{"input": "Down-regulation of interferon regulatory factor 4 gene expression in leukemic cells due to hypermethylation of CpG motifs in the promoter region \nAlthough the bcr-abl translocation has been shown to be the causative genetic aberration in chronic myeloid leukemia (CML), there is mounting evidence that the deregulation of other genes, such as the transcription factor interferon regulatory factor 4 (IRF-4), is also implicated in the pathogenesis of CML. Promoter methylation of CpG target sites or direct deletions/insertions of genes are mechanisms of a reversible or permanent silencing of gene expression, respectively. Therefore, we investigated whether IRF-4 promoter methylation or mutation may be involved in the regulation of IRF-4 expression in leukemia cells. Whereas promoter mutations or structural rearrangements could be excluded as a cause of altered IRF-4 expression in hematopoietic cells, the IRF-4 promoter methylation status was found to significantly influence IRF-4 transcription. First, treatment of IRF-4-negative lymphoid, myeloid and monocytic cell lines with the methylation-inhibitor 5-aza-2-deoxycytidine resulted in a time- and concentration-dependent increase of IRF-4 mRNA and protein levels. Second, using a restriction-PCR-assay and bisulfite-sequencing we identified specifically methylated CpG sites in IRF-4-negative but not in IRF-4-positive cells. Third, we clearly determined promoter methylation as a mechanism for IRF-4 down-regulation via reporter gene assays, but did not detect an association of methylational status and mRNA expression of DNA methyltransferases or methyl-CpG-binding proteins. Together, these data suggest CpG site-specific IRF-4 promoter methylation as a putative mechanism of down-regulated IRF-4 expression in leukemia. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 55, "end": 65}, "arguments": [{"role": "Theme", "text": "interferon regulatory factor 4", "start": 19, "end": 49}]}, {"trigger": {"text": "expression", "start": 741, "end": 751}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 735, "end": 740}]}, {"trigger": {"text": "expression", "start": 873, "end": 883}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 867, "end": 872}]}, {"trigger": {"text": "negative", "start": 1030, "end": 1038}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1024, "end": 1029}]}, {"trigger": {"text": "negative", "start": 1346, "end": 1354}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1340, "end": 1345}]}, {"trigger": {"text": "positive", "start": 1372, "end": 1380}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1366, "end": 1371}]}, {"trigger": {"text": "expression", "start": 1763, "end": 1773}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1757, "end": 1762}]}], "negative regulation": [{"trigger": {"text": "Down-regulation", "start": 0, "end": 15}, "arguments": [{"role": "Theme", "text": "expression", "start": 55, "end": 65}]}, {"trigger": {"text": "down-regulation", "start": 1463, "end": 1478}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1457, "end": 1462}]}, {"trigger": {"text": "down-regulated", "start": 1742, "end": 1756}, "arguments": [{"role": "Theme", "text": "expression", "start": 1763, "end": 1773}]}], "positive regulation": [{"trigger": {"text": "resulted", "start": 1135, "end": 1143}, "arguments": [{"role": "Theme", "text": "increase", "start": 1183, "end": 1191}]}, {"trigger": {"text": "increase", "start": 1183, "end": 1191}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1195, "end": 1200}]}], "regulation": [{"trigger": {"text": "deregulation", "start": 306, "end": 318}, "arguments": [{"role": "Theme", "text": "interferon regulatory factor 4", "start": 368, "end": 398}]}, {"trigger": {"text": "regulation", "start": 721, "end": 731}, "arguments": [{"role": "Theme", "text": "expression", "start": 741, "end": 751}]}, {"trigger": {"text": "altered", "start": 859, "end": 866}, "arguments": [{"role": "Theme", "text": "expression", "start": 873, "end": 883}]}, {"trigger": {"text": "influence", "start": 973, "end": 982}, "arguments": [{"role": "Theme", "text": "transcription", "start": 989, "end": 1002}]}], "transcription": [{"trigger": {"text": "transcription", "start": 989, "end": 1002}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 983, "end": 988}]}]}}, "schema": []}
{"input": "INTRODUCTION\nChronic myeloid leukemia (CML) is a clonal myeloproliferative disorder with a typical three phased course (chronic, accelerated and blastic phase) reflecting the loss of differentiation and malignant progress which inevitably leads to death after the blastic phase (1,2). The hallmark genetic aberration of CML is a reciprocal chromosomal translocation t(9;22) leading to expression of a bcr-abl fusion gene, an aberrant activated tyrosine kinase (2). Treatment with interferon alpha (IFN-alpha) prolongs survival of CML patients and is associated with a complete cytogenetic response in 5-33% of CML patients (1,2). Recently, we described an impaired expression of the interferon regulatory factor 4 (IRF-4) in CML, correlating with poor response to IFN-alpha treatment (3). The cause of the silencing of IRF-4 level remained unclear. \nInterferon regulatory factors (IRFs) are a family of transcriptional regulators defined by a characteristic homology in their DNA-binding domain. They play an important role in the regulation of various genes (such as IFNs, interleukins, MHC class I/II), apoptosis and differentiation/maturation (4-6). IRF-4 (ICSAT/Pip/MUM1/LSIRF) is one member with very restricted expression pattern: Predominately B- and activated T-lymphocytes are IRF-4 positive (7-11). In contrast to other IRFs, expression of IRF-4 cannot be induced by IFNs, but by antigen stimulation, crosslinking of T- or B-cell receptors or phorbol-myristate-acetate (10,11). Consistent with the restriction of expression to immunocompetent cells, mice with deletion of IRF-4 failed to develop mature and functionally active B- and T-lymphocytes (12), and the impaired expression of IRF-4 in CML was predominately found in T-cells (3). These data suggest a crucial role for IRF-4 in the function of immune cells. \nMethylation of dinucleotide cytosine-guanosine motifs (CpG), especially in CpG islands located in promoter regions, is one of the mechanisms of gene regulation in mammals and a common event of gene silencing in human neoplasias (13,14). As opposed to normal cells, hypermethylation of CpG islands is a frequently observed phenomenon in every cancer type. De novo DNA methylation of genes such as cell cycle, DNA repair, apoptosis and tumor suppressor genes is therefore thought to be involved in tumorigenesis (15-17). Examples for such aberrated genes are MGMT, DAPK, p14ARF, p15INK4b, p16INK4a, BRCA1, CDH13 and APAF-1 (17-19). In CML, methylation is known to regulate expression of the c-abl, the bcr gene and others (20-23), and the extent of methylation in the c-abl promoter has been shown to be associated with advanced disease (24). Hypermethylation due to overexpression of DNA methyltransferases (DNMTs) remains one possible explanation for de novo methylation in tumorigenesis. Recently, DNMTs have been shown to be up-regulated in hematopoietic malignancies (25). Methyl-CpG-binding proteins (MBPs) are thought to inhibit the binding of transcriptional factors to the promoter and are therefore discussed as one mechanism of transcription inhibition by hypermethylation (26). \nIn this work, we studied mechanisms of IRF-4 gene expression silencing in leukemic cells. We analyzed the IRF-4 promoter region for genetic aberrations and methylational status in IRF-4-positive and -negative hematopoietic cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "bcr-abl fusion gene", "start": 401, "end": 420}]}, {"trigger": {"text": "expression", "start": 665, "end": 675}, "arguments": [{"role": "Theme", "text": "interferon regulatory factor 4", "start": 683, "end": 713}]}, {"trigger": {"text": "expression", "start": 1217, "end": 1227}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1153, "end": 1158}]}, {"trigger": {"text": "positive", "start": 1292, "end": 1300}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1286, "end": 1291}]}, {"trigger": {"text": "expression", "start": 1336, "end": 1346}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1350, "end": 1355}]}, {"trigger": {"text": "expression", "start": 1681, "end": 1691}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1695, "end": 1700}]}, {"trigger": {"text": "expression", "start": 2497, "end": 2507}, "arguments": [{"role": "Theme", "text": "c-abl", "start": 2515, "end": 2520}]}, {"trigger": {"text": "expression", "start": 2497, "end": 2507}, "arguments": [{"role": "Theme", "text": "bcr", "start": 2526, "end": 2529}]}, {"trigger": {"text": "expression", "start": 3165, "end": 3175}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 3154, "end": 3159}]}, {"trigger": {"text": "positive", "start": 3301, "end": 3309}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 3295, "end": 3300}]}, {"trigger": {"text": "negative", "start": 3315, "end": 3323}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 3295, "end": 3300}]}], "negative regulation": [{"trigger": {"text": "impaired", "start": 656, "end": 664}, "arguments": [{"role": "Theme", "text": "expression", "start": 665, "end": 675}]}, {"trigger": {"text": "silencing", "start": 806, "end": 815}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 819, "end": 824}]}, {"trigger": {"text": "deletion", "start": 1570, "end": 1578}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1582, "end": 1587}]}, {"trigger": {"text": "silencing", "start": 3176, "end": 3185}, "arguments": [{"role": "Theme", "text": "expression", "start": 3165, "end": 3175}]}], "positive regulation": [{"trigger": {"text": "leading", "start": 374, "end": 381}, "arguments": [{"role": "Theme", "text": "expression", "start": 385, "end": 395}]}, {"trigger": {"text": "induced", "start": 1366, "end": 1373}, "arguments": [{"role": "Theme", "text": "expression", "start": 1336, "end": 1346}]}], "regulation": [{"trigger": {"text": "regulate", "start": 2488, "end": 2496}, "arguments": [{"role": "Theme", "text": "expression", "start": 2497, "end": 2507}]}]}}, "schema": []}
{"input": "Cell lines\nK-562, Jurkat and U-937 were obtained from the ATCC (American Type Culture Collection, Rockville, USA) and EM-2, LAMA-84, CML-T1, BV-173, SD-1 and RPMI-8226 from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany). All cell lines, except BV-173, SD-1 and RPMI-8226, were IRF-4-negative. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "negative", "start": 330, "end": 338}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 324, "end": 329}]}]}}, "schema": []}
{"input": "Cell culture and stimulation\nAll cell lines were maintained at 5% CO2 in RPMI 1640 medium with 1% glutamine (Gibco/BRL Eggenstein, Germany) supplemented with 10% fetal calf serum (Gibco/BRL), 1% penicillin/streptomycin (Biochrom, Berlin, Germany). When indicated, cells were treated with 5-aza-2-deoxycytidine (AzadC) or 5-azacytidine (AzaC) (Sigma, Taufkirchen, Germany) for different time periods. Owing to their chemical instability fresh substances were re-added every 24 h. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Sequencing of the IRF-4 promoter\nFor analysis of the IRF-4 promoter region for permanent aberrations such as insertions/deletions or mutation, we PCR-amplified two fragments from genomic DNA, which was extracted from depicted cell lines with a commercial kit (Qiagen, Hilde, Germany) as recommended. The primers were 1-forward: 5'-TTGAGATGGAGTCTTGCTCTGT-3', 1-reverse: 5'-CCAGGACCTCAGGAGGCCAGTCA-3'; 2-forward: 5'-AGCGGTGAAACTGAGAGTGCGAGGT-3', 2-reverse: 5'-GCCACATCGCTGCAGTTTAG-3'. The products were cloned with the 'TOPO TA cloning kit' (Invitrogen, Groningen, The Netherlands). After bacterial amplification of the cloned PCR fragments by standard procedures, at least three clones from each sample were sequenced with an automated sequencer (ABI Prism 377, Applied Bio-systems, Foster City, USA) as recommended by the manufacturer. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Expression analysis\nTo analyze the IRF-4 transcriptional level, RNA was extracted from cells using the commercial RNAzol-kit (Paesel, Frankfurt, Germany). An aliquot of 1 mug total RNA was used for cDNA synthesis as described previously (27). RNA expression analysis for IRF-4 and the reference gene beta-actin was carried out by semi-quantitative PCR as described previously (3,27). PCR products were verified by automated sequencing. PCR primers and conditions for expression analysis of DNMT or MBP (DNMT1 DNMT3A, DNMT3B, MeCP, MBD1, MBD2 and MBD4) were published elsewhere (28). \nFor analysis of IRF-4 protein expression, a standard immunoblotting assay was performed as described previously (29). Briefly, protein lysates were generated by incubating 1 x 106 cells in 100 microl RIPA buffer (1% NP-40, 0.5% sodiumdesoxycholate, 0.1% SDS, 100 microg/ml phenylmethylsulfonyl fluoride, 10 microl/ml protease-inhibitory-mix, 1 micromol/ml sodiumorthovanadate in phosphate-buffered saline) for 30 min on ice. After centrifugation, protein concentration of the supernatant was determined by BCA-method (Pierce, Rockford, IL) as recommended. Protein lysates (70-100 microg) were electrophoresed on polyacrylamide gels and transferred to a PVDF-membrane (Immobilon P, 0.45 microm; Millipore, Eschborn, Germany). Membranes were blocked with 2.5% blocking reagent (Boehringer Mannheim, Germany) in TBST buffer (4.44 g/l Tris-HCL, 2.65 g/l TrisOH, 8.07 g/l NaCl, 0.2 g/l KCl and 500 microl/l Tween-20 in H2O) and subsequently incubated with primary antibody as indicated and horseradish peroxidase-conjugated secondary antibody, anti-mouse or anti-goat IgG (DAKO, Hamburg, Germany), respectively. The membranes were then developed with an ECL detection kit (Amersham Pharmacia Biotech, Freiburg, Germany). The primary antibodies were goat anti-IRF-4/ICSAT (M-17) (Santa Cruz Biotechnology, Santa Cruz, CA) and mouse anti-beta-actin (AC-74) (Sigma). \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "(DNMT1", "start": 502, "end": 508}]}, {"trigger": {"text": "expression", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "DNMT3A", "start": 509, "end": 515}]}, {"trigger": {"text": "expression", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "DNMT3B", "start": 517, "end": 523}]}, {"trigger": {"text": "expression", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "MeCP", "start": 525, "end": 529}]}, {"trigger": {"text": "expression", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "MBD1", "start": 531, "end": 535}]}, {"trigger": {"text": "expression", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "MBD2", "start": 537, "end": 541}]}, {"trigger": {"text": "expression", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "MBD4", "start": 546, "end": 550}]}, {"trigger": {"text": "expression", "start": 614, "end": 624}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 600, "end": 605}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 41, "end": 56}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 35, "end": 40}]}, {"trigger": {"text": "RNA expression", "start": 243, "end": 257}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 271, "end": 276}]}, {"trigger": {"text": "RNA expression", "start": 243, "end": 257}, "arguments": [{"role": "Theme", "text": "beta-actin", "start": 300, "end": 310}]}]}}, "schema": []}
{"input": "Methylation-specific restriction-PCR-assay\nDNA was extracted with a commercial kit (Qiagen) as recommended. Since the restriction ability of several endonucleases is inhibited by methylation of their target sequence, we used methylation-sensitive enzymes HpaII and HaeII-isochizomer Bsp143II and Bsh1236I (MBI Fermentas, St Leon-Rot, Germany) (20,24). As control the methylation-resistant enzyme MspI and an enzyme with no recognition site in the target promoter, EcoRI, were used. DNA (0.8 microg) was digested by 40 U the respective enzyme for 6 h and, to ensure complete cleavage, additional 20 U for 16 h. Thereafter 100 ng of digested DNA was used to a PCR amplification of two fragments (F1 and F2) spanning part of the IRF-4 promoter (30) (GenBank U52683; see Figure 3A). The sequences of the primers were F1-forward: 5'-TTGAGATGGAGTCTTGCTCTGT-3', F1-reverse: ATCACTTCCAGACTTCAGTTCACCT-3' (341 bp); F2-forward: 5'-AAGGTGAACTGAAGTCTGGAAGTGA-3', F2-reverse: 5'-CCAGGACCTCAGGAGGCCAGTCA-3' (474 bp). The PCR conditions were described elsewhere (3). PCR was performed with an annealing temperature of 62degreesC and 35 cycles. When DNA was methylated at specific sites, the sensitive enzymes were not able to digest the DNA and amplification took place; in case of no methylation, DNA was digested and no product was generated. The PCR products were electrophoresed on a 3% agarose gel, were stained with ethidium bromide and photographed. PCR products were verified by automated sequencing. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Bisulfite treatment\nDNA was extracted as described above. Bisulfite treatment of DNA, leading to conversion of unmethylated cytosine to uracil residues and no change of methylated cytosine residues, was performed as described as follows. Briefly, 1 microg of DNA and 2 microg of poly(dA-dT)(poly(dA-dT) copolymers (Amersham Pharmacia Biotech) were denaturated for 20 min at 42degreesC in 0.3 M NaOH in a volume of 50 microl. Fresh solutions of 30 microl of 10 mM hydrochinon (Sigma) and 530 microl of 3 M sodium bisulfite (pH 5.0; Sigma) were added, the solution was gently mixed, overlayed with mineral oil and incubated in the dark for 12-13 h at 50degreesC. The aqueous phase was recovered using the 'Wizard DNA clean-up system' (Promega, Mannheim, Germany). The purified DNA was subsequently mixed with 1 M NaOH to a final concentration of 0.3 M and incubated for 20 min at 37degreesC to ensure complete desulfonisation. DNA was ethanol precipitated in the presence of 1/10 vol of 3 M sodium acetate, washed with 70% ethanol and resuspended in 50 microl H2O. Subsequent PCR amplification of 4 microl bisulfite-treated DNA was used for cloning of two fragments of the IRF-4 promoter (BS-I and BS-II) into pCR2.1 vector with the 'TOPO TA cloning kit' (Invitrogen) (see Figure 3A). The primers used for PCR amplification of the BS-I and BS-II fragments contain the putative altered sequence of the sense strand due to bisulfite treatment (converted cytosine residues are written in bold letters): BS-I-forward 5'-TATTTGGATTTTTAGGGAGTTTTTTTT-3', BS-I-reverse 5'-ACCCAACTCCCTTAAACTATTAAACT-3' (187 bp); BS-II-forward 5'-AGTTTAATAGTTTAAGGGAGTTGGGT-3', BS-II-reverse 5'-CTCACCCTAAACTCAAAACTAAAAAC-3' (674 bp). After bacterial amplification of the cloned PCR fragments by standard procedures, eight clones from each sample were sequenced with an automated sequencer (ABI Prism 377, Applied Biosystems). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "In vitro methylation and reporter gene assays\nThe IRF-4 promoter-reporter gene construct was generously provided by J.Hiscott (31). Constructs were methylated in vitro with CpG Methylase (M.Sss I) as recommended by the manufacturer (NE Biolabs) and complete methylation was checked via restriction analysis (Figure 5A). Reporter gene assays using the dual luciferase assay (Promega) were performed similar to previous reports (29). Briefly, 5 nM of the reporter construct and the transfection control construct expressing the renilla luciferase gene were transiently co-expressed via electroporation. The control construct served as an internal reference for transfection efficiency. Forty-eight hours after transfection, luciferase activity was measured with a LB 96 P microlumat (EG&G Berthold, Bad Wildbad, Germany). IRF-4 promoter activation was quantified as a ratio of measured firefly light units (flu) relative to renilla (rlu). Each experiment was carried out at least three times. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 511, "end": 521}, "arguments": [{"role": "Theme", "text": "luciferase", "start": 534, "end": 544}]}, {"trigger": {"text": "expressed", "start": 570, "end": 579}, "arguments": [{"role": "Theme", "text": "luciferase", "start": 534, "end": 544}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 835, "end": 845}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 820, "end": 825}, {"role": "Site", "text": "promoter", "start": 826, "end": 834}]}]}}, "schema": []}
{"input": "Absence of IRF-4 expression in leukemia cells is not due to promoter alterations\nWe have previously demonstrated a lack of IRF-4 expression in leukemia patients and specifically in CML T-cells (3). Here, we demonstrate the absence of IRF-4 expression in various hematopoietic cell lines, such as Jurkat, a T-cell leukemia, CML-T1, a bcr-abl-positive T-cell line, K-562, a bcr-abl-positve erythroleukemia, U-937, a monocytic leukemia, EM-2 and LAMA-84, bcr-abl-positve myeloid leukemia, but not in SD-1, a bcr-abl-positive acute lymphoblastic leukemia (pre B-ALL), RPMI-8226, a multiple myeloma and BV-173, a bcr-abl-positive B-cell line (Figures 1A and 5D). After sequencing of the IRF-4 promoter, it could be excluded that absence of IRF-4 expression in any of the above cell lines was due to genetic aberrations. However, 2 bp changes (nucleotide -1081, T-->C and -1068, A-->C) could be detected in both the IRF-4-positive BV-173 and the IRF-4-negative LAMA-84, EM-2 and K-562 (Figure 1B). At position -116 an A-->C substitution was found in EM-2, K-562 and CML-T1, whereas Jurkat, BV-173 and SD-1 exhibited a mixed A/C sequence and U-937, LAMA-84 and RPMI-8226 no substitution at all (Figure 1B). Consequently, these alterations are unlikely to affect IRF-4 expression. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 17, "end": 27}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 11, "end": 16}]}, {"trigger": {"text": "expression", "start": 129, "end": 139}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 123, "end": 128}]}, {"trigger": {"text": "expression", "start": 240, "end": 250}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 234, "end": 239}]}, {"trigger": {"text": "positive", "start": 341, "end": 349}, "arguments": [{"role": "Theme", "text": "bcr-abl", "start": 333, "end": 340}]}, {"trigger": {"text": "positve", "start": 380, "end": 387}, "arguments": [{"role": "Theme", "text": "bcr-abl", "start": 372, "end": 379}]}, {"trigger": {"text": "positve", "start": 460, "end": 467}, "arguments": [{"role": "Theme", "text": "bcr-abl", "start": 452, "end": 459}]}, {"trigger": {"text": "positive", "start": 513, "end": 521}, "arguments": [{"role": "Theme", "text": "bcr-abl", "start": 505, "end": 512}]}, {"trigger": {"text": "positive", "start": 616, "end": 624}, "arguments": [{"role": "Theme", "text": "bcr-abl", "start": 608, "end": 615}]}, {"trigger": {"text": "expression", "start": 741, "end": 751}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 735, "end": 740}]}, {"trigger": {"text": "positive", "start": 916, "end": 924}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 910, "end": 915}]}, {"trigger": {"text": "negative", "start": 946, "end": 954}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 940, "end": 945}]}, {"trigger": {"text": "expression", "start": 1261, "end": 1271}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1255, "end": 1260}]}], "negative regulation": [{"trigger": {"text": "Absence", "start": 0, "end": 7}, "arguments": [{"role": "Theme", "text": "expression", "start": 17, "end": 27}]}, {"trigger": {"text": "lack", "start": 115, "end": 119}, "arguments": [{"role": "Theme", "text": "expression", "start": 129, "end": 139}]}, {"trigger": {"text": "absence", "start": 724, "end": 731}, "arguments": [{"role": "Theme", "text": "expression", "start": 741, "end": 751}]}], "positive regulation": [{"trigger": {"text": "due", "start": 53, "end": 56}, "arguments": [{"role": "Theme", "text": "Absence", "start": 0, "end": 7}]}], "regulation": [{"trigger": {"text": "affect", "start": 1248, "end": 1254}, "arguments": [{"role": "Theme", "text": "expression", "start": 1261, "end": 1271}]}]}}, "schema": []}
{"input": "Increase of IRF-4 expression in hematopoietic cells after demethylating treatment\nWe next analyzed whether promoter methylation could be responsible for down-regulation of IRF-4 expression. A region including exon1 in the IRF-4 promoter exhibited a large number of CpG-rich sequences (Figure 3A). Several chemical substances such as 5-aza-2-deoxycytidine (AzadC) or 5-azacytidine (AzaC) inhibit de novo and maintenance methylation, and thus can be used to discern promoter methylation (32,33). We used AzadC to generate unmethylated DNA. A 72 h AzadC-treatment resulted in a concentration-dependent activation of IRF-4 transcription in Jurkat and CML-T1 T-cells as well as in U-937, K-562 and EM-2 cell lines (Figure 2A). IRF-4 transcription was induced in a time-dependent manner and was observed as early as 24 h after treatment with AzadC and increased over time until 72 h (Figure 2B). Time and strength of the appearance of IRF-4 transcripts varied among cell lines, i.e. CML-T1 responded strongest to AzadC-treatment (data not shown). In line with this, AzadC-treatment of CML-T1 and LAMA-84 cells also translated in an induction of IRF-4 protein expression (Figure 2C). Accordingly, treatment of the IRF-4-positive cell line BV-173, SD-1 and RPMI-8226 with AzadC had no effect on IRF-4 expression (Figure 2D). There was no difference in the effects of AzaC versus AzadC, as both increased the IRF-4 mRNA level in CML-T1 cells as well (data not shown). This implied that promoter methylation may control IRF-4 expression, but an alternative explanation may be activation of positive transcriptional regulators of IRF-4 by AzadC (or AzaC). \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 18, "end": 28}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 12, "end": 17}]}, {"trigger": {"text": "expression", "start": 178, "end": 188}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 172, "end": 177}]}, {"trigger": {"text": "positive", "start": 1213, "end": 1221}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1207, "end": 1212}]}, {"trigger": {"text": "expression", "start": 1293, "end": 1303}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1287, "end": 1292}]}, {"trigger": {"text": "expression", "start": 1516, "end": 1526}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1510, "end": 1515}]}], "positive regulation": [{"trigger": {"text": "Increase", "start": 0, "end": 8}, "arguments": [{"role": "Theme", "text": "expression", "start": 18, "end": 28}]}, {"trigger": {"text": "activation", "start": 599, "end": 609}, "arguments": [{"role": "Theme", "text": "transcription", "start": 619, "end": 632}]}, {"trigger": {"text": "induced", "start": 746, "end": 753}, "arguments": [{"role": "Theme", "text": "transcription", "start": 728, "end": 741}]}, {"trigger": {"text": "increased", "start": 846, "end": 855}, "arguments": [{"role": "Theme", "text": "transcription", "start": 728, "end": 741}]}, {"trigger": {"text": "increased", "start": 1386, "end": 1395}, "arguments": [{"role": "Theme", "text": "mRNA level", "start": 1406, "end": 1416}]}], "regulation": [{"trigger": {"text": "effect", "start": 1277, "end": 1283}, "arguments": [{"role": "Theme", "text": "expression", "start": 1293, "end": 1303}]}, {"trigger": {"text": "control", "start": 1502, "end": 1509}, "arguments": [{"role": "Theme", "text": "expression", "start": 1516, "end": 1526}]}], "transcription": [{"trigger": {"text": "transcription", "start": 619, "end": 632}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 613, "end": 618}]}, {"trigger": {"text": "transcription", "start": 728, "end": 741}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 722, "end": 727}]}, {"trigger": {"text": "transcripts", "start": 935, "end": 946}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 929, "end": 934}]}, {"trigger": {"text": "mRNA level", "start": 1406, "end": 1416}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1400, "end": 1405}]}]}}, "schema": []}
{"input": "Methylation-sensitive enzymes do not cut specific sites in the IRF-4 promoter in hematopoietic cells\nTo further investigate promoter methylation as a regulatory mechanism of IRF-4 gene expression, restriction-PCR-assays were performed (20,24), where only methylated DNA would not be cut enabling subsequent PCR amplification and vice versa. Genomic DNA from leukemic cells Jurkat, CML-T1, U-937, K-562, EM-2 and BV-173 was digested with the methylation-sensitive enzymes HpaII, Bsh1236I and HaeII-isochizomer Bsp143II. EcoRI, which has no recognition site within the IRF-4 promoter, and the methylation-resistant enzyme MspI served as controls. Two separate amplification reactions were performed, generating two fragments, F1 and F2 (Figure 3A). After digestion with HpaII and Bsp143II a sufficient PCR amplification of F1 and F2 was detected in DNA from IRF-4-negative Jurkat, CML-T1, U-937, K-562 and EM-2 cells, suggesting a promoter methylation (and restriction protection) at the respective recognition sites (Figure 3B and C). Notably, in IRF-4-positive SD-1 cells digestion with the methylation-sensitive enzymes completely inhibited amplification of F1 and F2. In IRF-4-positive BV-173 cells a HpaII, but not a Bsh1236I digestion, significantly reduced the amplifiable DNA message of F2 (Figure 3C), whereas amplification of F1 was not affected (Figure 3B). This implied that IRF-4 transcription in SD-1 and BV-173 cells is associated with less promoter methylation (in BV-173 especially at HpaII sites) as compared with the tested IRF-4-negative cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 185, "end": 195}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 174, "end": 179}]}, {"trigger": {"text": "negative", "start": 862, "end": 870}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 856, "end": 861}]}, {"trigger": {"text": "positive", "start": 1052, "end": 1060}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1046, "end": 1051}]}, {"trigger": {"text": "positive", "start": 1179, "end": 1187}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1173, "end": 1178}]}, {"trigger": {"text": "negative", "start": 1547, "end": 1555}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1541, "end": 1546}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1391, "end": 1404}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1385, "end": 1390}]}]}}, "schema": []}
{"input": "Specific CpG sites in the IRF-4 promoter are methylated in hematopoietic cells\nIn order to exactly map the methylation sites within the IRF-4 promoter, we treated DNA of Jurkat, CML-T1, U-937, K-562 and EM-2 cells as well as of SD-1, RPMI-8226 and BV-173 control cells with bisulfite, which chemically converts unmethylated cytosine to uracil, whereas it has no effect on methylated cytosine, i.e. in CpG (34). This technique is especially useful for detection of unknown methylation patterns. PCR amplification, cloning and sequencing of the bisulfite-treated DNA showed a specific methylation pattern of the analyzed 62 CpG sites in all cell lines (Figure 4 and Table 1). In general, the methylational status ranged from one cell line with a nearly non-methylated IRF-4 promoter (SD-1, IRF-4-positive) to a completely methylated IRF-4 promoter in CML-T1 (IRF-4-negative). Interestingly, the percentage of CpG methylation in the IRF-4 promoter from IRF-4-positive cells was very low (mean 24%) as compared with IRF-4-negative cells (mean 94%) (Figure 4A and Table 1). A 5'-region (R1) with 13 hypermethylated CpG sites (mean number of methylated clones 5.5 of 8 with 77% methylated CpGs) was found in most cells (except SD-1 and RPMI-8226) and a 3'-region (R3) of 6 hypomethylated CpG sites (mean number of methylated clones 1.7 of 8 with 33% methylated CpGs) was found in most cells (except CML-T1 and U-937) (Figure 4A and Table 1). \nIntriguingly, a stretch of 13 CpG sites (#10-22; R2) was detected in between these regions, which were highly methylated in IRF-4-negative (mean number of methylated clones 7.1 of 8 with 89% methylated CpGs) but totally non-methylated in IRF-4-positive cells (Figure 4A and B). Furthermore, three CpG sites at the 5' end (#54, 56, 58) and two CpG motifs at the 3' end (#1, 2) showed this direct correlation between high methylation status and absence of IRF-4 expression. In addition, two CpG sites located in a NFkappaB (#48) and a SP1element (#45) are less methylated in IRF-4-positive than in IRF-4-negative cells (mean number of methylated clones: 1/8 versus 8/8). These results indicate the involvement of CpG methylation in the regulation of IRF-4 expression in leukemic cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "positive", "start": 794, "end": 802}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 788, "end": 793}]}, {"trigger": {"text": "negative", "start": 863, "end": 871}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 857, "end": 862}]}, {"trigger": {"text": "positive", "start": 956, "end": 964}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 950, "end": 955}]}, {"trigger": {"text": "negative", "start": 1018, "end": 1026}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1012, "end": 1017}]}, {"trigger": {"text": "negative", "start": 1567, "end": 1575}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1561, "end": 1566}]}, {"trigger": {"text": "positive", "start": 1681, "end": 1689}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1675, "end": 1680}]}, {"trigger": {"text": "expression", "start": 1897, "end": 1907}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 1891, "end": 1896}]}, {"trigger": {"text": "positive", "start": 2016, "end": 2024}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 2010, "end": 2015}]}, {"trigger": {"text": "negative", "start": 2039, "end": 2047}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 2033, "end": 2038}]}, {"trigger": {"text": "expression", "start": 2191, "end": 2201}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 2185, "end": 2190}]}], "negative regulation": [{"trigger": {"text": "absence", "start": 1880, "end": 1887}, "arguments": [{"role": "Theme", "text": "expression", "start": 1897, "end": 1907}]}], "regulation": [{"trigger": {"text": "regulation", "start": 2171, "end": 2181}, "arguments": [{"role": "Theme", "text": "expression", "start": 2191, "end": 2201}]}]}}, "schema": []}
{"input": "In vitro methylation of an IRF-4 promoter-reporter construct decreases its activity\nTo provide evidence for a direct effect of methylational status on IRF-4 promoter activity we performed reporter gene assays with IRF-4 promoter constructs before and after their in vitro methylation. A complete methylation of these constructs was checked via restriction assays with methylation-sensitive endonucleases (Figure 5A). Intriguingly, methylation of the IRF-4 promoter significantly decreased promoter activity in IRF-4-positive SD-1 cells by 85.0% (Figure 5B). The silencing effect of CpG methylation was not restricted to IRF-4-positive cells, since in vitro methylation led to a 92.9% abrogation of promoter activity in IRF-4-negative Jurkat cells (Figure 5C). In contrast, control methylation of a reporter construct with a different promoter (FasL) as well as an empty vector had no effect on the reporter activity (data not shown). These data proved a direct association between methylation and activity of the IRF-4 promoter. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "positive", "start": 516, "end": 524}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 510, "end": 515}]}, {"trigger": {"text": "positive", "start": 626, "end": 634}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 620, "end": 625}]}, {"trigger": {"text": "negative", "start": 725, "end": 733}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 719, "end": 724}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 479, "end": 488}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 450, "end": 455}, {"role": "Site", "text": "promoter", "start": 489, "end": 497}]}, {"trigger": {"text": "abrogation", "start": 684, "end": 694}, "arguments": [{"role": "Site", "text": "promoter", "start": 698, "end": 706}, {"role": "Theme", "text": "IRF-4", "start": 719, "end": 724}]}]}}, "schema": []}
{"input": "mRNA expression of DNA methyltransferases and methyl-CpG-binding proteins may not be associated with IRF-4 promoter methylation\nSince abundance of DNMT and MBP contribute to promoter regulation via methylation (25,26,28), we studied their mRNA expression to investigate a possible mechanism for the observed methylation differences in the IRF-4 promoter. To this end, we did not detect a significant difference in DNMT (DNMT1, DNMT3A and DNMT3B) or MBP (MBD1, MBD2, MBD4 and MeCP) mRNA expression between IRF-4-positive and -negative cells (Figure 5D). In fact, all analyzed cells had moderate to high mRNA levels of these tested DNMT/MBPs and differences in expression were not correlated with IRF-4 status. These results indicate a distinct cause of the methylation differences in IRF-4-positive and -negative cells rather than changes in the DNMT and MBP mRNA transcription. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "positive", "start": 511, "end": 519}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 505, "end": 510}]}, {"trigger": {"text": "negative", "start": 525, "end": 533}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 505, "end": 510}]}, {"trigger": {"text": "positive", "start": 789, "end": 797}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 783, "end": 788}]}, {"trigger": {"text": "negative", "start": 803, "end": 811}, "arguments": [{"role": "Theme", "text": "IRF-4", "start": 783, "end": 788}]}], "regulation": [{"trigger": {"text": "regulation", "start": 183, "end": 193}, "arguments": [{"role": "Site", "text": "promoter", "start": 174, "end": 182}, {"role": "Theme", "text": "IRF-4", "start": 339, "end": 344}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 481, "end": 496}, "arguments": [{"role": "Theme", "text": "DNMT1", "start": 420, "end": 425}]}, {"trigger": {"text": "mRNA expression", "start": 481, "end": 496}, "arguments": [{"role": "Theme", "text": "DNMT3A", "start": 427, "end": 433}]}, {"trigger": {"text": "mRNA expression", "start": 481, "end": 496}, "arguments": [{"role": "Theme", "text": "DNMT3B", "start": 438, "end": 444}]}, {"trigger": {"text": "mRNA expression", "start": 481, "end": 496}, "arguments": [{"role": "Theme", "text": "MBD1", "start": 454, "end": 458}]}, {"trigger": {"text": "mRNA expression", "start": 481, "end": 496}, "arguments": [{"role": "Theme", "text": "MBD2", "start": 460, "end": 464}]}, {"trigger": {"text": "mRNA expression", "start": 481, "end": 496}, "arguments": [{"role": "Theme", "text": "MBD4", "start": 466, "end": 470}]}, {"trigger": {"text": "mRNA expression", "start": 481, "end": 496}, "arguments": [{"role": "Theme", "text": "MeCP", "start": 475, "end": 479}]}, {"trigger": {"text": "mRNA levels", "start": 602, "end": 613}, "arguments": [{"role": "Theme", "text": "DNMT1", "start": 420, "end": 425}]}, {"trigger": {"text": "mRNA levels", "start": 602, "end": 613}, "arguments": [{"role": "Theme", "text": "DNMT3A", "start": 427, "end": 433}]}, {"trigger": {"text": "mRNA levels", "start": 602, "end": 613}, "arguments": [{"role": "Theme", "text": "DNMT3B", "start": 438, "end": 444}]}, {"trigger": {"text": "mRNA levels", "start": 602, "end": 613}, "arguments": [{"role": "Theme", "text": "MBD1", "start": 454, "end": 458}]}, {"trigger": {"text": "mRNA levels", "start": 602, "end": 613}, "arguments": [{"role": "Theme", "text": "MBD2", "start": 460, "end": 464}]}, {"trigger": {"text": "mRNA levels", "start": 602, "end": 613}, "arguments": [{"role": "Theme", "text": "MBD4", "start": 466, "end": 470}]}, {"trigger": {"text": "mRNA levels", "start": 602, "end": 613}, "arguments": [{"role": "Theme", "text": "MeCP", "start": 475, "end": 479}]}, {"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "DNMT1", "start": 420, "end": 425}]}, {"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "DNMT3A", "start": 427, "end": 433}]}, {"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "DNMT3B", "start": 438, "end": 444}]}, {"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "MBD1", "start": 454, "end": 458}]}, {"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "MBD2", "start": 460, "end": 464}]}, {"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "MBD4", "start": 466, "end": 470}]}, {"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "MeCP", "start": 475, "end": 479}]}, {"trigger": {"text": "transcription", "start": 863, "end": 876}, "arguments": [{"role": "Theme", "text": "DNMT1", "start": 420, "end": 425}]}, {"trigger": {"text": "transcription", "start": 863, "end": 876}, "arguments": [{"role": "Theme", "text": "DNMT3A", "start": 427, "end": 433}]}, {"trigger": {"text": "transcription", "start": 863, "end": 876}, "arguments": [{"role": "Theme", "text": "DNMT3B", "start": 438, "end": 444}]}, {"trigger": {"text": "transcription", "start": 863, "end": 876}, "arguments": [{"role": "Theme", "text": "MBD1", "start": 454, "end": 458}]}, {"trigger": {"text": "transcription", "start": 863, "end": 876}, "arguments": [{"role": "Theme", "text": "MBD2", "start": 460, "end": 464}]}, {"trigger": {"text": "transcription", "start": 863, "end": 876}, "arguments": [{"role": "Theme", "text": "MBD4", "start": 466, "end": 470}]}, {"trigger": {"text": "transcription", "start": 863, "end": 876}, "arguments": [{"role": "Theme", "text": "MeCP", "start": 475, "end": 479}]}]}}, "schema": []}
{"input": "DISCUSSION\nMany genetic lesions are known to influence gene expression of tumor suppressor genes. Whereas mutations and deletions or insertions have permanent effects, reversible mechanisms are gene methylation, or expression and activation of transcription factors, respectively. We studied a putative cause for absent IRF-4 expression in leukemia cells and first focused on genetic aberrations of the promoter. We observed no genetic alterations in the IRF-4 promoter, which can account for the lack of IRF-4 expression: The detected base pair changes at position -1081 (T-->C substitution), at position -1068 (A-->C substitution) and at position -116 (A-->C substitution) are unlikely responsible for absent IRF-4-expression since the first two mutations were found both in IRF-4-positive and -negative cells whereas the latter change was not detected consistently in all IRF-4-negative or -positive cells and may thus be a polymorphism. All three substitutions did not change any known putative transcription factor binding sites (30,31) and also do not affect any restriction sites or primer binding sites of the used assays. However, permanent genetic variations in the IRF-4 coding sequence, such as deletions or mutations resulting in stop-codons have not been excluded by sequence analysis. Since IRF-4 expression in cell lines and CML can be induced by demethylation and successful IFN-alpha therapy (3), respectively, the existence of such genetic aberrations seems unlikely. \nWe then investigated whether the previously described down-regulation of IRF-4 expression in human myeloid leukemias was due to a differential hypermethylation of the promoter, since the presented re-expression due to AzadC-treatment might also be a result of activation of positive transcriptional regulators of IRF-4. Methylation of CpG sites is a common mechanism of silencing genes in leukemia and has also been shown for another IRF, IRF-7 (35) and for PU.1 (36), an interacting partner of IRF-4. To elucidate the relevance of this mechanism for the regulation of IRF-4 expression, various leukemic cells were treated with demethylating agents and promoters were sequenced after bisulfite treatment. We found that IRF-4 expression could indeed be connected to the methylation status of distinct CpG motifs in the IRF-4 promoter. In Figure 4A, those CpG sites are shown (bottom line), whose hypermethylation may account for the absence of IRF-4 expression in the respective cells. One of them (#54) is adjacent to an identified regulatory element (NFkappaB-site), indicating a possible involvement of this site. At two further CpG sites (#48, 45) the methylation status in IRF-4-positive was lower than that of IRF-4-negative cells. These CpG sites are located in an NFkappaB and an SP1 element (31) and thus may also play a role in regulation of IRF-4 expression. It has been shown that NFkappaB elements play an important role in IRF-4 induction as IRF-4 expression depends on binding of the transactivator c-Rel to these elements in the IRF-4 promoter (31,37). Furthermore, methylation of the central CpG in the NFkappaB element inhibits binding of the NFkappaB protein complexes (38), promoting the significance of the observed methylation differences in IRF-4-positive and -negative cells. \nVia in vitro methylation and reporter gene assays we could clearly appoint the silencing of the IRF-4 promoter to a methylation effect, which may thus be the mechanism of IRF-4 deregulation in vivo. One possible cause for the aberrant methylation in tumorigenesis is an increased level of DNMTs during the pathogenetic process. In colon, lung and hematologic malignancies, overexpression of DNMT1, a maintenance DNMT, has been detected (39-41). Furthermore, it has been shown that CML cells in the acute phase exhibited elevated levels of the three known DNMTs, while CML cells in chronic phase expressed normal levels of DNMTs if compared with normal bone marrow cells (25). Interestingly, a positive correlation between DNMT1 expression levels and hypermethylation of p15INK4b has been detected in AML (25). In this work, we did not detect significant mRNA expression differences of selected DNMT or MBP, making it an unlikely cause for the observed methylation and thus IRF-4 expression differences in leukemia cells. \nThe finding that IRF-4 expression is silenced by promoter hypermethylation might represent a mechanism that accounts for the previously observed loss of IRF-4 expression in CML. Indeed, several clinical trials with leukemia patients and patients with myelodysplastic syndromes demonstrated the potential clinical benefit of a treatment with demethylating agents (42-45). \nThe expression of another IRF, IFN consensus sequence binding protein (ICSBP/IRF-8), is impaired in myeloid leukemias especially CML (27,46,47). But in contrast to IRF-4, the loss of this IRF could not be reverted in ICSBP-negative cell lines (EM-2, CML-T1, K-562 and LAMA-84) by treatment with AzadC (Figure 6) and AzadC has no effect on ICSBP levels in ICSBP-positive U-937 cells (Figure 6). These data suggest a distinct regulatory mechanism for these two IRFs. \nIRF-4, similar to many other classical tumor suppressor genes p15INK4b, p16INK4a or p53, may thus be a subject of alterations in the promoter methylation status leading to expression changes, which might contribute to the initiation and/or progression of cancer. Still, the obvious functional diversity of IRF-4 remains remarkable and cannot be fully explained by the IRF-4 promoter methylation status. For example, IRF-4 is primarily known for its oncogenic features. In multiple myeloma (MM) a translocation on chromosome 14q was reported to lead to a fusion gene of immunoglobulin heavy-chain (IgH) and IRF-4 resulting in a subsequent overexpression of IRF-4 (48,49). In addition, abundant IRF-4 expression was found to be a marker for various subsets of lymphomas, such as diffuse large B-cell lymphomas, primary effusion lymphoma, and marginal zone lymphoma, and adult T-cell leukemia (11,31,50-52). This draws a more complex picture of the role of IRF-4. Down-regulation of IRF-4 may promote leukemogenesis in myeloid cell context (3), which was recently confirmed in IRF-4-/- ICSBP-/- double knock-out mice (53), while IRF-4 up-regulation may induce a growth advantage in lymphomas or MM (48). \nTaken together, our data suggest that IRF-4 promoter methylation regulates IRF-4 expression, and that aberrant expression of IRF-4 in certain types of leukemia may be a consequence of IRF-4 promoter hypermethylation. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacting", "start": 1960, "end": 1971}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1946, "end": 1950}, {"role": "Theme2", "text": "IRF-4", "start": 1983, "end": 1988}]}, {"trigger": {"text": "binding", "start": 2971, "end": 2978}, "arguments": [{"role": "Site2", "text": "NFkappaB elements", "start": 2880, "end": 2897}, {"role": "Theme", "text": "c-Rel", "start": 3001, "end": 3006}, {"role": "Theme2", "text": "IRF-4", "start": 3032, "end": 3037}]}, 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{"input": "Foxp3 Represses Retroviral Transcription by Targeting Both NF-kappaB and CREB Pathways \nForkhead box (Fox)/winged-helix transcription factors regulate multiple aspects of immune responsiveness and Foxp3 is recognized as an essential functional marker of regulatory T cells. Herein we describe downstream signaling pathways targeted by Foxp3 that may negatively impact retroviral pathogenesis. Overexpression of Foxp3 in HEK 293T and purified CD4+ T cells resulted in a dose-dependent and time-dependent decrease in basal levels of nuclear factor-kappaB (NF-kappaB) activation. Deletion of the carboxyl-terminal forkhead (FKH) domain, critical for nuclear localization and DNA-binding activity, abrogated the ability of Foxp3 to suppress NF-kappaB activity in HEK 293T cells, but not in Jurkat or primary human CD4+ T cells. We further demonstrate that Foxp3 suppressed the transcription of two human retroviral promoters (HIV-1 and human T cell lymphotropic virus type I [HTLV-I]) utilizing NF-kappaB-dependent and NF-kappaB-independent mechanisms. Examination of the latter identified the cAMP-responsive element binding protein (CREB) pathway as a target of Foxp3. Finally, comparison of the percent Foxp3+CD4+CD25+ T cells to the HTLV-I proviral load in HTLV-I-infected asymptomatic carriers and patients with HTLV-I-associated myelopathy/tropical spastic paraparesis suggested that high Foxp3 expression is associated with low proviral load and absence of disease. These results suggest an expanded role for Foxp3 in regulating NF-kappaB- and CREB-dependent cellular and viral gene expression. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 676, "end": 683}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 719, "end": 724}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1397, "end": 1407}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1391, "end": 1396}]}], "localization": [{"trigger": {"text": "localization", "start": 655, "end": 667}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 647, "end": 654}, {"role": "Theme", "text": "Foxp3", "start": 719, "end": 724}]}], "negative regulation": [{"trigger": {"text": "Deletion", "start": 577, "end": 585}, "arguments": [{"role": "Site", "text": "carboxyl-terminal forkhead (FKH) domain", "start": 593, "end": 632}, {"role": "Theme", "text": "Foxp3", "start": 719, "end": 724}]}], "positive regulation": [{"trigger": {"text": "Overexpression", "start": 393, "end": 407}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 411, "end": 416}]}, {"trigger": {"text": "critical", "start": 634, "end": 642}, "arguments": [{"role": "CSite", "text": "carboxyl-terminal forkhead (FKH) domain", "start": 593, "end": 632}, {"role": "Theme", "text": "localization", "start": 655, "end": 667}, {"role": "Cause", "text": "Foxp3", "start": 719, "end": 724}]}, {"trigger": {"text": "critical", "start": 634, "end": 642}, "arguments": [{"role": "CSite", "text": "carboxyl-terminal forkhead (FKH) domain", "start": 593, "end": 632}, {"role": "Theme", "text": "binding", "start": 676, "end": 683}, {"role": "Cause", "text": "Foxp3", "start": 719, "end": 724}]}, {"trigger": {"text": "high", "start": 1386, "end": 1390}, "arguments": [{"role": "Theme", "text": "expression", "start": 1397, "end": 1407}]}]}}, "schema": []}
{"input": "Synopsis\nOver the past several years, mounting evidence has shown that immune tolerance in healthy individuals can be maintained by a population of T lymphocytes known as regulatory T cells (Tregs). As a component of this system, a protein known as Foxp3 has been shown to be absolutely required for the development and function of Tregs. While Foxp3 plays an important role in maintaining immune tolerance by blocking T cell proliferation and production of inflammatory proteins known as cytokines, little is known about the molecular mechanisms that are used by Foxp3 to accomplish these events. The present study expands our understanding of how Foxp3 maintains a check on inappropriate immune responses by demonstrating that Foxp3 can block activation of key inducible proteins such as nuclear factor kappaB (NF-kappaB) and cAMP-responsive element binding protein (CREB). Since NF-kappaB and CREB are integrally involved in controlling cell cycle progression, inflammatory cytokine production, and the replication of numerous viruses at the level of transcription, understanding the mechanisms by which Foxp3 functions to regulate cellular and viral gene expression may aid in the discovery of therapeutic approaches designed to rescue the expression and/or function of Foxp3, which have been found to be deficient in several autoimmune diseases and virus-induced disorders. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1244, "end": 1254}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1274, "end": 1279}]}]}}, "schema": []}
{"input": "Introduction\nImmunological tolerance to self-antigens is the result of the deletion of self-reactive T lymphocytes in the thymus (central tolerance) and suppression of the activation of potentially self-reactive T lymphocytes in the periphery (peripheral tolerance) [1]. Suppression of pathogenic T cell responses is mediated by naturally arising CD4+CD25+ T regulatory cells (Tregs) [2,3]. Deficiencies in Treg development and function have been linked to the severe autoimmune disorder known as immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX) [4]. In addition, recent studies have provided strong evidence that dysregulation of Treg development and/or function may be a significant factor in the pathogenesis of several autoimmune disorders (e.g., multiple sclerosis [5], myasthenia gravis [6], and type 1 diabetes [7]) and virus-induced immunologic disorders (e.g., human T lymphotropic virus type I [HTLV-I]-associated myelopathy/tropical spastic paraparesis [HAM/TSP], and HIV-induced AIDS [8-10]). \nThe transcription factor Foxp3 is a 431-amino acid (48-kDa) protein expressed at very high levels in CD4+CD25hi T cells and has previously been shown to be absolutely critical for Treg development and function [11-14]. Foxp3 contains a proline-rich amino-terminal domain reported to function as a nuclear factor of activated T cells (NF-AT) and nuclear factor-kappaB (NF-kappaB) binding domain, a central region containing a zinc finger and leucine zipper potentially important for protein-protein interactions, and a carboxyl-terminal forkhead (FKH) domain required for nuclear localization and DNA-binding activity [14-16]. Functional inactivation of Foxp3 by genetic mutations affecting the Foxp3 coding region, as demonstrated in IPEX, or repression of Foxp3 expression by the HTLV-I-encoded transactivator protein Tax, as recently reported in patients with HAM/TSP, results in loss of regulatory activity in CD4+CD25hi T cells [4,8,17]. Although it is clear that Foxp3 regulates T cell proliferation and cytokine production, very little is known concerning the molecular mechanisms of Foxp3 function. \nThe first evidence to indicate how Foxp3 promotes the development and function of regulatory T cells came from a report by Ziegler and colleagues [16], which suggested that Foxp3 could inhibit transcriptional activation by physically interacting with forkhead binding sites located immediately adjacent to critical cis-acting NF-AT binding sites found in various cytokine promoters (e.g., IL-2 promoter). That study also demonstrated that Foxp3 could repress activation of a synthetic reporter vector containing an SV40 promoter and three tandem copies of a forkhead binding site. These results provided additional evidence suggesting that Foxp3 transcriptional repression was mediated by binding in a sequence-specific manner to promoters containing forkhead binding sites. A recent study by Bettelli and colleagues [15] further demonstrated that Foxp3 could inhibit NF-AT as well as NF-kappaB activation, although the mechanism of suppression was shown to involve direct protein-protein interactions between NF-AT or NF-kappaB and Foxp3 rather than binding of Foxp3 to promoter elements adjacent to cis-acting NF-AT or NF-kappaB sites. Collectively, these data suggested that Foxp3 may function as a transcriptional repressor, potentially through the formation of both DNA-protein and protein-protein interactions. \nIn the present study, we expanded upon these observations by defining additional requirements of Foxp3-mediated repression of NF-kappaB activation, and investigated whether Foxp3 could target additional signaling pathways by examining transcriptional activation of NF-kappaB-dependent and NF-kappaB-independent retroviral pathogens. The characterization of the molecular targets of Foxp3 and the mechanism(s) utilized by Foxp3 to support Treg development and function will aid in our understanding of the role Tregs play in the pathogenesis of human autoimmune disease. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "interactions", "start": 1535, "end": 1547}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1256, "end": 1261}]}, {"trigger": {"text": "binding", "start": 1637, "end": 1644}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1256, "end": 1261}]}, {"trigger": {"text": "interacting", "start": 2378, "end": 2389}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2317, "end": 2322}]}, {"trigger": {"text": "binding", "start": 2833, "end": 2840}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2784, "end": 2789}]}, {"trigger": {"text": "interactions", "start": 3133, "end": 3145}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 3177, "end": 3182}]}, {"trigger": {"text": "binding", "start": 3195, "end": 3202}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 3206, "end": 3211}]}, {"trigger": {"text": "interactions", "start": 3447, "end": 3459}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 3322, "end": 3327}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 1105, "end": 1114}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1062, "end": 1067}]}, {"trigger": {"text": "expression", "start": 1800, "end": 1810}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1794, "end": 1799}]}], "localization": [{"trigger": {"text": "localization", "start": 1616, "end": 1628}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1256, "end": 1261}, {"role": "ToLoc", "text": "nuclear", "start": 1608, "end": 1615}]}], "negative regulation": [{"trigger": {"text": "inactivation", "start": 1674, "end": 1686}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1690, "end": 1695}, {"role": "Cause", "text": "affecting", "start": 1717, "end": 1726}]}, {"trigger": {"text": "repression", "start": 1780, "end": 1790}, "arguments": [{"role": "Theme", "text": "expression", "start": 1800, "end": 1810}, {"role": "Cause", "text": "Tax", "start": 1856, "end": 1859}]}, {"trigger": {"text": "inhibit", "start": 2329, "end": 2336}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 2337, "end": 2363}, {"role": "Cause", "text": "interacting", "start": 2378, "end": 2389}]}], "positive regulation": [{"trigger": {"text": "important", "start": 1505, "end": 1514}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1256, "end": 1261}, {"role": "CSite", "text": "leucine zipper", "start": 1478, "end": 1492}, {"role": "Theme", "text": "interactions", "start": 1535, "end": 1547}]}, {"trigger": {"text": "required", "start": 1595, "end": 1603}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1256, "end": 1261}, {"role": "CSite", "text": "carboxyl-terminal forkhead (FKH) domain", "start": 1555, "end": 1594}, {"role": "Theme", "text": "localization", "start": 1616, "end": 1628}]}, {"trigger": {"text": "required", "start": 1595, "end": 1603}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1256, "end": 1261}, {"role": "CSite", "text": "carboxyl-terminal forkhead (FKH) domain", "start": 1555, "end": 1594}, {"role": "Theme", "text": "binding", "start": 1637, "end": 1644}]}, {"trigger": {"text": "transcriptional activation", "start": 2337, "end": 2363}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 2533, "end": 2537}, {"role": "Site", "text": "promoter", "start": 2538, "end": 2546}]}, {"trigger": {"text": "formation", "start": 3397, "end": 3406}, "arguments": [{"role": "Theme", "text": "interactions", "start": 3447, "end": 3459}]}], "regulation": [{"trigger": {"text": "affecting", "start": 1717, "end": 1726}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1731, "end": 1736}, {"role": "Site", "text": "coding region", "start": 1737, "end": 1750}]}]}}, "schema": []}
{"input": "Foxp3 Suppresses NF-kappaB Dependent Transcriptional Activation\nTo ascertain the molecular mechanisms by which Foxp3 functions to promote the regulatory function of CD4+CD25hi T cells, we first confirmed the function of Foxp3 as a repressor of activation of NF-kappaB, previously implicated as a target of other forkhead/winged-helix family transcription factors (e.g., Foxj1 and Foxo3a) [19,20]. We analyzed the effect of Foxp3 overexpression on NF-kappaB activation in HEK 293T cells in dose-response and time course analyses. Transfection of HEK 293T cells with an NF-kappaB luciferase reporter vector in the presence or absence of increasing concentrations of a Foxp3 expression vector or a control vector (enhanced green fluorescent protein [EGFP]) was performed, and cells were harvested after 24 h to assay for luciferase activity and Foxp3 mRNA expression. Results indicated that as the concentration of Foxp3 transfected into cells increases (from 50 to 2,400 ng), the level of NF-kappaB activation decreases proportionally (Figure 1A). Foxp3 mRNA was also assayed to monitor activity of the Foxp3 expression vector (Figure 1B). Since NF-kappaB activation was partially affected by transfection of high concentrations of the control vector, we determined the fold inhibition of NF-kappaB activation by Foxp3 compared to the control vector at each concentration (Figure 1A). Fold inhibition of NF-kappaB activation was directly proportional to the level of Foxp3 mRNA expression detected by real-time RT-PCR. To determine the level of Foxp3-mediated suppression of NF-kappaB activation over time, HEK 293T cells were transfected with an NF-kappaB luciferase reporter vector and an expression vector encoding Foxp3 or EGFP (control vector) and harvested over 4 d. As shown in Figure 1C, NF-kappaB activation was suppressed by overexpression of Foxp3 at all time points. Extending these results from established, in vitro HEK cell lines to primary human lymphocytes, overexpression of Foxp3 in purified CD4+ T cells from three healthy donors also down-regulated the steady-state level of NF-kappaB activation (Figure 1D). These results recapitulate those from Bettelli and colleagues [15] demonstrating that Foxp3 functions, in part, to block NF-kappaB-dependent transcription in human cell lines as well as in primary human CD4+ T cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 672, "end": 682}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 666, "end": 671}]}, {"trigger": {"text": "concentration", "start": 895, "end": 908}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 912, "end": 917}]}, {"trigger": {"text": "expression", "start": 1107, "end": 1117}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1101, "end": 1106}]}, {"trigger": {"text": "expression", "start": 1689, "end": 1699}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1716, "end": 1721}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 429, "end": 443}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 423, "end": 428}]}, {"trigger": {"text": "increases", "start": 941, "end": 950}, "arguments": [{"role": "Theme", "text": "concentration", "start": 895, "end": 908}]}, {"trigger": {"text": "overexpression", "start": 1833, "end": 1847}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1851, "end": 1856}]}, {"trigger": {"text": "overexpression", "start": 1973, "end": 1987}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1991, "end": 1996}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 848, "end": 863}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 842, "end": 847}]}, {"trigger": {"text": "mRNA expression", "start": 1471, "end": 1486}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1465, "end": 1470}]}]}}, "schema": []}
{"input": "The Carboxyl-Terminal FKH Domain Is Not Required for Suppression of NF-kappaB Activation in T Cells\nTo define the requirements of Foxp3 with respect to inhibition of NF-kappaB-dependent transcription, we utilized a mutant of Foxp3 lacking the FKH domain (Figure 2A) [16], similar to the scurfy mutant Foxp3 of mice, and a mutant Foxp3 protein from a patient with IPEX [4,11,14,17]. Unlike full-length Foxp3, which localizes almost exclusively to the nucleus and can bind in a sequence-specific manner to forkhead binding sites, the DeltaFKH mutant fails to localize to the nucleus and thus cannot interact with promoter elements or nuclear proteins [16]. Therefore, we utilized the DeltaFKH mutant to determine whether nuclear localization (or other function associated with the FKH domain) of Foxp3 was a prerequisite for inhibition of NF-kappaB activation. Although Foxp3 interaction with NF-kappaB presumably takes place in the nucleus, it may also be possible for a cytoplasmic Foxp3 protein to bind to NF-kappaB in the cytoplasm and prevent localization to the nucleus following an activation stimulus. Overexpression of full-length Foxp3, but not of DeltaFKH, was able to suppress activation of a cotransfected NF-kappaB reporter vector in HEK 293T cells (Figure 2B). Both Foxp3 and DeltaFKH were expressed at very high levels following transfection as detected by real-time RT-PCR (unpublished data). These data appear to suggest that the carboxyl-terminal FKH domain is critically important for Foxp3 to down-regulate NF-kappaB-dependent transcription. However, NF-kappaB activation was blocked to a similar extent by both full-length Foxp3 and DeltaFKH in Jurkat T cells (Figure 2C) and primary human CD4+ T cells (Figure 2D). Western blot analysis of NF-kappaB p65 expression demonstrated that Foxp3 and DeltaFKH does not block NF-kappaB activation at the level of p65 protein expression (Figure 2E). These results are very interesting with respect to Foxp3 function, because they suggest that the carboxyl-terminal FKH domain, and possibly nuclear localization, are dispensable for Foxp3 function in T cell populations. Alternative interpretations may include the possibility that the localization of DeltaFKH differ between epithelial cells and T cells. In either case, these results suggest a cell type-specific mechanism of action for this Foxp3 mutant. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 466, "end": 470}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 401, "end": 406}]}, {"trigger": {"text": "interact", "start": 597, "end": 605}, "arguments": [{"role": "Theme", "text": "DeltaFKH mutant", "start": 532, "end": 547}]}, {"trigger": {"text": "interaction", "start": 874, "end": 885}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 868, "end": 873}]}, {"trigger": {"text": "bind", "start": 999, "end": 1003}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 982, "end": 987}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1775, "end": 1785}, "arguments": [{"role": "Theme", "text": "p65", "start": 1771, "end": 1774}]}, {"trigger": {"text": "expression", "start": 1887, "end": 1897}, "arguments": [{"role": "Theme", "text": "p65", "start": 1875, "end": 1878}]}], "localization": [{"trigger": {"text": "localizes", "start": 414, "end": 423}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 401, "end": 406}, {"role": "ToLoc", "text": "nucleus", "start": 450, "end": 457}]}, {"trigger": {"text": "localize", "start": 557, "end": 565}, "arguments": [{"role": "Theme", "text": "DeltaFKH mutant", "start": 532, "end": 547}, {"role": "ToLoc", "text": "nucleus", "start": 573, "end": 580}]}, {"trigger": {"text": "localization", "start": 727, "end": 739}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 719, "end": 726}, {"role": "Theme", "text": "Foxp3", "start": 794, "end": 799}]}, {"trigger": {"text": "localization", "start": 1046, "end": 1058}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 982, "end": 987}, {"role": "ToLoc", "text": "nucleus", "start": 1066, "end": 1073}]}, {"trigger": {"text": "localization", "start": 2059, "end": 2071}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 2051, "end": 2058}, {"role": "Theme", "text": "Foxp3", "start": 2093, "end": 2098}]}, {"trigger": {"text": "localization", "start": 2196, "end": 2208}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 2212, "end": 2220}]}], "negative regulation": [{"trigger": {"text": "lacking", "start": 231, "end": 238}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 225, "end": 230}, {"role": "Site", "text": "FKH domain", "start": 243, "end": 253}]}, {"trigger": {"text": "prevent", "start": 1038, "end": 1045}, "arguments": [{"role": "Cause", "text": "bind", "start": 999, "end": 1003}, {"role": "Theme", "text": "localization", "start": 1046, "end": 1058}]}, {"trigger": {"text": "block", "start": 1832, "end": 1837}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1804, "end": 1809}, {"role": "Theme", "text": "expression", "start": 1887, "end": 1897}]}, {"trigger": {"text": "block", "start": 1832, "end": 1837}, "arguments": [{"role": "Cause", "text": "DeltaFKH", "start": 1814, "end": 1822}, {"role": "Theme", "text": "expression", "start": 1887, "end": 1897}]}], "positive regulation": [{"trigger": {"text": "following", "start": 1074, "end": 1083}, "arguments": [{"role": "Theme", "text": "localization", "start": 1046, "end": 1058}]}, {"trigger": {"text": "Overexpression", "start": 1108, "end": 1122}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1138, "end": 1143}]}, {"trigger": {"text": "Overexpression", "start": 1108, "end": 1122}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 1156, "end": 1164}]}, {"trigger": {"text": "expressed", "start": 1303, "end": 1312}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1279, "end": 1284}]}, {"trigger": {"text": "expressed", "start": 1303, "end": 1312}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 1289, "end": 1297}]}, {"trigger": {"text": "following", "start": 1333, "end": 1342}, "arguments": [{"role": "Theme", "text": "expressed", "start": 1303, "end": 1312}]}]}}, "schema": []}
{"input": "Foxp3 Suppresses HIV-1 Gene Expression in Part through Blocking Activation of NF-kappaB\nIf Foxp3 functions as a repressor of NF-kappaB-dependent gene expression, then we hypothesized that Foxp3 overexpression could selectively down-regulate transcription from promoters previously shown to be responsive to NF-kappaB. To address this question, we examined the transcriptional activation of the HIV-1 LTR, which contains two tandem cis-acting NF-kappaB binding sites located between positions -102 and -81 with respect to the transcription initiation site [21]. NF-kappaB plays a crucial role in regulating gene expression directed from the HIV-1 LTR in CD4+ T cells [21]. Overexpression of full-length Foxp3, but not DeltaFKH, in HEK 293T cells was able to inhibit basal activation of the HIV-1 LTR (Figure 3A), similar to what was previously demonstrated with the synthetic NF-kappaB reporter vector (Figure 2B). Furthermore, HIV-1 LTR activation was suppressed by full-length Foxp3 and DeltaFKH in Jurkat T cells (Figure 3B). To demonstrate that Foxp3-mediated HIV-1 LTR repression was associated with interactions with NF-kappaB bound to the HIV-1 LTR, we compared basal activation of the HIV-1 LTR or an identical HIV-1 LTR lacking the NF-kappaB sites located between -102 and -81 (HIV-1 Delta-kappaB LTR) (Figure 3C). This mutant HIV-1 LTR construct exhibited reduced levels of transcription compared to the parental HIV-1 LTR in purified healthy donor CD4+ T cells (unpublished data). However, directly comparing the effect of Foxp3 overexpression on the activation of these two viral promoters demonstrated that Foxp3 was more capable of suppressing transcriptional activation of the HIV-1 LTR (Figure 3D) compared to the mutated HIV-1 LTR (Figure 3E). These results suggest that Foxp3 down-regulation of HIV-1 LTR activation was mediated at least in part by cis-acting NF-kappaB binding sites. Residual levels of inhibition of the HIV-1 Delta-kappaB LTR by Foxp3 may be due to NF-AT binding sites located upstream of the NF-kappaB sites within the HIV-1 LTR [22,23]. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "interactions", "start": 1104, "end": 1116}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1048, "end": 1053}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 194, "end": 208}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 188, "end": 193}]}, {"trigger": {"text": "Overexpression", "start": 672, "end": 686}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 702, "end": 707}]}, {"trigger": {"text": "Overexpression", "start": 672, "end": 686}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 717, "end": 725}]}, {"trigger": {"text": "overexpression", "start": 1539, "end": 1553}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1533, "end": 1538}]}]}}, "schema": []}
{"input": "The Transactivation Functions of HTLV-I Tax Are Suppressed by Foxp3\nPrevious studies by Bettelli and colleagues have demonstrated that Foxp3 can repress both the basal levels of NF-kappaB activation as well as tumor necrosis factor-alpha-stimulated NF-kappaB activation [15]. Our next step was to determine whether Foxp3 could also suppress the activation of NF-kappaB caused by a strong viral transactivator protein. HTLV-I encodes a multifunctional transactivator protein, Tax, capable of activating both the NF-kappaB and CREB pathways [24-29]. Since the HTLV-I Tax protein can function at multiple levels in both the cytoplasm and the nucleus to stimulate activation of NF-kappaB [28,29], we hypothesized that overexpression of Foxp3 may interfere with this process. However, since Tax-dependent HTLV-I gene expression is independent of NF-kappaB [18], we also hypothesized that Foxp3 would not affect Tax-dependent activation of the HTLV-I LTR. To test these hypotheses, we overexpressed HTLV-I Tax, full-length Foxp3, and/or DeltaFKH in HEK 293T cells cotransfected with an HTLV-I LTR or NF-kappaB reporter vector. As shown in Figure 4A, HTLV-I Tax strongly up-regulated NF-kappaB-dependent transcriptional activation (~60-fold). Interestingly, overexpression of Foxp3, but not DeltaFKH, suppressed Tax-mediated activation of NF-kappaB-dependent transcription. These observations further suggest that the carboxyl-terminal FKH domain is required for inhibiting activation of NF-kappaB in the presence of Tax in HEK 293T cells, strikingly similar to the requirements of Foxp3 inhibition of basal NF-kappaB activation shown in Figure 2B. Transactivation of the HTLV-I LTR was stimulated about 55-fold by overexpression of Tax (Figure 4B), while transfection of Foxp3 suppressed Tax-dependent HTLV-I LTR activation, although HTLV-I LTR activation in the presence or absence of Tax is independent of NF-kappaB or NF-AT (another transcriptional activator known to interact with Foxp3). Furthermore, overexpression of DeltaFKH also led to suppression of HTLV-I transactivation by Tax to a similar extent as full-length Foxp3 (Figure 4B). The suppressive effects shown in Figure 4A and 4B were not the result of Foxp3 down-regulating the expression of the transfected Tax plasmid as determined by real-time RT-PCR (Figure 4C). These results strongly suggest that Foxp3 interacts with transcriptional regulators in addition to NF-kappaB and NF-AT, and that the carboxyl-terminal FKH domain, and therefore localization to the nucleus, are not required for inhibition of Tax-mediated HTLV-I LTR activation (even in HEK 293T cells). \nTo determine whether Foxp3 inhibited the transactivation functions of Tax by directly associating with this viral protein, we generated an expression vector in which HTLV-I Tax was fused in-frame to the carboxyl terminus of the Gal4 DNA-binding domain (Gal4-BD). This Gal4-BD-Tax fusion protein activated transcription of a synthetic promoter containing five Gal4 binding sites, while Gal4-BD was insufficient to stimulate transcription by itself (Figure 4D). Transactivation of the Gal4-resposive promoter by Gal4-BD-Tax remained relatively unaffected by overexpression of either EGFP (control), Foxp3, or DeltaFKH, suggesting that Foxp3 does not repress Tax transactivation by directly interfacing with the HTLV-I Tax protein. To confirm that Foxp3 had a direct effect on HTLV-I replication, we transfected HEK 293T cells with a well-characterized HTLV-I infectious molecular clone (termed ACH) [30] in the presence of full-length Foxp3, DeltaFKH, or control vector. ACH has been previously shown to direct the expression of viral antigens, produce infectious virus, and transform CD4+ T cells both in vitro and in vivo [31,32]. After 24 h, the amount of viral antigen expression, in this case Tax mRNA, was detected by a sensitive real-time RT-PCR assay. As illustrated in Figure 5, the level of Tax mRNA synthesized from ACH was down-regulated in the presence of Foxp3 compared to the level produced in the presence of the control vector. DeltaFKH did not have a discernable affect on Tax expression. These data indicate that Foxp3 is capable of repressing the expression of Tax from an infectious HTLV-I molecular clone. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 1965, "end": 1973}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1979, "end": 1984}]}, {"trigger": {"text": "interacts", "start": 2368, "end": 2377}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2362, "end": 2367}]}, {"trigger": {"text": "associating", "start": 2715, "end": 2726}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2650, "end": 2655}, {"role": "Theme2", "text": "Tax", "start": 2699, "end": 2702}]}], "gene expression": [{"trigger": {"text": "overexpression", "start": 1251, "end": 1265}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1269, "end": 1274}]}, {"trigger": {"text": "overexpression", "start": 1251, "end": 1265}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 1284, "end": 1292}]}, {"trigger": {"text": "transfection", "start": 1749, "end": 1761}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1765, "end": 1770}]}, {"trigger": {"text": "expression", "start": 2237, "end": 2247}, "arguments": [{"role": "Theme", "text": "Tax", "start": 2267, "end": 2270}]}, {"trigger": {"text": "expression", "start": 4122, "end": 4132}, "arguments": [{"role": "Theme", "text": "Tax", "start": 4118, "end": 4121}]}, {"trigger": {"text": "expression", "start": 4194, "end": 4204}, "arguments": [{"role": "Theme", "text": "Tax", "start": 4208, "end": 4211}]}], "localization": [{"trigger": {"text": "localization", "start": 2503, "end": 2515}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2362, "end": 2367}, {"role": "ToLoc", "text": "nucleus", "start": 2523, "end": 2530}]}], "negative regulation": [{"trigger": {"text": "down-regulating", "start": 2217, "end": 2232}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 2211, "end": 2216}, {"role": "Theme", "text": "expression", "start": 2237, "end": 2247}]}, {"trigger": {"text": "interfacing", "start": 3317, "end": 3328}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 3262, "end": 3267}, {"role": "Theme", "text": "Tax", "start": 3345, "end": 3348}]}, {"trigger": {"text": "down-regulated", "start": 3962, "end": 3976}, "arguments": [{"role": "Theme", "text": "synthesized", "start": 3937, "end": 3948}, {"role": "Cause", "text": "Foxp3", "start": 3996, "end": 4001}]}, {"trigger": {"text": "repressing", "start": 4179, "end": 4189}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 4159, "end": 4164}, {"role": "Theme", "text": "expression", "start": 4194, "end": 4204}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 714, "end": 728}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 732, "end": 737}]}, {"trigger": {"text": "overexpressed", "start": 979, "end": 992}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1000, "end": 1003}]}, {"trigger": {"text": "overexpressed", "start": 979, "end": 992}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1017, "end": 1022}]}, {"trigger": {"text": "overexpressed", "start": 979, "end": 992}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 1031, "end": 1039}]}, {"trigger": {"text": "overexpression", "start": 1708, "end": 1722}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1726, "end": 1729}]}, {"trigger": {"text": "overexpression", "start": 2000, "end": 2014}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 2018, "end": 2026}]}, {"trigger": {"text": "overexpression", "start": 3185, "end": 3199}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 3226, "end": 3231}]}, {"trigger": {"text": "overexpression", "start": 3185, "end": 3199}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 3236, "end": 3244}]}], "regulation": [{"trigger": {"text": "affect", "start": 4108, "end": 4114}, "arguments": [{"role": "Cause", "text": "DeltaFKH", "start": 4072, "end": 4080}, {"role": "Theme", "text": "expression", "start": 4122, "end": 4132}]}], "transcription": [{"trigger": {"text": "expression", "start": 3800, "end": 3810}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3825, "end": 3828}]}, {"trigger": {"text": "synthesized", "start": 3937, "end": 3948}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3928, "end": 3931}]}, {"trigger": {"text": "produced", "start": 4024, "end": 4032}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3928, "end": 3931}]}]}}, "schema": []}
{"input": "Increased Foxp3 Protein Expression Is Associated with Low HTLV-I Proviral Load\nSince Foxp3 is expressed almost exclusively within CD4+CD25+ T cells, a major viral reservoir for HTLV-I [33], it was important to determine whether there was an association between Foxp3 and HTLV-I replication in infected patients. We therefore quantitated the Foxp3 protein expression in CD4+CD25+ T cells by flow cytometry and the HTLV-I proviral load (a surrogate marker of viral replication) by real-time PCR from eight patients with HAM/TSP and eight asymptomatic carriers (ACs). The data from this analysis is summarized in Table 1. As expected, patients with HAM/TSP exhibited significantly higher proviral loads (indicated as HTLV-I proviral DNA copies/100 cells) (34.68 +/- 23.19) compared to ACs (4.75 +/- 5.47) (p = 0.0008). The percentage of Foxp3+ cells within the CD4+CD25+ T cell population was significantly greater in ACs (43.23 +/- 12.95) than in HAM/TSP patients (18.59 +/- 5.77) (p = 0.0033). These data suggest that high levels of Foxp3 protein expression are associated with reduced HTLV-I replication in vivo. They also support our recent reports that high proviral loads, which have been shown to correlate with high Tax mRNA in HTLV-I-infected patients, are associated with reduced Foxp3 expression [8,34]. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 24, "end": 34}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 10, "end": 15}]}, {"trigger": {"text": "expressed", "start": 94, "end": 103}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 85, "end": 90}]}, {"trigger": {"text": "expression", "start": 355, "end": 365}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 341, "end": 346}]}, {"trigger": {"text": "expression", "start": 1046, "end": 1056}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1032, "end": 1037}]}, {"trigger": {"text": "expression", "start": 1293, "end": 1303}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1287, "end": 1292}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 1279, "end": 1286}, "arguments": [{"role": "Theme", "text": "expression", "start": 1293, "end": 1303}]}], "positive regulation": [{"trigger": {"text": "Increased", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "Expression", "start": 24, "end": 34}]}, {"trigger": {"text": "high", "start": 1017, "end": 1021}, "arguments": [{"role": "Theme", "text": "expression", "start": 1046, "end": 1056}]}, {"trigger": {"text": "high", "start": 1216, "end": 1220}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1221, "end": 1224}]}]}}, "schema": []}
{"input": "CREB Is a Target for Transcriptional Repression by Foxp3\nAlthough Foxp3 could down-regulate Tax-dependent transactivation of the HTLV-I LTR (Figure 4B) and inhibit Tax expression from an infectious molecular clone (Figure 5), Foxp3 failed to modulate Tax function in the absence of the viral promoter (Figure 4D). These results led us to hypothesize that Foxp3 acts on HTLV-I gene expression by interacting with proteins important for driving HTLV-I LTR activity in vivo. Previous studies have demonstrated that the Tax-responsive elements within the HTLV-I LTR play a crucial role in driving Tax-mediated transactivation of the HTLV-I LTR [18]. The Tax-responsive elements have been shown to resemble CREB binding sites, bind CREB in vitro and in vivo, and facilitate HTLV-I LTR activation both in the presence and in the absence of Tax [35,36]. Ching and colleagues [18] demonstrated that addition of a dominant-negative CREB expression vector resulted in nearly complete inhibition of Tax-mediated activation of the HTLV-I LTR, while blocking NF-kappaB activation by addition of a dominant-negative IKKbeta expression vector had no effect on Tax transactivation of the HTLV-I LTR. Therefore, we hypothesized that Foxp3 may inhibit Tax transactivation of the HTLV-I LTR via disruption of the CREB signaling pathway. To test this possibility, HEK 293T cells were transfected with an HTLV-I LTR or synthetic CREB reporter vector along with a control expression vector (EGFP) or expression vectors encoding Foxp3 or DeltaFKH. As shown in Figure 6A, Foxp3 down-regulated basal activation of the HTLV-I LTR and transcription of a synthetic CREB reporter vector, suggesting that Foxp3 down-regulates HTLV-I LTR activation by targeting the CREB pathway. Deletion of the FKH domain of Foxp3 dampened the suppressive effect of Foxp3, but did not completely abrogate suppression, as is seen with NF-kappaB-responsive promoters in HEK 293T cells. Like NF-kappaB activation, CREB transcriptional activation was also suppressed by expression of Foxp3, and to a similar extent DeltaFKH, in healthy donor CD4+ T cells (Figure 6B). Similarly, Foxp3 and DeltaFKH also repressed basal HTLV-I LTR activation in primary human CD4+ T cells (Figure 6C). To our knowledge, this is the first evidence implicating CREB as a molecular target of Foxp3. As observed with NF-kappaB activation, DeltaFKH was a more potent inhibitor of CREB activation in CD4+ T cells than in HEK 293T cells, further indicating that a cell type-specific mechanism of action may govern the function of this Foxp3 mutant. \nTo determine whether Foxp3 functioned by directly signaling through CREB, we utilized expression vectors encoding CREB-1 or c-Jun (a member of the activator protein 1 family of transcription factors) fused in-frame to the Gal4-BD (Gal4-BD-CREB-1 and Gal4-BD-c-Jun). As shown in Figure 6D, activation of a Gal4-responsive reporter vector by Gal4-BD-CREB-1 was down-regulated by Foxp3 compared to control vector (EGFP), indicating that Foxp3 functions by directly or indirectly interacting with CREB-1. However, Foxp3 failed to markedly affect transcriptional activation of Gal4-BD-c-Jun (c-Jun has also been demonstrated to bind to the HTLV-I LTR) and Gal4-BD-Tax (see Figure 5). Importantly, the mechanism of Foxp3-mediated inhibition of CREB-dependent transcription was not due to a block in CREB-1 protein expression, as determined by Western blot analysis (Figure 6E). Although these results demonstrate that Foxp3 functions as a co-repressor of CREB activation (in addition to NF-kappaB and NF-AT), we were unable to detect a direct physical interaction between CREB-1 and Foxp3 by coimmunoprecipitation or mammalian two-hybrid analysis (unpublished data). Therefore, our data suggest that Foxp3 may interfere with CREB signaling at an upstream event, such as phosphorylation of CREB or recruitment/function of coactivator proteins CREB-binding protein (CBP)/p300. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacting", "start": 395, "end": 406}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 355, "end": 360}]}, {"trigger": {"text": "interacting", "start": 3051, "end": 3062}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 3009, "end": 3014}, {"role": "Theme2", "text": "CREB-1", "start": 3068, "end": 3074}]}, {"trigger": {"text": "bind", "start": 3198, "end": 3202}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 3162, "end": 3167}]}, {"trigger": {"text": "interaction", "start": 3621, "end": 3632}, "arguments": [{"role": "Theme", "text": "CREB-1", "start": 3641, "end": 3647}, {"role": "Theme2", "text": "Foxp3", "start": 3652, "end": 3657}]}, {"trigger": {"text": "recruitment", "start": 3866, "end": 3877}, "arguments": [{"role": "Theme", "text": "CREB-binding protein", "start": 3911, "end": 3931}]}, {"trigger": {"text": "recruitment", "start": 3866, "end": 3877}, "arguments": [{"role": "Theme", "text": "p300", "start": 3938, "end": 3942}]}], "gene expression": [{"trigger": {"text": "expression", "start": 168, "end": 178}, "arguments": [{"role": "Theme", "text": "Tax", "start": 164, "end": 167}]}, {"trigger": {"text": "expression", "start": 1110, "end": 1120}, "arguments": [{"role": "Theme", "text": "IKKbeta", "start": 1102, "end": 1109}]}, {"trigger": {"text": "expression", "start": 2020, "end": 2030}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2034, "end": 2039}]}, {"trigger": {"text": "expression", "start": 2020, "end": 2030}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 2065, "end": 2073}]}, {"trigger": {"text": "expression", "start": 2661, "end": 2671}, "arguments": [{"role": "Theme", "text": "Gal4-BD-CREB-1", "start": 2806, "end": 2820}]}, {"trigger": {"text": "expression", "start": 2661, "end": 2671}, "arguments": [{"role": "Theme", "text": "Gal4-BD-c-Jun", "start": 2825, "end": 2838}]}, {"trigger": {"text": "expression", "start": 3383, "end": 3393}, "arguments": [{"role": "Theme", "text": "CREB-1", "start": 3368, "end": 3374}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 156, "end": 163}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 66, "end": 71}, {"role": "Theme", "text": "expression", "start": 168, "end": 178}]}, {"trigger": {"text": "Deletion", "start": 1749, "end": 1757}, "arguments": [{"role": "Site", "text": "FKH domain", "start": 1765, "end": 1775}, {"role": "Theme", "text": "Foxp3", "start": 1779, "end": 1784}]}, {"trigger": {"text": "inhibitor", "start": 2394, "end": 2403}, "arguments": [{"role": "Cause", "text": "DeltaFKH", "start": 2367, "end": 2375}, {"role": "Theme", "text": "activation", "start": 2412, "end": 2422}]}, {"trigger": {"text": "block", "start": 3359, "end": 3364}, "arguments": [{"role": "Theme", "text": "expression", "start": 3383, "end": 3393}]}, {"trigger": {"text": "interfere", "start": 3779, "end": 3788}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 3769, "end": 3774}, {"role": "Theme", "text": "recruitment", "start": 3866, "end": 3877}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 2412, "end": 2422}, "arguments": [{"role": "Theme", "text": "CREB", "start": 2407, "end": 2411}]}], "regulation": [{"trigger": {"text": "modulate", "start": 242, "end": 250}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 226, "end": 231}, {"role": "Theme", "text": "Tax", "start": 251, "end": 254}]}]}}, "schema": []}
{"input": "Foxp3 Antagonizes CREB Transcriptional Activation by Disrupting Coactivator Recruitment\nStimulation of CREB-dependent transcription by reagents that activate adenylate cyclase and increase cAMP levels (e.g., forskolin) increase the transactivation potential of CREB through phosphorylation of serine 133 by protein kinase A, which permits binding and recruitment of coactivators CBP/p300 to the promoter [37,38]. Phosphorylation of serine 133 does not, however, affect the DNA-binding activity of CREB in most cases [39-41]. Addition of forskolin to HEK 293T cells stimulated activation of a CREB reporter vector about 65 fold (Figure 7A). Overexpression of Foxp3 was capable of down-regulating forskolin-induced CREB transcriptional activation. The functional interaction between Foxp3 and CREB did not affect the DNA-binding activity of CREB-1, but did show a modest decrease in activating transcription factor 2 (ATF-2) DNA-binding activity in the presence of forskolin as determined by transcription factor ELISA (Figure 7B). \nWhile Foxp3 has been shown to bind to and repress activation of both NF-kappaB and NF-AT, exactly how Foxp3 functions to bring about this affect has not been elucidated. To determine how Foxp3 blocks CREB-dependent transcription, we examined whether Foxp3 was capable of (1) disrupting the recruitment of coactivator proteins and/or (2) preventing phosphorylation of CREB at serine 133 (which is a prerequisite for coactivator recruitment). Since both of these events are required for CREB-dependent gene expression, we hypothesized that Foxp3 may affect CREB activation at both steps. To determine whether Foxp3 can disrupt the function/recruitment of the coactivator protein p300, we introduced a Gal4 reporter vector and a Gal4-BD-CREB-1 expression vector into HEK 293T cells in the absence or presence of Foxp3, p300, and/or control expression vectors (Figure 7C). As expected, p300 overexpression stimulated transcription of the Gal4-BD-CREB-1 fusion protein. Foxp3, again, repressed basal levels of Gal4-BD-CREB-1 activation by more than 2-fold, while effectively neutralizing Gal4-BD-CREB-1 activation in the presence of p300. We next analyzed the effect of Foxp3 on phosphorylation of CREB at serine 133 in forskolin-treated HEK 293T cells by Western blot analysis. Overexpression of Foxp3 failed to reduce the detectable levels of CREB phosphorylation using a phosphospecific antibody for CREB-1 (unpublished data). However, when we attempted to determine whether Foxp3 could physically interact with the coactivator protein p300, we found that p300 immunoprecipitated Foxp3 when both proteins were overexpressed in HEK 293T cells (Figure 7D). Collectively, these results suggest that Foxp3 antagonizes CREB-dependent gene expression by directly interacting with coactivator p300 and interfering with its function and/or recruitment to CREB-responsive promoter sequences. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 339, "end": 346}, "arguments": [{"role": "Theme", "text": "CBP", "start": 379, "end": 382}]}, {"trigger": {"text": "binding", "start": 339, "end": 346}, "arguments": [{"role": "Theme", "text": "p300", "start": 383, "end": 387}]}, {"trigger": {"text": "interaction", "start": 761, "end": 772}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 781, "end": 786}]}, {"trigger": {"text": "binding", "start": 819, "end": 826}, "arguments": [{"role": "Theme", "text": "CREB-1", "start": 839, "end": 845}]}, {"trigger": {"text": "binding", "start": 927, "end": 934}, "arguments": [{"role": "Theme", "text": "activating transcription factor 2", "start": 881, "end": 914}]}, {"trigger": {"text": "bind", "start": 1061, "end": 1065}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1037, "end": 1042}]}, {"trigger": {"text": "interact", "start": 2527, "end": 2535}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2504, "end": 2509}, {"role": "Theme2", "text": "p300", "start": 2565, "end": 2569}]}, {"trigger": {"text": "immunoprecipitated", "start": 2590, "end": 2608}, "arguments": [{"role": "Theme", "text": "p300", "start": 2585, "end": 2589}, {"role": "Theme2", "text": "Foxp3", "start": 2609, "end": 2614}]}, {"trigger": {"text": "interacting", "start": 2786, "end": 2797}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2725, "end": 2730}, {"role": "Theme2", "text": "p300", "start": 2815, "end": 2819}]}, {"trigger": {"text": "recruitment", "start": 2861, "end": 2872}, "arguments": [{"role": "Theme", "text": "p300", "start": 2815, "end": 2819}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1772, "end": 1782}, "arguments": [{"role": "Theme", "text": "Gal4-BD-CREB-1", "start": 1757, "end": 1771}]}, {"trigger": {"text": "expression", "start": 1868, "end": 1878}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1840, "end": 1845}]}, {"trigger": {"text": "expression", "start": 1868, "end": 1878}, "arguments": [{"role": "Theme", "text": "p300", "start": 1847, "end": 1851}]}, {"trigger": {"text": "overexpressed", "start": 2639, "end": 2652}, "arguments": [{"role": "Theme", "text": "p300", "start": 2585, "end": 2589}]}, {"trigger": {"text": "overexpressed", "start": 2639, "end": 2652}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2609, "end": 2614}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 869, "end": 877}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 781, "end": 786}, {"role": "Theme", "text": "binding", "start": 927, "end": 934}]}, {"trigger": {"text": "repressed", "start": 2010, "end": 2019}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1996, "end": 2001}, {"role": "Theme", "text": "activation", "start": 2051, "end": 2061}]}, {"trigger": {"text": "neutralizing", "start": 2101, "end": 2113}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1996, "end": 2001}, {"role": "Theme", "text": "activation", "start": 2129, "end": 2139}]}, {"trigger": {"text": "interfering", "start": 2824, "end": 2835}, "arguments": [{"role": "Cause", "text": "interacting", "start": 2786, "end": 2797}, {"role": "Theme", "text": "recruitment", "start": 2861, "end": 2872}]}], "positive regulation": [{"trigger": {"text": "permits", "start": 331, "end": 338}, "arguments": [{"role": "Theme", "text": "binding", "start": 339, "end": 346}]}, {"trigger": {"text": "Overexpression", "start": 640, "end": 654}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 658, "end": 663}]}, {"trigger": {"text": "overexpression", "start": 1918, "end": 1932}, "arguments": [{"role": "Theme", "text": "p300", "start": 1913, "end": 1917}]}, {"trigger": {"text": "stimulated", "start": 1933, "end": 1943}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 1918, "end": 1932}, {"role": "Theme", "text": "transcription", "start": 1944, "end": 1957}]}, {"trigger": {"text": "activation", "start": 2051, "end": 2061}, "arguments": [{"role": "Theme", "text": "Gal4-BD-CREB-1", "start": 2036, "end": 2050}]}, {"trigger": {"text": "activation", "start": 2129, "end": 2139}, "arguments": [{"role": "Theme", "text": "Gal4-BD-CREB-1", "start": 2114, "end": 2128}]}, {"trigger": {"text": "Overexpression", "start": 2305, "end": 2319}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 2323, "end": 2328}]}, {"trigger": {"text": "when", "start": 2615, "end": 2619}, "arguments": [{"role": "Theme", "text": "immunoprecipitated", "start": 2590, "end": 2608}, {"role": "Cause", "text": "overexpressed", "start": 2639, "end": 2652}]}], "regulation": [{"trigger": {"text": "affect", "start": 804, "end": 810}, "arguments": [{"role": "Cause", "text": "interaction", "start": 761, "end": 772}, {"role": "Theme", "text": "binding", "start": 819, "end": 826}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1944, "end": 1957}, "arguments": [{"role": "Theme", "text": "Gal4-BD-CREB-1", "start": 1965, "end": 1979}]}]}}, "schema": []}
{"input": "Discussion\nIn the present study, we show that Foxp3 functions as a potent repressor of NF-kappaB- and CREB-dependent transcriptional activation. Furthermore, the carboxyl-terminal FKH domain appears to be dispensable for mediating these effects, at least in T cell populations. This observation may become important in light of recent reports suggesting that Foxp3 expression in thymic epithelial cells was crucial for directing development of T cells in the thymus [42]. Interestingly, the majority of the genetic mutations associated with IPEX, a severe autoimmune disorder caused by functional inactivation of Foxp3, map to the carboxyl-terminal FKH domain or the leucine zipper domain in the central region of the protein. Only one mutation associated with IPEX to date has been mapped to the amino-terminal proline-rich region [43]. It is possible that the FKH domain has a complex tertiary structure that is particularly sensitive to misfolding caused by genetic mutations and that an intact FKH domain is absolutely critical for promoting Foxp3 function in the nucleus, whereas the structure of the amino-terminal proline-rich region may tolerate certain mutations as long as the NF-kappaB/NF-AT binding motif remains unaltered. This motif may also include the zinc finger domain. A logical region that may be targeted by the amino-terminal proline-rich region of Foxp3 is the Rel homology domain found in both NF-kappaB and NF-AT family proteins. A region that may also be important with respect to Foxp3 function is the leucine zipper domain, as demonstrated by the number of mutations associated with IPEX that have been mapped in this region of Foxp3. The role of this domain in Foxp3 function remains uncharacterized, but may play a role in dimer formation as it does in other Foxp family members [44]. \nBecause the pathogenesis of a number of retroviral-induced immunologic disorders such as HIV-1/AIDS and HTLV-I/HAM/TSP have been associated with dysregulation of Foxp3 expression [8,45], we also examined the role of Foxp3 in retroviral gene expression. HIV-1 LTR activation in CD4+ T cells is critically dependent on two tandem NF-kappaB sites located between nucleotide positions -102 and -81 within the HIV-1 enhancer region, whereas HTLV-I LTR activation in the presence or absence of the HTLV-I-encoded transactivator protein Tax is independent of NF-kappaB [18]. To our knowledge for the first time, Foxp3 was shown to have a direct effect on HIV-1 LTR transcription. Deletion of the NF-kappaB sites within the HIV-1 enhancer region reduced the responsiveness of the HIV-1 LTR to Foxp3-mediated suppression. In addition, the FKH domain of Foxp3 was required for this inhibitory effect in HEK 293T cells, but not in Jurkat T cells, similar to Foxp3-mediated suppression of a synthetic NF-kappaB reporter. The direct effect of Foxp3 down-regulating HIV-1 gene expression correlates well with recently reported evidence indicating that higher regulatory activity of CD4+CD25+ T cells from HIV-1-infected patients was associated with lower HIV-1 viral loads in these patients [46]. \nFoxp3 also affected two well-known functions of HTLV-I Tax: transactivation of the NF-kappaB pathway and, most surprisingly, transactivation of the HTLV-I LTR. Transactivation of the HTLV-I LTR by Tax involves the interaction of ATF/CREB factors with Tax in the nucleus. Binding of Tax enhances ATF/CREB dimerization and promotes assembly of Tax-ATF/CREB complexes onto specific sequences in the viral promoter known as Tax-responsive elements. This series of steps allows Tax to recruit coactivator proteins CBP/p300 to the viral promoter and facilitate a high level of viral gene expression [24-26]. Transactivation of the NF-kappaB pathway by Tax was inhibited by overexpression of full-length Foxp3, but not DeltaFKH, as seen with basal activation of the HIV-1 LTR and a synthetic NF-kappaB reporter in HEK 293T cells. However, Tax-mediated transactivation of the HTLV-I LTR was inhibited by overexpression of both full-length Foxp3 as well as DeltaFKH in both HEK 293T cells and CD4+ T cells. We demonstrated that Foxp3 did not directly affect the functioning of Tax, but rather Foxp3 targeted the transcription factors required for Tax transactivation (i.e., NF-kappaB and a then-unknown cellular factor, which we identified in this study as CREB). The negative effect of Foxp3 on HTLV-I gene expression was confirmed utilizing an HTLV-I infectious molecular clone. \nImportantly, we demonstrated that HTLV-I-infected individuals with the highest levels of Foxp3 protein expression within the CD4+CD25+ T cells population exhibited lower proviral loads than did individuals with the lowest levels of Foxp3 protein expression. Previous studies have demonstrated that the HTLV-I proviral load directly correlates with HTLV-I Tax mRNA load, the frequency of immunopathogenic virus-specific CD8+ T cells, and disease severity in patients with HAM/TSP [47]. These results have important implications on the utility of Foxp3 in controlling viral gene expression and thus pathogenesis of HAM/TSP. Therefore, Foxp3 becomes an attractive target for the development of novel therapeutic applications directed at modulating the expression of this important regulatory protein, especially in light of recent observations that the expression of Foxp3 can also be down-regulated by HTLV-I Tax [8]. \nAs the activation of the HTLV-I LTR depends primarily on ATF/CREB proteins (whether in the presence or the absence of Tax), we investigated whether Foxp3 could interact with this additional cellular signaling pathway. While the DNA-binding activity of CREB is, in most cases, constitutive, the transactivation potential of CREB is regulated by the phosphorylation of CREB and recruitment of CBP/p300 [48]. Our data demonstrate that Foxp3 interferes with the latter of these two processes and that the recruitment of the coactivator protein p300, and resulting transcriptional activation are blocked by Foxp3. This may be the result of the physical interaction we detected between Foxp3 and p300. With respect to HTLV-I LTR activity, while full-length Foxp3 inhibited both basal and Tax-dependent transcription by ~50%, DeltaFKH appeared less effective in suppressing basal activation (~25% inhibition) compared to Tax-dependent activation (~50% inhibition). The effect of DeltaFKH on basal activation of the HTLV-I LTR in HEK 293T cells was very similar to that shown for a synthetic CREB reporter, suggesting that the FKH domain of Foxp3 is important at some level. As observed with NF-kappaB activation, the Foxp3 mutant lacking the FKH domain was a stronger inhibitor of CREB activation in CD4+ T cells than in HEK 293T epithelial cells. Therefore, it appears that in CD4+ T cells, the FKH domain is dispensable for the proper functioning of Foxp3 with respect to both NF-kappaB and CREB activation. \nIn summary, this is, to our knowledge, the first direct evidence implicating a role for the Treg-specific transcription factor Foxp3 in regulating retroviral gene expression. In addition, we identify the CREB pathway as a molecular target of Foxp3. Since CREB has been shown to regulate multiple genes involved in transcription (e.g., JunD, c-Fos, signal transducer of activated T cells 3 [STAT3]), cell cycle (e.g., p15INK4b, cyclin A, cyclin D1), and immune regulation (e.g., IL-2, IL-6, T-cell receptor alpha) (reviewed in [48]), the findings presented in this report broaden the potential range of signaling pathways under the control of the regulatory protein Foxp3. Our evidence stresses the importance of Foxp3 expression and Treg function in the development and maintenance of protective immunity against HIV-1 and HTLV-I. Based on recent findings, Foxp3 may limit HIV-1 and HTLV-I transcription by interfering with activation of NF-kappaB and CREB pathways. However, observing that this inhibitory effect is not absolute, a low level of viral gene expression may persist in CD4+ T cells (in particular regulatory T cells, which are known reservoirs of HIV-1 and HTLV-I) and result in the accumulation of viral proteins that either stimulate NF-kappaB and/or CREB activation or directly inhibit Foxp3 expression or function. The imbalance of NF-kappaB and CREB activation caused by these viral gene products may be a crucial step in the pathogenesis of virus-induced immunological disorders such as AIDS and HAM/TSP. Future studies will be directed at identifying and characterizing cellular proteins that interact with Foxp3 both in the nucleus and cytoplasm, in order to better address how Foxp3 functions to guide the development and function of regulatory T cells in health and disease. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "targeted", "start": 1317, "end": 1325}, "arguments": [{"role": "Site", "text": "amino-terminal proline-rich region", "start": 1333, "end": 1367}, {"role": "Theme", "text": "Foxp3", "start": 1371, "end": 1376}]}, {"trigger": {"text": "dimer formation", "start": 1753, "end": 1768}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1690, "end": 1695}]}, {"trigger": {"text": "interaction", "start": 3314, "end": 3325}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3351, "end": 3354}]}, {"trigger": {"text": "Binding", "start": 3371, "end": 3378}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3382, "end": 3385}]}, {"trigger": {"text": "assembly", "start": 3430, "end": 3438}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3442, "end": 3445}]}, {"trigger": {"text": "recruit", "start": 3580, "end": 3587}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3573, "end": 3576}, {"role": "Theme2", "text": "CBP", "start": 3609, "end": 3612}]}, {"trigger": {"text": "recruit", "start": 3580, "end": 3587}, "arguments": [{"role": "Theme", "text": "Tax", "start": 3573, "end": 3576}, {"role": "Theme2", "text": "p300", "start": 3613, "end": 3617}]}, {"trigger": {"text": "recruitment", "start": 5766, "end": 5777}, "arguments": [{"role": "Theme", "text": "CBP", "start": 5781, "end": 5784}]}, {"trigger": {"text": "recruitment", "start": 5766, "end": 5777}, "arguments": [{"role": "Theme", "text": "p300", "start": 5785, "end": 5789}]}, {"trigger": {"text": "recruitment", "start": 5891, "end": 5902}, "arguments": [{"role": "Theme", "text": "p300", "start": 5930, "end": 5934}]}, {"trigger": {"text": "interaction", "start": 6038, "end": 6049}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 6070, "end": 6075}, {"role": "Theme2", "text": "p300", "start": 6080, "end": 6084}]}, {"trigger": {"text": "interact", "start": 8508, "end": 8516}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 8522, "end": 8527}]}], "gene expression": [{"trigger": {"text": "expression", "start": 365, "end": 375}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 359, "end": 364}]}, {"trigger": {"text": "expression", "start": 1984, "end": 1994}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 1978, "end": 1983}]}, {"trigger": {"text": "overexpression", "start": 3996, "end": 4010}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 4031, "end": 4036}]}, {"trigger": {"text": "overexpression", "start": 3996, "end": 4010}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 4048, "end": 4056}]}, {"trigger": {"text": "expression", "start": 4576, "end": 4586}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 4562, "end": 4567}]}, {"trigger": {"text": "expression", "start": 4719, "end": 4729}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 4705, "end": 4710}]}, {"trigger": {"text": "expression", "start": 5222, "end": 5232}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 5106, "end": 5111}]}, {"trigger": {"text": "expression", "start": 5323, "end": 5333}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 5337, "end": 5342}]}, {"trigger": {"text": "expression", "start": 7612, "end": 7622}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 7606, "end": 7611}]}, {"trigger": {"text": "expression", "start": 8203, "end": 8213}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 8197, "end": 8202}]}], "negative regulation": [{"trigger": {"text": "inactivation", "start": 597, "end": 609}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 613, "end": 618}]}, {"trigger": {"text": "lowest", "start": 4688, "end": 4694}, "arguments": [{"role": "Theme", "text": "expression", "start": 4719, "end": 4729}]}, {"trigger": {"text": "down-regulated", "start": 5355, "end": 5369}, "arguments": [{"role": "Theme", "text": "expression", "start": 5323, "end": 5333}, {"role": "Cause", "text": "Tax", "start": 5380, "end": 5383}]}, {"trigger": {"text": "interferes", "start": 5828, "end": 5838}, "arguments": [{"role": "Theme", "text": "recruitment", "start": 5766, "end": 5777}, {"role": "Cause", "text": "Foxp3", "start": 5822, "end": 5827}]}, {"trigger": {"text": "blocked", "start": 5981, "end": 5988}, "arguments": [{"role": "Theme", "text": "recruitment", "start": 5891, "end": 5902}, {"role": "Cause", "text": "Foxp3", "start": 5992, "end": 5997}]}, {"trigger": {"text": "lacking", "start": 6613, "end": 6620}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 6600, "end": 6605}, {"role": "Site", "text": "FKH domain", "start": 6625, "end": 6635}]}, {"trigger": {"text": "inhibit", "start": 8189, "end": 8196}, "arguments": [{"role": "Theme", "text": "expression", "start": 8203, "end": 8213}]}], "positive regulation": [{"trigger": {"text": "promotes", "start": 3421, "end": 3429}, "arguments": [{"role": "Cause", "text": "Binding", "start": 3371, "end": 3378}, {"role": "Theme", "text": "assembly", "start": 3430, "end": 3438}]}, {"trigger": {"text": "overexpression", "start": 3767, "end": 3781}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 3797, "end": 3802}]}, {"trigger": {"text": "overexpression", "start": 3767, "end": 3781}, "arguments": [{"role": "Theme", "text": "DeltaFKH", "start": 3812, "end": 3820}]}, {"trigger": {"text": "highest", "start": 4544, "end": 4551}, "arguments": [{"role": "Theme", "text": "expression", "start": 4576, "end": 4586}]}, {"trigger": {"text": "result", "start": 6015, "end": 6021}, "arguments": [{"role": "Theme", "text": "interferes", "start": 5828, "end": 5838}, {"role": "Cause", "text": "interaction", "start": 6038, "end": 6049}]}, {"trigger": {"text": "result", "start": 6015, "end": 6021}, "arguments": [{"role": "Theme", "text": "blocked", "start": 5981, "end": 5988}, {"role": "Cause", "text": "interaction", "start": 6038, "end": 6049}]}], "regulation": [{"trigger": {"text": "play a role", "start": 1738, "end": 1749}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1507, "end": 1512}, {"role": "CSite", "text": "leucine zipper domain", "start": 1529, "end": 1550}, {"role": "Theme", "text": "dimer formation", "start": 1753, "end": 1768}]}, {"trigger": {"text": "does", "start": 1775, "end": 1779}, "arguments": [{"role": "Cause", "text": "Foxp3", "start": 1507, "end": 1512}, {"role": "CSite", "text": "leucine zipper domain", "start": 1529, "end": 1550}, {"role": "Theme", "text": "dimer formation", "start": 1753, "end": 1768}]}, {"trigger": {"text": "dysregulation", "start": 1961, "end": 1974}, "arguments": [{"role": "Theme", "text": "expression", "start": 1984, "end": 1994}]}, {"trigger": {"text": "modulating", "start": 5207, "end": 5217}, "arguments": [{"role": "Theme", "text": "expression", "start": 5222, "end": 5232}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "JunD", "start": 7229, "end": 7233}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 7235, "end": 7240}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "signal transducer of activated T cells 3", "start": 7242, "end": 7282}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "p15INK4b", "start": 7311, "end": 7319}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "cyclin A", "start": 7321, "end": 7329}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "cyclin D1", "start": 7331, "end": 7340}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 7372, "end": 7376}]}, {"trigger": {"text": "regulate", "start": 7172, "end": 7180}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 7378, "end": 7382}]}]}}, "schema": []}
{"input": "Cell culture.\nHEK 293T cells were cultured in Dulbecco's modified Eagle medium (Invitrogen, Carlsbad, California, United States). Jurkat T cells and primary human CD4+ T cells were cultured in RPMI-1640 medium (Invitrogen). Media were supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 mug/ml streptomycin (Cambrex, East Rutherford, New Jersey, United States), and 10% fetal bovine serum (Atlanta Biologicals, Norcross, Georgia, United States). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Patients and cell preparation.\nPBMCs were prepared by centrifugation over Ficoll-Hypaque gradients (BioWhittaker, Walkersville, Maryland, United States) from eight HAM/TSP patients and eight ACs, and the cells were viably cryopreserved in liquid nitrogen until tested. HAM/TSP was diagnosed according to WHO guidelines [49]. HTLV-I seropositivity was determined by ELISA (Abbott Laboratories, Abbott Park, Illinois, United States), with confirmation by Western blot analysis (Genelabs Technologies, Redwood City, California, United States). Blood samples were obtained after informed consent as part of a clinical protocol reviewed and approved by the NIH institutional review panel. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Plasmids.\nExpression vectors encoding human Foxp3 (pCMV-Foxp3-IRES-EGFP) and human Foxp3 lacking the forkhead (FKH) domain (pCMV-DeltaFKH-IRES-EGFP) were generous gifts from S. Ziegler (Benaroya Research Institute). pEGFP-C2 was provided by I. Lipinski (NIDDK/NIH). pcDNA3 was provided by K. T. Jeang (NIAID/NIH). pCMV4-Tax was a generous gift from W. Greene (University of California San Francisco). pGL4-luc2 and pGL4-TKhRluc2 were purchased from Promega (Madison, Wisconsin, United States). pUC18 was purchased from Stratagene (La Jolla, California, United States). HIV-1 wt LTR and HIV-1 Delta-kappaB LTR luciferase reporter vectors were constructed by cloning the XhoI/HindIII LTR fragments from pHIV-CAT and pDelta-kappaB-HIV-CAT (AIDS Research and Reference Reagent Program, NIAID/NIH) into the multiple cloning site of pGL4-luc2. NF-kappaB, HTLV-I LTR, and CREB luciferase reporter and pCMV-p300-HA expression vectors were generously provided by B. Wigdahl (Drexel University College of Medicine). HTLV-I pACH infectious molecular clone has been described previously [30]. pFR-luc, pFA-CMV, pFA2-CREB-1, and pFA2-c-Jun were purchased from Stratagene. pFA-Tax (encoding a fusion protein consisting of the Gal4 DNA-binding domain fused in-frame to HTLV-I Tax) was constructed by PCR amplification of HTLV-I Tax using pCMV4-Tax as a template and BamHI/BglII-tagged primers. The amplified insert was digested and ligated into the BamHI/BglII sites of pFA-CMV. Plasmid contents were confirmed by DNA sequencing. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 10, "end": 20}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 44, "end": 49}]}, {"trigger": {"text": "Expression", "start": 10, "end": 20}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 83, "end": 88}]}, {"trigger": {"text": "expression", "start": 907, "end": 917}, "arguments": [{"role": "Theme", "text": "luciferase", "start": 870, "end": 880}]}, {"trigger": {"text": "expression", "start": 907, "end": 917}, "arguments": [{"role": "Theme", "text": "p300", "start": 899, "end": 903}]}], "negative regulation": [{"trigger": {"text": "lacking", "start": 89, "end": 96}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 83, "end": 88}, {"role": "Site", "text": "forkhead (FKH) domain", "start": 101, "end": 122}]}]}}, "schema": []}
{"input": "Isolation of primary human CD4+ T cells.\nCD4+ T cells were isolated from cryopreserved healthy donor PBMCs by negative selection with the CD4+ T Cell Isolation Kit II (Miltenyi Biotech, Bergisch Gladbach, Germany) according to manufacturer's guidelines. Purity of negatively selected CD4+ T cells was consistently higher than 96% as determined by flow cytometry. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Transient expression and luciferase assays.\nHEK 293T cells were plated at a density of 5 x 105 cells/well in six-well culture plates (BD Biosciences, San Diego, California, United States) 1 d prior to transfection with the appropriate plasmid DNA (~2 mug total) using FuGene 6 transfection reagent (Roche, Basel, Switzerland). Jurkat T cells were plated at 1 x 106 cells/well in six-well culture plates the day of transfection with the appropriate plasmid DNA (~2 mug total) using FuGene 6 transfection reagent. Primary human CD4+ T cells (2 x 106) were nucleofected with the specified plasmid DNA (5 mug total) using the Human T Cell Nucleofection Kit (Amaxa, Gaithersburg, Maryland, United States). Forskolin (10 muM; Calbiochem, San Diego, California, United States) was added in some experiments 20 h posttransfection. Cells were harvested 24 h posttransfection and luciferase activity was analyzed using the Dual-luciferase Reporter Assay System (Promega) and a Monolight 2010 luminometer (Analytical Luminescence Laboratory, San Diego, California, United States) according to manufacturer's guidelines. pGL4-TKhRluc2 was used as an internal control to normalize for transfection efficiency. Nucleofected CD4+ T cells were also monitored for transfection efficiency and cell viability 24 h posttransfection as follows. Transfection efficiency was routinely ~30% as determined by flow cytometric analysis of EGFP expression. Cell viability, determined by staining with 7-amino-actinomycin D (7-AAD; BD Biosciences), was routinely ~70%. Both transfection efficiency and cell viability in nucleofected CD4+ T cells was independent of the plasmids used. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Foxp3 and HTLV-I Tax expression analysis by real-time RT-PCR.\nReal-time RT-PCR analysis of Foxp3 and HTLV-I Tax expression was performed as previously described [8,47]. Briefly, total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, California, United States) according to manufacturer's guidelines, and cDNA was synthesized by reverse transcription using TaqMan Gold RT-PCR Kit using random hexamer primers (Applied Biosystems, Foster City, California, United States). Foxp3 and HTLV-I Tax mRNA expression was quantified by real-time PCR using ABI PRISM 7700 Sequence Detection System (Applied Biosystems). The normalized values in each sample were calculated as the relative quantity of Foxp3 or HTLV-I Tax mRNA expression divided by the relative quantity of HPRT mRNA expression. The values were calculated by the following formula: normalized Foxp3 or HTLV-I Tax expression = 2Ct value of HPRT - Ct value of Foxp3 or HTLV-I Tax. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 21, "end": 31}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 0, "end": 5}]}, {"trigger": {"text": "expression", "start": 21, "end": 31}, "arguments": [{"role": "Theme", "text": "Tax", "start": 17, "end": 20}]}, {"trigger": {"text": "expression", "start": 112, "end": 122}, "arguments": [{"role": "Theme", "text": "Tax", "start": 108, "end": 111}]}, {"trigger": {"text": "expression", "start": 112, "end": 122}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 91, "end": 96}]}, {"trigger": {"text": "expression", "start": 881, "end": 891}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 861, "end": 866}]}, {"trigger": {"text": "expression", "start": 881, "end": 891}, "arguments": [{"role": "Theme", "text": "Tax", "start": 877, "end": 880}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 505, "end": 520}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 484, "end": 489}]}, {"trigger": {"text": "mRNA expression", "start": 505, "end": 520}, "arguments": [{"role": "Theme", "text": "Tax", "start": 501, "end": 504}]}, {"trigger": {"text": "mRNA expression", "start": 723, "end": 738}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 703, "end": 708}]}, {"trigger": {"text": "mRNA expression", "start": 723, "end": 738}, "arguments": [{"role": "Theme", "text": "Tax", "start": 719, "end": 722}]}, {"trigger": {"text": "mRNA expression", "start": 780, "end": 795}, "arguments": [{"role": "Theme", "text": "HPRT", "start": 775, "end": 779}]}]}}, "schema": []}
{"input": "Real-time PCR.\nReal-time PCR analysis of HTLV-I (Tax) proviral load was performed as previously described [47,50]. DNA was extracted from 1 x 106 cells using Puregene DNA Isolation Kit (Gentra, Minneapolis, Minnesota, United States), and 100 ng of the sample DNA solution was analyzed by this system. The HTLV-I proviral DNA load was calculated by the following formula: copy number of HTLV-I (pX) per 100 cells = (copy number of pX)/(copy number of beta-actin/2) x 100. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Western blot analysis.\nHEK 293T cells were plated at a density of 5 x 105 cells/well in six-well culture plates (BD Biosciences) 1 d prior to transfection with the appropriate plasmid DNA (2 mug total) using FuGene 6 transfection reagent (Roche). Cells were harvested 24 h posttransfection for whole-cell lysates in RIPA buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 1% Igepal (NP-40), 0.5% sodium deoxycholate, 1 mM EDTA, 1 mM DTT, 1 mM PMSF, and 1x Complete Mini Protease Inhibitor [Roche]). Protein concentration was determined by Lowry assay (Bio-Rad, Hercules, California, United States) and colorimetric reactions were read using a VersaMax microplate reader (Molecular Devices, Sunnyvale, California, United States) at an absorbance of 750 nm. Size fractionation was performed on 20 mug of protein/sample by SDS-PAGE, and the protein was transferred to nitrocellulose or PVDF membranes and subjected to immunoblotting using the indicated antibodies. Foxp3 was detected using rabbit anti-human Foxp3 polyclonal antibody (ab4728 or ab10563; Abcam, Cambridge, United Kingdom) and anti-rabbit IgG-HRP secondary antibody (Cell Signaling Technology, Beverly, Massachusetts, United States). NF-kappaB p65 and CREB-1 were detected using rabbit anti-human polyclonal (p65) or monoclonal antibody (CREB-1; 48H2) (Cell Signaling Technology). Beta-actin was detected using a mouse monoclonal antibody (AC-15; Sigma, St. Louis, Missouri, United States). For coimmunoprecipitation analysis, cell lysates were precleared with 30 mul of protein A/G plus-agarose beads (Santa Cruz Biotechnology, Santa Cruz, California, United States) and then incubated with mouse monoclonal anti-HA antibody (6E2; 1:100; Cell Signaling Technology) and 30 mul of protein A/G plus-agarose beads overnight. The immunoprecipitates were washed four times with RIPA buffer, resuspended in SDS sample buffer, and heated at 95 degreesC for 5 min. Proteins were then treated as described for Western blot analysis. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Transcription factor DNA-binding analysis (TF-ELISA).\nCREB-1 and ATF-2 DNA-binding activity was analyzed with the TransFactor Profiling (Inflammation 1) Kit (BD Biosciences) according to the manufacturer's protocol. Nuclear extracts were prepared from HEK 293T cells transfected with a control vector (EGFP) or Foxp3 expression vector (1,000 ng) in the presence or absence of forskolin (10 muM for 4 h) using the TransFactor Extraction Kit (BD Biosciences). Protein concentration was determined using a Biophotometer (Eppendorf, Hamburg, Germany). Nuclear extracts (20 mug) were incubated in preblocked wells containing plate-bound double-stranded oligonucleotides corresponding to an ATF/CREB consensus sequence (emTGACATCAem). Wells were washed, incubated with the appropriate primary antibody, washed, incubated with secondary antibody (HRP-labeled), washed again, and finally developed with TMB substrate. Colorimetric reactions were read using a VersaMax microplate reader (Molecular Devices) at an absorbance of 655 nm. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 75, "end": 82}, "arguments": [{"role": "Theme", "text": "CREB-1", "start": 54, "end": 60}]}, {"trigger": {"text": "binding", "start": 75, "end": 82}, "arguments": [{"role": "Theme", "text": "ATF-2", "start": 65, "end": 70}]}], "gene expression": [{"trigger": {"text": "expression", "start": 317, "end": 327}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 311, "end": 316}]}]}}, "schema": []}
{"input": "Flow cytometric analysis of Foxp3 protein expression.\nCryopreserved PBMCs from HAM/TSP patients or HTLV-I-infected ACs were thawed and washed with FACS buffer (1x PBS, 0.1% NaN3, 5% FBS). Cells (1.5 x 106) were fixed by sequential formaldehyde/methanol fixation as follows. Cells were carefully resuspended in FACS buffer and fixed with 100 mul of reagent A (Fix & Perm kit; Caltag Laboratories, Burlingame, California, United States) at room temperature for 3 min followed by 2 ml of 70% methanol for 5 min at 4 degreesC. Cells were washed twice and permeabilized with 100 mul of reagent B (Fix & Perm kit) and stained for intracellular Foxp3 with mouse anti-human Foxp3 monoclonal antibody (0.5 mug of ab22510; Abcam) or the appropriate isotype control for 30 min. Cells were washed twice and stained with Cy5-conjugated goat anti-mouse immunoglobulin F(ab')2 secondary antibody (Caltag Laboratories) for an additional 30 min. Cells were washed twice and stained for surface CD4 expression with PE-labeled anti-CD4 (BD) and CD25 expression with FITC-labeled anti-CD25 (BD). Cells were washed twice and analyzed on a FACSCalibur (BD). Data analysis was performed using FlowJo (Tree Star, Ashland, Oregon, United States). \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 42, "end": 52}, "arguments": [{"role": "Theme", "text": "Foxp3", "start": 28, "end": 33}]}, {"trigger": {"text": "expression", "start": 981, "end": 991}, "arguments": [{"role": "Theme", "text": "CD4", "start": 977, "end": 980}]}, {"trigger": {"text": "expression", "start": 1031, "end": 1041}, "arguments": [{"role": "Theme", "text": "CD25", "start": 1026, "end": 1030}]}]}}, "schema": []}
{"input": "Statistical analyses.\nThe Mann-Whitney U test was used to compare the data between patients with HAM/TSP and AC. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "EBV Latent Membrane Protein 1 Activates Akt, NFkappaB, and Stat3 in B Cell Lymphomas \nLatent membrane protein 1 (LMP1) is the major oncoprotein of Epstein-Barr virus (EBV). In transgenic mice, LMP1 promotes increased lymphoma development by 12 mo of age. This study reveals that lymphoma develops in B-1a lymphocytes, a population that is associated with transformation in older mice. The lymphoma cells have deregulated cell cycle markers, and inhibitors of Akt, NFkappaB, and Stat3 block the enhanced viability of LMP1 transgenic lymphocytes and lymphoma cells in vitro. Lymphoma cells are independent of IL4/Stat6 signaling for survival and proliferation, but have constitutively activated Stat3 signaling. These same targets are also deregulated in wild-type B-1a lymphomas that arise spontaneously through age predisposition. These results suggest that Akt, NFkappaB, and Stat3 pathways may serve as effective targets in the treatment of EBV-associated B cell lymphomas. \nAuthor Summary\nEpstein-Barr virus (EBV) is linked to the development of multiple cancers, including post-transplant lymphoma, Hodgkin disease, and nasopharyngeal carcinoma. Latent membrane protein 1 (LMP1) is expressed in many EBV-associated cancers and is responsible for most of the altered cellular growth properties that are induced by EBV infection. This study reveals that LMP1 induces lymphomas in B-1a lymphocytes, a cell type that is susceptible to transformation in aged mice. The lymphomas require Akt, NFkappaB, and Stat3 signaling for enhanced growth and survival. The activation of the Stat3, Akt, and NFkappaB signaling pathways likely underlies the ability of LMP1 to promote malignant transformation. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 1186, "end": 1195}, "arguments": [{"role": "Theme", "text": "Latent membrane protein 1", "start": 1150, "end": 1175}]}], "negative regulation": [{"trigger": {"text": "inhibitors", "start": 445, "end": 455}, "arguments": [{"role": "Theme", "text": "Akt", "start": 459, "end": 462}]}, {"trigger": {"text": "inhibitors", "start": 445, "end": 455}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 478, "end": 483}]}], "positive regulation": [{"trigger": {"text": "Activates", "start": 30, "end": 39}, "arguments": [{"role": "Cause", "text": "Latent Membrane Protein 1", "start": 4, "end": 29}, {"role": "Theme", "text": "Akt", "start": 40, "end": 43}]}, {"trigger": {"text": "Activates", "start": 30, "end": 39}, "arguments": [{"role": "Cause", "text": "Latent Membrane Protein 1", "start": 4, "end": 29}, {"role": "Theme", "text": "Stat3", "start": 59, "end": 64}]}], "regulation": [{"trigger": {"text": "deregulated", "start": 738, "end": 749}, "arguments": [{"role": "Theme", "text": "IL4", "start": 607, "end": 610}]}, {"trigger": {"text": "deregulated", "start": 738, "end": 749}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 611, "end": 616}]}, {"trigger": {"text": "deregulated", "start": 738, "end": 749}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 693, "end": 698}]}]}}, "schema": []}
{"input": "Introduction\nEpstein-Barr virus (EBV) is a ubiquitous gamma-herpesvirus that infects humans predominantly at an early age with greater than 90% of the adult population infected with EBV [1]. EBV is linked to the development of both B lymphocyte and epithelial cell malignancies, including Burkitt lymphoma, Hodgkin disease (HD), and nasopharyngeal carcinoma (NPC), and cancers linked to immunosuppression, including post-transplant lymphoma and AIDS-associated lymphomas [2,3]. In vitro infection of B lymphocytes with EBV induces permanent growth transformation, and this ability to affect cell growth regulation likely contributes to the development of cancer. \nMany of the viral proteins expressed in transformed cells, including the EBV nuclear antigens and latent membrane proteins, have profound effects on cell growth regulation and are required for EBV latent infection and B cell transformation [1]. Latent membrane protein 1 (LMP1) is considered the major oncoprotein of EBV, as it transforms rodent fibroblasts to tumorigenicity in nude mice and is expressed in HD, NPC, and immunosuppression-associated tumors [4-8]. In B lymphocytes, LMP1 mimics CD40 signaling, and both LMP1 and CD40 are essential for EBV-mediated B cell transformation [9-11]. While CD40 interacts with CD40 ligand expressed on activated T cells to induce B cell activation and differentiation, LMP1 acts as a constitutive signal through ligand-independent oligomerization. LMP1 and CD40 interact with the same tumor necrosis factor receptor-associated factors (TRAFs) leading to activation of NFkappaB, c-Jun N terminal kinase (JNK), and p38 MAPK signaling pathways [12-16]. Activation of NFkappaB is required for EBV-induced B cell transformation and its inhibition rapidly results in cell death [17,18]. Recent studies indicate that LMP1 also activates phosphatidylinositol 3 kinase (PI3K)/Akt signaling and that this activation is required for LMP1-mediated transformation of rodent fibroblasts [5,19]. \nIn vitro, primary B cells can be maintained by CD40 ligation in combination with IL4 treatment. In vivo, CD40 signaling is necessary for germinal center (GC) formation such that mice deficient for CD40 or CD40L are unable to form GCs in response to T cell-dependent antigens [20,21]. Both the membrane proximal and distal cytoplasmic regions of CD40 that bind TRAF6 and TRAFs2/3/5, respectively, are necessary for GC formation, but either region is sufficient to induce extrafollicular B cell differentiation and restore low affinity antibody production [22]. Functionally, LMP1 can rescue CD40-deficient mice and restore immunoglobulin (Ig) class switching, most likely because LMP1 recruits similar TRAF molecules, TRAFs 1/2/3/5 and TRAF6, through the C-terminal activation regions 1 and 2 domains, respectively. However, LMP1 is unable to restore affinity maturation and GC formation [23]. \nSeveral EBV transforming proteins have been studied in transgenic mouse models, however, only LMP1 induces tumor development when expressed under the control of the Ig heavy chain promoter and enhancer [24-26]. The LMP1 transgenic mice (IgLMP1) express LMP1 in B lymphocytes, and in mice older than 12 mo, lymphoma develops with increased incidence (40%-50%) compared to wild-type control mice (11%), suggesting that LMP1 contributes to tumor development [26]. The LMP1 lymphomas have rearranged Ig genes and have activated Akt, JNK, p38, and NFkappaB, with specific activation of the NFkappaB family member cRel [27]. \nIn this study, the LMP1 transgenic lymphocytes and lymphomas were further characterized and their growth properties in vitro were determined. To obtain pure populations of malignant lymphocytes and to enable more detailed biochemical analyses, examples of primary lymphomas were inoculated and passaged in SCID mice. Interestingly, lymphoma development was restricted to B-1a lymphocytes, a self-replenishing population of cells that are prone to malignancy [28,29]. LMP1 transgenic lymphocytes had increased viability in vitro and viability was increased by the addition of IL4. In contrast, both LMP1-positive and -negative lymphoma cells were independent of IL4 co-stimulation for survival and proliferation in vitro with a complete absence of activated Stat6, the IL4 target. The lymphomas were also distinguished by constitutive activation of Stat3 and deregulation of the Rb cell cycle pathway. Inhibition of the PI3K/Akt, NFkappaB, and Stat3 signaling pathways blocked the enhanced growth of both LMP1 transgenic and malignant lymphocytes, suggesting that these pathways are required for their growth and survival. These appear to be the same targets that are deregulated in wild-type B-1a lymphomas that arise spontaneously through age predisposition. This study reveals that LMP1 promotes malignancy in cells with the inherent ability to proliferate and that the Akt, NFkappaB, and Stat3 signaling pathways are required for its growth stimulatory effects. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 1270, "end": 1279}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1265, "end": 1269}, {"role": "Theme2", "text": "CD40 ligand", "start": 1285, "end": 1296}]}, {"trigger": {"text": "oligomerization", "start": 1439, "end": 1454}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1377, "end": 1381}]}, {"trigger": {"text": "interact", "start": 1470, "end": 1478}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1456, "end": 1460}]}, {"trigger": {"text": "interact", "start": 1470, "end": 1478}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1465, "end": 1469}]}, {"trigger": {"text": "ligation", "start": 2042, "end": 2050}, "arguments": [{"role": "Theme", "text": 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"C-terminal activation regions 1", "start": 2744, "end": 2775}]}, {"trigger": {"text": "recruits", "start": 2674, "end": 2682}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2669, "end": 2673}, {"role": "Theme2", "text": "5", "start": 2719, "end": 2720}, {"role": "Site", "text": "C-terminal activation regions 1", "start": 2744, "end": 2775}]}, {"trigger": {"text": "recruits", "start": 2674, "end": 2682}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2669, "end": 2673}, {"role": "Theme2", "text": "TRAF6", "start": 2725, "end": 2730}, {"role": "Site", "text": "2 domains", "start": 2780, "end": 2789}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 1060, "end": 1069}, "arguments": [{"role": "Theme", "text": "Latent membrane protein 1", "start": 909, "end": 934}]}, {"trigger": {"text": "expressed", "start": 1297, "end": 1306}, "arguments": [{"role": "Theme", "text": "CD40 ligand", "start": 1285, "end": 1296}]}, {"trigger": {"text": "expressed", "start": 3014, "end": 3023}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2978, "end": 2982}]}, {"trigger": {"text": "express", "start": 3129, "end": 3136}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 3137, "end": 3141}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 2173, "end": 2182}, "arguments": [{"role": "Theme", "text": "CD40", "start": 2187, "end": 2191}]}, {"trigger": {"text": "deficient", "start": 2173, "end": 2182}, "arguments": [{"role": "Theme", "text": "CD40L", "start": 2195, "end": 2200}]}, {"trigger": {"text": "rescue", "start": 2573, "end": 2579}, "arguments": [{"role": "Theme", "text": "deficient", "start": 2585, "end": 2594}]}, {"trigger": {"text": "deficient", "start": 2585, "end": 2594}, "arguments": [{"role": "Theme", "text": "CD40", "start": 2580, "end": 2584}]}, {"trigger": {"text": "absence", "start": 4240, "end": 4247}, "arguments": [{"role": "Theme", "text": "activated", "start": 4251, "end": 4260}]}], "positive regulation": [{"trigger": {"text": "under the control", "start": 3024, "end": 3041}, "arguments": [{"role": "Theme", "text": "expressed", "start": 3014, "end": 3023}]}, {"trigger": {"text": "activated", "start": 3398, "end": 3407}, "arguments": [{"role": "Theme", "text": "Akt", "start": 3408, "end": 3411}]}, {"trigger": {"text": "activation", "start": 3451, "end": 3461}, "arguments": [{"role": "Theme", "text": "cRel", "start": 3492, "end": 3496}]}, {"trigger": {"text": "activated", "start": 4251, "end": 4260}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 4261, "end": 4266}]}, {"trigger": {"text": "activation", "start": 4338, "end": 4348}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 4352, "end": 4357}]}], "regulation": [{"trigger": {"text": "target", "start": 4276, "end": 4282}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 4261, "end": 4266}, {"role": "Cause", "text": "IL4", "start": 4272, "end": 4275}]}, {"trigger": {"text": "deregulated", "start": 4671, "end": 4682}, "arguments": [{"role": "Theme", "text": "Akt", "start": 4428, "end": 4431}]}, {"trigger": {"text": "deregulated", "start": 4671, "end": 4682}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 4447, "end": 4452}]}]}}, "schema": []}
{"input": "High Levels of LMP1 Expression Correlates with the Development of Lymphoma\nLMP1 expression in IgLMP1 mice was directed to B cells under the control of the Ig heavy chain promoter and enhancer. It has previously been shown that in these transgenic mice, LMP1 expression was restricted to B220+ B cells with lymphoma detected in greatly enlarged spleens [23,26]. To investigate whether LMP1 expression contributes to lymphoma development, B cells were purified from splenocytes by positive selection using anti-CD19 MACS magnetic beads, and equivalent amounts of B cells were analyzed by immunoblotting. LMP1 was detectable in LMP1 transgenic B cells, but upon development of lymphoma, LMP1 expression was stronger in 5/7 lymphomas analyzed with concomitant appearance of degradation products (Figure 1A). To determine whether the higher level of LMP1 detected was due to an expansion of malignant lymphocytes, expression of LMP1 in the spleen was further evaluated by immunohistochemical staining. Immunohistochemistry analysis of spleen sections detected LMP1 in the plasma membrane of cells in both the follicular white pulp and circulating lymphocytes in the red pulp (Figure 1B). LMP1 expression was heterogeneous with strong LMP1 staining interspersed amongst a background of cells staining weakly for LMP1. Upon development to lymphoma, LMP1 expression was more abundantly detected with multiple foci of intense LMP1 staining. This demonstrates that the increased LMP1 detected by immunoblotting upon malignant progression reflects an increase in LMP1 expression and an accumulation of cells expressing high levels of LMP1. This correlation between high LMP1 expression and the development of lymphoma suggests that progression to lymphoma results from increased levels of LMP1. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 20, "end": 30}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 15, "end": 19}]}, {"trigger": {"text": "expression", "start": 80, "end": 90}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 75, "end": 79}]}, {"trigger": {"text": "expression", "start": 258, "end": 268}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 253, "end": 257}]}, {"trigger": {"text": "expression", "start": 389, "end": 399}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 384, "end": 388}]}, {"trigger": {"text": "detectable", "start": 611, "end": 621}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 602, "end": 606}]}, {"trigger": {"text": "expression", "start": 689, "end": 699}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 684, "end": 688}]}, {"trigger": {"text": "expression", "start": 909, "end": 919}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 923, "end": 927}]}, {"trigger": {"text": "detected", "start": 1046, "end": 1054}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1055, "end": 1059}]}, {"trigger": {"text": "expression", "start": 1188, "end": 1198}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1183, "end": 1187}]}, {"trigger": {"text": "expression", "start": 1347, "end": 1357}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1342, "end": 1346}]}, {"trigger": {"text": "expression", "start": 1557, "end": 1567}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1552, "end": 1556}]}, {"trigger": {"text": "expressing", "start": 1597, "end": 1607}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1623, "end": 1627}]}, {"trigger": {"text": "expression", "start": 1664, "end": 1674}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1659, "end": 1663}]}, {"trigger": {"text": "levels", "start": 1768, "end": 1774}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1778, "end": 1782}]}], "positive regulation": [{"trigger": {"text": "High Levels", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "Expression", "start": 20, "end": 30}]}, {"trigger": {"text": "restricted", "start": 273, "end": 283}, "arguments": [{"role": "Theme", "text": "expression", "start": 258, "end": 268}]}, {"trigger": {"text": "stronger", "start": 704, "end": 712}, "arguments": [{"role": "Theme", "text": "expression", "start": 689, "end": 699}]}, {"trigger": {"text": "higher level", "start": 829, "end": 841}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 845, "end": 849}]}, {"trigger": {"text": "strong", "start": 1222, "end": 1228}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1229, "end": 1233}]}, {"trigger": {"text": "weakly", "start": 1295, "end": 1301}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1306, "end": 1310}]}, {"trigger": {"text": "abundantly", "start": 1367, "end": 1377}, "arguments": [{"role": "Theme", "text": "expression", "start": 1347, "end": 1357}]}, {"trigger": {"text": "intense", "start": 1409, "end": 1416}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1417, "end": 1421}]}, {"trigger": {"text": "increased", "start": 1459, "end": 1468}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1469, "end": 1473}]}, {"trigger": {"text": "increase", "start": 1540, "end": 1548}, "arguments": [{"role": "Theme", "text": "expression", "start": 1557, "end": 1567}]}, {"trigger": {"text": "high levels", "start": 1608, "end": 1619}, "arguments": [{"role": "Theme", "text": "expressing", "start": 1597, "end": 1607}]}, {"trigger": {"text": "high", "start": 1654, "end": 1658}, "arguments": [{"role": "Theme", "text": "expression", "start": 1664, "end": 1674}]}, {"trigger": {"text": "increased", "start": 1758, "end": 1767}, "arguments": [{"role": "Theme", "text": "levels", "start": 1768, "end": 1774}]}], "regulation": [{"trigger": {"text": "under the control", "start": 130, "end": 147}, "arguments": [{"role": "Theme", "text": "expression", "start": 80, "end": 90}]}]}}, "schema": []}
{"input": "LMP1 Promotes B-1a Lymphomas That Can Escape Allelic Exclusion\nTo determine if LMP1 signaling affects B cell differentiation and to immunophenotype the lymphomas that arise from LMP1 expression, surface Ig expression of heavy chains (IgM, IgG, IgD) and light chains (kappa, lambda) were analyzed by flow cytometry. Similar numbers of naive (IgM+IgD+IgG-) splenic B cells with a strong bias towards kappa light chain were detected from wild-type or LMP1 transgenic mice, indicating that LMP1 signaling does not affect B cell maturation (unpublished data). Flow cytometry analysis of the SCID-passaged wild-type and LMP1 transgenic lymphomas revealed an IgMhighIgDlow phenotype (Figure 2A), indicative of marginal zone, B-1, or memory B cells. B-1 cells are further separated into CD5+ (B-1a) and CD5- (B-1b) subsets. To differentiate between these cell types, lymphoma cells were further analyzed for the B-1a marker CD5. All (5/5) of the tested LMP1 transgenic lymphomas displayed an IgMhighIgDlowCD5+ phenotype (Figure 2A), an expression pattern that distinguishes B-1a cells. Interestingly, a spontaneous wild-type lymphoma also developed in B-1a cells (Figure 2A). These cells are an interesting population that is self replenishing with an increased likelihood to become malignant in aged mice [30]. Analysis of LMP1 transgenic mice before the development of lymphoma showed similar numbers of splenic B-1a (CD19+CD5+) and B-1b or B-2 populations (CD19+CD5-), indicating that LMP1 does not affect B cell differentiation (Figure 2B). \nDue to allelic exclusion, mature B cells that have been exposed to antigen will typically express only one heavy chain isotype (IgG, IgE, or IgA) and either a kappa or lambda light chain. Interestingly, 2/5 LMP1 transgenic lymphomas analyzed (lymphomas 2 and 4) were doubly positive for low levels of both kappa and lambda light chains (Figure 2A). Previous characterization of the LMP1 lymphomas had revealed that the lymphomas were clonal as determined by Ig heavy chain rearrangement [26], and analysis of kappa chain rearrangement (Figure S1) of the samples analyzed in this study confirmed clonality. To further assess light chain expression, the passaged samples were tested by immunoblotting for kappa and lambda light chains (Figure 2C). Interestingly, very low levels of expression of both light chains were detected by flow cytometry. The low levels of expression may reflect a limitation of the total number of light chains that can be expressed on the surface of a B cell. In agreement with the flow cytometry analysis, LMP1 transgenic lymphomas 2 and 4 were also positive for kappa and lambda light chains by immunoblot analysis (Figure 2C), confirming that these lymphomas express both light chains. \nA previous study of mice that developed leukemia due to an expansion of self-reactive B-1a cells determined that the B-1a leukemias were also doubly positive for kappa and lambda light chains [31]. These findings indicate that expression of LMP1 in B-1a cells promotes the development of malignancy and can result in the aberrant escape from allelic exclusion. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 183, "end": 193}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 178, "end": 182}]}, {"trigger": {"text": "expression", "start": 2980, "end": 2990}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2994, "end": 2998}]}]}}, "schema": []}
{"input": "LMP1 Promotes B Cell Survival and Proliferation In Vitro\nPrimary B cell cultures can be maintained through CD40 ligation and supplementation with IL4 [32]. To investigate whether LMP1 affects primary B cell survival and proliferation, splenocytes were cultured in the presence or absence of IL4 and analyzed by MTS as a metabolic marker, by ethidium monoazide (EMA) exclusion for viability, and by 5-bromo-2'-deoxy-uridine (BrdU) incorporation for proliferation. In the MTS assay, as expected, splenocytes from wild-type mice did not survive even with the addition of IL4 due to a lack of CD40 ligation (Figure 3A). In contrast, LMP1 splenocytes had increased metabolism even in the absence of IL4, which was further enhanced upon addition of IL4. Wild-type and LMP1 transgenic lymphoma cells had high levels of MTS activity even in the absence of IL4 (Figure 3A). The LMP1 transgenic lymphoma cells had approximately 4-fold higher MTS activity than the normal transgenic lymphocytes and were at least 2-fold higher than the control lymphoma. As previously published, lymphoma usually develops in mice over 12 mo of age and all mice are sacrificed by 18-20 mo. The ages of the transgenic mice with or without lymphoma ranged between 6 and 20 mo old. There was no correlation between age and MTS activity. \nEMA exclusion of CD19+ gated B cells prepared from two wild-type and two LMP1 transgenic mice indicated a 2-fold increase in viability in the LMP1 transgenic lymphocytes compared to wild-type lymphocytes. Two examples of LMP1 transgenic lymphoma cells had greatly increased viability that was not increased by IL4 treatment, indicating that the lymphoma cells are independent of IL4 co-stimulation (Figure 3B). Enhancement in MTS activity was observed in LMP1 transgenic lymphoma cells by the addition of IL4; however, EMA exclusion did not reveal a similar increase. This could reflect a difference for IL4 requirement in the metabolic activity versus the viability of LMP1 transgenic lymphoma cells. Although expression of LMP1 could enhance survival of non-malignant primary lymphocytes, BrdU incorporation revealed that LMP1 expression alone was not sufficient to induce proliferation in culture (unpublished data). Only lymphoma cells had detectable levels of BrdU incorporation detected by flow cytometry (Figure 3C). Interestingly, LMP1 lymphoma cells had significantly higher levels of proliferation in comparison to the spontaneous lymphoma that developed in an LMP1-negative littermate (25% versus 4%). This higher level of proliferation was observed in lymphomas that express both high (Table 1, LMP1-L2 and LMP1-L3) and low (Table 1, LMP1-L5) levels of LMP1, suggesting that even small amounts of LMP1 is sufficient to induce dramatic effects in proliferation. The level of proliferation was not enhanced upon IL4 addition, confirming the IL4 independence observed in the viability studies (Figure 3C; Table1). \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 112, "end": 120}, "arguments": [{"role": "Theme", "text": "CD40", "start": 107, "end": 111}]}, {"trigger": {"text": "ligation", "start": 594, "end": 602}, "arguments": [{"role": "Theme", "text": "CD40", "start": 589, "end": 593}]}], "gene expression": [{"trigger": {"text": "expression", "start": 2017, "end": 2027}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2031, "end": 2035}]}, {"trigger": {"text": "expression", "start": 2135, "end": 2145}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2130, "end": 2134}]}, {"trigger": {"text": "express", "start": 2585, "end": 2592}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2671, "end": 2675}]}], "negative regulation": [{"trigger": {"text": "lack", "start": 581, "end": 585}, "arguments": [{"role": "Theme", "text": "ligation", "start": 594, "end": 602}]}, {"trigger": {"text": "absence", "start": 683, "end": 690}, "arguments": [{"role": "Theme", "text": "IL4", "start": 694, "end": 697}]}, {"trigger": {"text": "absence", "start": 837, "end": 844}, "arguments": [{"role": "Theme", "text": "IL4", "start": 848, "end": 851}]}, {"trigger": {"text": "negative", "start": 2482, "end": 2490}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2477, "end": 2481}]}], "positive regulation": [{"trigger": {"text": "high", "start": 2598, "end": 2602}, "arguments": [{"role": "Theme", "text": "express", "start": 2585, "end": 2592}]}, {"trigger": {"text": "low", "start": 2638, "end": 2641}, "arguments": [{"role": "Theme", "text": "express", "start": 2585, "end": 2592}]}]}}, "schema": []}
{"input": "Wild-Type and LMP1 Transgenic Lymphoma Cells Do Not Require IL4 and Stat6 Signaling\nTo investigate whether IL4 independence was due to endogenous IL4 expression, IL4 transcription was assessed by an Rnase protection assay (RPA). IL4 transcription was detectable with control RNA and faintly in the mouse lymphoma cell line K46mu (Figure 4A). However, IL4 transcription was not detectable in CD19+ MACS-purified B cells from wild-type lymphocytes (unpublished data), LMP1 transgenic lymphocytes, or lymphoma cells, although the GAPDH and L32 controls were effectively protected (Figure 4A). Activated Stat6 (pStat6), a target of the IL4 receptor pathway, was detected in the wild-type and LMP1 transgenic lymphocytes (Figure 4B). In contrast, pStat6 was barely detected in either the wild-type or LMP1 transgenic lymphoma cells. However, the pathway was not disabled, as treatment of the lymphoma cells with IL4 induced Stat6 phosphorylation (Figure 4C). \nAlthough wild-type lymphocytes cannot be maintained in culture with IL4 supplementation alone (Figure 3A), slight enhancement in MTS activity could be detected if the cells were analyzed at an earlier time point, at 1 d (Figure 4D) versus 3 d (Figure 3A) post-harvest. The enhancement of MTS activity induced by IL4 in wild-type lymphocytes could be neutralized by the addition of IL4 antibody (Figure 4D). However, neutralizing antibodies to IL4 did not affect the MTS activity of LMP1 transgenic lymphoma cells (Figure 4E). In summary, the wild-type and LMP1 transgenic lymphoma cells grew independently of IL4 treatment and did not require Stat6 signaling. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 150, "end": 160}, "arguments": [{"role": "Theme", "text": "IL4", "start": 146, "end": 149}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 925, "end": 940}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 919, "end": 924}]}], "positive regulation": [{"trigger": {"text": "Activated", "start": 590, "end": 599}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 600, "end": 605}]}, {"trigger": {"text": "induced", "start": 911, "end": 918}, "arguments": [{"role": "Cause", "text": "IL4", "start": 907, "end": 910}, {"role": "Theme", "text": "phosphorylation", "start": 925, "end": 940}]}], "regulation": [{"trigger": {"text": "target", "start": 618, "end": 624}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 600, "end": 605}]}], "transcription": [{"trigger": {"text": "transcription", "start": 166, "end": 179}, "arguments": [{"role": "Theme", "text": "IL4", "start": 162, "end": 165}]}, {"trigger": {"text": "transcription", "start": 233, "end": 246}, "arguments": [{"role": "Theme", "text": "IL4", "start": 229, "end": 232}]}, {"trigger": {"text": "transcription", "start": 355, "end": 368}, "arguments": [{"role": "Theme", "text": "IL4", "start": 351, "end": 354}]}]}}, "schema": []}
{"input": "LMP1 Upregulates IL10 and Constitutively Activates Stat3\nTo identify cytokines that may contribute to the increased survival and growth of lymphomas, the expression levels of a panel of cytokines were screened on CD19+ MACS-purified B cells, using an RPA probe set for IL4, IL5, IL10, IL13, IL15, IL9, IL2, IL6, and IFNgamma. Expression levels were quantified with a phosphorimager and normalized to the ribosomal housekeeping gene L32. None of the tested cytokines were detected in wild-type lymphocytes, therefore cytokine:L32 ratios were set to 1 in the mouse B cell lymphoma line 967. Transcription of IL10, IL15, and IFNgamma were reproducibly detected in LMP1 transgenic lymphocytes and lymphoma cells and was higher than in the B cell lymphoma cell lines 967 and K46mu (Figure 5A). There was no significant difference in the expression of IL15 and IFNgamma between LMP1 transgenic lymphocytes and lymphoma cells, suggesting that upregulation of IL15 and IFNgamma is induced by LMP1 expression in healthy lymphocytes but is not a unique property of malignant lymphocytes. Strikingly, IL10, a B lymphocyte stimulatory cytokine, was increased 1.5- to 5-fold in the wild-type and LMP1 transgenic lymphoma cells compared to LMP1 transgenic lymphocytes (Figure 5A). Production of IL15 and IFNgamma has been associated with induction of cytotoxic effector responses in cells latently infected with EBV [33,34]. However, transformation and growth properties induced by EBV are associated with the upregulation of IL10 [35-38]; hence, the effects of IL10 upregulation on the growth properties of the lymphoma cells were further examined. Immunoblot analysis indicated that LMP1 transgenic lymphocytes and wild-type and LMP1 transgenic lymphoma cells had corresponding increased levels of phosphorylated alpha and beta isoforms of activated Stat3, a target of the IL10 receptor (Figure 5B). However, when comparing the same lymphomas, there was no correlation between the levels of IL10 induction and the levels of Stat3 activation. This suggests that the activation of Stat3 is not solely induced by IL10 or that Stat3 activation may be constitutive. Additionally, there was no correlation between the levels of LMP1 expression and the levels of IL10 induction (Figures 1A and 5A). This indicates that the induction of IL10 is a general property associated with enhanced survival and may only be indirectly affected by LMP1. Neutralizing antibodies to IL10 did not affect the survival of lymphoma cells as determined by the MTS assay (unpublished data), suggesting constitutive activation of Stat3. This was confirmed by immunoblot analysis such that in the presence of anti-IL10 neutralizing antibodies, pStat3 levels remained activated in lymphoma cells isolated from wild-type and LMP1 transgenic lymphomas (Figure 5C). Exogenous addition of IL10 enhanced pStat3 activation above constitutive levels, indicating that lymphoma cells are responsive to IL10 treatment (Figure 5C). This means that although the lymphoma cells have constitutive Stat3 activation, it may be further enhanced by IL10 induction. The neutralizing effect of the anti-IL10 antibody was confirmed by pre-incubation of IL10 with anti-IL10 antibody compared to a rat IgG1 isotype control (Figure 5C). \nNuclear translocation of pStat3 is a consequence of activation, and nuclear pStat3 was not detected by immunohistochemistry staining of spleen sections from control mice. However, nuclear pStat3 was detectable in LMP1 transgenic mice and wild-type lymphomas and was detected more homogeneously in LMP1 transgenic lymphomas (Figure 5D). The constitutive activation of pStat3 and abundant nuclear Stat3 suggests that Stat3 signaling contributes to LMP1-mediated lymphoma development. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "detected", "start": 471, "end": 479}, "arguments": [{"role": "Theme", "text": "IL4", "start": 269, "end": 272}]}, {"trigger": {"text": "detected", "start": 471, "end": 479}, "arguments": [{"role": "Theme", "text": "IL5", "start": 274, "end": 277}]}, {"trigger": {"text": "detected", "start": 471, "end": 479}, "arguments": [{"role": "Theme", "text": "IL10", "start": 279, "end": 283}]}, {"trigger": {"text": "detected", "start": 471, "end": 479}, "arguments": [{"role": "Theme", "text": "IL13", "start": 285, "end": 289}]}, {"trigger": {"text": "detected", "start": 471, "end": 479}, "arguments": [{"role": "Theme", "text": "IL15", "start": 291, "end": 295}]}, {"trigger": {"text": "detected", "start": 471, "end": 479}, "arguments": [{"role": "Theme", "text": "IL9", "start": 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{"input": "LMP1 Activates Akt Signaling and Deregulates the Rb Cell Cycle Pathway\nLMP1 transformation of rodent fibroblasts requires activation of PI3K and Akt [5]. Additionally, activated pAkt is frequently detected in NPC and the neoplastic Reed-Sternberg cells of classical HD [39,40]. To determine if Akt signaling is activated in LMP1 transgenic mice, pAkt and several of its targets were assessed by immunoblotting of splenic CD19+ MACS-purified B cells. LMP1 transgenic B cells had increased levels of pAkt compared to wild-type lymphocytes; however, progression to lymphoma in both LMP1-positive and -negative lymphoma cells did not further increase pAkt levels. The Akt target glycogen synthase kinase 3 (GSK3) is inactivated by phosphorylation; however, increased phosphorylated GSK3 was not detected in the transgenic lymphocytes and was almost absent in the lymphoma samples (Figure 6A). This finding indicates that GSK3 is not a target of activated Akt in the LMP1 transgenic lymphocytes and lymphoma cells. Similarly, activation of Akt without phosphorylation of GSK3 has been previously shown in EBV-positive HD [40]. In contrast, the wild-type lymphocytes lacked activated Akt but did have detectable phosphorylated GSK3. This further suggests that additional pathways are involved in the regulation of GSK3. \nTo identify other potential Akt targets, immunoblot analysis for p-mTOR was performed. Activated p-mTOR was not increased in LMP1 transgenic lymphocytes or lymphoma cells, indicating that this pathway is not affected by LMP1-induced Akt activation and does not contribute to lymphoma development (Figure 6B). Akt is also known to phosphorylate and induce the degradation of the pro-apoptotic Forkhead family of transcription factors, leading to cell cycle progression and survival in some human tumors [41,42]. Immunoblot analysis of splenic B cells did not consistently detect p-FoxO1 levels, a signal that targets FoxO1 for degradation. Hence, degradation of FoxO1 was assessed by detection of total FoxO1 levels. Immunoblot analysis indicated that total FoxO1 levels were greatly decreased in wild-type and LMP1 transgenic lymphomas (Figure 6B), suggesting that inhibition of the Forkhead signaling pathway is an important target of Akt in lymphoma development. However, considering that Akt activation did not induce FoxO1 degradation in LMP1 transgenic B cells, Akt may not be the sole regulator of FoxO1, and it may be that progression to lymphoma requires modulation of multiple pathways. \nThe Forkhead family of transcription factors is known to induce the expression of the Cdk inhibitor p27 [43,44]. LMP1-transformed rodent fibroblasts have decreased expression of p27, upregulation of Cdk2, and subsequent phosphorylation and inactivation of the tumor suppressor gene Rb [45]. To investigate whether LMP1 affected cell cycle regulation through the Rb pathway in B cells, immunoblot analyses for pRb, Cdk2, and p27 were performed on splenic CD19+ MACS-purified B cells. LMP1 transgenic B cells had enhanced levels of pRb with concomitant stabilization of total Rb levels and Cdk2 compared to wild-type B lymphocytes (Figure 6C). Progression to lymphoma in both wild-type and LMP1 transgenic lymphoma cells led to increased levels of Rb, correspondingly high levels of Cdk2, and decreased levels of p27 (Figure 6C). These data indicate that the Rb pathway is deregulated in LMP1 transgenic lymphocytes and that lymphoma cells are distinguished by loss of FoxO1 and decreased p27. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "target", "start": 668, "end": 674}, "arguments": [{"role": "Theme", "text": "Akt", "start": 664, "end": 667}, {"role": "Theme2", "text": "glycogen synthase kinase 3", "start": 675, "end": 701}]}, {"trigger": {"text": "target", "start": 931, "end": 937}, "arguments": [{"role": "Theme", "text": "GSK3", "start": 917, "end": 921}, {"role": "Theme2", "text": "Akt", "start": 951, "end": 954}]}, {"trigger": {"text": "targets", "start": 1347, "end": 1354}, "arguments": [{"role": "Theme", "text": "Akt", "start": 1343, "end": 1346}]}], "gene expression": [{"trigger": {"text": "expression", "start": 2580, "end": 2590}, "arguments": [{"role": "Theme", "text": "p27", "start": 2612, "end": 2615}]}], "negative regulation": [{"trigger": {"text": "inactivated", "start": 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{"input": "LMP1 Promotes Tumor Growth and Survival through Activation of Akt, NFkappaB, and Stat3 Pathways\nTo explore which pathways were required for the enhanced growth and survival of LMP1-induced lymphomas, splenocytes from wild-type and LMP1 transgenic mice were cultured in the presence of inhibitors for Akt, NFkappaB, Stat3, mTOR, or MAPK and assayed for growth and survival by the MTS assay. As previously shown, wild-type lymphocytes were not viable in culture and could not be tested with the inhibitors. However, the enhanced viability of LMP1 transgenic lymphocytes was effectively blocked by treatment with triciribine, BAY11-7085, cucurbitacin I, and slightly with SB203580, but not by treatment with rapamycin, U0126, or AG490 (Figure 7). Triciribine inhibits the activation of Akt and at 20 muM has been shown to induce growth arrest in cancer cells with aberrant Akt activity [46]. The effects of triciribine on cell growth of the transgenic lymphocytes and lymphomas were apparent as low as 1 muM, suggesting that activation of Akt is required for the survival and growth of LMP1 transgenic lymphocytes and lymphoma cells (Figure 7). The effects of the inhibitors were assessed by identifying phosphorylated Akt, Stat3, and total levels of IkappaBalpha (Figure 8). Treatment with triciribine effectively blocked phosphorylation of Akt, and phosphorylated Akt was no longer detected past 5 muM. Phosphorylated Stat3 and IkappaBalpha were still present at 25 muM. These findings suggest that triciribine specifically targets Akt and that Akt activation is required for the enhanced viability of the transgenic lymphocytes and lymphoma cells. \nInhibition of NFkappaB signaling rapidly induces cell death of EBV-transformed lymphocytes [17,18]. BAY11-7085, an inhibitor of NFkappaB signaling, also greatly decreased the viability of the LMP1 transgenic lymphocytes and lymphoma cells at doses as low as 1 muM, and at 5 muM the cells were completely nonviable (Figure 7). This is well within the reported IC50 of 10 muM. Phosphorylated Akt, Stat3, and total IkappaBalpha were still present up to treatment with 15 muM and then were no longer detected (Figure 8). This finding suggests that inhibition of NFkappaB can induce cell death in LMP1 transgenic lymphocytes and lymphoma cells without significant effects on activation of Akt or Stat3. \nCucurbitacin I inhibits activation of Stat3 by suppressing the activation of its kinase JAK2. It has been shown to selectively inhibit the growth of tumors with constitutively activated Stat3 [47]. Similarly, LMP1 transgenic lymphocytes and lymphoma cells were susceptible to cucurbitacin I treatment starting at 0.1 muM, a dose that corresponds closely to the reported IC50 of 500 nM (Figure 7) [47]. Phosphorylated Akt, Stat3, and total IkappaBalpha were not detectable past 1 muM and at higher doses all protein levels were greatly decreased, indicative of the total loss of viability (Figure 8). A second reported inhibitor of Stat3, AG490, had no effect on growth (Figure 7), but activation of Akt, Stat3, or levels of IkappaBalpha were also not affected (Figure 8). These findings suggest that inhibition of Stat3 can induce cell death in LMP1 transgenic lymphocytes and lymphoma cells, but Stat3 inhibition also has considerable crossover effects on Akt and NFkappaB signaling. \nLMP1 has also been shown to activate JNK and p38 MAPK pathways [13,48], and LMP1 transgenic lymphocytes were mildly susceptible to growth inhibition by SB202190, an inhibitor of p38 MAPK, but not U0126, an inhibitor of MEK1/2 activity. However, effects of SB202190 were only apparent at high doses (>10 muM), much higher than the reported IC50 of 0.35 muM, suggesting that p38 MAPK does not significantly contribute to the enhanced viability in LMP1 transgenic lymphocytes or lymphoma cells (Figure 7). Interestingly, both wild-type and LMP1 transgenic lymphomas were similarly susceptible to triciribine, BAY11-7085, and cucurbitacin I treatments, but not SB202190, AG490, or U0126 treatment, suggesting that activation of Akt, NFkappaB, and Stat3 but not MAPK pathways are characteristics associated with malignant transformation (Figure 7). rapamycin, an inhibitor of mTOR, did not affect the viability of the transgenic lymphocytes or lymphoma cells, confirming that mTOR is not targeted by Akt activation in LMP1 transgenic lymphocytes or malignant lymphoma cells (Figure 7). \n", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitors", "start": 285, "end": 295}, "arguments": [{"role": "Theme", "text": "Akt", "start": 300, "end": 303}]}, {"trigger": {"text": "inhibitors", "start": 285, "end": 295}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 315, "end": 320}]}, {"trigger": {"text": "inhibitors", "start": 285, "end": 295}, "arguments": [{"role": 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{"input": "Discussion\nThis study defines the oncogenic properties of LMP1 in promoting B cell lymphomagenesis. LMP1 transgenic mice have a higher incidence of lymphoma [26] and the progression to lymphoma correlates with higher expression levels of LMP1 (Figure 1A and 1B), suggesting that LMP1 is directly involved in tumor development. Table 1 summarizes the biological and molecular properties that were identified in wild-type and LMP1 transgenic lymphomas. Although many of the molecular properties studied were similar between wild-type and LMP1 transgenic lymphomas, there were distinguishing biological properties, namely the ability of LMP1 transgenic lymphomas to induce higher levels of survival and proliferation. Interestingly, although LMP1 transgenic mice develop lymphomas in the same B-1a cell type as spontaneous wild-type lymphomas (Figure 2), some signaling effects induced by LMP1 may explain the enhanced promotion to lymphomagenesis. Since CD40-deficient mice have decreased numbers of IgMhighIgDlow cells, a phenotype associated with B-1, marginal zone, and memory B cells, the mimicry of CD40 signaling by LMP1 could possibly contribute to the expansion of B-1 cells [20]. It is noteworthy that expression of LMP1 in transgenic mice has been shown to inhibit the formation of GCs [23,49], preventing typical B-2 cells from antigen-driven selection and expansion. The lack of GC reactions may contribute to the bias of LMP1 transgenic mice towards B-1 cell lymphomas. Interestingly, LMP2 signaling also favors development of B-1 cells, but this occurs in the absence of transformation. These results suggest that the mimicry of B cell receptor signaling by LMP2 promotes B-1 cell differentiation but not transformation [24,50,51]. This promotion of B-1 differentiation may account for the ability of LMP2 to exacerbate autoimmunity and bypass anergy induction [52,53]. In contrast, the preponderance of tumors of B-1a origin does not reflect effects of LMP1 signaling on B cell differentiation, as splenic B cells from healthy LMP1 transgenic mice contain similar numbers of B-1 and B-2 cells as wild-type mice. In support of this lack of effect, the differentiation of B-1 versus B-2 cells is thought to be independent of CD40 signaling [54]. \nB-1 cells constitute the predominant lymphocyte population in the peritoneal and pleuropericardial cavities, while B-2 cells are mainly found in the spleen, lymph node, and peripheral blood. B-1 cells produce the main source of IgM and IgA antibodies in serum, which are involved in T cell-independent responses to common microbial antigens. Importantly, B-1 cells have the unique capacity to self replenish and are also predisposed to transformation [28,29]. Clonal expansion of B-1 cells can be detected in aging mice above 18 mo of age, and B-1 cells are thought to be the murine progenitor of B cell chronic lymphocytic leukemia [30]. The data presented in this study indicate that although LMP1 is expressed in all B lymphocytes in the transgenic mice, malignancy develops in this specific subset of B cells. The elevated expression of LMP1 in B-1a cells and the activation of specific pathways apparently induce malignant growth. These same pathways can also become sporadically activated in aged mice and also result in lymphoma development. This is similar to EBV-associated cancers in vivo, where pathways that are activated by LMP1 are also activated in the less prevalent EBV-negative forms of the cancers [40,55-58]. Thus, the contribution of EBV and LMP1 to tumor development is apparently the continuous activation of pathways that can also be sporadically activated and contribute to tumor development. \nThe lymphomas were marked by the upregulation of IL10, constitutive activation of Stat3 signaling, and a requirement for activation of Akt, NFkappaB, and Stat3 pathways (Figures 5 and 7). Induction of IL10 is associated with the transformation of B-1 lymphomas in mice [59,60] and is frequently associated with EBV-positive B cell malignancies acting as a B cell growth factor [35-38]. In addition, LMP1 has been shown to stimulate IL10 expression in Burkitt lymphoma cell lines [61,62]. This suggests that although Stat3 is constitutively activated in the lymphoma cells, the induction of IL10 may further enhance Stat3 activation or may contribute to other IL10-responsive signaling pathways. \nLMP1 activates both the canonical and non-canonical pathways of NFkappaB signaling [14,63-65], and inhibition of NFkappaB blocked the survival of LMP1 transgenic lymphocytes and LMP1-positive and -negative lymphoma cells. NFkappaB and PI3K signaling are crucial for CD40-induced proliferation, and mice deficient for cRel or the p85 regulatory subunit of PI3K are unresponsive to mitogenic stimuli, including CD40 ligation [66-68]. We have previously shown that cRel is specifically activated in both wild-type and LMP1 transgenic lymphomas, suggesting that activation of cRel is associated with B cell transformation [27]. Our observations suggest that similar to CD40-induced proliferation, LMP1 induces proliferation through PI3K-mediated activation of Akt and activation of NFkappaB components such as cRel. CD40 also induces downregulation of the cell cycle inhibitor p27 through a PI3K-dependent manner, and the LMP1 lymphoma cells also had decreased levels of p27 with phosphorylation of Rb and increased Cdk2 (Figure 6C) [66]. Although LMP1 has been shown to deregulate the Rb pathway in epithelial cells [69], to our knowledge this is the first demonstration of this property in B lymphocytes. \nThe requirement for Akt activation was confirmed by the striking inhibition of lymphoma viability by triciribine, an Akt inhibitor. However, the activated pAkt did not lead to phosphorylation and inactivation of the downstream target GSK3 (Figure 6A). This effect has also been described in EBV-positive HD biopsies [40]. In contrast, rapamycin, U0126, and SB202190 did not affect the survival of LMP1 transgenic lymphocytes or the wild-type and LMP1 transgenic lymphoma cells (Figure 7A, 7C, and 7E). This lack of effect by rapamycin confirmed the absence of activated p-mTOR levels (Figure 6B). These findings suggest that other Akt targets contribute to malignant progression. One key target is likely the inhibition of the Fox01 transcription factors. Repression of the pro-apoptotic transcription factor FoxO1 in a PI3K-dependent manner can inhibit expression of bcl6, a transcription factor necessary for GC formation [49,70]. It has been shown that overstimulation of CD40 signaling with agonistic antibodies inhibits GC formation [71]. Similarly, due to mimicry of CD40 signaling, transgenic LMP1 mice are also defective in GC formation [23,49]. The constitutive signaling by LMP1 likely blocks GC formation through downregulation of bcl6. Interestingly, clinical studies indicate that expression of LMP1 and bcl6 are mutually exclusive in non-HD and classical HD [72,73]. Thus, the LMP1 transgenic lymphomas mirror aspects of EBV-induced HD. Although the activation of Akt and the lack of Fox01 in the lymphoma cells suggest that LMP1 affects bcl6 and GC formation through this pathway, regulation of other Forkhead targets involved in cell cycle progression, such as p27 and CyclinD2, likely contribute to malignant transformation. Indeed, loss of FoxO1 expression in lymphoma cells correlated with a loss of p27 (Figure 6B and 6C). CyclinD2 has also been shown to be upregulated by LMP1 through release of FoxO1-mediated repression [70]. \nIn summary, in this transgenic model of lymphomagenesis, LMP1 promotes malignancy in B-1a cells, a population that is predisposed to clonal expansion with age. The malignant lymphocytes were distinguished by constitutively active Stat3 signaling, decreased p27, and activated Akt and NFkappaB pathways, properties that are associated with promoting the growth and survival of B lymphocytes. Importantly, Akt, NFkappaB, and Stat3 pathways were critically required for the growth and survival of malignant lymphocytes as well as healthy LMP1 transgenic lymphocytes. The growth of EBV-transformed lymphocytes also requires activation of NFkappaB, and these studies provide insight into how LMP1 contributes to EBV-associated transformation. The transgenic lymphomas mirror multiple aspects of EBV-induced tumors and suggest that in vivo these properties of LMP1 are major factors in the development of cancer. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 4787, "end": 4795}, "arguments": [{"role": "Theme", "text": "CD40", "start": 4782, "end": 4786}]}], "gene expression": [{"trigger": {"text": "expression", "start": 217, "end": 227}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 238, "end": 242}]}, {"trigger": {"text": "expression", "start": 1209, "end": 1219}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1223, "end": 1227}]}, {"trigger": {"text": "expressed", "start": 2961, "end": 2970}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 2953, "end": 2957}]}, {"trigger": {"text": "expression", "start": 3085, "end": 3095}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 3099, "end": 3103}]}, {"trigger": {"text": "expression", "start": 4114, 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"deficient", "start": 4676, "end": 4685}, "arguments": [{"role": "Theme", "text": "p85", "start": 4702, "end": 4705}]}, {"trigger": {"text": "downregulation", "start": 5203, "end": 5217}, "arguments": [{"role": "Theme", "text": "p27", "start": 5246, "end": 5249}]}, {"trigger": {"text": "decreased", "start": 5320, "end": 5329}, "arguments": [{"role": "Theme", "text": "p27", "start": 5340, "end": 5343}]}, {"trigger": {"text": "inhibitor", "start": 5698, "end": 5707}, "arguments": [{"role": "Theme", "text": "Akt", "start": 5694, "end": 5697}]}, {"trigger": {"text": "inactivation", "start": 5773, "end": 5785}, "arguments": [{"role": "Theme", "text": "GSK3", "start": 5811, "end": 5815}]}, {"trigger": {"text": "absence", "start": 6126, "end": 6133}, "arguments": [{"role": "Theme", "text": "activated", "start": 6137, "end": 6146}]}, {"trigger": {"text": "inhibition", "start": 6286, "end": 6296}, "arguments": [{"role": "Theme", "text": "Fox01", "start": 6304, "end": 6309}]}, {"trigger": {"text": "Repression", "start": 6333, "end": 6343}, "arguments": [{"role": "Theme", "text": "FoxO1", "start": 6386, "end": 6391}]}, {"trigger": {"text": "inhibit", "start": 6423, "end": 6430}, "arguments": [{"role": "Cause", "text": "Repression", "start": 6333, "end": 6343}, {"role": "Theme", "text": "expression", "start": 6431, "end": 6441}]}, {"trigger": {"text": "downregulation", "start": 6801, "end": 6815}, "arguments": [{"role": "Theme", "text": "bcl6", "start": 6819, "end": 6823}]}, {"trigger": {"text": "exclusive", "start": 6912, "end": 6921}, "arguments": [{"role": "Cause", "text": "expression", "start": 6871, "end": 6881}, {"role": "Theme", "text": "expression", "start": 6871, "end": 6881}]}, {"trigger": {"text": "lack", "start": 7067, "end": 7071}, "arguments": [{"role": "Theme", "text": "Fox01", "start": 7075, "end": 7080}]}, {"trigger": {"text": "loss", "start": 7327, "end": 7331}, "arguments": [{"role": "Theme", "text": "expression", "start": 7341, "end": 7351}]}, {"trigger": {"text": "loss", "start": 7388, "end": 7392}, "arguments": [{"role": "Theme", "text": "p27", "start": 7396, "end": 7399}]}, {"trigger": {"text": "decreased", "start": 7774, "end": 7783}, "arguments": [{"role": "Theme", "text": "p27", "start": 7784, "end": 7787}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 5349, "end": 5364}, "arguments": [{"role": "Theme", "text": "Rb", "start": 5368, "end": 5370}]}, {"trigger": {"text": "phosphorylation", "start": 5753, "end": 5768}, "arguments": [{"role": "Theme", "text": "GSK3", "start": 5811, "end": 5815}]}], "positive regulation": [{"trigger": {"text": "higher", "start": 210, "end": 216}, "arguments": [{"role": "Theme", "text": "expression", "start": 217, "end": 227}]}, {"trigger": {"text": "elevated", "start": 3076, "end": 3084}, "arguments": [{"role": "Theme", "text": "expression", "start": 3085, "end": 3095}]}, {"trigger": {"text": "upregulation", "start": 3710, "end": 3722}, "arguments": [{"role": "Theme", "text": "IL10", "start": 3726, "end": 3730}]}, {"trigger": {"text": "Induction", "start": 3865, "end": 3874}, "arguments": [{"role": "Theme", "text": "IL10", "start": 3878, "end": 3882}]}, {"trigger": {"text": "stimulate", "start": 4099, "end": 4108}, "arguments": [{"role": "Cause", "text": "LMP1", "start": 4076, "end": 4080}, {"role": "Theme", "text": "expression", "start": 4114, "end": 4124}]}, {"trigger": {"text": "activated", "start": 4217, "end": 4226}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 4193, "end": 4198}]}, {"trigger": {"text": "induction", "start": 4254, "end": 4263}, "arguments": [{"role": "Theme", "text": "IL10", "start": 4267, "end": 4271}]}, {"trigger": {"text": "enhance", "start": 4284, "end": 4291}, "arguments": [{"role": "Cause", "text": "induction", "start": 4254, "end": 4263}, {"role": "Theme", "text": "activation", "start": 4298, "end": 4308}]}, {"trigger": {"text": "activation", "start": 4298, "end": 4308}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 4292, "end": 4297}]}, {"trigger": {"text": "activated", "start": 4856, "end": 4865}, "arguments": [{"role": "Theme", "text": "cRel", "start": 4835, "end": 4839}]}, {"trigger": {"text": "activation", "start": 4931, "end": 4941}, "arguments": [{"role": "Theme", "text": "cRel", "start": 4945, "end": 4949}]}, {"trigger": {"text": "induces", "start": 5071, "end": 5078}, "arguments": [{"role": "Cause", "text": "LMP1", "start": 5066, "end": 5070}, {"role": "Theme", "text": "activation", "start": 5115, "end": 5125}]}, {"trigger": {"text": "induces", "start": 5071, "end": 5078}, "arguments": [{"role": "Cause", "text": "LMP1", "start": 5066, "end": 5070}, {"role": "Theme", "text": "activation", "start": 5137, "end": 5147}]}, {"trigger": {"text": "activation", "start": 5115, "end": 5125}, "arguments": [{"role": "Theme", "text": "Akt", "start": 5129, "end": 5132}]}, {"trigger": {"text": "activation", "start": 5137, "end": 5147}, "arguments": [{"role": "Theme", "text": "cRel", "start": 5179, "end": 5183}]}, {"trigger": {"text": "induces", "start": 5195, "end": 5202}, "arguments": [{"role": "Cause", "text": "CD40", "start": 5185, "end": 5189}, {"role": "Theme", "text": "downregulation", "start": 5203, "end": 5217}]}, {"trigger": {"text": "increased", "start": 5375, "end": 5384}, "arguments": [{"role": "Theme", "text": "Cdk2", "start": 5385, "end": 5389}]}, {"trigger": {"text": "requirement", "start": 5581, "end": 5592}, "arguments": [{"role": "Theme", "text": "activation", "start": 5601, "end": 5611}]}, {"trigger": {"text": "activation", "start": 5601, "end": 5611}, "arguments": [{"role": "Theme", "text": "Akt", "start": 5597, "end": 5600}]}, {"trigger": {"text": "activated", "start": 5722, "end": 5731}, "arguments": [{"role": "Theme", "text": "pAkt", "start": 5732, "end": 5736}]}, {"trigger": {"text": "lead", "start": 5745, "end": 5749}, "arguments": [{"role": "Cause", "text": "activated", "start": 5722, "end": 5731}, {"role": "Theme", "text": "phosphorylation", "start": 5753, "end": 5768}]}, {"trigger": {"text": "lead", "start": 5745, "end": 5749}, "arguments": [{"role": "Cause", "text": "activated", "start": 5722, "end": 5731}, {"role": "Theme", "text": "inactivation", "start": 5773, "end": 5785}]}, {"trigger": {"text": "activated", "start": 6137, "end": 6146}, "arguments": [{"role": "Theme", "text": "p-mTOR", "start": 6147, "end": 6153}]}, {"trigger": {"text": "activation", "start": 7041, "end": 7051}, "arguments": [{"role": "Theme", "text": "Akt", "start": 7055, "end": 7058}]}, {"trigger": {"text": "correlated", "start": 7370, "end": 7380}, "arguments": [{"role": "Cause", "text": "loss", "start": 7327, "end": 7331}, {"role": "Theme", "text": "loss", "start": 7388, "end": 7392}]}, {"trigger": {"text": "upregulated", "start": 7455, "end": 7466}, "arguments": [{"role": "Theme", "text": "CyclinD2", "start": 7420, "end": 7428}]}], "regulation": [{"trigger": {"text": "target", "start": 6265, "end": 6271}, "arguments": [{"role": "Cause", "text": "Akt", "start": 6208, "end": 6211}, {"role": "Theme", "text": "inhibition", "start": 6286, "end": 6296}]}, {"trigger": {"text": "affects", "start": 7121, "end": 7128}, "arguments": [{"role": "Theme", "text": "bcl6", "start": 7129, "end": 7133}, {"role": "Cause", "text": "pathway", "start": 7164, "end": 7171}]}, {"trigger": {"text": "pathway", "start": 7164, "end": 7171}, "arguments": [{"role": "Theme", "text": "Fox01", "start": 7075, "end": 7080}, {"role": "Cause", "text": "LMP1", "start": 7116, "end": 7120}]}, {"trigger": {"text": "regulation", "start": 7173, "end": 7183}, "arguments": [{"role": "Theme", "text": "p27", "start": 7254, "end": 7257}]}, {"trigger": {"text": "regulation", "start": 7173, "end": 7183}, "arguments": [{"role": "Theme", "text": "CyclinD2", "start": 7262, "end": 7270}]}]}}, "schema": []}
{"input": "Transgenic mice.\nGeneration of LMP1 mice under the Ig heavy chain promoter and enhancer have been described previously and were maintained as heterozygotes on a Balbc background [26]. LMP1 mice were genotyped by Southern blot and PCR analysis of tail DNA as described previously [26]. Spleen and liver sections were fixed in 4% paraformaldehyde and embedded in paraffin, and 5-mum sections were stained with hematoxylin and eosin for histopathological analysis. Lymphomas were passaged by intraperitoneal injection of 1 x 108 splenocytes into SCID mice and sacrificed upon development of an extended abdomen. Animals were housed in the Association for Assessment and Accreditation for Animal Care-approved animal facility at the University of North Carolina at Chapel Hill. All protocols were approved by the Institutional Animal Care and Use Committee. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Isolation and growth of B cells.\nSplenocytes were prepared by homogenizing spleen tissue with two frosted slides and debris was filtered through a 100-mum cell strainer. Erythrocytes were lysed using 0.8% ammonium chloride solution (StemCell Technologies) for 10 min on ice and washed twice with PBS. B cells were isolated using CD19-MACS beads according to the manufacturer's instructions (Miltenyi Biotec) and grown in Iscove's medium supplemented with heat-inactivated 10% fetal bovine serum and antibiotic/antimycotic (GIBCO). Splenocytes isolated from SCID-passaged lymphomas consisted of 80%-90% B cells as determined by flow cytometry, and were hence not further purified with CD19-MACS beads. Splenocytes were seeded at 1.25 x 106 cells/ml and where applicable, recombinant mouse IL4 was added at 100 ng/ml, recombinant mouse IL10 at 10 ng/ml, and rat IgG1 anti-mouse IL10 and rat IgG1 isotype control at 10 mug/ml (R&D Systems). For BrdU incorporation assays, splenocytes were pulsed for 24 h with 10 muM BrdU 1 d post-harvest. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "MTS assay.\nThe 3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) cell cytotoxicity/proliferation assays were performed using the CellTiter 96 aqueous one-solution cell proliferation assay (Promega), according to manufacturer's instructions. For IL4 studies, splenocytes were cultured for 3 d in the presence or absence of 100 ng/ml IL4. Cells were seeded on day 3 in triplicate in a 96-well plate at 2.5 x 106 cells/ml at 100 mul per well. MTS reagent was added for 4 h and absorbance was read at 540 nm; values plotted were subtracted from blanks. For neutralization assays, splenocytes were seeded at 5 x 106 cells/ml at 100 mul per well on day of harvest and IL4, rat IgG1 anti-mouse IL4, or rat IgG1 isotype control (R&D Systems) were added at the concentrations indicated in the figures. Cultures were pulsed for 4 h with MTS reagent 1 d post-seeding. For inhibitor studies, splenocytes were seeded at 1 x 107 cells/ml at 100 mul per well on day of harvest, and inhibitors were added at the concentrations indicated in the figures. The inhibitors BAY11-7085, rapamycin, triciribine, U0126, SB202190, and cucurbitacin I were purchased from EMD Biosciences. For non-malignant splenocyte cultures, B cell activation was induced with 10 mug/ml of goat F(ab') anti-mouse IgM (Jackson ImmunoResearch). Cultures were pulsed for 4 h with MTS reagent 1 d post-seeding. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Immunohistochemistry.\nParaffin-embedded spleen sections were deparaffinized in Histoclear (National Diagnostics) and rehydrated in graded ethanol. Sections were antigen retrieved by microwaving in citrate buffer (pH 6.0) for 15 min (LMP1 staining) and 10 min (pStat3 staining). For LMP1 staining, sections were blocked with 1% BSA and 0.1% cold fish skin gelatin followed with streptavidin/biotin block (Vector Labs). Rat IgG anti-LMP1 (clones 8G3 and 1G6, Ascenion) were used at 1:10 dilution from tissue culture supernatants, followed with 8 mug/ml biotinylated mouse F(ab') anti-rat IgG (H+L) pre-adsorbed to mouse serum (Jackson ImmunoResearch) and 2 mug/ml streptavidin-alkaline phosphatase conjugate (Jackson ImmunoResearch). Stains were developed with BCIP/NBT and counterstained in Nuclear Fast Red (Dako). Phospho-Stat3 was detected with 4 mug/ml of pStat3 antibody (Tyr705, Cell Signaling) and detected with anti-rabbit Poly-HRP IHC detection kit (Chemicon). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Flow cytometry.\nOne million splenocytes were stained with the appropriate primary antibody unconjugated or conjugated to FITC, PE, or APC diluted in stain buffer (PBS with 3% FBS). For BrdU detection, the FITC-BrdU flow kit was used as instructed by the manufacturer (BD Bioscience). Briefly, cells were exposed to EMA (Molecular Probes) for exclusion of dead cells, stained for surface antigens, fixed in paraformaldehyde, and permeabilized with saponin. To expose BrdU epitopes, cells were treated with Dnase and stained with FITC-conjugated anti-BrdU antibody. Flow cytometry was performed on FACScalibur using the CellQuest program (Becton Dickinson). Further analysis was conducted on the Summit v4.2 program (Dako). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Rnase protection assay.\nTotal RNA was isolated from CD19+ MACS-purified B cells using the Rneasy midi purification kit with Dnase treatment, according to the manufacturer's instructions (Qiagen). The mCK-1 probe template set (BD Biosciences) was labeled using the In Vitro Transcription Kit according to the manufacturer's instructions (BD Biosciences). Briefly, 50 ng of mCK-1 probe set was labeled with [alpha-32P]UTP using T7 RNA polymerase and purified using Sephadex G-50 columns (NucAway Spin column, Ambion). The labeled probe was quantitated using a scintillation counter, and 6 x 105 cherenkov cpm was used to hybridize to 4 mug of total RNA using the RPA kit (BD Biosciences). Samples were denatured at 90 degreesC and hybridized at 56 degreesC overnight. Single-stranded RNA was digested with a mixture of Rnase A and T1, and precipitated using isopropanol. Protected probes were resolved on a denaturing 4.75% acrylamide gel, dried, and imaged using a phosphorImager (Molecular Dynamics). Densitometry was performed using the ImageQuant TL v2005 software (GE Healthcare). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "PCR analysis of kappa chain rearrangement.\nDNA was isolated from splenocytes using the Dneasy Tissue Kit (Qiagen), with Rnase treatment. PCR reactions contained 100 ng of genomic DNA, 0.2 muM each primer, 0.2 mM dNTPs, and 2.5 U Taq DNA polymerase (NEB) performed in 1X ThermoPol buffer (NEB). Primers used were Vkappacon and Jkappa5-1degrees and have been described previously [74]. PCR conditions were 94 degreesC for 2 min, 40 cycles of 94 degreesC for 30 s, 63 degreesC for 90 s, and 72 degreesC for 1 min, followed by 1 cycle of 72 degreesC for 5 min. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Immunoblot analysis.\nWhole cell lysates were prepared in radioimmunoprecipitation assay (RIPA) buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with 2 mM phenylmethylsulfonyl fluoride, 1 mM Na3VO4, and 1:100 protease/phosphatase inhibitor cocktails (Sigma). Crude lysates were centrifuged at 13,000 rpm for 10 min at 4 degreesC and the supernatants were collected for further analysis. Protein concentrations were determined with the Bio-Rad DC protein assay system. Lysates were boiled in the presence of 2.5% beta-mecaptoethanol, separated by denaturing SDS-PAGE, and transferred to 0.45-mum Optitran membranes (Schleicher & Schuell) in a Bio-Rad transfer unit. Membranes were immunoblotted with the appropriate primary antibody followed by horseradish peroxidase-tagged secondary antibodies (Amersham Biosciences and Dako) and detected with the SuperSignal West Pico System (Pierce). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Antibodies.\nFITC-conjugated goat anti-mouse IgM, rat IgG2akappa anti-mouse IgD (clone 11-26), rat IgG1kappa anti-mouse kappa (clone 187.1), rat IgG2bkappa anti-mouse lambda (clone JC5-1); PE-conjugated goat anti-mouse IgG; un-conjugated goat anti-mouse kappa and anti-mouse lambda were purchased from Southern Biotech. APC-conjugated rat IgG2akappa anti-mouse CD19 (clone 6D5), PE-conjugated mouse IgG2akappa anti-LMP1 (clone S12), un-conjugated mouse IgG2a anti-Rb (clone 2), and anti-Cdk2 (clone 55) were purchased from BD Bioscience. PE-conjugated rat IgG2akappa anti-mouse CD5 (clone 53-7.3) was purchased from eBioscience. Rat anti-LMP1 (clones 8G3, 1G6, 7E10, and 7G8) was purchased from Ascenion. Rabbit anti-pAkt (Ser473), anti-pGSK3alpha/beta (Ser21/9), anti-pStat3 (Tyr705), anti-pStat6 (Tyr641), anti-pmTOR (Ser2448), anti-Stat6, anti-Akt, anti-FoxO1, and anti-p27 were purchased from Cell Signaling. Rabbit anti-Stat3 (H-190), anti-IkappaBalpha (C-21), and goat anti-beta actin (I-19) were purchased from Santa Cruz Biotechnology. Mouse IgG1kappa anti-GSK3 was purchased from Upstate Biotechnology. Rabbit anti-pRb (Thr373) was purchased from EMD Biosciences. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Accession Numbers\nThe GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) accession number for the EBV genome sequence is AJ507799. The gene identifier for LMP1 is BNLF1. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "High LMP1 Expression Correlates with the Development of Lymphoma\nLMP1 expression is shown by (A) immunoblotting of purified B cells (CD19+) and (B) immunohistochemistry staining of spleen tissue from wild-type (WT) and LMP1 transgenic mice. \n(A) Lymphomas are identified with a number (1-7). Arrows indicate the LMP1-specific band and its degradation products as well as a non-specific band. Actin was used as a loading control. \n(B) White and red pulps are shown, but this architecture is lost upon development of lymphoma. Scale bar, 20 mum. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 10, "end": 20}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 5, "end": 9}]}, {"trigger": {"text": "expression", "start": 70, "end": 80}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 65, "end": 69}]}], "positive regulation": [{"trigger": {"text": "High", "start": 0, "end": 4}, "arguments": [{"role": "Theme", "text": "Expression", "start": 10, "end": 20}]}]}}, "schema": []}
{"input": "LMP1 Promotes B-1a Lymphomas That Can Escape Allelic Exclusion\n(A) Flow cytometry analysis of splenocytes from a WT or LMP1 transgenic lymphoma for the pan-B cell (CD19), B-1a cell (CD5), and Ig heavy chain (IgM and IgD) and light chain (kappa and lambda) markers. Shown are the results from WT lymphoma 1 and LMP1 transgenic lymphoma 4. This analysis was repeated on four other LMP1 transgenic lymphomas (1, 2, 3, and 6) showing a similar B-1a phenotype, of which lymphomas 2 and 4 were also doubly positive for kappa and lambda light chains. \n(B) Flow cytometry analysis of WT or LMP1 transgenic splenocytes for B-1a (CD19+CD5+) and B-1b or B2 subsets (CD19+CD5-). Percentages of B-1a and B-1b or B2 subsets are shown in each quadrant. This analysis was repeated on three other WT and two other LMP1 transgenic mice with similar results. \n(C) Immunoblot analysis for kappa and lambda light chains of B cells (CD19+) purified from WT and LMP1 transgenic mice. Actin was used as a loading control. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "LMP1 Promotes B Cell Survival and Proliferation In Vitro\n(A) MTS assay of splenocytes from WT and LMP1 transgenic mice. Splenocytes were cultured in the presence (grey bars) or absence (black bars) of IL4 for 3 d. The results are the mean +/- SEM of triplicate samples averaged from multiple mice where \"n\" the number of mice analyzed is as follows: n = 2 for WT lymphocytes and WT lymphomas, n = 11 for LMP1 transgenic lymphocytes, and n = 13 for LMP1 transgenic lymphomas. \n(B) EMA exclusion of CD19+ gated splenocytes from WT and LMP1 transgenic mice showing percentage of viable B cells cultured with (white bars) or without (black bars) IL4 for 2 d. \n(C) Flow cytometry analysis for incorporated BrdU in WT and LMP1 transgenic lymphoma cells cultured with or without IL4 for 2 d. Shown are the results from WT lymphoma 1 and LMP1 transgenic lymphoma 2. Percentages of cells in each quadrant are shown. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Summary of Analysis Performed on Wild-Type and LMP1 Transgenic Lymphomas \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Transgenic", "start": 52, "end": 62}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 47, "end": 51}]}]}}, "schema": []}
{"input": "Wild-Type and LMP1 Transgenic Lymphoma Cells Survive Independently of IL4/Stat6 Signaling in Culture\n(A) Rnase protection assay for IL4 mRNA from purified B cells (CD19+) from WT and LMP1 transgenic splenocytes. The L32 and GAPDH housekeeping genes were used as a loading control. Arrow indicates the position of the protected probe. \n(B and C) Immunoblot analysis of WT and LMP1 transgenic mice for activated pStat6 in (B) purified B cells (CD19+) at the time of harvest or in (C) whole splenocytes cultured with or without IL4. (B) Actin was used as a loading control, and the white line indicates that intervening lanes have been spliced out. \n(D and E) MTS assay of (D) WT lymphocytes and (E) LMP1 transgenic lymphoma cells cultured with IL4, a neutralizing antibody to IL4, or a rat IgG isotype control at the indicated concentrations. Shown are the results from LMP1 transgenic lymphoma 3. The results are the mean +/- SEM of triplicate samples from a single representative experiment that was repeated twice with similar results. \n", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "activated", "start": 400, "end": 409}, "arguments": [{"role": "Theme", "text": "pStat6", "start": 410, "end": 416}]}]}}, "schema": []}
{"input": "LMP1 Upregulates IL10 Expression and Constitutively Activates Stat3\n(A) Relative expression of IL10, IL15, and IFNgamma mRNA in WT and LMP1 transgenic B cells (CD19+), as detected with an Rnase protection assay. Mouse lymphoma cell lines 967 and K46mu were used as controls. Expression levels were quantified with a phosphorimager and values were normalized to the ribosomal housekeeping gene L32. The cytokine:L32 ratio was set to 1 in the mouse B cell lymphoma line 967. \n(B and C) Immunoblot analysis of activated pStat3 in purified B cells (CD19+) from WT and LMP1 transgenic mice (B) at the time of harvest, and (C) 4 h after culture with or without IL10, a neutralizing antibody to IL10, or a rat IgG1 isotype control. (C) Shown are the results for WT lymphoma 1 and LMP1 transgenic lymphoma 1. Arrows indicate the positions of the alpha and beta isoforms of Stat3. Actin was used as a loading control. \n(D) Immunohistochemistry detection of activated nuclear pStat3 in the spleens of WT and LMP1 transgenic mice. Scale bar, 20 mum. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 22, "end": 32}, "arguments": [{"role": "Theme", "text": "IL10", "start": 17, "end": 21}]}], "positive regulation": [{"trigger": {"text": "Upregulates", "start": 5, "end": 16}, "arguments": [{"role": "Cause", "text": "LMP1", "start": 0, "end": 4}, {"role": "Theme", "text": "Expression", "start": 22, "end": 32}]}, {"trigger": {"text": "Activates", "start": 52, "end": 61}, "arguments": [{"role": "Cause", "text": "LMP1", "start": 0, "end": 4}, {"role": "Theme", "text": "Stat3", "start": 62, "end": 67}]}, {"trigger": {"text": "activated", "start": 507, "end": 516}, "arguments": [{"role": "Theme", "text": "pStat3", "start": 517, "end": 523}]}, {"trigger": {"text": "activated", "start": 948, "end": 957}, "arguments": [{"role": "Theme", "text": "pStat3", "start": 966, "end": 972}]}], "transcription": [{"trigger": {"text": "expression", "start": 81, "end": 91}, "arguments": [{"role": "Theme", "text": "IL15", "start": 101, "end": 105}]}, {"trigger": {"text": "expression", "start": 81, "end": 91}, "arguments": [{"role": "Theme", "text": "IFNgamma", "start": 111, "end": 119}]}, {"trigger": {"text": "expression", "start": 81, "end": 91}, "arguments": [{"role": "Theme", "text": "IL10", "start": 95, "end": 99}]}]}}, "schema": []}
{"input": "LMP1 Activates Akt Signaling and Deregulates the Rb Cell Cycle Pathway\n(A and B) Immunoblot analysis of purified B cells (CD19+) from the spleens of WT and LMP1 transgenic mice for Akt signaling, probing for (A) activated pAkt and downstream targets, including inactivated pGSK3alpha/beta, and (B) activated p-mTOR, and total levels of FoxO1. Arrows indicate the positions of alpha and beta isoforms of GSK3. The white line indicates that intervening lanes have been spliced out. \n(C) Immunoblot analysis for cell cycle proteins regulating the Rb pathway, probing for activated pRb, and total levels of Cdk2 and the Cdk inhibitor p27. Actin was used as a loading control. \n", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "inactivated", "start": 261, "end": 272}, "arguments": [{"role": "Theme", "text": "pGSK3alpha", "start": 273, "end": 283}]}, {"trigger": {"text": "inactivated", "start": 261, "end": 272}, "arguments": [{"role": "Theme", "text": "beta", "start": 284, "end": 288}]}, {"trigger": {"text": "activated", "start": 298, "end": 307}, "arguments": [{"role": "Theme", "text": "p-mTOR", "start": 308, "end": 314}]}, {"trigger": {"text": "activated", "start": 568, "end": 577}, "arguments": [{"role": "Theme", "text": "pRb", "start": 578, "end": 581}]}], "regulation": [{"trigger": {"text": "targets", "start": 242, "end": 249}, "arguments": [{"role": "Theme", "text": "pGSK3alpha", "start": 273, "end": 283}]}, {"trigger": {"text": "targets", "start": 242, "end": 249}, "arguments": [{"role": "Theme", "text": "beta", "start": 284, "end": 288}]}]}}, "schema": []}
{"input": "Akt, NFkappaB, and Stat3 Signaling Are Required for the Growth and Survival of Lymphoma Cells\nMTS assay of splenocytes from (A and B) WT or (C and D) LMP1 transgenic lymphomas and (E and F) LMP1 transgenic lymphoctyes. Splenocytes were cultured with or without inhibitors of NFkappaB (BAY11), mTOR (rapamycin), Akt (triciribine), MEK1/2 (U0126), p38 (SB202190), or Stat3 (cucurbitacin I and AG490) at the indicated concentrations. The results are the mean +/- SEM of triplicate samples. Shown are the results for (A and B) WT lymphoma 1, (C and D) LMP1 transgenic lymphoma 2, and (E and F) one out of two LMP1 transgenic mice analyzed. This analysis was repeated with LMP1 transgenic lymphoma 4 yielding similar results. \n", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitors", "start": 261, "end": 271}, "arguments": [{"role": "Theme", "text": "mTOR", "start": 293, "end": 297}]}, {"trigger": {"text": "inhibitors", "start": 261, "end": 271}, "arguments": [{"role": "Theme", "text": "Akt", "start": 311, "end": 314}]}, {"trigger": {"text": "inhibitors", "start": 261, "end": 271}, "arguments": [{"role": "Theme", "text": "MEK1", "start": 330, "end": 334}]}, {"trigger": {"text": "inhibitors", "start": 261, "end": 271}, "arguments": [{"role": "Theme", "text": "2", "start": 335, "end": 336}]}, {"trigger": {"text": "inhibitors", "start": 261, "end": 271}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 365, "end": 370}]}]}}, "schema": []}
{"input": "Analysis of Akt, NFkappaB, and Stat3 Pathways in Contribution to the Growth and Survival of Lymphoma Cells\n(A-D) Immunoblot analysis of wild-type and LMP1 transgenic lymphomas for Akt, NFkappaB, and Stat3 signaling after treatment with (A) an Akt inhibitor, triciribine, (B) an NFkappaB inhibitor, BAY11-7085, and the Stat3 inhibitors (C) cucurbitacin I and (D) AG490, at the indicated concentrations. Arrows indicate the positions of alpha and beta isoforms of Stat3. Actin was used as a loading control. \n", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitor", "start": 247, "end": 256}, "arguments": [{"role": "Theme", "text": "Akt", "start": 243, "end": 246}]}, {"trigger": {"text": "inhibitors", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "Stat3", "start": 318, "end": 323}]}]}}, "schema": []}
{"input": "Lymphomas Are Clonal by kappa Light Chain Rearrangement\nPCR analysis of total spleen genomic DNA for the mouse kappa locus. Primers were designed to amplify all V-J rearrangements, including VJ1, VJ2, VJ4, and VJ5. Specific PCR products for the four rearrangements corresponding to the calculated sizes are indicated with arrows. Bands of other sizes are due to non-specific products. If a tumor was present in the background of normal spleen cells, a single band appears brighter than all the other specific bands. Wild-type and LMP1 transgenic lymphocytes are positive for all four V-J rearrangements and serve as positive controls. Clonality is determined by the appearance of a predominant band at the correct size for a single V-J rearrangement. \n(739 KB PDF) \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Click here for additional data file. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Runx3 and T-box proteins cooperate to establish the transcriptional program of effector CTLs \nActivation of naive CD8+ T cells with antigen induces their differentiation into effector cytolytic T lymphocytes (CTLs). CTLs lyse infected or aberrant target cells by exocytosis of lytic granules containing the pore-forming protein perforin and a family of proteases termed granzymes. We show that effector CTL differentiation occurs in two sequential phases in vitro, characterized by early induction of T-bet and late induction of Eomesodermin (Eomes), T-box transcription factors that regulate the early and late phases of interferon (IFN) gamma expression, respectively. In addition, we demonstrate a critical role for the transcription factor Runx3 in CTL differentiation. Runx3 regulates Eomes expression as well as expression of three cardinal markers of the effector CTL program: IFN-gamma, perforin, and granzyme B. Our data point to the existence of an elaborate transcriptional network in which Runx3 initially induces and then cooperates with T-box transcription factors to regulate gene transcription in differentiating CTLs. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 645, "end": 655}, "arguments": [{"role": "Theme", "text": "interferon (IFN) gamma", "start": 622, "end": 644}]}, {"trigger": {"text": "expression", "start": 796, "end": 806}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 790, "end": 795}]}, {"trigger": {"text": "expression", "start": 818, "end": 828}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 884, "end": 893}]}, {"trigger": {"text": "expression", "start": 818, "end": 828}, "arguments": [{"role": "Theme", "text": "perforin", "start": 895, "end": 903}]}, {"trigger": {"text": "expression", "start": 818, "end": 828}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 909, "end": 919}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 488, "end": 497}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 501, "end": 506}]}, {"trigger": {"text": "induction", "start": 516, "end": 525}, "arguments": [{"role": "Theme", "text": "Eomesodermin", "start": 529, "end": 541}]}], "regulation": [{"trigger": {"text": "regulate", "start": 584, "end": 592}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 501, "end": 506}, {"role": "Theme", "text": "expression", "start": 645, "end": 655}]}, {"trigger": {"text": "regulate", "start": 584, "end": 592}, "arguments": [{"role": "Cause", "text": "Eomesodermin", "start": 529, "end": 541}, {"role": "Theme", "text": "expression", "start": 645, "end": 655}]}, {"trigger": {"text": "regulates", "start": 780, "end": 789}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 774, "end": 779}, {"role": "Theme", "text": "expression", "start": 796, "end": 806}]}, {"trigger": {"text": "regulates", "start": 780, "end": 789}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 774, "end": 779}, {"role": "Theme", "text": "expression", "start": 818, "end": 828}]}]}}, "schema": []}
{"input": "INTRODUCTION\nNaive CD8+ T cells differentiate into effector CTLs with the ability to lyse antigen-bearing target cells by exocytosis of lytic granules containing perforin and granzymes, and to produce inflammatory cytokines such as IFN-gamma and TNF upon restimulation through the TCR (1, 2). In vivo experiments have elucidated many critical parameters governing the development and evolution of primary CTL responses (3, 4). In this study, we have used in vitro systems such as those developed to study CD4+ T cell differentiation to define the molecular basis of effector CTL differentiation (5, 6). \nThe T-box transcription factors Eomesodermin (Eomes) and T-bet are needed for important aspects of effector and memory CTL differentiation (7). In uninfected mice, compound deletion of the Tbx21 (encoding T-bet) and eomesodermin genes is associated with a selective loss of CD8+ T cells with an IL-2Rbeta-high, memory phenotype (8). Mice deficient for both T-bet and Eomes in T cells have impaired expression of cytolytic mediators, manifest poor cytolytic activity, and fail to control acute lymphocytic choriomeningitis virus infection (9). Nevertheless, the specific roles of T-bet and Eomes in clonal expansion and CTL differentiation have not yet been resolved: in particular, it is not known whether these transcription factors function redundantly to control effector CD8+ T cell differentiation, and whether they do so directly by targeting specific effector cytokine and cytolytic genes. \nRunx proteins, a family of three DNA-binding transcription factors, control thymocyte differentiation and the CD4/CD8 lineage decision (10-13). Runx3 and perforin mRNA are expressed by double-positive (DP) thymocytes and CD8+ single-positive (SP) thymocytes but not in CD4+ SP cells (14). Although Runx3 is not expressed in naive CD4+ T cells, its expression is up-regulated during Th1 cell differentiation, and Runx3 influences Th1 cell differentiation and function through direct regulation of the Il4 and Ifng cytokine genes (15, 16). In contrast, all three Runx proteins are expressed in mature CD8+ T cells (10, 12), and Runx3-deficient CD8+ T cells show reduced cytolytic activity (12, 13). We therefore tested whether Runx3 influenced cytolytic T cell differentiation. \nIn this report, we show that Runx3 and T-box factors synergistically regulate CTL differentiation and function. T-bet is induced quickly upon TCR stimulation and is required for early programming of cytokine production (17), whereas Eomes is induced later during differentiation and sustains IFN-gamma expression. Runx3 is required for Eomes and perforin expression, and both Eomes and Runx3 bind at the Prf1 locus; in contrast, perforin expression is unaffected in T-bet-deficient cells. T cells lacking Runx3 show decreased expression of IFN-gamma and granzyme B, and Runx3 also binds the promoter regions of the Ifng and Gzmb genes. Collectively, these results provide evidence for a complex transcriptional network in which Runx3 is a primary regulator of Gzmb expression but synergizes with T-bet and Eomes, respectively, to promote transcription of the Ifng and Prf1 genes. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "targeting", "start": 1443, "end": 1452}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1183, "end": 1188}]}, {"trigger": {"text": "targeting", "start": 1443, "end": 1452}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 1193, "end": 1198}]}, {"trigger": {"text": "bind", "start": 2671, "end": 2675}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2655, "end": 2660}, {"role": "Theme2", "text": "Prf1", "start": 2683, "end": 2687}]}, {"trigger": {"text": "bind", "start": 2671, "end": 2675}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 2665, "end": 2670}, {"role": "Theme2", "text": "Prf1", "start": 2683, "end": 2687}]}, {"trigger": {"text": "binds", "start": 2860, "end": 2865}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 2849, "end": 2854}, {"role": "Site2", "text": "promoter regions", "start": 2870, "end": 2886}, {"role": "Theme2", "text": "Ifng", "start": 2894, "end": 2898}]}, {"trigger": {"text": "binds", "start": 2860, "end": 2865}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 2849, "end": 2854}, {"role": "Site2", "text": "promoter regions", "start": 2870, "end": 2886}, {"role": "Theme2", "text": "Gzmb", "start": 2903, "end": 2907}]}], "gene expression": [{"trigger": {"text": "produce", "start": 193, "end": 200}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 232, "end": 241}]}, {"trigger": {"text": "produce", "start": 193, "end": 200}, "arguments": [{"role": "Theme", "text": "TNF", "start": 246, "end": 249}]}, {"trigger": {"text": "expressed", "start": 1813, "end": 1822}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 1800, "end": 1805}]}, {"trigger": {"text": "expression", "start": 1850, "end": 1860}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 1800, "end": 1805}]}, {"trigger": {"text": "expression", "start": 2581, "end": 2591}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 2571, "end": 2580}]}, {"trigger": {"text": "expression", "start": 2634, "end": 2644}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2615, "end": 2620}]}, {"trigger": {"text": "expression", "start": 2634, "end": 2644}, "arguments": [{"role": "Theme", "text": "perforin", "start": 2625, "end": 2633}]}, {"trigger": {"text": "expression", "start": 2717, "end": 2727}, "arguments": [{"role": "Theme", "text": "perforin", "start": 2708, "end": 2716}]}, {"trigger": {"text": "expression", "start": 2805, "end": 2815}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 2819, "end": 2828}]}, {"trigger": {"text": "expression", "start": 2805, "end": 2815}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 2833, "end": 2843}]}, {"trigger": {"text": "expression", "start": 3044, "end": 3054}, "arguments": [{"role": "Theme", "text": "Gzmb", "start": 3039, "end": 3043}]}], "negative regulation": [{"trigger": {"text": "deletion", "start": 777, "end": 785}, "arguments": [{"role": "Theme", "text": "Tbx21", "start": 793, "end": 798}]}, {"trigger": {"text": "deletion", "start": 777, "end": 785}, "arguments": [{"role": "Theme", "text": "eomesodermin", "start": 820, "end": 832}]}, {"trigger": {"text": "deficient", "start": 942, "end": 951}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 961, "end": 966}]}, {"trigger": {"text": "deficient", "start": 942, "end": 951}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 971, "end": 976}]}, {"trigger": {"text": "deficient", "start": 2134, "end": 2143}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 2128, "end": 2133}]}, {"trigger": {"text": "deficient", "start": 2751, "end": 2760}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 2745, "end": 2750}]}, {"trigger": {"text": "lacking", "start": 2776, "end": 2783}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 2784, "end": 2789}]}, {"trigger": {"text": "decreased", "start": 2795, "end": 2804}, "arguments": [{"role": "Cause", "text": "lacking", "start": 2776, "end": 2783}, {"role": "Theme", "text": "expression", "start": 2805, "end": 2815}]}], "positive regulation": [{"trigger": {"text": "up-regulated", "start": 1864, "end": 1876}, "arguments": [{"role": "Theme", "text": "expression", "start": 1850, "end": 1860}]}, {"trigger": {"text": "induced", "start": 2400, "end": 2407}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 2391, "end": 2396}]}, {"trigger": {"text": "induced", "start": 2521, "end": 2528}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2512, "end": 2517}]}, {"trigger": {"text": "sustains", "start": 2562, "end": 2570}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 2512, "end": 2517}, {"role": "Theme", "text": "expression", "start": 2581, "end": 2591}]}, {"trigger": {"text": "required", "start": 2602, "end": 2610}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 2593, "end": 2598}, {"role": "Theme", "text": "expression", "start": 2634, "end": 2644}]}, {"trigger": {"text": "promote", "start": 3109, "end": 3116}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 3075, "end": 3080}, {"role": "Theme", "text": "transcription", "start": 3117, "end": 3130}]}, {"trigger": {"text": "promote", "start": 3109, "end": 3116}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 3085, "end": 3090}, {"role": "Theme", "text": "transcription", "start": 3117, "end": 3130}]}], "regulation": [{"trigger": {"text": "regulation", "start": 1984, "end": 1994}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 1914, "end": 1919}, {"role": "Theme", "text": "Il4", "start": 2002, "end": 2005}]}, {"trigger": {"text": "regulation", "start": 1984, "end": 1994}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 1914, "end": 1919}, {"role": "Theme", "text": "Ifng", "start": 2010, "end": 2014}]}, {"trigger": {"text": "unaffected", "start": 2731, "end": 2741}, "arguments": [{"role": "Theme", "text": "expression", "start": 2717, "end": 2727}, {"role": "Cause", "text": "deficient", "start": 2751, "end": 2760}]}, {"trigger": {"text": "regulator", "start": 3026, "end": 3035}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 3007, "end": 3012}, {"role": "Theme", "text": "expression", "start": 3044, "end": 3054}]}], "transcription": [{"trigger": {"text": "expressed", "start": 1674, "end": 1683}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 1646, "end": 1651}]}, {"trigger": {"text": "expressed", "start": 1674, "end": 1683}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1656, "end": 1664}]}, {"trigger": {"text": "transcription", "start": 3117, "end": 3130}, "arguments": [{"role": "Theme", "text": "Ifng", "start": 3138, "end": 3142}]}, {"trigger": {"text": "transcription", "start": 3117, "end": 3130}, "arguments": [{"role": "Theme", "text": "Prf1", "start": 3147, "end": 3151}]}]}}, "schema": []}
{"input": "A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions. \nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for >8 d. We limited our analysis to the first 6-8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Distinct expression kinetics of perforin and granzyme B during CTL development in culture\nOur experiments revealed clear differences in the kinetics of perforin, granzyme B, and cytokine expression during CD8+ T cell activation (Fig. 1). Naive T cells showed detectable expression of perforin mRNA as well as perforin protein (Fig. 1, A-D). Relative to its expression in naive T cells, perforin (Prf1) mRNA expression did not increase appreciably at day 2 but showed a reproducible decrease at day 4, followed by robust reexpression between days 4 and 8 (Fig. 1, A-D). In contrast, granzyme B (Gzmb) mRNA was low or undetectable in naive T cells but was strongly up-regulated by day 2 after stimulation and increased progressively until day 6 (Fig. 1, A and B); similarly, granzyme B protein was expressed by day 4 and remained high until day 6 (Fig. 1 E). As expected, a small fraction of naive T cells expressed the cytokines IFN-gamma and TNF in response to stimulation, and this capacity increased significantly in differentiated cells (Fig. 1 E; see also Fig. 2 A). \nWe evaluated antigen-dependent cytolytic function in a short-term assay in which target cell death was measured within 2 h (Fig. 1 F). By limiting the duration of TCR stimulation, this strategy minimizes cytolysis secondary to new gene expression during the period of the assay. Naive T cells did not display significant cytolytic function in this short-term assay (unpublished data), most likely because they express immature (unprocessed) forms of perforin and lack the capacity to degranulate (18, 19). Even after activation for 2 or 4 d, the cells showed poor cytolytic activity (Fig. 1 F), in striking contrast to their capacity for efficient cytokine production (Fig. 1 E). Only cells cultured until day 6 displayed robust cytotoxicity, as judged by their ability to induce apoptosis in a large number of target cells (Fig. 1 F). \nThese results show that after a strong priming stimulus through TCRs and co-stimulatory receptors in vitro, granzyme B expression and the ability to produce effector cytokines are programmed early, whereas perforin expression and cytolytic function are induced later, during the phase of clonal expansion in IL-2. Therefore, the two major effector functions of CTL, cytokine production and cytolytic activity, are not intrinsically coregulated. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 9, "end": 19}, "arguments": [{"role": "Theme", "text": "perforin", "start": 32, "end": 40}]}, {"trigger": {"text": "expression", "start": 9, "end": 19}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 45, "end": 55}]}, {"trigger": {"text": "expression", "start": 187, "end": 197}, "arguments": [{"role": "Theme", "text": "perforin", "start": 152, "end": 160}]}, {"trigger": {"text": "expression", "start": 187, "end": 197}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 162, "end": 172}]}, {"trigger": {"text": "expression", "start": 270, "end": 280}, "arguments": [{"role": "Theme", "text": "perforin", "start": 284, "end": 292}]}, {"trigger": {"text": "expression", "start": 270, "end": 280}, "arguments": [{"role": "Theme", "text": "perforin", "start": 309, "end": 317}]}, {"trigger": {"text": "expression", "start": 357, "end": 367}, "arguments": [{"role": "Theme", "text": "perforin", "start": 386, "end": 394}]}, {"trigger": {"text": "expressed", "start": 904, "end": 913}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 928, "end": 937}]}, {"trigger": {"text": "expressed", "start": 904, "end": 913}, "arguments": [{"role": "Theme", "text": "TNF", "start": 942, "end": 945}]}, {"trigger": {"text": "express", "start": 1482, "end": 1489}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1522, "end": 1530}]}, {"trigger": {"text": "expression", "start": 2028, "end": 2038}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 2017, "end": 2027}]}, {"trigger": {"text": "expression", "start": 2124, "end": 2134}, "arguments": [{"role": "Theme", "text": "perforin", "start": 2115, "end": 2123}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 482, "end": 490}, "arguments": [{"role": "Theme", "text": "mRNA expression", "start": 402, "end": 417}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 426, "end": 434}, "arguments": [{"role": "Theme", "text": "mRNA expression", "start": 402, "end": 417}]}, {"trigger": {"text": "reexpression", "start": 520, "end": 532}, "arguments": [{"role": "Theme", "text": "mRNA expression", "start": 402, "end": 417}]}, {"trigger": {"text": "up-regulated", "start": 663, "end": 675}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 582, "end": 592}]}, {"trigger": {"text": "increased", "start": 707, "end": 716}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 582, "end": 592}]}, {"trigger": {"text": "remained high", "start": 819, "end": 832}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 773, "end": 783}]}, {"trigger": {"text": "increased", "start": 992, "end": 1001}, "arguments": [{"role": "Theme", "text": "expressed", "start": 904, "end": 913}]}, {"trigger": {"text": "induced", "start": 2162, "end": 2169}, "arguments": [{"role": "Theme", "text": "expression", "start": 2124, "end": 2134}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 402, "end": 417}, "arguments": [{"role": "Theme", "text": "perforin", "start": 386, "end": 394}]}, {"trigger": {"text": "low or undetectable", "start": 609, "end": 628}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 582, "end": 592}]}]}}, "schema": []}
{"input": "Distinct kinetics of T-bet and Eomes expression during CTL differentiation\nThe T-box transcription factors T-bet and Eomes have been linked to the regulation of genes encoding effector cytokines (e.g., Ifng) and genes important for cytolytic function (e.g., Prf1 and GzmB) (20). We investigated the kinetics of expression of these transcription factors in our in vitro cultures (Fig. 1, A-D). T-bet mRNA and protein were not detectable in naive CD8+ T cells, but were strongly induced upon TCR priming (day 2) and remained expressed through day 6 of differentiation (Fig. 1, A and C; quantified in Fig. 1, B and D). In contrast, Eomes expression was low or undetectable at both the mRNA and protein levels in naive CD8+ T cells, and TCR priming in culture had only a modest effect on its expression at day 2 (Fig. 1, A and C). Strong induction of Eomes mRNA and protein was only observed at day 4 and later (Fig. 1, A and C). T-bet mRNA expression slightly preceded the expression of GzmB mRNA; similarly, Eomes mRNA and protein were expressed approximately1 d ahead of the reexpression of perforin mRNA and protein, respectively (Fig. 1, B and D). \nThis detailed kinetic analysis suggested that, under our culture conditions, T-bet and Eomes contribute to distinct aspects of gene transcription during CTL differentiation. T-bet is required early for IFN-gamma production, and our data suggested that Eomes might not function during this early period but rather might contribute later to the control of perforin expression. Our data seemed most consistent with a model in which TCR signals induce T-bet, which in turn induces IFN-gamma (17) and possibly granzyme B; subsequently, Eomes is induced during the period of clonal expansion in IL-2 and activates perforin expression. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 37, "end": 47}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 21, "end": 26}]}, {"trigger": {"text": "expression", "start": 37, "end": 47}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 31, "end": 36}]}, {"trigger": {"text": "expression", "start": 311, "end": 321}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 107, "end": 112}]}, {"trigger": {"text": "expression", "start": 311, "end": 321}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 117, "end": 122}]}, {"trigger": {"text": "detectable", "start": 425, "end": 435}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 393, "end": 398}]}, {"trigger": {"text": "expressed", "start": 523, "end": 532}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 393, "end": 398}]}, {"trigger": {"text": "expression", "start": 635, "end": 645}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 629, "end": 634}]}, {"trigger": {"text": "expression", "start": 788, "end": 798}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 629, "end": 634}]}, {"trigger": {"text": "expression", "start": 970, "end": 980}, "arguments": [{"role": "Theme", "text": "GzmB", "start": 984, "end": 988}]}, {"trigger": {"text": "expressed", "start": 1034, "end": 1043}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 1006, "end": 1011}]}, {"trigger": {"text": "reexpression", "start": 1074, "end": 1086}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1090, "end": 1098}]}, {"trigger": {"text": "production", "start": 1362, "end": 1372}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1352, "end": 1361}]}, {"trigger": {"text": "expression", "start": 1513, "end": 1523}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1504, "end": 1512}]}, {"trigger": {"text": "expression", "start": 1767, "end": 1777}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1758, "end": 1766}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 477, "end": 484}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 393, "end": 398}]}, {"trigger": {"text": "remained", "start": 514, "end": 522}, "arguments": [{"role": "Theme", "text": "expressed", "start": 523, "end": 532}]}, {"trigger": {"text": "low or undetectable", "start": 650, "end": 669}, "arguments": [{"role": "Theme", "text": "expression", "start": 635, "end": 645}]}, {"trigger": {"text": "induction", "start": 834, "end": 843}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 847, "end": 852}]}, {"trigger": {"text": "required", "start": 1333, "end": 1341}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1324, "end": 1329}, {"role": "Theme", "text": "production", "start": 1362, "end": 1372}]}, {"trigger": {"text": "contribute", "start": 1469, "end": 1479}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1402, "end": 1407}, {"role": "Theme", "text": "control", "start": 1493, "end": 1500}]}, {"trigger": {"text": "induce", "start": 1591, "end": 1597}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1598, "end": 1603}]}, {"trigger": {"text": "induces", "start": 1619, "end": 1626}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1598, "end": 1603}, {"role": "Theme", "text": "IFN-gamma", "start": 1627, "end": 1636}]}, {"trigger": {"text": "induces", "start": 1619, "end": 1626}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1598, "end": 1603}, {"role": "Theme", "text": "granzyme B", "start": 1655, "end": 1665}]}, {"trigger": {"text": "induced", "start": 1690, "end": 1697}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 1681, "end": 1686}]}, {"trigger": {"text": "activates", "start": 1748, "end": 1757}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1681, "end": 1686}, {"role": "Theme", "text": "expression", "start": 1767, "end": 1777}]}], "regulation": [{"trigger": {"text": "linked", "start": 133, "end": 139}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 107, "end": 112}, {"role": "Theme", "text": "regulation", "start": 147, "end": 157}]}, {"trigger": {"text": "linked", "start": 133, "end": 139}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 117, "end": 122}, {"role": "Theme", "text": "regulation", "start": 147, "end": 157}]}, {"trigger": {"text": "regulation", "start": 147, "end": 157}, "arguments": [{"role": "Theme", "text": "Ifng", "start": 202, "end": 206}]}, {"trigger": {"text": "regulation", "start": 147, "end": 157}, "arguments": [{"role": "Theme", "text": "Prf1", "start": 258, "end": 262}]}, {"trigger": {"text": "regulation", "start": 147, "end": 157}, "arguments": [{"role": "Theme", "text": "GzmB", "start": 267, "end": 271}]}, {"trigger": {"text": "effect", "start": 774, "end": 780}, "arguments": [{"role": "Theme", "text": "expression", "start": 788, "end": 798}]}, {"trigger": {"text": "control", "start": 1493, "end": 1500}, "arguments": [{"role": "Theme", "text": "expression", "start": 1513, "end": 1523}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 932, "end": 947}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 926, "end": 931}]}]}}, "schema": []}
{"input": "Perforin and granzyme B expression are not appreciably regulated by T-bet\nTo test the model outlined in the previous paragraph directly, we compared the expression of IFN-gamma, perforin, and granzyme B in CD8+ T cells from WT and Tbx21 (T-bet)-deficient mice. As expected (17, 21), naive Tbx21-/- CD8+ T cells produced IFN-gamma poorly upon activation (Fig. 2 A). Notably, this deleterious effect of T-bet deficiency was only observed in differentiating CD8+ T cells until day 4 of culture but was almost completely mitigated by day 6 (Fig. 2 A). This most likely reflected compensation by Eomes, which was strongly induced between days 4 and 6 (Fig. 1). In contrast, T-bet-deficient T cells cultured for 6 d showed no defect in perforin mRNA expression (Fig. 2 B, compare lanes 1 and 4). We consistently observed a modest reduction in GzmB mRNA in T-bet-deficient T cells (Fig. 2 B, compare lanes 1 and 4), which did not translate into a decrease in expression of granzyme B protein (Fig. 2 C). \nTo examine the role of Eomes, we transduced naive CD8+ T cells from WT and Tbx21-/- mice with retroviruses containing internal ribosome entry site (IRES)-GFP that were either empty or encoded a strongly transactivating version of Eomes (Eo-VP16) (8), and expanded them for 6 d under our culture conditions. Eo-VP16, but not the empty GFP retrovirus, increased perforin expression in both WT and T-bet-deficient CD8+ T cells (Fig. 2 B, lanes 2, 3, 5, and 6). As expected, Eo-VP16 also rescued the early defect in IFN-gamma production observed in T-bet-deficient CD8+ T cells (Fig. 2 D). However, Eo-VP16 did not induce GzmB mRNA expression in either WT or T-bet-deficient cells; thus, the partial T-bet dependence of GzmB mRNA expression cannot be compensated for by Eo-VP16. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 24, "end": 34}, "arguments": [{"role": "Theme", "text": "Perforin", "start": 0, "end": 8}]}, {"trigger": {"text": "expression", "start": 24, "end": 34}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 13, "end": 23}]}, {"trigger": {"text": "expression", "start": 153, "end": 163}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 167, "end": 176}]}, {"trigger": {"text": "expression", "start": 153, "end": 163}, "arguments": [{"role": "Theme", "text": "perforin", "start": 178, "end": 186}]}, {"trigger": {"text": "expression", "start": 153, "end": 163}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 192, "end": 202}]}, {"trigger": {"text": "produced", "start": 311, "end": 319}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 320, "end": 329}]}, {"trigger": {"text": "expression", "start": 952, "end": 962}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 966, "end": 976}]}, {"trigger": {"text": "expression", "start": 1367, "end": 1377}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1358, "end": 1366}]}, {"trigger": {"text": "production", "start": 1520, "end": 1530}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1510, "end": 1519}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 245, "end": 254}, "arguments": [{"role": "Theme", "text": "Tbx21", "start": 231, "end": 236}]}, {"trigger": {"text": "deficiency", "start": 407, "end": 417}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 401, "end": 406}]}, {"trigger": {"text": "deficient", "start": 675, "end": 684}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 669, "end": 674}]}, {"trigger": {"text": "defect", "start": 720, "end": 726}, "arguments": [{"role": "Cause", "text": "deficient", "start": 675, "end": 684}, {"role": "Theme", "text": "mRNA expression", "start": 739, "end": 754}]}, {"trigger": {"text": "reduction", "start": 824, "end": 833}, "arguments": [{"role": "Theme", "text": "GzmB", "start": 837, "end": 841}, {"role": "Cause", "text": "deficient", "start": 856, "end": 865}]}, {"trigger": {"text": "deficient", "start": 856, "end": 865}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 850, "end": 855}]}, {"trigger": {"text": "decrease", "start": 940, "end": 948}, "arguments": [{"role": "Theme", "text": "expression", "start": 952, "end": 962}]}, {"trigger": {"text": "deficient", "start": 1399, "end": 1408}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1393, "end": 1398}]}, {"trigger": {"text": "rescued", "start": 1482, "end": 1489}, "arguments": [{"role": "Cause", "text": "Eo-VP16", "start": 1469, "end": 1476}, {"role": "Theme", "text": "defect", "start": 1500, "end": 1506}]}, {"trigger": {"text": "defect", "start": 1500, "end": 1506}, "arguments": [{"role": "Theme", "text": "production", "start": 1520, "end": 1530}, {"role": "Cause", "text": "deficient", "start": 1549, "end": 1558}]}, {"trigger": {"text": "deficient", "start": 1549, "end": 1558}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1543, "end": 1548}]}, {"trigger": {"text": "deficient", "start": 1659, "end": 1668}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1653, "end": 1658}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 617, "end": 624}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 591, "end": 596}]}, {"trigger": {"text": "increased", "start": 1348, "end": 1357}, "arguments": [{"role": "Cause", "text": "Eo-VP16", "start": 1305, "end": 1312}, {"role": "Theme", "text": "expression", "start": 1367, "end": 1377}]}, {"trigger": {"text": "induce", "start": 1609, "end": 1615}, "arguments": [{"role": "Cause", "text": "Eo-VP16", "start": 1593, "end": 1600}, {"role": "Theme", "text": "mRNA expression", "start": 1621, "end": 1636}]}, {"trigger": {"text": "dependence", "start": 1700, "end": 1710}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1694, "end": 1699}, {"role": "Theme", "text": "mRNA expression", "start": 1719, "end": 1734}]}], "regulation": [{"trigger": {"text": "regulated", "start": 55, "end": 64}, "arguments": [{"role": "Theme", "text": "expression", "start": 24, "end": 34}, {"role": "Cause", "text": "T-bet", "start": 68, "end": 73}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 739, "end": 754}, "arguments": [{"role": "Theme", "text": "perforin", "start": 730, "end": 738}]}, {"trigger": {"text": "mRNA expression", "start": 1621, "end": 1636}, "arguments": [{"role": "Theme", "text": "GzmB", "start": 1616, "end": 1620}]}, {"trigger": {"text": "mRNA expression", "start": 1719, "end": 1734}, "arguments": [{"role": "Theme", "text": "GzmB", "start": 1714, "end": 1718}]}]}}, "schema": []}
{"input": "Runx3 controls multiple aspects of the CTL differentiation program, in part through induction of Eomes\nBecause Runx3 is highly expressed in peripheral CD8+ T cells, and because of the T-bet-Runx3 cooperation we observed earlier in CD4+ T cells (15), we examined the role of Runx3 in effector CTL differentiation. We isolated CD8+ T cells from Runx3-/- (KO) mice of the outbred ICR background and their WT Runx3+/+ littermates by positive selection with anti-CD8 magnetic beads (Figs. S1 and S2, available at http://www.jem.org/cgi/content/full/jem.20081242/DC1). Strikingly, Runx3-/- CD8+ T cells were strongly impaired in their ability to differentiate into effector CTLs, as judged by expression of perforin, granzyme B, and IFN-gamma (Fig. 3). Compared with WT T cells, perforin mRNA and protein expression were essentially undetectable in Runx3-/- T cells at day 6 of culture (Fig. 3, A and B). Runx3-/- T cells also had no detectable Eomes expression; in contrast, T-bet expression was unimpaired (Fig. 3 A). Furthermore, Runx3 was required for maximal production of IFN-gamma, but not TNF or IL-2, by CD8+ T cells restimulated at day 6 (Fig. 3 C). \nWe previously reported that Th1 cell differentiation was regulated through a feed-forward loop in which T-bet is up-regulated early and induces Runx3, after which T-bet and Runx3 cooperate to induce IFN-gamma and silence IL-4, thus promoting stable differentiation toward the Th1 lineage (15, 22). Because (a) Runx3 appeared necessary for Eomes induction (Fig. 3 A), (b) the kinetics of Eomes expression paralleled those of perforin expression (Fig. 2), and (c) overexpression of Eo-VP16 in either WT or T-bet-deficient T cells led to an increase in both perforin and IFN-gamma expression (Fig. 2, B and D), we asked whether CTL differentiation was also potentially regulated by a feed-forward loop involving these same two classes of Runx and T-box transcription factors. Specifically, we asked whether Runx3, which was necessary for Eomes induction, then cooperated with Eomes to regulate transcription of the effector CTL markers perforin, IFN-gamma, and granzyme B. \nTo test this hypothesis, we used chromatin immunoprecipitation (ChIP) assays to ask whether Eomes and Runx3 bound regulatory regions of the Prf1, Ifng, and Gzmb genes (Fig. 3 D). Both proteins associated with gene regulatory regions in differentiated CTLs. Runx3 bound to the Prf1 and Gzmb transcription start sites (TSS); to a known IL-2 responsive enhancer located near -1 kb of the Prf1 gene (23); to the distal CTL-specific DNase I hypersensitive site 9 in the Prf1 locus (24); to the Ifng promoter near the TSS, as previously reported for Th1 cells (10); and to several DNase I hypersensitive sites in the Ifng locus (Fig. 3 D and not depicted) (25). Eomes bound primarily to the Prf1 TSS and the -1 kb enhancer; this binding was substantially greater than that observed at the promoter of the Il2rb gene, a known direct target of Eomes (8), and comparable to that observed at the Ifng TSS, a known target of T-box proteins in both Th1 and CD8+ T cells (Fig. 3 D) (17). \nTo determine whether Runx3 controlled the expression of CTL effector genes through its induction of Eomes, we retrovirally expressed Runx3 and Eo-VP16 in CD8+ T cells from Runx3-/- mice. Because of the limited number of CD8+ T cells in these mice, and because we saw no difference between Runx3-/- CD8+CD4- SP and CD8+CD4+ DP cells in our previous experiments, we used total Runx3-/- CD8+ T cells without further fractionation as recipients for retroviral transduction. Reconstitution of Runx3-/- CD8+ T cells with Runx3 restored expression of Eomes as well as perforin, granzyme B, and IFN-gamma (Fig. 4, A and B). In addition, Runx3-/- T cells showed a compensatory up-regulation of Runx1, which was suppressed upon reconstitution with Runx3, indicating that Runx1 is a target of repression by Runx3. Notably, Eo-VP16 did not up-regulate perforin expression when expressed in Runx3-/- cells, even though it restored the capacity to induce IFN-gamma expression upon TCR restimulation (Fig. 4, A and B). This result suggests strongly that perforin expression requires Runx3 and Eomes. \nAs expected from their defect in perforin and granzyme B expression, Runx3-/- CD8+ T cells showed defective cytolytic activity in a mixed lymphocyte reaction (12). However, TCR-stimulated Runx3-/- CD8+ cells were as effective as WT cells in killing tumor cells in a redirected CTL assay (12). Furthermore, CD8+ cells from the peritoneal cavity of Runx3-/- mice immunized with certain tumor cells effectively killed these targets (13). Therefore, although activation of the perforin/granzyme B machinery is defective in Runx3-/- CD8+ cells, these cells are not entirely devoid of cytolytic activity and could still effectively kill targets, possibly by alternative mechanisms such as the Fas-Fas ligand pathway. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 2234, "end": 2239}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2218, "end": 2223}, {"role": "Site2", "text": "regulatory regions", "start": 2240, "end": 2258}, {"role": "Theme2", "text": "Prf1", "start": 2266, "end": 2270}]}, {"trigger": {"text": "bound", "start": 2234, "end": 2239}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 2228, "end": 2233}, {"role": "Site2", "text": "regulatory regions", "start": 2240, "end": 2258}, {"role": "Theme2", "text": "Prf1", "start": 2266, "end": 2270}]}, {"trigger": {"text": "bound", "start": 2234, "end": 2239}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 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{"input": "Runx3 and T-box factors control a complex program of transcriptional regulation during CTL differentiation\nCollectively, these data provide evidence that Runx3, together with T-box factors, orchestrates a complex program of transcriptional regulation in differentiating CTL (Fig. 4 C). Runx3 is present in naive CD8+ T cells before activation (12). It represses Runx1 and has a positive role in the induction of Eomes, granzyme B, perforin, and IFN-gamma. Runx3 binds to promoters and putative regulatory regions of the latter three genes, suggesting a direct effect on gene expression. Additional experiments are needed to determine whether Eomes and Runx1 are also direct target genes of Runx3. \nSurprisingly, Runx3 contributed to the optimal expression of TNF, IL-2, and IFN-gamma at day 4 (Fig. S2). For TNF and IL-2, the requirement for Runx3 subsides by day 6 (Fig. 3 C), possibly because of compensation by Runx1, which is derepressed in Runx3-/- cells (Fig. 4 A). Runx3 continues to be required for IFN-gamma expression even at day 6, perhaps because of its role in the induction of Eomes expression (Fig. 4 A). \nAn unexpected finding was that the two T-box transcription factors, T-bet and Eomes, are up-regulated with very different kinetics in CD8+ T cells under our culture conditions and have nonredundant roles in the subsequent expression of key effector proteins (Fig. 4 C). T-bet is needed early to confer on activated CD8+ T cells the competence to produce IFN-gamma upon restimulation, but its function is less important at later times. Eomes, which is induced late and functions downstream of Runx3, may substitute for T-bet in promoting the acute expression of IFN-gamma in restimulated CTLs (8). Indeed, T-bet and Eomes both contribute to perforin expression in NK cells (8, 26), and Eomes induces granzyme B as effectively as T-bet in developing Th2 cells (7); thus, the relative roles of these T-box transcription factors vary depending on cell type. \nSurprisingly, however, Eomes and T-bet appeared nonredundant in their ability to induce two other markers of CTL function, Prf1 and Gzmb (Fig. 4 C). Rather, T-bet and Eomes were involved in regulating granzyme B and perforin expression, respectively: up-regulation of T-bet and Eomes mRNA and protein closely preceded up-regulation of Gzmb and Prf1 mRNA and protein, respectively. T-bet had no role in perforin expression under our culture conditions, and Eo-VP16 did not affect granzyme B expression when expressed in T-bet-/- or Runx3-/- cells. Because conventional Eomes-deficient mice die before precursor cells can be isolated for bone marrow transfers (27) and because T cells conditionally deficient in Eomes have only recently been described (9), we were unable to introduce Runx3 into Eomes-deficient CD8+ T cells to test formally whether Eomes cooperated with Runx3 to induce perforin expression. \nCollectively, our data are consistent with a transcriptional network in which preexisting Runx3 cooperates with the induced T-box factors T-bet and Eomes and IL-2Rbeta signals (unpublished data) to orchestrate CTL differentiation (Fig. 4 C). Our data recall the \"feed-forward\" interaction between T-bet and Runx3 that we previously described in CD4+ (Th1) T cells (15) but are distinct in two respects: in differentiating Th1 cells, T-bet is induced by TCR signals and IFN-gamma, and in turn induces Runx3 (15), whereas in differentiating CD8+ T cells, preexisting Runx3 is required to induce the T-box transcription factor Eomes. 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"end": 361}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 286, "end": 291}, {"role": "Theme", "text": "Runx1", "start": 362, "end": 367}]}, {"trigger": {"text": "subsides", "start": 848, "end": 856}, "arguments": [{"role": "Theme", "text": "requirement", "start": 826, "end": 837}, {"role": "Cause", "text": "Runx1", "start": 914, "end": 919}]}, {"trigger": {"text": "derepressed", "start": 930, "end": 941}, "arguments": [{"role": "Theme", "text": "Runx1", "start": 914, "end": 919}]}, {"trigger": {"text": "deficient", "start": 2550, "end": 2559}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2544, "end": 2549}]}, {"trigger": {"text": "deficient", "start": 2673, "end": 2682}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2686, "end": 2691}]}, {"trigger": {"text": "deficient", "start": 2776, "end": 2785}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2770, "end": 2775}]}], "positive regulation": [{"trigger": {"text": "has a positive role", "start": 372, "end": 391}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 286, "end": 291}, {"role": "Theme", "text": "induction", "start": 399, "end": 408}]}, {"trigger": {"text": "induction", "start": 399, "end": 408}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 412, "end": 417}]}, {"trigger": {"text": "induction", "start": 399, "end": 408}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 419, "end": 429}]}, {"trigger": {"text": "induction", "start": 399, "end": 408}, "arguments": [{"role": "Theme", "text": "perforin", "start": 431, "end": 439}]}, {"trigger": {"text": "induction", "start": 399, "end": 408}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 445, "end": 454}]}, {"trigger": {"text": "contributed", "start": 718, "end": 729}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 712, "end": 717}, {"role": "Theme", "text": "expression", "start": 745, "end": 755}]}, {"trigger": {"text": "requirement", "start": 826, "end": 837}, "arguments": [{"role": "Theme", "text": "TNF", "start": 808, "end": 811}, {"role": "Cause", "text": "Runx3", "start": 842, "end": 847}]}, {"trigger": {"text": "requirement", "start": 826, "end": 837}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 816, "end": 820}, {"role": "Cause", "text": "Runx3", "start": 842, "end": 847}]}, {"trigger": {"text": "required", "start": 994, "end": 1002}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 972, "end": 977}, {"role": "Theme", "text": "expression", "start": 1017, "end": 1027}]}, {"trigger": {"text": "induction", "start": 1078, "end": 1087}, "arguments": [{"role": "Theme", "text": "expression", "start": 1097, "end": 1107}]}, {"trigger": {"text": "up-regulated", "start": 1210, "end": 1222}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1189, "end": 1194}]}, {"trigger": {"text": "up-regulated", "start": 1210, "end": 1222}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 1199, "end": 1204}]}, {"trigger": {"text": "needed", "start": 1400, "end": 1406}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1391, "end": 1396}, {"role": "Theme", "text": "produce", "start": 1467, "end": 1474}]}, {"trigger": {"text": "induced", "start": 1572, "end": 1579}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 1556, "end": 1561}]}, {"trigger": {"text": "promoting", "start": 1648, "end": 1657}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1556, "end": 1561}, {"role": "Theme", "text": "expression", "start": 1668, "end": 1678}]}, {"trigger": {"text": "promoting", "start": 1648, "end": 1657}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1639, "end": 1644}, {"role": "Theme", "text": "expression", "start": 1668, "end": 1678}]}, {"trigger": {"text": "contribute", "start": 1747, "end": 1757}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1726, "end": 1731}, {"role": "Theme", "text": "expression", "start": 1770, "end": 1780}]}, {"trigger": {"text": "contribute", "start": 1747, "end": 1757}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1736, "end": 1741}, {"role": "Theme", "text": "expression", "start": 1770, "end": 1780}]}, {"trigger": {"text": "induces", "start": 1812, "end": 1819}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1806, "end": 1811}, {"role": "Theme", "text": "granzyme B", "start": 1820, "end": 1830}]}, {"trigger": {"text": "induces", "start": 1812, "end": 1819}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 1820, "end": 1830}, {"role": "Cause", "text": "T-bet", "start": 1849, "end": 1854}]}, {"trigger": {"text": "induce", "start": 2057, "end": 2063}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1999, "end": 2004}, {"role": "Theme", "text": "Prf1", "start": 2099, "end": 2103}]}, {"trigger": {"text": "induce", "start": 2057, "end": 2063}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1999, "end": 2004}, {"role": "Theme", "text": "Gzmb", "start": 2108, "end": 2112}]}, {"trigger": {"text": "induce", "start": 2057, "end": 2063}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 2009, "end": 2014}, {"role": "Theme", "text": "Prf1", "start": 2099, "end": 2103}]}, {"trigger": {"text": "induce", "start": 2057, "end": 2063}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 2009, "end": 2014}, {"role": "Theme", "text": "Gzmb", "start": 2108, "end": 2112}]}, {"trigger": {"text": "up-regulation", "start": 2227, "end": 2240}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 2244, "end": 2249}]}, {"trigger": {"text": "up-regulation", "start": 2227, "end": 2240}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 2254, "end": 2259}]}, {"trigger": {"text": "preceded", "start": 2285, "end": 2293}, "arguments": [{"role": "Cause", "text": "up-regulation", "start": 2227, "end": 2240}, {"role": "Theme", "text": "up-regulation", "start": 2294, "end": 2307}]}, {"trigger": {"text": "up-regulation", "start": 2294, "end": 2307}, "arguments": [{"role": "Theme", "text": "Gzmb", "start": 2311, "end": 2315}]}, {"trigger": {"text": "up-regulation", "start": 2294, "end": 2307}, "arguments": [{"role": "Theme", "text": "Prf1", "start": 2320, "end": 2324}]}, {"trigger": {"text": "induce", "start": 2855, "end": 2861}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 2824, "end": 2829}, {"role": "Theme", "text": "expression", "start": 2871, "end": 2881}]}, {"trigger": {"text": "induce", "start": 2855, "end": 2861}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 2846, "end": 2851}, {"role": "Theme", "text": "expression", "start": 2871, "end": 2881}]}, {"trigger": {"text": "induced", "start": 3000, "end": 3007}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 3022, "end": 3027}]}, {"trigger": {"text": "induced", "start": 3000, "end": 3007}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 3032, "end": 3037}]}, {"trigger": {"text": "induced", "start": 3326, "end": 3333}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 3317, "end": 3322}, {"role": "Cause", "text": "IFN-gamma", "start": 3353, "end": 3362}]}, {"trigger": {"text": "induces", "start": 3376, "end": 3383}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 3317, "end": 3322}, {"role": "Theme", "text": "Runx3", "start": 3384, "end": 3389}]}, {"trigger": {"text": "required", "start": 3458, "end": 3466}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 3449, "end": 3454}, {"role": "Theme", "text": "induce", "start": 3470, "end": 3476}]}, {"trigger": {"text": "induce", "start": 3470, "end": 3476}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 3508, "end": 3513}]}], "regulation": [{"trigger": {"text": "effect", "start": 560, "end": 566}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 456, "end": 461}, {"role": "Theme", "text": "expression", "start": 575, "end": 585}]}, {"trigger": {"text": "role", "start": 1066, "end": 1070}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 972, "end": 977}, {"role": "Theme", "text": "induction", "start": 1078, "end": 1087}]}, {"trigger": {"text": "functions downstream", "start": 1589, "end": 1609}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 1556, "end": 1561}, {"role": "Cause", "text": "Runx3", "start": 1613, "end": 1618}]}, {"trigger": {"text": "regulating", "start": 2166, "end": 2176}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 2133, "end": 2138}, {"role": "Theme", "text": "expression", "start": 2201, "end": 2211}]}, {"trigger": {"text": "regulating", "start": 2166, "end": 2176}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 2143, "end": 2148}, {"role": "Theme", "text": "expression", "start": 2201, "end": 2211}]}, {"trigger": {"text": "had no role", "start": 2363, "end": 2374}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 2357, "end": 2362}, {"role": "Theme", "text": "expression", "start": 2387, "end": 2397}]}, {"trigger": {"text": "affect", "start": 2448, "end": 2454}, "arguments": [{"role": "Cause", "text": "Eo-VP16", "start": 2432, "end": 2439}, {"role": "Theme", "text": "expression", "start": 2466, "end": 2476}]}, {"trigger": {"text": "interaction", "start": 3161, "end": 3172}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 3181, "end": 3186}, {"role": "Theme", "text": "T-bet", "start": 3181, "end": 3186}]}, {"trigger": {"text": "interaction", "start": 3161, "end": 3172}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 3181, "end": 3186}, {"role": "Theme", "text": "Runx3", "start": 3191, "end": 3196}]}, {"trigger": {"text": "interaction", "start": 3161, "end": 3172}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 3181, "end": 3186}, {"role": "Cause", "text": "Runx3", "start": 3191, "end": 3196}]}, {"trigger": {"text": "interaction", "start": 3161, "end": 3172}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 3191, "end": 3196}, {"role": "Theme", "text": "Runx3", "start": 3191, "end": 3196}]}]}}, "schema": []}
{"input": "Antibodies and reagents.\nThe following antibodies used for intracellular or surface stains were obtained from eBioscience: anti-IL-2, anti-IFN-gamma, anti-TNF, anti-granzyme B, anti-CD8, anti-CD25, and anti-CD44. Anti-CD69 was purchased from BD. For ChIP experiments, the anti-Eomes antibody was obtained from Abcam and the anti-Runx3 antibody was produced by the Groner laboratory. The following antibodies were used for immunoblotting: antiperforin (Abcam), anti-Eomes (Abcam), and anti-Pol-II (Santa Cruz Biotechnology, Inc.). The T-bet antibody was provided by L. Glimcher (Harvard School of Public Health, Boston, MA). \nThe following reagents were used for the experiments presented in this report: Annexin V-FITC Apoptosis Detection Kit (BD), CD8 Negative Isolation Kit (Invitrogen), CD8 MicroBeads (Miltenyi Biotec), and SYBR Green PCR Core Reagents (Applied Biosystems). The Gp33 peptide (KAVYNFATC) was synthesized by the Tufts University Core Facility, and 10 mM of stock solutions was prepared in DMSO. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Isolation and culture of primary CD8+ T cells.\nCD8+ T cells from 4-8-wk-old Tcra-/- x P14 TCR transgenic (Taconic), C57BL/6J WT, or Tbx21-/- (The Jackson Laboratory) mice were purified (>95% purity) by negative selection (Invitrogen) from pooled spleen and lymph node cells. CD8+ T cells from Runx3-/- mice on the ICR background were purified by positive selection (Miltenyi Biotec). All mice were maintained in specific pathogen-free barrier facilities and used according to protocols approved by the Immune Disease Institute and the Harvard Medical School Animal Care and Use Committees. For stimulation, purified CD8+ T cells were cultured at 106 cells/ml (10 ml) in T25 flasks coated with 1 mug/ml each of anti-CD3 (clone 2C11) and anti-CD28 (clone 37.51) by pretreatment with 300 mug/ml goat anti-hamster IgG. After 48 h, cells were removed from the TCR stimulation and recultured at a concentration of 5 x 105 cells/ml in media supplemented with 100 U/ml rhIL-2. Every 24 h, viable cells were counted and readjusted to 5 x 105 cells/ml with fresh media containing the corresponding amount of rhIL-2. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Isolation of CD8+ T cells from Runx3-/- mice.\nRunx3-deficient T cells fail to silence CD4 expression normally (Fig. S1) (12, 13). We therefore further fractionated the positively selected CD8+ T cells from Runx3 KO mice into CD8+CD4- SP or CD8+CD4+ DP cells by separation using anti-CD4 magnetic beads. This yielded a Runx3 KO SP \"enriched\" population that contained 75% CD8+CD4- cells and a KO DP enriched population that contained 85% CD8+CD4+ cells (Fig. S1). The cells were stimulated with anti-CD3+ anti-CD28 for 2 d before removing them from the TCR stimulus and culturing them in media containing 100 U/ml IL-2. As previously reported, TCR-induced proliferation of Runx3-/- CD8+ T cells was severely impaired, irrespective of CD4 expression (Fig. S1) (12, 13). However, the Runx3-/- cells showed cell-surface expression patterns indicative of activated cells, including up-regulation of CD25 and CD69 (Fig. S1). As expected from their ability to up-regulate CD25, Runx3-/- CD8+ T cells responded to IL-2 supplementation after day 2 and efficiently expanded until day 6 of the culture period, albeit at slower rates compared with WT cells (Fig. S1). Although a fraction of the KO DP cells silenced CD4 expression after activation, the ratio of SP/DP cells in each enriched population remained constant thereafter, and we did not observe any major differences between these two populations throughout the culture period, indicating that in terms of effector CTL differentiation and under our culture conditions, Runx3-/- CD8+ T cells that also coexpress CD4 are indistinguishable from those that do not. The data presented in Fig. S2 are from Runx3 KO SP cells, whereas those shown in Figs. 3 and 4 are from total Runx3 KO CD8 cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 90, "end": 100}, "arguments": [{"role": "Theme", "text": "CD4", "start": 86, "end": 89}]}, {"trigger": {"text": "expression", "start": 737, "end": 747}, "arguments": [{"role": "Theme", "text": "CD4", "start": 733, "end": 736}]}, {"trigger": {"text": "expression", "start": 1208, "end": 1218}, "arguments": [{"role": "Theme", "text": "CD4", "start": 1204, "end": 1207}]}, {"trigger": {"text": "coexpress", "start": 1549, "end": 1558}, "arguments": [{"role": "Theme", "text": "CD4", "start": 1559, "end": 1562}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 52, "end": 61}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 46, "end": 51}]}, {"trigger": {"text": "silence", "start": 78, "end": 85}, "arguments": [{"role": "Cause", "text": "deficient", "start": 52, "end": 61}, {"role": "Theme", "text": "expression", "start": 90, "end": 100}]}, {"trigger": {"text": "silenced", "start": 1195, "end": 1203}, "arguments": [{"role": "Theme", "text": "expression", "start": 1208, "end": 1218}]}], "positive regulation": [{"trigger": {"text": "up-regulation", "start": 877, "end": 890}, "arguments": [{"role": "Theme", "text": "CD25", "start": 894, "end": 898}]}, {"trigger": {"text": "up-regulation", "start": 877, "end": 890}, "arguments": [{"role": "Theme", "text": "CD69", "start": 903, "end": 907}]}, {"trigger": {"text": "up-regulate", "start": 953, "end": 964}, "arguments": [{"role": "Theme", "text": "CD25", "start": 965, "end": 969}]}]}}, "schema": []}
{"input": "FACS-based cytotoxicity assay.\nTo measure cytotoxicity, EL4 thymoma target cells were loaded with 0 or 1 muM Gp33 peptide for 2 h before a 2-h coincubation with P14 CD8+ T cells at the effector-to-target ratios indicated in the figures in 96-well round-bottom plates. After the coincubation period, cells were stained with Annexin V-FITC and anti-CD8-allophycocyanin. Data analysis was performed with FlowJo software (Tree Star, Inc.); EL4 target cells (CD8-negative events) were gated, and the percentage of Annexin V+ target cells was determined. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Cytokine and surface marker staining.\nTo assess cytokine production, cells were restimulated with 10 nM PMA + 1 muM ionomycin for 6 h (unless indicated otherwise in the figures), and intracellular cytokine stains were performed as previously described (28). To detect expression of surface molecules, cells were washed in PBS, resuspended in FACS wash buffer (3% FBS, 0.1% sodium azide, 30 mM Hepes, 1x PBS) containing the antibodies indicated in the figures at previously optimized concentrations, incubated for 15 min at room temperature (RT), washed, and resuspended in 2% formaldehyde fixative solution before acquisition on a FACSCalibur (BD). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Retroviral transduction of primary CD8+ T cells.\nFor transduction experiments, viral supernatants were generated by calcium phosphate transfection of Phoenix cells and concentration by overnight centrifugation at 6,000 g. At approximately42 h after the initial TCR activation of 106 CD8+ T cells per well in 12-well plates, the culture media was removed and replaced with complete media supplemented with 8 mug/ml polybrene containing fresh plus concentrated virus. The plates were centrifuged at 700 g for 1 h at RT before returning to 37degreesC for an additional 5 h. Retroviral constructs for Eomes-VP16 and the MIG control empty vector were a gift from S.L. Reiner (University of Pennsylvania, Philadelphia, PA) (8). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "ChIP and real-time PCR analysis.\n20 x 106 CD8+ T cells per immunoprecipitation were fixed by adding a 1/10th volume of fixation solution (11.1% formaldehyde, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM Hepes) to 1 volume of culture media and were incubated for 10 or 30 min at RT. Fixation was stopped with 120 mM glycine on ice for 5 min. Fixed cells were washed 2x with cold PBS, 1x with cold solution I (10 mM Tris [pH 7.5], 10 mM EDTA, 0.5 mM EGTA, 1% Triton X-100), and 1x with cold solution II (10 mM Tris [pH 7.5], 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). After washes, cell pellets were resuspended at 40 x 106 cells/ml in ChIP lysis buffer (150 mM NaCl, 25 mM Tris [pH 7.5], 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate plus protease and phosphatase inhibitors), and chromatin was sheared with a sonicator to yield 0.5-1-kb DNA fragments. After preclearing the sheared chromatin with protein A-sepharose beads and removing 5% as input chromatin, immunoprecipitation was performed by adding optimized antibody amounts (per 20 x 106 cell equivalents: 2.5 mug anti-Eomes, 1:100 dilution anti-Runx3), followed by overnight incubation at 4degreesC; protein A-sepharose beads were added for the last 3 h of the incubation period. Beads were washed 2x with RIPA buffer (50 mM Tris [pH 8], 150 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% deoxycholate), 1x with high salt buffer (50 mM Tris [pH 8], 500 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS), and 1x with TE buffer. After the last wash, DNA was eluted by resuspending the beads in elution buffer (1% SDS, 100 mM NaHCO3). Both input and ChIP chromatin were then treated with RNase A (5 mug total) for 1 h at 37degreesC, followed by the addition of proteinase K (100 mug total) and overnight incubation at 65degreesC to reverse cross-linking. DNA was then purified with QIAquick columns (Gel Extraction Kit; QIAGEN) according to the manufacturer's instructions and resuspended in a 50-mul volume. For real-time PCR detection of immunoprecipitated targets using the SYBR Green PCR Kit, a standard curve was obtained with serial dilutions of input DNA for each sample, and 1 mul ChIP DNA was used per PCR reaction (performed in duplicates). Melt curves and agarose gels were analyzed to ensure amplification of specific target sequences. Refer to Table S1 (available at http://www.jem.org/cgi/content/full/jem.20081242/DC1) for a list of primer sets. The data are presented as the number of immunoprecipitated target sequences relative to input chromatin, assuming two copies of target sequence per cell equivalent used for the ChIP. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Northern and Western blot analyses.\nRNA isolation and Northern blot analysis was performed as previously described (29). In brief, 10 mug of total RNA was loaded per lane and transferred to positively charged nylon membranes (Hybond-N+; GE Healthcare), which was confirmed by ethidium bromide staining of ribosomal RNA species on the membrane. Membranes were hybridized with 1 ng/ml alpha-[32P]dCTP-labeled trichloroacetic acid precipitable probe in ExpressHyb hybridization buffer (Clontech Laboratories, Inc.). All cDNA probes were confirmed to have the appropriate single-copy specificity under these conditions using genomic Southern blot analysis. Band intensities were acquired by phosphorimaging analysis. \nFor Western analysis, whole-cell protein lysates were obtained from CD8+ T cells at the time points indicated in the figures during clonal expansion in 100 U/ml IL-2 with lysis buffer (50 mM Tris [pH 7.5], 150 mM NaCl, 10% glycerol, 5 mM EDTA, 1% NP-40) by resuspending samples in 10 mul per 106 cells and incubating on ice for 30 min in the presence of protease inhibitors. Immunoblot analysis was performed with the antibodies indicated in the figures after SDS-PAGE (10-30 mug of total protein was loaded per well). Quantification of detected protein was performed with an Intelligent Dark Box unit (LAS-3000; Fujifilm) and normalized for loading with the amount of RNA Pol-II detected in each lane. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Online supplemental material.\nFig. S1 shows the characterization of peripheral CD8+ T cells from Runx3-/- mice. Fig. S2 shows effector protein expression by Runx3 WT and KO cells at day 4 of in vitro culture. Primer sequences used for ChIP experiments are shown in Table S1. Online supplemental material is available at http://www.jem.org/cgi/content/full/jem.20081242/DC1. \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Supplementary Material\n[Supplemental Material Index]\n", "output": {"json_structures": {}}, "schema": []}
{"input": "Kinetics of gene expression during CD8+ T cell differentiation. (A) Kinetics of Prf1, Gzmb, Tbx21 (T-bet), and Eomes mRNA expression in differentiating P14 CD8+ T cells analyzed by Northern blotting. RNA from day 7 Th1 cells was used as a control. Sizes of mRNA transcripts are indicated. (B) Quantification of relative mRNA amounts by phosphorimager analysis. (C) Kinetics of protein expression in differentiating P14 CD8+ T cells analyzed by immunoblotting. Sizes of protein bands are indicated. (D) Relative protein amounts quantified from the Western blots. (E) Intracellular staining for granzyme B, IFN-gamma, and TNF. Granzyme B staining was specific relative to an isotype control (not depicted). Cells were restimulated with PMA and ionomycin for 4 h. (F) FACS-based assay to measure cytolytic activity of P14 CD8+ T cells against EL4 targets loaded with 0 (-) or 1 (+) muM Gp33 peptide (effector-to-target ratio = 5:1). Percentage of Annexin V+ (apoptotic) target cells in the CD8-negative EL4 target population (dot plots) was determined (histograms). Cytolytic activity was blocked by incubation with 2 mM EGTA (not depicted), confirming involvement of the granule exocytosis (perforin-granzyme B) pathway. Data are representative of at least five (A-E) or three (F) independent experiments. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "staining", "start": 580, "end": 588}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 593, "end": 603}]}, {"trigger": {"text": "staining", "start": 580, "end": 588}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 605, "end": 614}]}, {"trigger": {"text": "staining", "start": 580, "end": 588}, "arguments": [{"role": "Theme", "text": "TNF", "start": 620, "end": 623}]}, {"trigger": {"text": "staining", "start": 636, "end": 644}, "arguments": [{"role": "Theme", "text": "Granzyme B", "start": 625, "end": 635}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 117, "end": 132}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 111, "end": 116}]}, {"trigger": {"text": "mRNA expression", "start": 117, "end": 132}, "arguments": [{"role": "Theme", "text": "Prf1", "start": 80, "end": 84}]}, {"trigger": {"text": "mRNA expression", "start": 117, "end": 132}, "arguments": [{"role": "Theme", "text": "Gzmb", "start": 86, "end": 90}]}, {"trigger": {"text": "mRNA expression", "start": 117, "end": 132}, "arguments": [{"role": "Theme", "text": "Tbx21", "start": 92, "end": 97}]}]}}, "schema": []}
{"input": "Regulation of perforin, granzyme B, and IFN-gamma expression by T-bet and Eomes in differentiating CTLs. (A) IFN-gamma expression by WT (Tbx21+/+) and T-bet-deficient (Tbx21-/-) T cells. Naive CD8+ T cells, or cells activated and cultured for 4 or 6 d, were restimulated with PMA and ionomycin for 6 h, and IFN-gamma expression was assessed by intracellular staining. Numbers show the percentage of IFN-gamma+ cells. (B) Northern blot analysis of Prf1 and GzmB mRNA expression in WT or T-bet-deficient CD8+ T cells activated and either left uninfected (uninf) or transduced with retroviruses expressing Eomes-VP16 (Eo-VP16) or an empty IRES-GFP cassette (GFP). Total cellular RNA was analyzed on day 6 of culture. The frequency of transduced cells in the cultures was equivalent for both constructs (approximately65-70% GFP+ cells; not depicted). (C) Granzyme B and IFN-gamma expression by Tbx21+/+ and Tbx21-/- T cells analyzed in restimulated cells that had been cultured for 5 d. (D) IFN-gamma production by cells transduced with Eo-VP16 or control (GFP) retroviruses (RV) measured on day 4 after 6 h of restimulation with PMA and ionomycin. Numbers show the percentage of GFP+ IFN-gamma+ cells. Results are representative of three (A and C) or two (B and D) independent experiments. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 50, "end": 60}, "arguments": [{"role": "Theme", "text": "perforin", "start": 14, "end": 22}]}, {"trigger": {"text": "expression", "start": 50, "end": 60}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 24, "end": 34}]}, {"trigger": {"text": "expression", "start": 50, "end": 60}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 40, "end": 49}]}, {"trigger": {"text": "expression", "start": 119, "end": 129}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 109, "end": 118}]}, {"trigger": {"text": "expression", "start": 317, "end": 327}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 307, "end": 316}]}, {"trigger": {"text": "expressing", "start": 592, "end": 602}, "arguments": [{"role": "Theme", "text": "Eomes-VP16", "start": 603, "end": 613}]}, {"trigger": {"text": "expression", "start": 876, "end": 886}, "arguments": [{"role": "Theme", "text": "Granzyme B", "start": 851, "end": 861}]}, {"trigger": {"text": "expression", "start": 876, "end": 886}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 866, "end": 875}]}, {"trigger": {"text": "production", "start": 997, "end": 1007}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 987, "end": 996}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 157, "end": 166}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 151, "end": 156}]}, {"trigger": {"text": "deficient", "start": 492, "end": 501}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 486, "end": 491}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 50, "end": 60}, {"role": "Cause", "text": "T-bet", "start": 64, "end": 69}]}, {"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 50, "end": 60}, {"role": "Cause", "text": "Eomes", "start": 74, "end": 79}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 461, "end": 476}, "arguments": [{"role": "Theme", "text": "Prf1", "start": 447, "end": 451}]}, {"trigger": {"text": "mRNA expression", "start": 461, "end": 476}, "arguments": [{"role": "Theme", "text": "GzmB", "start": 456, "end": 460}]}]}}, "schema": []}
{"input": "Key role for Runx3 in effector CTL differentiation. (A) Western analysis of Runx3, Eomes, T-bet, and perforin expression in Runx3+/+ versus Runx3-/- CD8+ SP T cells differentiated for 6 d. beta-Actin was used as a loading control. (B) Northern blot analysis of Prf1 mRNA expression in Runx3+/+ versus Runx3-/- CD8+ T cells differentiated for 6 d. beta-Actin was used as a loading control. (C) Expression of granzyme B, IFN-gamma, TNF, and IL-2 by resting or restimulated (6 h) Runx3+/+ versus Runx3-/- CD8+ SP T cells differentiated for 6 d. The vertical gray line indicates the granzyme B MFI for WT GFP+ cells. Results in A-C are representative of two independent experiments. (D) ChIP analysis of binding of endogenous Runx3 and Eomes to the Prf1 locus. Enrichment of the indicated genomic regions was evaluated by real-time PCR of DNA from immunoprecipitated and input chromatin. The data are the means of duplicate measurements from two chromatin preparations from two independent CD8+ T cell differentiations. The efficiency of recovery of input for the -1-kb region of Prf1 was 0.97% for the Runx3 ChIP and 0.5% for the Eomes ChIP. \n", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 700, "end": 707}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 722, "end": 727}, {"role": "Theme2", "text": "Prf1", "start": 745, "end": 749}]}, {"trigger": {"text": "binding", "start": 700, "end": 707}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 732, "end": 737}, {"role": "Theme2", "text": "Prf1", "start": 745, "end": 749}]}], "gene expression": [{"trigger": {"text": "expression", "start": 110, "end": 120}, "arguments": [{"role": "Theme", "text": "perforin", "start": 101, "end": 109}]}, {"trigger": {"text": "expression", "start": 110, "end": 120}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 76, "end": 81}]}, {"trigger": {"text": "expression", "start": 110, "end": 120}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 83, "end": 88}]}, {"trigger": {"text": "expression", "start": 110, "end": 120}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 90, "end": 95}]}, {"trigger": {"text": "Expression", "start": 393, "end": 403}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 407, "end": 417}]}, {"trigger": {"text": "Expression", "start": 393, "end": 403}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 419, "end": 428}]}, {"trigger": {"text": "Expression", "start": 393, "end": 403}, "arguments": [{"role": "Theme", "text": "TNF", "start": 430, "end": 433}]}, {"trigger": {"text": "Expression", "start": 393, "end": 403}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 439, "end": 443}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 266, "end": 281}, "arguments": [{"role": "Theme", "text": "Prf1", "start": 261, "end": 265}]}]}}, "schema": []}
{"input": "Runx3 controls Eomes, perforin, granzyme B, and IFN-gamma expression in effector CTLs. Runx3+/+ or Runx3-/- CD8+ T cells were activated and transduced with retroviruses bearing an empty IRES-GFP cassette (GFP) or also encoding Eomes-VP16 (Eo-VP16) or Myc-Runx3 (Runx3). The frequency of transduced cells in the cultures was equivalent for all constructs (approximately75-90% GFP+ cells; not depicted). (A) Protein expression in whole-cell extracts (day 6) was analyzed by immunoblotting. Overexpression of Eomes-VP16 cannot be detected with the Eomes antibody, as the C-terminal epitope is within the region that has been replaced with the VP16 transactivation domain. (B) Expression of granzyme B and IFN-gamma after culture for 6 d and restimulation for 4 h with PMA and ionomycin was determined by intracellular staining. The percentage of positively stained cells is shown above the gate; the mean fluorescence intensity (MFI) of granzyme B staining for the total population is shown below the gate. The vertical gray lines indicate the MFI for WT GFP+ cells. Results are representative of at least two independent experiments. (C) Schematic diagram of the transcriptional network involving Runx3 and T-box factors. T-bet is induced by TCR signals and is essential for early IFN-gamma expression. Runx3 is present in naive CD8+ T cells and represses Runx1 and induces Eomes, perforin, granzyme B, and IFN-gamma expression. Eomes may participate in sustaining late IFN-gamma expression, whereas Runx3 and Eomes (but not T-bet) may cooperate to activate perforin expression. The dotted line indicates the partial effect of T-bet deficiency on Gzmb mRNA but not granzyme B protein expression. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 58, "end": 68}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 15, "end": 20}]}, {"trigger": {"text": "expression", "start": 58, "end": 68}, "arguments": [{"role": "Theme", "text": "perforin", "start": 22, "end": 30}]}, {"trigger": {"text": "expression", "start": 58, "end": 68}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 32, "end": 42}]}, {"trigger": {"text": "expression", "start": 58, "end": 68}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 48, "end": 57}]}, {"trigger": {"text": "Expression", "start": 673, "end": 683}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 687, "end": 697}]}, {"trigger": {"text": "Expression", "start": 673, "end": 683}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 702, "end": 711}]}, {"trigger": {"text": "staining", "start": 945, "end": 953}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 934, "end": 944}]}, {"trigger": {"text": "expression", "start": 1289, "end": 1299}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1279, "end": 1288}]}, {"trigger": {"text": "present", "start": 1310, "end": 1317}, "arguments": [{"role": "Theme", "text": "Runx3", "start": 1301, "end": 1306}]}, {"trigger": {"text": "expression", "start": 1415, "end": 1425}, "arguments": [{"role": "Theme", "text": "Eomes", "start": 1372, "end": 1377}]}, {"trigger": {"text": "expression", "start": 1415, "end": 1425}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1379, "end": 1387}]}, {"trigger": {"text": "expression", "start": 1415, "end": 1425}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 1389, "end": 1399}]}, {"trigger": {"text": "expression", "start": 1415, "end": 1425}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1405, "end": 1414}]}, {"trigger": {"text": "expression", "start": 1478, "end": 1488}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1468, "end": 1477}]}, {"trigger": {"text": "expression", "start": 1565, "end": 1575}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1556, "end": 1564}]}, {"trigger": {"text": "expression", "start": 1682, "end": 1692}, "arguments": [{"role": "Theme", "text": "Gzmb", "start": 1645, "end": 1649}]}, {"trigger": {"text": "expression", "start": 1682, "end": 1692}, "arguments": [{"role": "Theme", "text": "granzyme B", "start": 1663, "end": 1673}]}], "negative regulation": [{"trigger": {"text": "represses", "start": 1344, "end": 1353}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 1301, "end": 1306}, {"role": "Theme", "text": "Runx1", "start": 1354, "end": 1359}]}, {"trigger": {"text": "deficiency", "start": 1631, "end": 1641}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1625, "end": 1630}]}], "positive regulation": [{"trigger": {"text": "Overexpression", "start": 488, "end": 502}, "arguments": [{"role": "Theme", "text": "Eomes-VP16", "start": 506, "end": 516}]}, {"trigger": {"text": "induced", "start": 1229, "end": 1236}, "arguments": [{"role": "Theme", "text": "T-bet", "start": 1220, "end": 1225}]}, {"trigger": {"text": "essential", "start": 1259, "end": 1268}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1220, "end": 1225}, {"role": "Theme", "text": "expression", "start": 1289, "end": 1299}]}, {"trigger": {"text": "induces", "start": 1364, "end": 1371}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 1301, "end": 1306}, {"role": "Theme", "text": "expression", "start": 1415, "end": 1425}]}, {"trigger": {"text": "activate", "start": 1547, "end": 1555}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 1498, "end": 1503}, {"role": "Theme", "text": "expression", "start": 1565, "end": 1575}]}, {"trigger": {"text": "activate", "start": 1547, "end": 1555}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1508, "end": 1513}, {"role": "Theme", "text": "expression", "start": 1565, "end": 1575}]}, {"trigger": {"text": "activate", "start": 1547, "end": 1555}, "arguments": [{"role": "Cause", "text": "T-bet", "start": 1523, "end": 1528}, {"role": "Theme", "text": "expression", "start": 1565, "end": 1575}]}], "regulation": [{"trigger": {"text": "controls", "start": 6, "end": 14}, "arguments": [{"role": "Cause", "text": "Runx3", "start": 0, "end": 5}, {"role": "Theme", "text": "expression", "start": 58, "end": 68}]}, {"trigger": {"text": "participate", "start": 1437, "end": 1448}, "arguments": [{"role": "Cause", "text": "Eomes", "start": 1427, "end": 1432}, {"role": "Theme", "text": "expression", "start": 1478, "end": 1488}]}, {"trigger": {"text": "effect", "start": 1615, "end": 1621}, "arguments": [{"role": "Cause", "text": "deficiency", "start": 1631, "end": 1641}, {"role": "Theme", "text": "expression", "start": 1682, "end": 1692}]}]}}, "schema": []}
{"input": "[Supplemental Material Index]\n", "output": {"json_structures": {}}, "schema": []}
{"input": "Interleukin-10 Production by Th1 Cells Requires Interleukin-12-Induced STAT4 Transcription Factor and ERK MAP Kinase Activation by High Antigen Dose \nSummary\nCD4+ Tcells producing interleukin-10 (IL-10) and interferon-gamma (IFN-gamma) are reported in chronic infections. However, the signals that direct the development of IL-10-producing T helper 1 (Th1) cells are undefined. We showed that development of IL-10-producing Th1 cells required high Tcell receptor (TCR) ligation, sustained ERK1 and ERK2 MAP kinases phosphorylation, and IL-12-induced STAT4 transcription factor activation. Repeated TCR triggering led to enhanced IL-10 production by Th1 cells, and continued IL-12 action and high-dose TCR signaling were required for the development and maintenance of IL-10-producing Th1 cells. Although Th1, Th2, and Th17 cells require the activation of distinct STATs for their differentiation, activation of ERK1 and ERK2 wasa common requirement for production of IL-10 by all Th cell subsets. IL-10 expression also correlated with c-maf expression. Despite having distinct functions in protection against pathogens, all Th cells share the important task of controlling overexuberant immune responses by means of IL-10 production. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Production", "start": 15, "end": 25}, "arguments": [{"role": "Theme", "text": "Interleukin-10", "start": 0, "end": 14}]}, {"trigger": {"text": "producing", "start": 170, "end": 179}, "arguments": [{"role": "Theme", "text": "interleukin-10", "start": 180, "end": 194}]}, {"trigger": {"text": "producing", "start": 170, "end": 179}, "arguments": [{"role": "Theme", "text": "interferon-gamma", "start": 207, "end": 223}]}, {"trigger": {"text": "producing", "start": 330, "end": 339}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 324, "end": 329}]}, {"trigger": {"text": "producing", "start": 414, "end": 423}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 408, "end": 413}]}, {"trigger": {"text": "production", "start": 635, "end": 645}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 629, "end": 634}]}, {"trigger": {"text": "producing", "start": 774, "end": 783}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 768, "end": 773}]}, {"trigger": {"text": "production", "start": 953, "end": 963}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 967, "end": 972}]}, {"trigger": {"text": "expression", "start": 1003, "end": 1013}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 997, "end": 1002}]}, {"trigger": {"text": "expression", "start": 1041, "end": 1051}, "arguments": [{"role": "Theme", "text": "c-maf", "start": 1035, "end": 1040}]}, {"trigger": {"text": "production", "start": 1222, "end": 1232}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1216, "end": 1221}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 515, "end": 530}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 489, "end": 493}]}, {"trigger": {"text": "phosphorylation", "start": 515, "end": 530}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 498, "end": 502}]}], "positive regulation": [{"trigger": {"text": "Requires", "start": 39, "end": 47}, "arguments": [{"role": "Theme", "text": "Production", "start": 15, "end": 25}, {"role": "Cause", "text": "Activation", "start": 117, "end": 127}]}, {"trigger": {"text": "Requires", "start": 39, "end": 47}, "arguments": [{"role": "Theme", "text": "Production", "start": 15, "end": 25}, {"role": "Cause", "text": "Induced", "start": 63, "end": 70}]}, {"trigger": {"text": "Induced", "start": 63, "end": 70}, "arguments": [{"role": "Cause", "text": "Interleukin-12", "start": 48, "end": 62}, {"role": "Theme", "text": "STAT4", "start": 71, "end": 76}]}, {"trigger": {"text": "Activation", "start": 117, "end": 127}, "arguments": [{"role": "Theme", "text": "ERK", "start": 102, "end": 105}]}, {"trigger": {"text": "induced", "start": 542, "end": 549}, "arguments": [{"role": "Cause", "text": "IL-12", "start": 536, "end": 541}, {"role": "Theme", "text": "activation", "start": 577, "end": 587}]}, {"trigger": {"text": "activation", "start": 577, "end": 587}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 550, "end": 555}]}, {"trigger": {"text": "enhanced", "start": 620, "end": 628}, "arguments": [{"role": "Theme", "text": "production", "start": 635, "end": 645}]}, {"trigger": {"text": "required", "start": 720, "end": 728}, "arguments": [{"role": "Theme", "text": "producing", "start": 774, "end": 783}]}, {"trigger": {"text": "activation", "start": 897, "end": 907}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 911, "end": 915}]}, {"trigger": {"text": "activation", "start": 897, "end": 907}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 920, "end": 924}]}, {"trigger": {"text": "requirement", "start": 937, "end": 948}, "arguments": [{"role": "Cause", "text": "activation", "start": 897, "end": 907}, {"role": "Theme", "text": "production", "start": 953, "end": 963}]}]}}, "schema": []}
{"input": "Introduction\nInterleukin-10 (IL-10) is a cytokine with broad anti-inflammatory properties that inhibits macrophage and dendritic cell (DC) function (Moore etal., 2001). IL-10 limits the immune and inflammatory responses to pathogens and gut flora and prevents damage to the host (Moore etal., 2001; O'Garra and Vieira, 2004), but when dysregulated may result in chronic infection (Brooks etal., 2006; Ejrnaes etal., 2006; Moore etal., 2001). IL-10 is expressed by T helper 2 (Th2) cells, B cells, DCs, and macrophages (Moore etal., 2001), and also by Th1 cells (Anderson etal., 2007; Assenmacher etal., 1994; Del Prete etal., 1993; Gerosa etal., 1996; Jankovic etal., 2007; Pohl-Koppe etal., 1998) and (reviewed in O'Garra and Vieira, 2007; Trinchieri, 2007), certain regulatory (Treg) Tcells (Moore etal., 2001; O'Garra and Vieira, 2004; Roncarolo etal., 2006), and Th17 cells (Awasthi etal., 2007; Fitzgerald etal., 2007; McGeachy etal., 2007; Stumhofer etal., 2007). \nIn vitro human CD4+ and CD8+ Tcell clones, or mouse CD4+ Tcells that produce both interferon-gamma (IFN-gamma) and IL-10, can be differentiated by Tcell receptor (TCR)-stimulation in the presence of IL-12 (Chang etal., 2007; Gerosa etal., 1996; Jeannin etal., 1996; Meyaard etal., 1996; Windhagen etal., 1996). Furthermore, Th1 cell clones coproducing IFN-gamma and IL-10 have been isolated from bronchoalveolar lavage (BAL) of active pulmonary tuberculosis (TB) patients (Gerosa etal., 1999). IL-10 production by Th1 cells was also reported in animals infected with Toxoplasma gondii (Jankovic etal., 2002; Shaw etal., 2006) or with Leishmania major (Anderson etal., 2007) and shown to be required for regulation of the immune response in these infections (Anderson etal., 2007; Jankovic etal., 2007). The relative amounts of IL-10 and IFN-gamma produced by Th1 cells may influence the balance between clearance and persistent infection with certain pathogens (Moore etal., 2001; Trinchieri, 2007), thus determining whether chronic infection or immunopathology ensues. \nTh1, Th2, and Th17 cell responses differentiate along distinct signaling pathways (Glimcher and Murphy, 2000; Ivanov etal., 2007; Stockinger and Veldhoen, 2007). Th1 cell development requires signal transducer and activator of transcription (STAT)1activation, induced by type I IFN or IFN-gamma, the transcription factor T-box 21 (T-bet), and IL-12-induced STAT4 signaling, which can couple with IL-18-induced IRAK and NF-kappaB transcription factors to drive the high amounts of IFN-gamma required to eradicate intracellular pathogens (Glimcher and Murphy, 2000). Th2 cell development, with expression of IL-4, IL-5, and IL-13, requires IL-4, STAT6, and the transcription factor GATA binding protein (GATA)-3 (Glimcher and Murphy, 2000). The development of Th17 cells requires IL-6, TGF-beta, and the STAT3-dependent expression of the transcription factor RORgammat (Ivanov etal., 2007; Stockinger and Veldhoen, 2007). \nTh1 and Th2 cell responses can also be induced by varying the dose of antigen presented to the naive Tcell by the antigen-presenting cell (APC). Whereas high doses of antigen, with sustained TCR signaling and extracellular-signal regulated (ERK) mitogen-activated protein kinase (MAPK) phosphorylation, result in Th1 cells producing IFN-gamma via an IL-12-independent mechanism, low doses of antigen, with transient ERK1 and ERK2 activation, favor Th2 responses and IL-4 secretion (Constant etal., 1995; Hosken etal., 1995; Jorritsma etal., 2003; Yamane etal., 2005). \nBecause Th1 and Th2 cells cross regulate each other's development and function and can suppress Th17 cell responses, and all differentiate along distinct signaling pathways (Glimcher and Murphy, 2000; Stockinger and Veldhoen, 2007), IL-10 produced by all these Th cells may thus act as a feedback regulator to control the pathology associated with an overexuberant, albeit efficacious, inflammatory response. Whether IL-10 production by these different Th cell subsets is induced by independent and/or common mechanisms is unknown. \nHere, we showed that invitro differentiation of IL-10-producing Th1 cells from naive CD4+ Tcells required IL-12-induced STAT4 signaling, strong TCR activation (high antigen dose), and sustained ERK1 and ERK2 phosphorylation. Furthermore, we showed that activation of ERK1 and ERK2 is a requirement for production of IL-10 by Th1, Th2, and Th17 cell subsets. This common but highly regulated pathway for IL-10 induction and maintenance ensures its function as a feedback loop to control damage to the host and also allows a protective response to ensue as opposed to chronic infection. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 451, "end": 460}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 442, "end": 447}]}, {"trigger": {"text": "produce", "start": 1040, "end": 1047}, "arguments": [{"role": "Theme", "text": "interferon-gamma", "start": 1053, "end": 1069}]}, {"trigger": {"text": "produce", "start": 1040, "end": 1047}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1086, "end": 1091}]}, {"trigger": {"text": "coproducing", "start": 1311, "end": 1322}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1323, "end": 1332}]}, {"trigger": {"text": "coproducing", "start": 1311, "end": 1322}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1337, "end": 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{"input": "IL-12 and High Doses of Antigen Induce the Development of Th1 Cells Producing IL-10\nTo study the differentiation of Th1 cells coproducing IFN-gamma and IL-10, we cultured purified TCR-transgenic DO11.10 naive CD4+ Tcells with purified DCs as APCs and increasing doses of ovalbumin peptide 323-339 (OVA). Culture with high doses of antigen for 7 days gave rise to Th1 cells expressing IFN-gamma upon restimulation (Constant etal., 1995; Hosken etal., 1995), but not IL-10 (FigureS1A available online). Culture with low antigen doses under the same conditions led to the differentiation of Th2 cells, which expressed both IL-4 and IL-10 upon restimulation (FigureS1A). Culture of naive CD4+ Tcells in an APC-free system by stimulation with anti-CD3 and anti-CD28 antibodies in the presence of IL-12 resulted in IFN-gamma-producing Th1 cells, a proportion of which coproduced IL-10, as did Th2 cells resulting from culture in IL-4 (FigureS1B). \nTo investigate whether the lack of IL-10 produced by Th1 cells resulted from inhibition of IL-10 production by DCs and high antigen dose or alternatively required IL-12, we cultured naive CD4+ Tcells with increasing doses of antigen presented by DC in the presence of IL-12. At low doses of antigen, IL-12 abrogated the development of Th2 cells and induced IFN-gamma expression but only low levels of IL-10 expression, suggesting that IL-12 per se was not sufficient to induce significant IL-10 production in Th1 cells (Figure1A). Strikingly, as the antigen dose was increased, Th1 populations driven with IL-12 now contained higher numbers of IL-10-producing cells (Figure1A) and produced more IL-10 protein upon restimulation (Figures 1A and 1B). Thus, the development of Th1 cells producing IL-10 required both IL-12 and high doses of antigen. Th1 cells differentiated to produce large amounts of IL-10 and IFN-gamma and lost theircapacity to produce IL-2 (Figure1B). Because the presence of IL-12 reduced the proliferation of CD4+ Tcells at both high andlow antigen doses (Table S1), and only the former showed IL-10 production, the development of high IL-10-producing cellsis most likely not related to limited IL-2. Naive CD4+ Tcells from DO11.10/recombination-activating gene 1 (Rag1)-deficient animals, cultured with high doses of antigen in the presence of IL-12, also resulted in IL-10 expression by Th1 cells, showing that this expression was not dependent on the presence of effector or memory Tcells or Treg cells (FigureS2). Although it has been suggested that TGF-beta can induce IL-10 in CD4+ Tcells (Kitani etal., 2003; Schiott etal., 2000), we found that in developing Th1 and Th2 cells this was not the case (data not shown). In fact, neutralization of TGF-beta led to increased IL-10 production by both Tcell subsets (FigureS3). Thus, the development of IL-10-producing Th1 cells only depended on the presence of IL-12 together with high antigen dose and not on other soluble factors such as IL-2 or TGF-beta or on the presence of other Tcell types. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Producing", "start": 68, "end": 77}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 78, "end": 83}]}, {"trigger": {"text": "coproducing", "start": 126, "end": 137}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 138, "end": 147}]}, {"trigger": {"text": "coproducing", "start": 126, "end": 137}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 152, "end": 157}]}, {"trigger": {"text": "expressing", "start": 373, "end": 383}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 384, "end": 393}]}, {"trigger": {"text": "expressing", "start": 373, "end": 383}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 465, "end": 470}]}, {"trigger": 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{"input": "IL-10 Production by Th1 Cells Is Dependent on STAT4 but Not on STAT6, IFN-gamma, or IL-4 Signaling\nTo further elucidate the mechanisms required for the development of Th1 cells producing IL-10, we investigated the role of STAT4, one of the signaling pathways activated by IL-12 (Murphy etal., 2000). Naive CD4+ D011.10 Tcells deficient in STAT4 (Ouyang etal., 1998) were cultured in the presence of IL-12 and OVA. Again, IL-10-producing Th1 cells were differentiated at the high antigen dose in the presence of IL-12 in DO11.10 Tcells (Figure2A). In contrast, in the absence of STAT4, the percentage of cells expressing IFN-gamma was dramatically diminished as expected and resulted in an increase in the percentage of cells expressing IL-4, but not IL-10 (Figure2A), suggesting that STAT4 contributes to IL-10 expression by Th1 cells. \nBecause IL-10 expression is associated with an IL-4-induced Th2 cell phenotype, we investigated whether the differentiation of the IL-10-producing Th1 cells depended on signaling through the IL-4 receptor via STAT6 activation (Glimcher and Murphy, 2000; Murphy etal., 2000). The absence of STAT6 did not impair the differentiation of IL-10-producing Th1 cells in the presence of IL-12 and OVA (Figure2A). In fact, a higher percentage of STAT6-deficient cells compared with WT cells produced both IL-10 and IFN-gamma (Figure2A), which may be the result of the loss of Th2 cell control over a Th1 cell response. As expected, lack of STAT6 abrogated both IL-4 and IL-10 production by Tcells developed with IL-4 or with low antigen dose (Figures 2B and 2C). However, in the absence of STAT4 signaling, IL-10 and IL-4 production by Th2 cells was if anything increased (Figures 2B and 2C). Thus, in contrast to what was observed under Th1 conditions, IL-10 expression by Th2 cells depended on STAT6, but not on STAT4, signaling (Figures 2B and 2C). \nTo investigate whether the inability of STAT4-deficient Tcells to produce IL-10 might be due to the absence of IFN-gamma, as suggested before (Shaw etal., 2006), we differentiated DO11.10 or DO11.10 IFN-gamma-deficient naive CD4+ Tcells in the presence of IL-12 and increasing doses of OVA. The secretion of IL-10 as induced by high antigen dose, and IL-12 was not affected by an absence of IFN-gamma (Figure2D), showing that the expression ofIL-10 by Th1 cells is independent of IFN-gamma. In the absence of IFN-gamma, we observed an increase in the secreted IL-4 as expected (data not shown). \nWe also tested for any potential role of IL-4 in the development of Th1 cells producing IL-10 by culturing DO11.10 or DO11.10 IL-4-deficient naive CD4+ Tcells with IL-12 and increasing doses of antigen. As observed in the absence of STAT6 (Figure2A), IL-4 deficiency had no effect on the development of Th1 cells producing IL-10 (Figure2E), but compromised the development of Th2 cells producing IL-10 (Figure2F). Thus, our data suggested that IL-10 production by Th1 or Th2 cells was dependent on the specific signaling pathways required for their differentiation, given that STAT4 is required for the induction of IL-10 production by Th1 cells and STAT6 for Th2 cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Production", "start": 6, "end": 16}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 0, "end": 5}]}, {"trigger": {"text": "producing", "start": 177, "end": 186}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 187, "end": 192}]}, {"trigger": {"text": "producing", "start": 427, "end": 436}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 421, "end": 426}]}, {"trigger": {"text": "expressing", "start": 609, "end": 619}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 620, "end": 629}]}, {"trigger": {"text": "expressing", "start": 725, "end": 735}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 736, "end": 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{"trigger": {"text": "production", "start": 1504, "end": 1514}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1489, "end": 1493}]}, {"trigger": {"text": "production", "start": 1504, "end": 1514}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1498, "end": 1503}]}, {"trigger": {"text": "production", "start": 1650, "end": 1660}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1635, "end": 1640}]}, {"trigger": {"text": "production", "start": 1650, "end": 1660}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1645, "end": 1649}]}, {"trigger": {"text": "expression", "start": 1788, "end": 1798}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1782, "end": 1787}]}, {"trigger": {"text": "produce", "start": 1947, "end": 1954}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1955, "end": 1960}]}, {"trigger": {"text": "expression", "start": 2311, "end": 2321}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 2324, "end": 2329}]}, {"trigger": {"text": "producing", "start": 2555, "end": 2564}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 2565, "end": 2570}]}, {"trigger": {"text": "producing", "start": 2790, "end": 2799}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 2800, "end": 2805}]}, {"trigger": {"text": "producing", "start": 2863, "end": 2872}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 2873, "end": 2878}]}, {"trigger": {"text": "production", "start": 2927, "end": 2937}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 2921, "end": 2926}]}, {"trigger": {"text": "production", "start": 3099, "end": 3109}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 3093, "end": 3098}]}], "localization": [{"trigger": {"text": "secretion", "start": 2176, "end": 2185}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 2189, "end": 2194}]}, {"trigger": {"text": "secreted", "start": 2432, "end": 2440}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 2441, "end": 2445}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 326, "end": 335}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 339, "end": 344}]}, {"trigger": {"text": "absence", "start": 567, "end": 574}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 578, "end": 583}]}, {"trigger": {"text": "diminished", "start": 647, "end": 657}, "arguments": [{"role": "Cause", "text": "absence", "start": 567, "end": 574}, {"role": "Theme", "text": "expressing", "start": 609, "end": 619}]}, {"trigger": {"text": "absence", "start": 1116, "end": 1123}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1127, "end": 1132}]}, {"trigger": {"text": "deficient", "start": 1280, "end": 1289}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1274, "end": 1279}]}, {"trigger": {"text": "lack", "start": 1460, "end": 1464}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1468, "end": 1473}]}, {"trigger": {"text": "abrogated", "start": 1474, "end": 1483}, "arguments": [{"role": "Cause", "text": "lack", "start": 1460, "end": 1464}, {"role": "Theme", "text": "production", "start": 1504, "end": 1514}]}, {"trigger": {"text": "inability", "start": 1908, "end": 1917}, "arguments": [{"role": "Cause", "text": "deficient", "start": 1927, "end": 1936}, {"role": "Theme", "text": "produce", "start": 1947, "end": 1954}]}, {"trigger": {"text": "deficient", "start": 1927, "end": 1936}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 1921, "end": 1926}]}, {"trigger": {"text": "absence", "start": 1981, "end": 1988}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1992, "end": 2001}]}, {"trigger": {"text": "deficient", "start": 2090, "end": 2099}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 2080, "end": 2089}]}, {"trigger": {"text": "absence", "start": 2261, "end": 2268}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 2272, "end": 2281}]}, {"trigger": {"text": "absence", "start": 2379, "end": 2386}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 2390, "end": 2399}]}, {"trigger": {"text": "deficient", "start": 2608, "end": 2617}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 2603, "end": 2607}]}, {"trigger": {"text": "absence", "start": 2699, "end": 2706}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 2710, "end": 2715}]}, {"trigger": {"text": "deficiency", "start": 2733, "end": 2743}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 2728, "end": 2732}]}], "positive regulation": [{"trigger": {"text": "Dependent", "start": 33, "end": 42}, "arguments": [{"role": "Theme", "text": "Production", "start": 6, "end": 16}]}, {"trigger": {"text": "activated", "start": 259, "end": 268}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 222, "end": 227}, {"role": "Cause", "text": "IL-12", "start": 272, "end": 277}]}, {"trigger": {"text": "increase", "start": 689, "end": 697}, "arguments": [{"role": "Cause", "text": "absence", "start": 567, "end": 574}, {"role": "Theme", "text": "expressing", "start": 725, "end": 735}]}, {"trigger": {"text": "contributes", "start": 790, "end": 801}, "arguments": [{"role": "Cause", "text": "STAT4", "start": 784, "end": 789}, {"role": "Theme", "text": "expression", "start": 811, "end": 821}]}, {"trigger": {"text": "activation", "start": 1052, "end": 1062}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1046, "end": 1051}]}, {"trigger": {"text": "in the presence of", "start": 1197, "end": 1215}, "arguments": [{"role": "Theme", "text": "producing", "start": 1177, "end": 1186}, {"role": "Cause", "text": "IL-12", "start": 1216, "end": 1221}]}, {"trigger": {"text": "in the presence of", "start": 1197, "end": 1215}, "arguments": [{"role": "Theme", "text": "producing", "start": 1177, "end": 1186}, {"role": "Cause", "text": "OVA", "start": 1226, "end": 1229}]}, {"trigger": {"text": "increased", "start": 1690, "end": 1699}, "arguments": [{"role": "Theme", "text": "production", "start": 1650, "end": 1660}]}, {"trigger": {"text": "depended", "start": 1812, "end": 1820}, "arguments": [{"role": "Theme", "text": "expression", "start": 1788, "end": 1798}]}, {"trigger": {"text": "due", "start": 1970, "end": 1973}, "arguments": [{"role": "Theme", "text": "inability", "start": 1908, "end": 1917}, {"role": "Cause", "text": "absence", "start": 1981, "end": 1988}]}, {"trigger": {"text": "induced", "start": 2198, "end": 2205}, "arguments": [{"role": "Theme", "text": "secretion", "start": 2176, "end": 2185}]}, {"trigger": {"text": "increase", "start": 2416, "end": 2424}, "arguments": [{"role": "Cause", "text": "absence", "start": 2379, "end": 2386}, {"role": "Theme", "text": "secreted", "start": 2432, "end": 2440}]}, {"trigger": {"text": "induction", "start": 3080, "end": 3089}, "arguments": [{"role": "Cause", "text": "STAT4", "start": 3054, "end": 3059}, {"role": "Theme", "text": "production", "start": 3099, "end": 3109}]}, {"trigger": {"text": "induction", "start": 3080, "end": 3089}, "arguments": [{"role": "Theme", "text": "production", "start": 3099, "end": 3109}, {"role": "Cause", "text": "STAT6", "start": 3127, "end": 3132}]}], "regulation": [{"trigger": {"text": "role", "start": 214, "end": 218}, "arguments": [{"role": "Theme", "text": "producing", "start": 177, "end": 186}, {"role": "Cause", "text": "STAT4", "start": 222, "end": 227}]}, {"trigger": {"text": "affected", "start": 2246, "end": 2254}, "arguments": [{"role": "Theme", "text": "IL-12", "start": 2232, "end": 2237}, {"role": "Cause", "text": "absence", "start": 2261, "end": 2268}]}, {"trigger": {"text": "independent", "start": 2346, "end": 2357}, "arguments": [{"role": "Theme", "text": "expression", "start": 2311, "end": 2321}, {"role": "Cause", "text": "IFN-gamma", "start": 2361, "end": 2370}]}, {"trigger": {"text": "role", "start": 2510, "end": 2514}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 2518, "end": 2522}, {"role": "Theme", "text": "producing", "start": 2555, "end": 2564}]}]}}, "schema": []}
{"input": "High Antigen Doses and STAT4 Are Required for the In Vivo Generation of IL-10-Producing Th1 Cells\nTo address the mechanisms regulating IL-10 production by Th1 cells invivo, we transferred DO11.10 cells into BALB/c recipient mice and immunized the recipients with very high doses of OVA-protein with or without added lipopolysacharide (LPS). Tcells were recovered from the inguinal lymph nodes 3 days after priming and restimulated invitro with OVA peptide for 48 hr. This invivo immunization induced IL-10 and IFN-gamma production, and the amount of IL-10 production was enhanced by addition of LPS in the immunization (Figure3A) and with higher doses of OVA (3 muM versus 1 muM, data not shown). To test the role of STAT4 and STAT6 signaling in the invivo development of IL-10-producing Th1 cells, we transferred STAT4- or STAT6-deficient or WT DO11.10 cells into recipient BALB/c mice and immunized with OVA-protein plus LPS as before. In vivo expression of both IL-10 and IFN-gamma was markedly reduced but not completely abrogated in the absence of STAT4 signaling (Figures 3B and 3C), suggesting the existence of compensatory mechanisms that were absent in the invitro system. Signaling through STAT6 had no effect on IL-10 production by Th1 cells as shown by intracellular cytokine staining (ICS) and by immunoassay in STAT6-deficient Tcells (Figures 3B and 3C). \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Producing", "start": 78, "end": 87}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 72, "end": 77}]}, {"trigger": {"text": "production", "start": 141, "end": 151}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 135, "end": 140}]}, {"trigger": {"text": "production", "start": 520, "end": 530}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 500, "end": 505}]}, {"trigger": {"text": "production", "start": 520, "end": 530}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 510, "end": 519}]}, {"trigger": {"text": "production", "start": 556, "end": 566}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 550, "end": 555}]}, {"trigger": {"text": "producing", "start": 778, "end": 787}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 772, "end": 777}]}, {"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 965, "end": 970}]}, {"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 975, "end": 984}]}, {"trigger": {"text": "production", "start": 1229, "end": 1239}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1223, "end": 1228}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 830, "end": 839}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 814, "end": 819}]}, {"trigger": {"text": "deficient", "start": 830, "end": 839}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 824, "end": 829}]}, {"trigger": {"text": "reduced", "start": 998, "end": 1005}, "arguments": [{"role": "Theme", "text": "expression", "start": 946, "end": 956}]}, {"trigger": {"text": "completely abrogated", "start": 1014, "end": 1034}, "arguments": [{"role": "Theme", "text": "expression", "start": 946, "end": 956}]}, {"trigger": {"text": "deficient", "start": 1331, "end": 1340}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1325, "end": 1330}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 492, "end": 499}, "arguments": [{"role": "Theme", "text": "production", "start": 520, "end": 530}]}, {"trigger": {"text": "enhanced", "start": 571, "end": 579}, "arguments": [{"role": "Theme", "text": "production", "start": 556, "end": 566}, {"role": "Cause", "text": "OVA", "start": 655, "end": 658}]}], "regulation": [{"trigger": {"text": "regulating", "start": 124, "end": 134}, "arguments": [{"role": "Theme", "text": "production", "start": 141, "end": 151}]}, {"trigger": {"text": "effect", "start": 1213, "end": 1219}, "arguments": [{"role": "Theme", "text": "production", "start": 1229, "end": 1239}]}]}}, "schema": []}
{"input": "IL-10 Production Is Maintained by High TCR Signal Strength and IL-12\nWe next investigated whether repeated strong TCR activation is a compensatory signal for IL-12-induced STAT4 signaling in the induction of IL-10 in Th1 cells. For this, CD4+ Tcells were differentiated for 2 consecutive weeks with high antigen doses in the presence or absence of IL-12 throughout (Figures 4A-4D). High antigen dose and IL-12 cooperated to induce maximal IL-10 production (Figures 4A and 4B), given that this combination resulted in the highest numbers of IL-10-producing Th1 cells. Repeated high antigen dose stimulation in the absence of exogenously added IL-12 resulted in the production of IL-10 by Th1 cells, suggesting that repeated strong TCR triggering may overcome the need for IL-12 for IL-10 induction (Figures 4C and 4D). However, IL-10 induction under these conditions was abrogated when IL-12p40-deficient DCs were used as APCs (Figure4E). Thus, IL-12 is essential during both primary and secondary antigenic stimulation for production of IL-10 by Th1 cells. \nTo determine the requirements for stability of the IL-10-producing Th1 cells, we differentiated CD4+ Tcells for 1 week with high antigen doses with or without IL-12 (Figures 4A and 4C), washed them, and then restimulated them for an additional week with a low antigen dose, in the absence or presence of IL-12 (Figure4F). Th1 cells induced in the first week to produce IL-10 by culture with high antigen doses and IL-12 lost their ability to express IL-10 when recultured with low doses of OVA, which could be compensated for, to some extent, by addition of IL-12 to the secondary cultures (Figure4F), again suggesting that antigen dose and IL-12 signals cooperate for the induction of IL-10. Finally, DO11.10 CD4+ cells that were exposed to low doses of antigen and IL-12 during the primary differentiation phase produced high amounts of IFN-gamma but little IL-10, but they could be induced to produce IL-10 when both high antigen dose and IL-12 were present during the recall phase (FigureS4). Thus, high antigen dose and IL-12 are required for sustaining the induction of IL-10 production by Th1 cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Production", "start": 6, "end": 16}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 0, "end": 5}]}, {"trigger": {"text": "production", "start": 445, "end": 455}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 439, "end": 444}]}, {"trigger": {"text": "producing", "start": 546, "end": 555}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 540, "end": 545}]}, {"trigger": {"text": "production", "start": 664, "end": 674}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 678, "end": 683}]}, {"trigger": {"text": "production", "start": 1023, "end": 1033}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1037, "end": 1042}]}, {"trigger": {"text": "producing", "start": 1115, "end": 1124}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1109, "end": 1114}]}, {"trigger": {"text": "produce", "start": 1419, "end": 1426}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1427, "end": 1432}]}, {"trigger": {"text": "express", "start": 1500, "end": 1507}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1508, "end": 1513}]}, {"trigger": {"text": "induction", "start": 1731, "end": 1740}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1744, "end": 1749}]}, {"trigger": {"text": "produced", "start": 1872, "end": 1880}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1897, "end": 1906}]}, {"trigger": {"text": "produced", "start": 1872, "end": 1880}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1918, "end": 1923}]}, {"trigger": {"text": "produce", "start": 1954, "end": 1961}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1962, "end": 1967}]}, {"trigger": {"text": "production", "start": 2140, "end": 2150}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 2134, "end": 2139}]}], "negative regulation": [{"trigger": {"text": "abrogated", "start": 870, "end": 879}, "arguments": [{"role": "Theme", "text": "induction", "start": 833, "end": 842}, {"role": "Cause", "text": "deficient", "start": 894, "end": 903}]}, {"trigger": {"text": "deficient", "start": 894, "end": 903}, "arguments": [{"role": "Theme", "text": "IL-12p40", "start": 885, "end": 893}]}, {"trigger": {"text": "lost", "start": 1478, "end": 1482}, "arguments": [{"role": "Theme", "text": "express", "start": 1500, "end": 1507}, {"role": "Cause", "text": "OVA", "start": 1548, "end": 1551}]}, {"trigger": {"text": "compensated", "start": 1568, "end": 1579}, "arguments": [{"role": "Theme", "text": "lost", "start": 1478, "end": 1482}, {"role": "Cause", "text": "IL-12", "start": 1616, "end": 1621}]}], "positive regulation": [{"trigger": {"text": "Maintained", "start": 20, "end": 30}, "arguments": [{"role": "Theme", "text": "Production", "start": 6, "end": 16}, {"role": "Cause", "text": "IL-12", "start": 63, "end": 68}]}, {"trigger": {"text": "induction", "start": 195, "end": 204}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 208, "end": 213}]}, {"trigger": {"text": "induce", "start": 424, "end": 430}, "arguments": [{"role": "Cause", "text": "IL-12", "start": 404, "end": 409}, {"role": "Theme", "text": "production", "start": 445, "end": 455}]}, {"trigger": {"text": "resulted", "start": 648, "end": 656}, "arguments": [{"role": "Theme", "text": "production", "start": 664, "end": 674}]}, {"trigger": {"text": "need", "start": 762, "end": 766}, "arguments": [{"role": "Cause", "text": "IL-12", "start": 771, "end": 776}, {"role": "Theme", "text": "induction", "start": 787, "end": 796}]}, {"trigger": {"text": "induction", "start": 787, "end": 796}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 781, "end": 786}]}, {"trigger": {"text": "induction", "start": 833, "end": 842}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 827, "end": 832}]}, {"trigger": {"text": "essential", "start": 953, "end": 962}, "arguments": [{"role": "Cause", "text": "IL-12", "start": 944, "end": 949}, {"role": "Theme", "text": "production", "start": 1023, "end": 1033}]}, {"trigger": {"text": "induced", "start": 1390, "end": 1397}, "arguments": [{"role": "Theme", "text": "produce", "start": 1419, "end": 1426}, {"role": "Cause", "text": "IL-12", "start": 1472, "end": 1477}]}, {"trigger": {"text": "addition", "start": 1604, "end": 1612}, "arguments": [{"role": "Theme", "text": "IL-12", "start": 1616, "end": 1621}]}, {"trigger": {"text": "cooperate", "start": 1713, "end": 1722}, "arguments": [{"role": "Theme", "text": "induction", "start": 1731, "end": 1740}]}, {"trigger": {"text": "induced", "start": 1943, "end": 1950}, "arguments": [{"role": "Theme", "text": "produce", "start": 1954, "end": 1961}, {"role": "Cause", "text": "IL-12", "start": 2000, "end": 2005}]}, {"trigger": {"text": "induction", "start": 2121, "end": 2130}, "arguments": [{"role": 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{"input": "IL-10 Production by Th1 Cells Requires ERK1 and ERK2 Activation\nOur data showed that the maintenance of IL-10 induction in Th1 cells required stimulation with high antigen dose, which to some extent could be compensated for by the addition of IL-12. Signaling through the TCR with high doses of antigen induced stronger ERK1 and ERK2 activation than that induced by low antigen dose, not only in naive CD4+ Tcells (data not shown) as previously demonstrated (Jorritsma etal., 2003) but also in CD4+ Tcells restimulated with the same high and low antigen doses (Figure5A). Although the apparent peak and amount of ERK1 and ERK2 activation varied slightly between experiments, a consistent finding was that high antigen dose differentiated Th1 cells always showed enhanced and prolonged ERK1 and ERK2 activation in the presence of IL-12, regardless of whether they were restimulated with high or low antigen dose (Figure5B). \nWe then investigated whether ERK1 and ERK2 activation was required for the induction of IL-10 in Th1 cells by using U0126 (Figure5C), a compound that blocks downstream ERK activation. To ensure that only Tcell signaling was being affected by U0126, we used an APC-free system in which the Tcells were differentiated in the presence of increasing doses of anti-CD3 and a constant amount of IL-12. As in the APC-driven cultures, stronger TCR stimulation together with IL-12 led to higher percentages of cells producing both IL-10 and IFN-gamma after 1 week of culture (Figure5C). Addition of U0126 to the cultures abrogated the production of IL-10 at all doses of anti-CD3 (Figure5C). Because U0126 inhibits the MEK5-catalyzed activation of ERK5, as well as the MEK1- and MEK2-catalyzed activation of ERK1 and ERK2 (Bain etal., 2007; Mody etal., 2001), we also used the more specific, structurally unrelated MEK1 and MEK2 inhibitor PD184352 at concentrations in which it inhibits MEK1 and MEK2 but not MEK5 (Bain etal., 2007; Mody etal., 2001). PD184352 caused a similar inhibition of IL-10 production by Th1 cells in a dose-dependent fashion (Figure5D and FigureS5A). Upon addition of inhibitors to othersignaling pathways, including a p38 MAPK inhibitor, SB203580, or the GSK3beta inhibitor, CT99021 (Bain etal., 2007), no effect on IL-10 production was observed (FigureS5B). Our data thus suggested that IL-10 production by Th1 cells in response to high antigen dose and IL-12 requires ERK1 and ERK2 signaling, but not the activation of the p38 or the GSK3beta pathways. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Production", "start": 6, "end": 16}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 0, "end": 5}]}, {"trigger": {"text": "induction", "start": 110, "end": 119}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 104, "end": 109}]}, {"trigger": {"text": "producing", "start": 1431, "end": 1440}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1446, "end": 1451}]}, {"trigger": {"text": "producing", "start": 1431, "end": 1440}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1456, "end": 1465}]}, {"trigger": {"text": "production", "start": 1550, "end": 1560}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1564, "end": 1569}]}, {"trigger": {"text": "production", 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{"input": "IL-10 Production by Th2 and Th17 Cells Also Requires ERK1 and ERK2 Activation\nTo address whether IL-10 production by Th2 and Th17 cells was also dependent on ERK1 and ERK2 activation, we differentiated these cells with anti-CD3 and anti-CD28 in the absence of APCs (Shoemaker etal., 2006; Veldhoen etal., 2009; Veldhoen etal., 2006), in the presence or absence of the MEK inhibitor (PD184352). We showed that ERK1 and ERK2 activation is a common pathway required for induction of IL-10 in different Th cell subsets because IL-10 production by both Th2 and Th17 cells was markedly inhibited in the presence of the MEK inhibitor (PD184352) (Figure5D and FigureS5B). In contrast, inhibitors of p38 MAPK or of GSK-3beta activation did not affect the expression of IL-10 by these subsets (FigureS5B). Activation of the ERK1 and ERK2 signaling pathway is therefore a common requirement for the induction of IL-10 production by Th1, Th2, and Th17 cells. \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Production", "start": 6, "end": 16}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 0, "end": 5}]}, {"trigger": {"text": "production", "start": 103, "end": 113}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 97, "end": 102}]}, {"trigger": {"text": "induction", "start": 467, "end": 476}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 480, "end": 485}]}, {"trigger": {"text": "production", "start": 529, "end": 539}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 523, "end": 528}]}, {"trigger": {"text": "expression", "start": 746, "end": 756}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 760, "end": 765}]}, {"trigger": {"text": "production", "start": 907, "end": 917}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 901, "end": 906}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 372, "end": 381}, "arguments": [{"role": "Theme", "text": "MEK", "start": 368, "end": 371}]}, {"trigger": {"text": "inhibited", "start": 580, "end": 589}, "arguments": [{"role": "Theme", "text": "production", "start": 529, "end": 539}, {"role": "Cause", "text": "inhibitor", "start": 617, "end": 626}]}, {"trigger": {"text": "inhibitor", "start": 617, "end": 626}, "arguments": [{"role": "Theme", "text": "MEK", "start": 613, "end": 616}]}, {"trigger": {"text": "inhibitors", "start": 677, "end": 687}, "arguments": [{"role": "Theme", "text": "activation", "start": 716, "end": 726}]}], "positive regulation": [{"trigger": {"text": "Requires", "start": 44, "end": 52}, "arguments": [{"role": "Theme", "text": "Production", "start": 6, "end": 16}, {"role": "Cause", "text": "Activation", "start": 67, "end": 77}]}, {"trigger": {"text": "Activation", "start": 67, "end": 77}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 53, "end": 57}]}, {"trigger": {"text": "Activation", "start": 67, "end": 77}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 62, "end": 66}]}, {"trigger": {"text": "dependent", "start": 145, "end": 154}, "arguments": [{"role": "Theme", "text": "production", "start": 103, "end": 113}, {"role": "Cause", "text": "activation", "start": 172, "end": 182}]}, {"trigger": {"text": "activation", "start": 172, "end": 182}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 158, "end": 162}]}, {"trigger": {"text": "activation", "start": 172, "end": 182}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 167, "end": 171}]}, {"trigger": {"text": "activation", "start": 423, "end": 433}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 409, "end": 413}]}, {"trigger": {"text": "activation", "start": 423, "end": 433}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 418, "end": 422}]}, {"trigger": {"text": "required", "start": 454, "end": 462}, "arguments": [{"role": "Cause", "text": "activation", "start": 423, "end": 433}, {"role": "Theme", "text": "induction", "start": 467, "end": 476}]}, {"trigger": {"text": "activation", "start": 716, "end": 726}, "arguments": [{"role": "Theme", "text": "p38 MAPK", "start": 691, "end": 699}]}, {"trigger": {"text": "activation", "start": 716, "end": 726}, "arguments": [{"role": "Theme", "text": "GSK-3beta", "start": 706, "end": 715}]}, {"trigger": {"text": "requirement", "start": 868, "end": 879}, "arguments": [{"role": "Theme", "text": "induction", "start": 888, "end": 897}]}, {"trigger": {"text": "induction", "start": 888, "end": 897}, "arguments": [{"role": "Theme", "text": "production", "start": 907, "end": 917}]}], "regulation": [{"trigger": {"text": "affect", "start": 735, "end": 741}, "arguments": [{"role": "Cause", "text": "inhibitors", "start": 677, "end": 687}, {"role": "Theme", "text": "expression", "start": 746, "end": 756}]}]}}, "schema": []}
{"input": "c-maf Expression Correlates with IL-10 Production in Th1, Th2, and Th17 Cells\nTo investigate further the downstream factors involved in regulating IL-10 production, we differentiated DO11.10 CD4+ Tcells with increasing doses of OVA, in the presence or absence of IL-12, and quantified the expression of cytokines and transcription factors by real-time RT-PCR. Low-dose antigen resulted in transcription of Il4 and this was abrogated by both high antigen doses and IL-12 (Figure6A). A low amount of transcription of Ifngamma was induced by IL-12 when cells were differentiated with low antigen dose, but this effect of IL-12 was markedly upregulated with increasing doses of antigen (Figure6A). A low amount of Il10 transcription was observed at low doses of antigen accompanying Il4 expression (Th2 cell response), and this was abrogated by increased doses of antigen as was Il4 expression (Figure6A). At low doses of antigen, IL-12 had little effect to increase IL-10 mRNA expression (Figure6A) in keeping with the protein data (Figure1A). However, IL-12 induced a high amount of Il10 transcription as well as Ifngamma expression with increased antigen doses (Figure6A), again in keeping with the protein data (Figure1A). \nCD4+ Tcells differentiated with increasing doses of antigen did not express high amounts of Tbx-21 (T-bet) mRNA, unless they were cocultured with IL-12 (Figure6B). In contrast, high amounts of GATA-3 mRNA expression were only observed under Th2 cell differentiation conditions (low-dose antigen) (Figure6B), and this expression was markedly downregulated by both increasing antigen dose and coculture in IL-12 (Figure6B). Differentiation of Tcells under low antigen dose led to expression of c-maf, in keeping with the Th2 cell profile (Ho etal., 1996), which was almost completely abrogated by increasing doses of antigen (Figure6B). Interestingly, IL-12 sustained the high expression of c-Maf mRNA even at the highest antigen dose (Figure6B). Moreover, IL-12 maintenance of c-maf expression required STAT4 activation (data not shown). \nIn Th17 cells that expressed IL-17a as well as IL-10 mRNA (Figure6C), T-bet and GATA-3 mRNA were undetectable (data not shown), whereas that of ROR-gammat was high (Figure6C) (Ivanov etal., 2007). Th17 cells also expressed high amounts of c-maf (Figure6C), confirming a recent report (Bauquet etal., 2009). c-Maf is therefore expressed in all IL-10-expressing Tcell populations tested (Figures 6B and 6C) and may not be just a Th2 cell-specific transcription factor as originally thought (Ho etal., 1996). We showed also that like Il10 expression, c-maf expression was inhibited in Th1 and Th17 cells in the presence of the MEK1 and MEK2 inhibitor (PD184352), whereas T-bet and RORgammat expression was hardly affected (Figure6D). \n", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 6, "end": 16}, "arguments": [{"role": "Theme", "text": "c-maf", "start": 0, "end": 5}]}, {"trigger": {"text": "Production", "start": 39, "end": 49}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 33, "end": 38}]}, {"trigger": {"text": "production", "start": 153, "end": 163}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 147, "end": 152}]}, {"trigger": {"text": "expression", "start": 783, "end": 793}, "arguments": [{"role": "Theme", "text": "Il4", "start": 779, "end": 782}]}, {"trigger": {"text": "expression", "start": 879, "end": 889}, "arguments": [{"role": "Theme", "text": "Il4", "start": 875, "end": 878}]}, {"trigger": {"text": "expression", 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{"input": "Discussion\nIL-10 expression by cells of the innate and adaptive immune systems reflects the importance of this cytokine in the tight regulation of the immune response, to minimize pathology during infection. IL-10 expression by Th1 cells has been reported to regulate the immune response in leishmaniasis and toxoplasmosis. However, in many situations, IL-10 is not produced by Th1 cells in response to antigenic stimulation. Our goal was to address the molecular signals that determine whether Th1 cells develop to produce IL-10 (Trinchieri, 2007). Here, we showed that Th1 cells required high-antigen-dose-induced ERK1 and ERK2 phosphorylation and IL-12-induced STAT-4 activation to produce IL-10. Our findings that ERK1 and ERK2 activation was a common pathway required for the production of IL-10 by Th1, Th2, and Th17 cell subsets, which differentiate along distinct pathways, such that IL-10 provides a highly regulated feedback loop to avoid the extremes of excessive inflammation or chronic infections and also allow a protective response to diverse pathogens. \nIn certain viral or parasitic infections (Anderson etal., 2007; Brooks etal., 2006; Ejrnaes etal., 2006), high amounts of stimulation may lead to the chronic nonhealing infection shown to be regulated by IL-10. During the course of infection, after initial triggering with antigen, Tcells migrate to the tissue encountering high doses of antigen and factors produced by the innate immune response. Under these conditions, we speculate that Th1 cells will be induced to express high amounts of IL-10, in keeping with reports that IL-10-producing Th1 cells were found in CD4+ clones isolated from BAL but not blood of TB patients (Gerosa etal., 1999). Similarly, the immune response to a clinical isolate of L. major, which produces heavily infected nonhealing lesions, was found to be regulated by IL-10 derived from Foxp3- Th1 cells that coproduce IL-10 and IFN-gamma (Anderson etal., 2007), and the immune response during T. gondii infection was found also to be regulated by Foxp3- Th1 cells (Jankovic etal., 2007). It is likely that IL-10 production by Th1 cells is evoked under conditions of high inflammation and antigenic stimulation, whereas regulatory CD4+ Tcells producing IL-10 may operate to regulate the immune response under conditions in which the pathogen is clinically controlled, such as in infection with L. major (Friedlin strain) (Belkaid etal., 2002; Suffia etal., 2006). We now also reported that CD4+ Tcells cultured with high antigen dose and IL-12 differentiate into canonical Th1 effector cells , which, in addition to expressing large amounts of IFN-gamma and IL-10, lose their IL-2 expression as described before in certain chronic infection models (Sallusto etal., 2004). Our demonstration that loss of IL-2 is accompanied by production of IL-10 offers potential additional mechanisms whereby effector Tcell responses may be dampened during chronic disease. \nUsing an invivo transfer model of DO11.10 TCR transgenic cells (Castro etal., 2000), we showed that IL-10-producing Th1 cells were differentiated in the presence of high doses of OVA protein and LPS. We showed here that this induction of IL-10 inTh1 cells invivo was markedly, but not totally, reduced in STAT4-deficient Tcells as observed during T. gondii infection (Jankovic etal., 2002). A high antigenic activation during T. gondii infection or high antigen doses delivered in the presence of LPS, as seen in our system, may compensate for an absolute requirement for IL-12 in the induction of IL-10 by Th1 cells. \nIn our invitro system, repeated stimulation of Th1 cells with high antigen doses allowed the development of Th1 cells producing IL-10 in an IL-12-dependent manner. IL-10 production by Th1 cells induced by high antigen dose and IL-12 was independent of IFN-gamma, in keeping with previous findings (Jankovic etal., 2002). However, a role for IFN-gamma in mediating IL-10 reactivation by Th1 cells during secondary infection with T. gondii has been suggested (Shaw etal., 2006). We have found that CD4+ Tcells exposed to a high dose of antigen do not express IL-10 upon restimulation, but can be induced to produce IL-10 upon re-exposure to a high dose of antigen in the recall phase in the absence of added IL-12. However, this is dependent on the induction of IL-12 by antigen-presenting DCs. The combination of both high antigen dose and IL-12 resulted in the highest levels of IL-10 production and correlated with the high levels of ERK1 and ERK2 activation. The increased expression of IFN-gamma observed during the secondary phase will induce increased IL-12 production by DCs and suggests that repeated high-level TCR activation feeds back to upregulate IL-12 production by DC. It is thus likely that in T. gondii infection invivo (Shaw etal., 2006), the requirement for IFN-gamma to induce IL-10, was for feedback upregulation of IL-12 by DCs, which in turn induced IL-10 in the Th1 cells. \nAlthough IL-10 may be differentially regulated in Th1 and Th2 cells as has been reported (Chang etal., 2007; Wang etal., 2005), some studies suggest the existence of common pathways, but the molecular basis for these is as yet unclear. Costimulatory OX-40 signals have been shown to negatively regulate IL-10 production (Ito etal., 2005) both in Th1 and Th2 cells, whereas ICOS signaling has been suggested to induce IL-10 (Ito etal., 2007; Witsch etal., 2002) in both Th1 and Th2 cells. However, in some cases, ICOS signaling also regulates IL-4 production and Th2 responses (Greenwald etal., 2005). We now provide a common mechanism of ERK1 and ERK2 activation for the regulation of IL-10 production in Th1, Th2, and Th17 cells, although each subset differentiates along a distinct and subset-specific transcriptional pathway. This reinforces the fact that IL-10 is not a Th cell-subset-specific cytokine, but instead is produced in a tightly regulated fashion during each differentiation pathway. Of note, a role for ERK1 and ERK2 activation in the induction of IL-10 production has already been described for macrophages and DC (Agrawal etal., 2006; Hacker etal., 1999). \nDifferential transcriptional regulation of IL-10 in Th1 and Th2 cells has been suggested (Chang etal., 2007; Wang etal., 2005), and extensive histone acetylation of the IL-10 gene is detectable in fully polarized Th2 cells, but not Th1cells (Chang etal., 2007). We provide evidence that IL-10 is produced in canonical Th1 cells and that its expression correlates with the expression of T-bet and the highest IFN-gamma production, in keeping with our observations that high-dose antigen stimulation and IL-12 signaling are required for IL-10 and IFN-gamma expression. It has also been shown that maintenance of IL-10 expression is conditional on IL-12 or IL-4 unless the IL-10 gene is imprinted by GATA-3 (Chang etal., 2007), which can remodel the IL-10 locus, thus explaining the highest amounts of IL-10 produced by Th2 cells (Chang etal., 2007; Shoemaker etal., 2006). We show here that high antigen dose and IL-12 drastically downregulate Gata-3 expression, suggesting that additional factors are in place to induce IL-10 expression in Th1 cells, albeit transiently. Expression of c-maf was greatly diminished by high antigen doses in Tcells and yet was unexpectedly maintained by IL-12 and present in Th17 cells. That c-maf expression is common to IL-10-producing Th1, Th2, and Th17 cells and, like IL-10, is dependent on ERK activation in Th1 and Th17 cells for its expression is of interest because c-Maf has been shown to be an essential transcription factor for IL-10 expression in macrophages (Cao etal., 2005). \nIn summary, we show that although Th1, Th2, and Th17 CD4+ Tcell subsets differentiate along distinct signaling and transcriptional pathways, they can all be induced to make IL-10. ERK1 and ERK2 activation is required for IL-10 production by all these Th cell subsets. With regard to the expression of IL-10 by Th1 cells, our data provide a mechanism for how IL-10 expression is induced and then amplified and regulated by the levels of antigen and IL-12 encountered in the environment. This provides a mechanism whereby a Th1 cell responds to extrinsic signals, reflecting increased inflammation in the tissue, to tightly regulate the production of IL-10 so as to allow a protective response to eradicate a pathogen with minimal damage to the host and also prevent chronic infection. 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"increased", "start": 4624, "end": 4633}, "arguments": [{"role": "Theme", "text": "production", "start": 4640, "end": 4650}]}, {"trigger": {"text": "upregulate", "start": 4725, "end": 4735}, "arguments": [{"role": "Theme", "text": "production", "start": 4742, "end": 4752}]}, {"trigger": {"text": "requirement", "start": 4837, "end": 4848}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 4853, "end": 4862}, {"role": "Theme", "text": "induce", "start": 4866, "end": 4872}]}, {"trigger": {"text": "induce", "start": 4866, "end": 4872}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 4873, "end": 4878}]}, {"trigger": {"text": "upregulation", "start": 4897, "end": 4909}, "arguments": [{"role": "Theme", "text": "IL-12", "start": 4913, "end": 4918}]}, {"trigger": {"text": "induced", "start": 4941, "end": 4948}, "arguments": [{"role": "Cause", "text": "upregulation", "start": 4897, "end": 4909}, {"role": "Theme", "text": "IL-10", "start": 4949, "end": 4954}]}, {"trigger": {"text": "induce", "start": 5384, "end": 5390}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 5391, "end": 5396}]}, {"trigger": {"text": "activation", "start": 5626, "end": 5636}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 5612, "end": 5616}]}, {"trigger": {"text": "activation", "start": 5626, "end": 5636}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 5621, "end": 5625}]}, {"trigger": {"text": "activation", "start": 6008, "end": 6018}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 5994, "end": 5998}]}, {"trigger": {"text": "activation", "start": 6008, "end": 6018}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 6003, "end": 6007}]}, {"trigger": {"text": "induction", "start": 6026, "end": 6035}, "arguments": [{"role": "Theme", "text": "production", "start": 6045, "end": 6055}]}, {"trigger": {"text": "required", "start": 6672, "end": 6680}, "arguments": [{"role": "Theme", "text": "expression", "start": 6705, "end": 6715}]}, {"trigger": {"text": "maintenance", "start": 6745, "end": 6756}, "arguments": [{"role": "Theme", "text": "expression", "start": 6766, "end": 6776}]}, {"trigger": {"text": "conditional", "start": 6780, "end": 6791}, "arguments": [{"role": "Theme", "text": "maintenance", "start": 6745, "end": 6756}, {"role": "Cause", "text": "IL-12", "start": 6795, "end": 6800}]}, {"trigger": {"text": "conditional", "start": 6780, "end": 6791}, "arguments": [{"role": "Theme", "text": "maintenance", "start": 6745, "end": 6756}, {"role": "Cause", "text": "IL-4", "start": 6804, "end": 6808}]}, {"trigger": {"text": "induce", "start": 7162, "end": 7168}, "arguments": [{"role": "Theme", "text": "expression", "start": 7175, "end": 7185}]}, {"trigger": {"text": "maintained", "start": 7320, "end": 7330}, "arguments": [{"role": "Theme", "text": "Expression", "start": 7220, "end": 7230}, {"role": "Cause", "text": "IL-12", "start": 7334, "end": 7339}]}, {"trigger": {"text": "dependent", "start": 7463, "end": 7472}, "arguments": [{"role": "Theme", "text": "expression", "start": 7378, "end": 7388}, {"role": "Cause", "text": "activation", "start": 7480, "end": 7490}]}, {"trigger": {"text": "dependent", "start": 7463, "end": 7472}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 7453, "end": 7458}, {"role": "Cause", "text": "activation", "start": 7480, "end": 7490}]}, {"trigger": {"text": "activation", "start": 7480, "end": 7490}, "arguments": [{"role": "Theme", "text": "ERK", "start": 7476, "end": 7479}]}, {"trigger": {"text": "essential", "start": 7585, "end": 7594}, "arguments": [{"role": "Cause", "text": "c-Maf", "start": 7555, "end": 7560}, {"role": "Theme", "text": "expression", "start": 7626, "end": 7636}]}, {"trigger": {"text": "induced", "start": 7829, "end": 7836}, "arguments": [{"role": "Theme", "text": "make", "start": 7840, "end": 7844}]}, {"trigger": {"text": "activation", "start": 7866, "end": 7876}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 7852, "end": 7856}]}, {"trigger": {"text": "activation", "start": 7866, "end": 7876}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 7861, "end": 7865}]}, {"trigger": {"text": "required", "start": 7880, "end": 7888}, "arguments": [{"role": "Cause", "text": "ERK1", "start": 7852, "end": 7856}, {"role": "Theme", "text": "production", "start": 7899, "end": 7909}]}, {"trigger": {"text": "required", "start": 7880, "end": 7888}, "arguments": [{"role": "Cause", "text": "ERK2", "start": 7861, "end": 7865}, {"role": "Theme", "text": "production", "start": 7899, "end": 7909}]}, {"trigger": {"text": "induced", "start": 8050, "end": 8057}, "arguments": [{"role": "Theme", "text": "expression", "start": 8036, "end": 8046}]}, {"trigger": {"text": "amplified", "start": 8067, "end": 8076}, "arguments": [{"role": "Theme", "text": "expression", "start": 8036, "end": 8046}, {"role": "Cause", "text": "IL-12", "start": 8120, "end": 8125}]}], "regulation": [{"trigger": {"text": "provides a highly regulated feedback loop", "start": 898, "end": 939}, "arguments": [{"role": "Theme", "text": "production", "start": 781, "end": 791}, {"role": "Cause", "text": "IL-10", "start": 892, "end": 897}]}, {"trigger": {"text": "independent", "start": 3814, "end": 3825}, "arguments": [{"role": "Theme", "text": "induced", "start": 3771, "end": 3778}, {"role": "Cause", "text": "IFN-gamma", "start": 3829, "end": 3838}]}, {"trigger": {"text": "regulated", "start": 5011, "end": 5020}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 4983, "end": 4988}]}, {"trigger": {"text": "regulates", "start": 5506, "end": 5515}, "arguments": [{"role": "Theme", "text": "production", "start": 5521, "end": 5531}]}, {"trigger": {"text": "regulation", "start": 5645, "end": 5655}, "arguments": [{"role": "Cause", "text": "ERK1", "start": 5612, "end": 5616}, {"role": "Theme", "text": "production", "start": 5665, "end": 5675}]}, {"trigger": {"text": "regulation", "start": 5645, "end": 5655}, "arguments": [{"role": "Cause", "text": "ERK2", "start": 5621, "end": 5625}, {"role": "Theme", "text": "production", "start": 5665, "end": 5675}]}, {"trigger": {"text": "regulated", "start": 5919, "end": 5928}, "arguments": [{"role": "Theme", "text": "produced", "start": 5897, "end": 5905}]}, {"trigger": {"text": "role", "start": 5985, "end": 5989}, "arguments": [{"role": "Cause", "text": "activation", "start": 6008, "end": 6018}, {"role": "Theme", "text": "induction", "start": 6026, "end": 6035}]}, {"trigger": {"text": "regulation", "start": 6179, "end": 6189}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 6193, "end": 6198}]}, {"trigger": {"text": "regulated", "start": 8081, "end": 8090}, "arguments": [{"role": "Theme", "text": "expression", "start": 8036, "end": 8046}, {"role": "Cause", "text": "IL-12", "start": 8120, "end": 8125}]}, {"trigger": {"text": "regulate", "start": 8294, "end": 8302}, "arguments": [{"role": "Theme", "text": "production", "start": 8307, "end": 8317}]}, {"trigger": {"text": "regulation", "start": 8515, "end": 8525}, "arguments": [{"role": "Theme", "text": "production", "start": 8535, "end": 8545}]}]}}, "schema": []}
{"input": "Mice, Cytokines, Antibodies, and Other Reagents\nBALB/c DO11.10 mice transgenic for OVA-specific TCR WT or crossed back with Rag1-, IL-4-,IFN-gamma-, STAT4-, and STAT6-deficient mice were used as a source of antigen-specific Tcells (Murphy etal., 1990; Ouyang etal., 1998; Shoemaker etal., 2006) and were bred and maintained under SPF conditions at the NIMR, London, Home Office, UK, Animals (Scientific Procedures) Act 1986 or at the Washington University School of Medicine. Female mice were used at 8-12 weeks old, and animal protocols were approved according to the Animals (Scientific Procedures) Act 1986, Home Office, UK. Reagents, including antibodies for Tcell and DC preparation, purification and culture, media, cytokines, and cytokine mAbs have been described (Hosken etal., 1995; Shoemaker etal., 2006; Veldhoen etal., 2009; Veldhoen etal., 2006). LPS (S. minnesota) was from Alexis, chicken ovalbumin protein (OVA protein) was from from Sigma-Aldrich, and ovalbumin peptide323-339 (OVA) (endotoxin-free) was from Biosynthesis. U0126 was from BioMol International. PD184352 (MEK inhibitors), SB203580 (p38 inhibitor), and CT99021 (GSK3beta inhibitor) were kind gifts from P. Cohen and N.Shpiro, University of Dundee, UK. \n", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "deficient", "start": 167, "end": 176}, "arguments": [{"role": "Theme", "text": "Rag1", "start": 124, "end": 128}]}, {"trigger": {"text": "deficient", "start": 167, "end": 176}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 131, "end": 135}]}, {"trigger": {"text": "deficient", "start": 167, "end": 176}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 137, "end": 146}]}, {"trigger": {"text": "deficient", "start": 167, "end": 176}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 149, "end": 154}]}, {"trigger": {"text": "deficient", "start": 167, "end": 176}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 161, "end": 166}]}, {"trigger": {"text": "inhibitors", "start": 1091, "end": 1101}, "arguments": [{"role": "Theme", "text": "MEK", "start": 1087, "end": 1090}]}, {"trigger": {"text": "inhibitor", "start": 1118, "end": 1127}, "arguments": [{"role": "Theme", "text": "p38", "start": 1114, "end": 1117}]}, {"trigger": {"text": "inhibitor", "start": 1152, "end": 1161}, "arguments": [{"role": "Theme", "text": "GSK3beta", "start": 1143, "end": 1151}]}]}}, "schema": []}
{"input": "Isolation of CD4+ T Cells and of Splenic DC and Cell Culture for T Cell Phenotype Differentiation\nT cells were sorted for CD4+CD62Lhi, CD4+CD62LhiCD25-, or CD4+CD44loCD25- to >98% on a Moflo cytometer (Cytomation) as before (Shoemaker etal., 2006; Veldhoen etal., 2009). In most cases, experiments were reproduced with each type of purified CD4+ Tcell population with similar results obtained. Splenic DCs were prepared as described (Hosken etal., 1995), and sort purified CD11c+ cells were added to the Tcell culture. Purified DO11.10 CD4+ Tcells (1 x 105 cells/ml) were cultured as before (Hosken etal., 1995), in a total volume of 1 ml cRPMI medium in a 48-well plate, with splenic DCs (2 x 104 cells/ml), and varying amounts of OVA and of IL-12. APC-independent differentiation of naive CD4+ Tcells into Th1 and Th2 cells used stimulation with anti-CD3 and anti-CD28 and appropriate cytokine conditions, and control Th1 and Th2 cells were cultured as described before (Hosken etal., 1995; Shoemaker etal., 2006). Culture conditions for Th17 cells were as described before (Veldhoen etal., 2006). Importantly, Th1 and Th2 cells could be differentiated in cRPMI or IMDM (Hosken etal., 1995; Shoemaker etal., 2006; Veldhoen etal., 2006), but Th17 cells were only differentiated optimally in IMDM (Veldhoen etal., 2009). When indicated, U0126 or PD184352 (MEK inhibitors), SB203580 (p38 inhibitor), CT99021 (GSK3beta inhibitor), or a similar amount of DMSO were present in the culture. More details of specific culture conditions are provided in Figures S6 and S7. \n", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitors", "start": 1360, "end": 1370}, "arguments": [{"role": "Theme", "text": "MEK", "start": 1356, "end": 1359}]}, {"trigger": {"text": "inhibitor", "start": 1387, "end": 1396}, "arguments": [{"role": "Theme", "text": "p38", "start": 1383, "end": 1386}]}, {"trigger": {"text": "inhibitor", "start": 1417, "end": 1426}, "arguments": [{"role": "Theme", "text": "GSK3beta", "start": 1408, "end": 1416}]}]}}, "schema": []}
{"input": "Cytokine Detection by ICS and ELISA\nAt day 5 or 7, cells were restimulated with immobilized anti-CD3 (2 mug/ml) and anti-CD28 (2 mug/ml) (4 hr with BrefeldinA [10 mug/ml] in the last 2 hr) or with PdBU and Ionomycin (5 hr with BrefeldinA [1 mug/ml]). After ICS FACS, data were collected on a FACSCalibur (Becton Dickinson) and analyzed with FlowJo (Tree Star). For ELISA, cells were similarly restimulated for 48 hr and supernatant was collected and analyzed for IL-4, IL-10, and IFN-gamma as described before (Shoemaker etal., 2006). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "In Vivo Studies\nBALB/c mice were injected intravenously (i.v.) with a red blood cell-depleted single-cell spleen suspension (2.5 x 107 cells) (Castro etal., 2000) from DO11.10 WT or STAT-deficient mice. After 48 hr, they were injected subcutaneously with PBS or with OVA protein (5 mg) plus LPS (5 mug). The inguinal lymph nodes were removed 48 hr later. A single-cell suspension (1 x 106 cells) was restimulated for 24 or 48 hr with 1 muM or 3 muM of OVA and with BrefeldinA for the last 6 hr. Half of the supernatant was removed before the addition of BrefeldinA for use in an ELISA assay. The cells were fixed and stained as before. Those positive for KJ1-26-Bio and for CD4-PerCP were gated, and IFN-gamma and IL-10 staining was examined for this population and analyzed as before. \n", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "deficient", "start": 187, "end": 196}, "arguments": [{"role": "Theme", "text": "STAT", "start": 182, "end": 186}]}]}}, "schema": []}
{"input": "Real-Time Quantitative RT-PCR\nCells were harvested and restimulated in the presence of immobilized anti-CD3 (2 mug/ml) plus anti-CD28 (2 mug/ml) for 3 hr or immediately lysed. RNA was extracted and reverse-transcribed and cDNA was analyzed for the expression of cytokines and transcription factors by real-time PCR assay as before (Shoemaker etal., 2006). Target gene mRNA expression was quantified either with SYBR Green (Applied Biosystems) or with Master Mix (Applied Biosystems) and normalized to ubiquitin or HPRT mRNA levels, respectively. \n", "output": {"json_structures": {"transcription": [{"trigger": {"text": "mRNA levels", "start": 519, "end": 530}, "arguments": [{"role": "Theme", "text": "ubiquitin", "start": 501, "end": 510}]}, {"trigger": {"text": "mRNA levels", "start": 519, "end": 530}, "arguments": [{"role": "Theme", "text": "HPRT", "start": 514, "end": 518}]}]}}, "schema": []}
{"input": "Immunoblotting\nDifferentiated CD4+ Tcells were rested for 5 hr in 1% FCS-containing medium and restimulated as described for specific experiments. Cell lysates were prepared, equal amounts of protein were separated by SDS-PAGE, and phosphorylated or total ERK and actin were detected as described before (Beinke etal., 2004). \n", "output": {"json_structures": {}}, "schema": []}
{"input": "Reactive oxygen intermediate-dependent NF-kappaB activation by interleukin-1beta requires 5-lipoxygenase or NADPH oxidase activity. \nWe previously reported that the role of reactive oxygen intermediates (ROIs) in NF-kappaB activation by proinflammatory cytokines was cell specific. However, the sources for ROIs in various cell types are yet to be determined and might include 5-lipoxygenase (5-LOX) and NADPH oxidase. 5-LOX and 5-LOX activating protein (FLAP) are coexpressed in lymphoid cells but not in monocytic or epithelial cells. Stimulation of lymphoid cells with interleukin-1beta (IL-1beta) led to ROI production and NF-kappaB activation, which could both be blocked by antioxidants or FLAP inhibitors, confirming that 5-LOX was the source of ROIs and was required for NF-kappaB activation in these cells. IL-1beta stimulation of epithelial cells did not generate any ROIs and NF-kappaB induction was not influenced by 5-LOX inhibitors. However, reintroduction of a functional 5-LOX system in these cells allowed ROI production and 5-LOX-dependent NF-kappaB activation. In monocytic cells, IL-1beta treatment led to a production of ROIs which is independent of the 5-LOX enzyme but requires the NADPH oxidase activity. This pathway involves the Rac1 and Cdc42 GTPases, two enzymes which are not required for NF-kappaB activation by IL-1beta in epithelial cells. In conclusion, three different cell-specific pathways lead to NF-kappaB activation by IL-1beta: a pathway dependent on ROI production by 5-LOX in lymphoid cells, an ROI- and 5-LOX-independent pathway in epithelial cells, and a pathway requiring ROI production by NADPH oxidase in monocytic cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "coexpressed", "start": 465, "end": 476}, "arguments": [{"role": "Theme", "text": "5-LOX", "start": 419, "end": 424}]}, {"trigger": {"text": "coexpressed", "start": 465, "end": 476}, "arguments": [{"role": "Theme", "text": "FLAP", "start": 455, "end": 459}]}]}}, "schema": []}
{"input": "Activation-dependent transcriptional regulation of the human Fas promoter requires NF-kappaB p50-p65 recruitment. \nFas (CD95) and Fas ligand (CD95L) are an interacting receptor-ligand pair required for immune homeostasis. Lymphocyte activation results in the upregulation of Fas expression and the acquisition of sensitivity to FasL-mediated apoptosis. Although Fas upregulation is central to the preservation of immunologic tolerance, little is known about the molecular machinery underlying this process. To investigate the events involved in activation-induced Fas upregulation, we have examined mRNA accumulation, fas promoter activity, and protein expression in the Jurkat T-cell line treated with phorbol myristate acetate and ionomycin (P/I), pharmacological mimics of T-cell receptor activation. Although resting Jurkat cells express Fas, Fas mRNA was induced approximately 10-fold in 2 h upon P/I stimulation. Using sequential deletion mutants of the human fas promoter in transient transfection assays, we identified a 47-bp sequence (positions -306 to -260 relative to the ATG) required for activation-driven fas upregulation. Sequence analysis revealed the presence of a previously unrecognized composite binding site for both the Sp1 and NF-kappaB transcription factors at positions -295 to -286. Electrophoretic mobility shift assay (EMSA) and supershift analyses of this region documented constitutive binding of Sp1 in unactivated nuclear extracts and inducible binding of p50-p65 NF-kappaB heterodimers after P/I activation. Sp1 and NF-kappaB transcription factor binding was shown to be mutually exclusive by EMSA displacement studies with purified recombinant Sp1 and recombinant p50. The functional contribution of the kappaB-Sp1 composite site in P/I-inducible fas promoter activation was verified by using kappaB-Sp1 concatamers (-295 to -286) in a thymidine kinase promoter-driven reporter construct and native promoter constructs in Jurkat cells overexpressing IkappaB-alpha. Site-directed mutagenesis of the critical guanine nucleotides in the kappaB-Sp1 element documented the essential role of this site in activation-dependent fas promoter induction. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacting receptor-ligand pair", "start": 156, "end": 188}, "arguments": [{"role": "Theme", "text": "CD95", "start": 120, "end": 124}, {"role": "Theme2", "text": "CD95L", "start": 142, "end": 147}]}, {"trigger": {"text": "binding", "start": 1417, "end": 1424}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1428, "end": 1431}]}, {"trigger": {"text": "binding", "start": 1478, "end": 1485}, "arguments": [{"role": "Theme", "text": "p50", "start": 1489, "end": 1492}]}, {"trigger": {"text": "binding", "start": 1478, "end": 1485}, "arguments": [{"role": "Theme", "text": "p65", "start": 1493, "end": 1496}]}, {"trigger": {"text": "binding", "start": 1581, "end": 1588}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1542, "end": 1545}]}], "gene expression": [{"trigger": {"text": "expression", "start": 279, "end": 289}, "arguments": [{"role": "Theme", "text": "Fas", "start": 275, "end": 278}]}, {"trigger": {"text": "expression", "start": 653, "end": 663}, "arguments": [{"role": "Theme", "text": "Fas", "start": 564, "end": 567}]}, {"trigger": {"text": "express", "start": 834, "end": 841}, "arguments": [{"role": "Theme", "text": "Fas", "start": 842, "end": 845}]}], "negative regulation": [{"trigger": {"text": "mutually exclusive", "start": 1605, "end": 1623}, "arguments": [{"role": "Theme", "text": "binding", "start": 1581, "end": 1588}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 11, "end": 20}, "arguments": [{"role": "Theme", "text": "regulation", "start": 37, "end": 47}]}, {"trigger": {"text": "requires", "start": 74, "end": 82}, "arguments": [{"role": "Theme", "text": "regulation", "start": 37, "end": 47}, {"role": "Cause", "text": "recruitment", "start": 101, "end": 112}]}, {"trigger": {"text": "recruitment", "start": 101, "end": 112}, "arguments": [{"role": "Theme", "text": "p50", "start": 93, "end": 96}]}, {"trigger": {"text": "recruitment", "start": 101, "end": 112}, "arguments": [{"role": "Theme", "text": "p65", "start": 97, "end": 100}]}, {"trigger": {"text": "upregulation", "start": 259, "end": 271}, "arguments": [{"role": "Theme", "text": "expression", "start": 279, "end": 289}]}, {"trigger": {"text": "upregulation", "start": 366, "end": 378}, "arguments": [{"role": "Theme", "text": "Fas", "start": 362, "end": 365}]}, {"trigger": {"text": "induced", "start": 556, "end": 563}, "arguments": [{"role": "Theme", "text": "upregulation", "start": 568, "end": 580}]}, {"trigger": {"text": "upregulation", "start": 568, "end": 580}, "arguments": [{"role": "Theme", "text": "Fas", "start": 564, "end": 567}]}, {"trigger": {"text": "induced", "start": 860, "end": 867}, "arguments": [{"role": "Theme", "text": "Fas", "start": 847, "end": 850}]}, {"trigger": {"text": "required", "start": 1089, "end": 1097}, "arguments": [{"role": "Theme", "text": "upregulation", "start": 1124, "end": 1136}]}, {"trigger": {"text": "upregulation", "start": 1124, "end": 1136}, "arguments": [{"role": "Theme", "text": "fas", "start": 1120, "end": 1123}]}, {"trigger": {"text": "inducible", "start": 1468, "end": 1477}, "arguments": [{"role": "Theme", "text": "binding", "start": 1478, "end": 1485}]}, {"trigger": {"text": "activation", "start": 1795, "end": 1805}, "arguments": [{"role": "Theme", "text": "fas", "start": 1782, "end": 1785}, {"role": "Site", "text": "promoter", "start": 1786, "end": 1794}]}, {"trigger": {"text": "essential role", "start": 2103, "end": 2117}, "arguments": [{"role": "Theme", "text": "induction", "start": 2168, "end": 2177}]}, {"trigger": {"text": "induction", "start": 2168, "end": 2177}, "arguments": [{"role": "Theme", "text": "fas", "start": 2155, "end": 2158}, {"role": "Site", "text": "promoter", "start": 2159, "end": 2167}]}], "regulation": [{"trigger": {"text": "regulation", "start": 37, "end": 47}, "arguments": [{"role": "Theme", "text": "Fas", "start": 61, "end": 64}, {"role": "Site", "text": "promoter", "start": 65, "end": 73}]}]}}, "schema": []}
{"input": "RFLAT-1: a new zinc finger transcription factor that activates RANTES gene expression in T lymphocytes. \nRANTES (Regulated upon Activation, Normal T cell Expressed and Secreted) is a chemoattractant cytokine (chemokine) important in the generation of inflammatory infiltrate and human immunodeficiency virus entry into immune cells. RANTES is expressed late (3-5 days) after activation in T lymphocytes. Using expression cloning, we identified the first \"late\" T lymphocyte associated transcription factor and named it \"RANTES Factor of Late Activated T Lymphocytes-1\" (RFLAT-1). RFLAT-1 is a novel, phosphorylated, zinc finger transcription factor that is expressed in T cells 3 days after activation, coincident with RANTES expression. While Rel proteins play the dominant role in RANTES gene expression in fibroblasts, RFLAT-1 is a strong transactivator for RANTES in T cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 75, "end": 85}, "arguments": [{"role": "Theme", "text": "RANTES", "start": 63, "end": 69}]}, {"trigger": {"text": "expressed", "start": 343, "end": 352}, "arguments": [{"role": "Theme", "text": "RANTES", "start": 333, "end": 339}]}, {"trigger": {"text": "expressed", "start": 657, "end": 666}, "arguments": [{"role": "Theme", "text": "RFLAT-1", "start": 580, "end": 587}]}, {"trigger": {"text": "expression", "start": 726, "end": 736}, "arguments": [{"role": "Theme", "text": "RANTES", "start": 719, "end": 725}]}, {"trigger": {"text": "expression", "start": 795, "end": 805}, "arguments": [{"role": "Theme", "text": "RANTES", "start": 783, "end": 789}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 600, "end": 614}, "arguments": [{"role": "Theme", "text": "RFLAT-1", "start": 580, "end": 587}]}], "positive regulation": [{"trigger": {"text": "activates", "start": 53, "end": 62}, "arguments": [{"role": "Cause", "text": "RFLAT-1", "start": 0, "end": 7}, {"role": "Theme", "text": "expression", "start": 75, "end": 85}]}, {"trigger": {"text": "dominant role", "start": 766, "end": 779}, "arguments": [{"role": "Theme", "text": "expression", "start": 795, "end": 805}]}, {"trigger": {"text": "transactivator", "start": 842, "end": 856}, "arguments": [{"role": "Cause", "text": "RFLAT-1", "start": 822, "end": 829}, {"role": "Theme", "text": "RANTES", "start": 861, "end": 867}]}]}}, "schema": []}
{"input": "Interleukin-10 inhibits expression of both interferon alpha- and interferon gamma- induced genes by suppressing tyrosine phosphorylation of STAT1. \nInterleukin-10 (IL-10) helps maintain polarized T-helper cells in a T-helper lymphocyte 2 (Th2) phenotype. Part of this process involves the prevention of the development of Th1 cells, which are a primary source of interferon gamma (IFNgamma), a potent activator of monocytes and an inhibitor of Th2 proliferation. Because monocytes and macrophages are important mediators of Th1-type responses, such as delayed-type hypersensitivity, we sought to determine if IL-10 could directly mediate inhibition of IFNgamma- and IFNalpha-induced gene expression in these cells. Highly purified monocytes were incubated with IL-10 for 60 to 90 minutes before the addition of IFNgamma or IFNalpha. IL-10 preincubation resulted in the inhibition of gene expression for several IFN-induced genes, such as IP-10, ISG54, and intercellular adhesion molecule-1. The reduction in gene expression resulted from the ability of IL-10 to suppress IFN-induced assembly of signal transducer and activator of transcription (STAT) factors to specific promoter motifs on IFNalpha- and IFNgamma-inducible genes. This was accomplished by preventing the IFN-induced tyrosine phosphorylation of STAT1, a component of both IFNalpha- and IFNgamma-induced DNA binding complexes. Therefore, IL-10 can directly inhibit STAT-dependent early response gene expression induced by both IFNalpha and IFNgamma in monocytes by suppressing the tyrosine phosphorylation of STAT1. This may occur through the ability of IL-10 to induce expression of the gene, suppressor of cytokine signaling 3 (SOCS3). ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "primary source", "start": 345, "end": 359}, "arguments": [{"role": "Theme", "text": "IFNgamma", "start": 381, "end": 389}]}, {"trigger": {"text": "expression", "start": 888, "end": 898}, "arguments": [{"role": "Theme", "text": "IP-10", "start": 938, "end": 943}]}, {"trigger": {"text": "expression", "start": 888, "end": 898}, "arguments": [{"role": "Theme", "text": "ISG54", "start": 945, "end": 950}]}, {"trigger": {"text": "expression", "start": 888, "end": 898}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 956, "end": 989}]}, {"trigger": {"text": "expression", "start": 1634, "end": 1644}, "arguments": [{"role": "Theme", "text": "SOCS3", "start": 1694, "end": 1699}]}], "negative regulation": [{"trigger": {"text": "suppressing", "start": 100, "end": 111}, "arguments": [{"role": "Cause", "text": "Interleukin-10", "start": 0, "end": 14}, {"role": "Theme", "text": "phosphorylation", "start": 121, "end": 136}]}, {"trigger": {"text": "inhibition", "start": 869, "end": 879}, "arguments": [{"role": "Theme", "text": "expression", "start": 888, "end": 898}]}, {"trigger": {"text": "preventing", "start": 1255, "end": 1265}, "arguments": [{"role": "Theme", "text": "induced", "start": 1274, "end": 1281}]}, {"trigger": {"text": "suppressing", "start": 1529, "end": 1540}, "arguments": [{"role": "Cause", "text": "IL-10", "start": 1402, "end": 1407}, {"role": "Theme", "text": "phosphorylation", "start": 1554, "end": 1569}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 121, "end": 136}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 112, "end": 120}, {"role": "Theme", "text": "STAT1", "start": 140, "end": 145}]}, {"trigger": {"text": "phosphorylation", "start": 1291, "end": 1306}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1282, "end": 1290}, {"role": "Theme", "text": "STAT1", "start": 1310, "end": 1315}]}, {"trigger": {"text": "phosphorylation", "start": 1554, "end": 1569}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1545, "end": 1553}, {"role": "Theme", "text": "STAT1", "start": 1573, "end": 1578}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 915, "end": 922}, "arguments": [{"role": "Theme", "text": "IP-10", "start": 938, "end": 943}]}, {"trigger": {"text": "induced", "start": 915, "end": 922}, "arguments": [{"role": "Theme", "text": "ISG54", "start": 945, "end": 950}]}, {"trigger": {"text": "induced", "start": 915, "end": 922}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 956, "end": 989}]}, {"trigger": {"text": "resulted", "start": 1024, "end": 1032}, "arguments": [{"role": "Theme", "text": "inhibition", "start": 869, "end": 879}]}, {"trigger": {"text": "accomplished", "start": 1239, "end": 1251}, "arguments": [{"role": "Theme", "text": "resulted", "start": 1024, "end": 1032}, {"role": "Cause", "text": "preventing", "start": 1255, "end": 1265}]}, {"trigger": {"text": "induced", "start": 1274, "end": 1281}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1291, "end": 1306}]}, {"trigger": {"text": "induced", "start": 1360, "end": 1367}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1310, "end": 1315}, {"role": "Cause", "text": "IFNgamma", "start": 1351, "end": 1359}]}, {"trigger": {"text": "induced", "start": 1360, "end": 1367}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1310, "end": 1315}]}, {"trigger": {"text": "induce", "start": 1627, "end": 1633}, "arguments": [{"role": "Cause", "text": "IL-10", "start": 1618, "end": 1623}, {"role": "Theme", "text": "expression", "start": 1634, "end": 1644}]}]}}, "schema": []}
{"input": "The Megakaryocyte/Platelet-specific enhancer of the alpha2beta1 integrin gene: two tandem AP1 sites and the mitogen-activated protein kinase signaling cascade. \nThe alpha2beta1 integrin, a collagen receptor on platelets and megakaryocytes, is required for normal platelet function. Transcriptional regulation of the alpha2 integrin gene in cells undergoing megakaryocytic differentiation requires a core promoter between bp -30 and -92, a silencer between bp -92 and -351, and megakaryocytic enhancers in the distal 5' flank. We have now identified a 229-bp region of the distal 5' flank of the alpha2 integrin gene required for high-level enhancer activity in cells with megakaryocytic features. Two tandem AP1 binding sites with dyad symmetry are required for enhancer activity and for DNA-protein complex formation with members of the c-fos/c-jun family. The requirement for AP1 activation suggested a role for the mitogen-activated protein kinase (MAPK) signaling pathway in regulating alpha2 integrin gene expression. Inhibition of the MAP kinase cascade with PD98059, a specific inhibitor of MAPK kinase 1, prevented the expression of the alpha2 integrin subunit in cells induced to become megakaryocytic. We provide a model of megakaryocytic differentiation in which expression of the alpha2 integrin gene requires signaling via the MAP kinase pathway to activate two tandem AP1 binding sites in the alpha2 integrin enhancer. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complex formation", "start": 800, "end": 817}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 838, "end": 843}]}, {"trigger": {"text": "complex formation", "start": 800, "end": 817}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 844, "end": 849}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1011, "end": 1021}, "arguments": [{"role": "Theme", "text": "alpha2 integrin", "start": 990, "end": 1005}]}, {"trigger": {"text": "expression", "start": 1127, "end": 1137}, "arguments": [{"role": "Theme", "text": "alpha2 integrin", "start": 1145, "end": 1160}]}, {"trigger": {"text": "expression", "start": 1274, "end": 1284}, "arguments": [{"role": "Theme", "text": "alpha2 integrin", "start": 1292, "end": 1307}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 1085, "end": 1094}, "arguments": [{"role": "Theme", "text": "MAPK kinase 1", "start": 1098, "end": 1111}]}, {"trigger": {"text": "prevented", "start": 1113, "end": 1122}, "arguments": [{"role": "Theme", "text": "expression", "start": 1127, "end": 1137}]}], "positive regulation": [{"trigger": {"text": "requires", "start": 388, "end": 396}, "arguments": [{"role": "Theme", "text": "Transcriptional regulation", "start": 282, "end": 308}]}, {"trigger": {"text": "required", "start": 749, "end": 757}, "arguments": [{"role": "Theme", "text": "complex formation", "start": 800, "end": 817}]}, {"trigger": {"text": "requirement", "start": 862, "end": 873}, "arguments": [{"role": "Theme", "text": "regulating", "start": 979, "end": 989}]}, {"trigger": {"text": "role", "start": 905, "end": 909}, "arguments": [{"role": "Theme", "text": "regulating", "start": 979, "end": 989}]}, {"trigger": {"text": "requires", "start": 1313, "end": 1321}, "arguments": [{"role": "Theme", "text": "expression", "start": 1274, "end": 1284}]}], "regulation": [{"trigger": {"text": "Transcriptional regulation", "start": 282, "end": 308}, "arguments": [{"role": "Theme", "text": "alpha2 integrin", "start": 316, "end": 331}]}, {"trigger": {"text": "regulating", "start": 979, "end": 989}, "arguments": [{"role": "Theme", "text": "expression", "start": 1011, "end": 1021}]}]}}, "schema": []}
{"input": "Differential expression and phosphorylation of CTCF, a c-myc transcriptional regulator, during differentiation of human myeloid cells. \nCTCF is a transcriptional repressor of the c-myc gene. Although CTCF has been characterized in some detail, there is very little information about the regulation of CTCF activity. Therefore we investigated CTCF expression and phosphorylation during induced differentiation of human myeloid leukemia cells. We found that: (i) both CTCF mRNA and protein are down-regulated during terminal differentiation in most cell lines tested; (ii) CTCF down-regulation is retarded and less pronounced than that of c-myc; (iii) CTCF protein is differentially phosphorylated and the phosphorylation profiles depend on the differentiation pathway. We concluded that CTCF expression and activity is controlled at transcriptional and post-transcriptional levels. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 13, "end": 23}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 47, "end": 51}]}, {"trigger": {"text": "expression", "start": 347, "end": 357}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 342, "end": 346}]}, {"trigger": {"text": "expression", "start": 791, "end": 801}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 786, "end": 790}]}], "negative regulation": [{"trigger": {"text": "transcriptional repressor", "start": 146, "end": 171}, "arguments": [{"role": "Cause", "text": "CTCF", "start": 136, "end": 140}, {"role": "Theme", "text": "c-myc", "start": 179, "end": 184}]}, {"trigger": {"text": "down-regulated", "start": 492, "end": 506}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 466, "end": 470}]}, {"trigger": {"text": "down-regulation", "start": 576, "end": 591}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 571, "end": 575}]}, {"trigger": {"text": "down-regulation", "start": 576, "end": 591}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 637, "end": 642}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 28, "end": 43}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 47, "end": 51}]}, {"trigger": {"text": "phosphorylation", "start": 362, "end": 377}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 342, "end": 346}]}, {"trigger": {"text": "phosphorylated", "start": 681, "end": 695}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 650, "end": 654}]}], "positive regulation": [{"trigger": {"text": "depend", "start": 729, "end": 735}, "arguments": [{"role": "Theme", "text": "phosphorylated", "start": 681, "end": 695}]}], "regulation": [{"trigger": {"text": "transcriptional regulator", "start": 61, "end": 86}, "arguments": [{"role": "Cause", "text": "CTCF", "start": 47, "end": 51}, {"role": "Theme", "text": "c-myc", "start": 55, "end": 60}]}, {"trigger": {"text": "regulation", "start": 287, "end": 297}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 301, "end": 305}]}, {"trigger": {"text": "controlled at transcriptional and post-transcriptional levels", "start": 818, "end": 879}, "arguments": [{"role": "Theme", "text": "CTCF", "start": 786, "end": 790}]}, {"trigger": {"text": "controlled at transcriptional and post-transcriptional levels", "start": 818, "end": 879}, "arguments": [{"role": "Theme", "text": "expression", "start": 791, "end": 801}]}]}}, "schema": []}
{"input": "T-cell expression of the human GATA-3 gene is regulated by a non-lineage-specific silencer. \nThe GATA-3 transcription factor is required for development of the T-cell lineage and Th2 cytokine gene expression in CD4 T-cells. We have mapped the DNase-I-hypersensitive (HS) regions of the human GATA-3 gene in T-cells and non-T-cells and studied their transcriptional activities. HS I-III, located 5' from the transcriptional initiation site, were found in hematopoietic and non-hematopoietic cells, whereas HS IV-VII, located 3' from the transcriptional start site, were exclusively observed in T-cells. Among these hypersensitive sites, two transcriptional control elements were found, one in the first intron of the GATA-3 gene and the other between 8.3 and 5.9 kilobases 5' from the GATA-3 transcriptional initiation site. The first intron acted as a strong transcriptional activator in a position-dependent manner and with no cell-type specificity. The upstream regulatory element could confer T-cell specificity to the GATA-3 promoter activity, and analysis of this region revealed a 707-base pair silencer that drastically inhibited GATA-3 promoter activity in non-T-cells. Two CAGGTG E-boxes, located at the 5'- and 3'-ends of the silencer, were necessary for this silencer activity. The 3'-CAGGTG E-box could bind USF proteins, the ubiquitous repressor ZEB, or the basic helix-loop-helix proteins E2A and HEB, and we showed that a competition between ZEB and E2A/HEB proteins is involved in the silencer activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 1315, "end": 1319}, "arguments": [{"role": "Theme", "text": "ZEB", "start": 1359, "end": 1362}]}, {"trigger": {"text": "bind", "start": 1315, "end": 1319}, "arguments": [{"role": "Theme", "text": "E2A", "start": 1403, "end": 1406}]}, {"trigger": {"text": "bind", "start": 1315, "end": 1319}, "arguments": [{"role": "Theme", "text": "HEB", "start": 1411, "end": 1414}]}], "gene expression": [{"trigger": {"text": "expression", "start": 7, "end": 17}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 31, "end": 37}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1127, "end": 1136}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 1137, "end": 1143}, {"role": "Site", "text": "promoter", "start": 1144, "end": 1152}]}, {"trigger": {"text": "competition", "start": 1437, "end": 1448}, "arguments": [{"role": "Theme", "text": "bind", "start": 1315, "end": 1319}, {"role": "Cause", "text": "ZEB", "start": 1457, "end": 1460}]}], "positive regulation": [{"trigger": {"text": "confer", "start": 989, "end": 995}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 1022, "end": 1028}, {"role": "Site", "text": "promoter", "start": 1029, "end": 1037}]}, {"trigger": {"text": "necessary", "start": 1251, "end": 1260}, "arguments": [{"role": "Theme", "text": "inhibited", "start": 1127, "end": 1136}]}], "regulation": [{"trigger": {"text": "regulated", "start": 46, "end": 55}, "arguments": [{"role": "Theme", "text": "expression", "start": 7, "end": 17}]}, {"trigger": {"text": "involved", "start": 1485, "end": 1493}, "arguments": [{"role": "Theme", "text": "inhibited", "start": 1127, "end": 1136}, {"role": "Cause", "text": "competition", "start": 1437, "end": 1448}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 349, "end": 364}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 292, "end": 298}]}]}}, "schema": []}
{"input": "AML and Ets proteins regulate the I alpha1 germ-line promoter. \nThe immunoglobulin heavy chain (IgH) class switch recombination of B lymphocytes preferentially targets unrearranged IgH genes that have already been rendered transcriptionally active. Transcription of the germ-line IgH genes is controlled by intervening (I) regions upstream of their switch regions. The I alpha1 promoter activates transcription of the human germ-line C alpha1 gene for IgA1 and mediates the transforming growth factor (TGF)-beta1 responsiveness of this locus. Here we show that the I alpha1 promoter contains several binding sites for the AML/PEBP2/CBF family of transcription factors and that AML and Ets proteins are major regulators of the basal and TGF-beta-inducible promoter activity. Our data constitute a starting point for studies to elucidate the molecular mechanism by which TGF-beta regulates IgA production. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Peripheral blood mononuclear cells isolated from patients with diabetic nephropathy show increased activation of the oxidative-stress sensitive transcription factor NF-kappaB. \nIncreased oxidative stress and subsequent activation of the transcription factor NF-kappaB has been linked to the development of late diabetic complications. To determine whether oxidative stress dependent NF-kappaB activation is evident in patients with diabetic nephropathy we used an Electrophoretic Mobility Shift Assay based semiquantitative detection system which enabled us to determine NF-kappaB activation in ex vivo isolated peripheral blood mononuclear cells. We examined 33 patients with diabetes mellitus (Type I and Type II). Patients with diabetic nephropathy showed higher NF-kappaB binding activity in Electrophoretic Mobility Shift Assays and stronger immunohistological staining for activated NF-kappaBp65 than patients without renal complications. NF-kappaB binding activity correlated with the degree of albuminuria (r = 0.316) and with thrombomodulin plasma concentrations (r = 0.33), indicative for albuminuria associated endothelial dysfunction. In a 3 day intervention study in which 600 mg of the antioxidant thioctic acid (alpha-lipoic acid) per day were given to nine patients with diabetic nephropathy oxidative stress in plasma samples was decreased by 48% and NF-kappaB binding activity in ex vivo isolated peripheral blood mononuclear cells by 38%. In conclusion, activation of the transcription factor NF-kappaB in ex vivo isolated peripheral blood mononuclear cells of patients with diabetes mellitus correlates with the degree of diabetic nephropathy. NF-kappaB activation is at least in part dependent on oxidative stress since thioctic acid (alpha-lipoic acid) reduced NF-kappaB binding activity. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "stronger", "start": 838, "end": 846}, "arguments": [{"role": "Theme", "text": "activated", "start": 879, "end": 888}]}, {"trigger": {"text": "activated", "start": 879, "end": 888}, "arguments": [{"role": "Theme", "text": "NF-kappaBp65", "start": 889, "end": 901}]}]}}, "schema": []}
{"input": "Activation of human immunodeficiency virus type 1 expression by Gardnerella vaginalis. \nBacterial vaginosis (BV) is associated with an increased rate of sexual transmission of human immunodeficiency virus (HIV) type 1, and Gardnerella vaginalis is frequently isolated from the genital tracts of women with BV. G. vaginalis lysates were found to significantly stimulate HIV expression in monocytoid cells. Stimulation was significantly higher when lysates were heated at 100 degrees C for 5 min but was reduced by treatment with lysozyme or protease. G. vaginalis lysates also activated HIV expression in certain T cell lines. G. vaginalis lysates activated HIV long-terminal repeat transcription in HIV-infected cells and increased NF-kappaB binding activity, indicating an effect by G. vaginalis on HIV transcription. The activation of HIV production by G. vaginalis suggests that genital tract infection with G. vaginalis increases the risk of HIV transmission by increasing HIV expression in the genital tract. This may explain, at least in part, the increased rate of HIV transmission in women with BV. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Interferon-alpha activates multiple STAT proteins and upregulates proliferation-associated IL-2Ralpha, c-myc, and pim-1 genes in human T cells. \nInterferon-alpha (IFN-alpha) is a pleiotropic cytokine that has antiviral, antiproliferative, and immunoregulatory functions. There is increasing evidence that IFN-alpha has an important role in T-cell biology. We have analyzed the expression of IL-2Ralpha, c-myc, and pim-1 genes in anti-CD3-activated human T lymphocytes. The induction of these genes is associated with interleukin-2 (IL-2)-induced T-cell proliferation. Treatment of T lymphocytes with IFN-alpha, IL-2, IL-12, and IL-15 upregulated IL-2Ralpha, c-myc, and pim-1 gene expression. IFN-alpha also sensitized T cells to IL-2-induced proliferation, further suggesting that IFN-alpha may be involved in the regulation of T-cell mitogenesis. When we analyzed the nature of STAT proteins capable of binding to IL-2Ralpha, pim-1, and IRF-1 GAS elements after cytokine stimulation, we observed IFN-alpha-induced binding of STAT1, STAT3, and STAT4, but not STAT5 to all of these elements. Yet, IFN-alpha was able to activate binding of STAT5 to the high-affinity IFP53 GAS site. IFN-alpha enhanced tyrosine phosphorylation of STAT1, STAT3, STAT4, STAT5a, and STAT5b. IL-12 induced STAT4 and IL-2 and IL-15 induced STAT5 binding to the GAS elements. Taken together, our results suggest that IFN-alpha, IL-2, IL-12, and IL-15 have overlapping activities on human T cells. These findings thus emphasize the importance of IFN-alpha as a T-cell regulatory cytokine. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 904, "end": 911}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 915, "end": 925}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}]}, {"trigger": {"text": "binding", "start": 904, "end": 911}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 927, "end": 932}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}]}, {"trigger": {"text": "binding", "start": 904, "end": 911}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 938, "end": 943}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 915, "end": 925}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT1", "start": 1026, "end": 1031}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 927, "end": 932}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT1", "start": 1026, "end": 1031}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 938, "end": 943}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT1", "start": 1026, "end": 1031}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 915, "end": 925}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT3", "start": 1033, "end": 1038}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 927, "end": 932}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT3", "start": 1033, "end": 1038}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 938, "end": 943}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT3", "start": 1033, "end": 1038}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 915, "end": 925}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT4", "start": 1044, "end": 1049}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 927, "end": 932}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT4", "start": 1044, "end": 1049}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 938, "end": 943}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}, {"role": "Theme2", "text": "STAT4", "start": 1044, "end": 1049}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 915, "end": 925}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 927, "end": 932}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}]}, {"trigger": {"text": "binding", "start": 1015, "end": 1022}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 938, "end": 943}, {"role": "Site", "text": "GAS elements", "start": 944, "end": 956}]}, {"trigger": {"text": "binding", "start": 1322, "end": 1329}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 1283, "end": 1288}]}], "gene expression": [{"trigger": {"text": "expression", "start": 377, "end": 387}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 391, "end": 401}]}, {"trigger": {"text": "expression", "start": 377, "end": 387}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 403, "end": 408}]}, {"trigger": {"text": "expression", "start": 377, "end": 387}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 414, "end": 419}]}, {"trigger": {"text": "expression", "start": 680, "end": 690}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 646, "end": 656}]}, {"trigger": {"text": "expression", "start": 680, "end": 690}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 658, "end": 663}]}, {"trigger": {"text": "expression", "start": 680, "end": 690}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 669, "end": 674}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1209, "end": 1224}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1200, "end": 1208}, {"role": "Theme", "text": "STAT1", "start": 1228, "end": 1233}]}, {"trigger": {"text": "phosphorylation", "start": 1209, "end": 1224}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1200, "end": 1208}, {"role": "Theme", "text": "STAT3", "start": 1235, "end": 1240}]}, {"trigger": {"text": "phosphorylation", "start": 1209, "end": 1224}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1200, "end": 1208}, {"role": "Theme", "text": "STAT4", "start": 1242, "end": 1247}]}, {"trigger": {"text": "phosphorylation", "start": 1209, "end": 1224}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1200, "end": 1208}, {"role": "Theme", "text": "STAT5a", "start": 1249, "end": 1255}]}, {"trigger": {"text": "phosphorylation", "start": 1209, "end": 1224}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1200, "end": 1208}, {"role": "Theme", "text": "STAT5b", "start": 1261, "end": 1267}]}], "positive regulation": [{"trigger": {"text": "upregulates", "start": 54, "end": 65}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 103, "end": 108}]}, {"trigger": {"text": "upregulates", "start": 54, "end": 65}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 114, "end": 119}]}, {"trigger": {"text": "upregulates", "start": 54, "end": 65}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 91, "end": 101}]}, {"trigger": {"text": "induction", "start": 473, "end": 482}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 391, "end": 401}]}, {"trigger": {"text": "induction", "start": 473, "end": 482}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 403, "end": 408}]}, {"trigger": {"text": "induction", "start": 473, "end": 482}, "arguments": [{"role": "Theme", "text": "pim-1", "start": 414, "end": 419}]}, {"trigger": {"text": "upregulated", "start": 634, "end": 645}, "arguments": [{"role": "Theme", "text": "expression", "start": 680, "end": 690}]}, {"trigger": {"text": "induced", "start": 1007, "end": 1014}, "arguments": [{"role": "Theme", "text": "binding", "start": 1015, "end": 1022}]}, {"trigger": {"text": "enhanced", "start": 1191, "end": 1199}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1209, "end": 1224}]}, {"trigger": {"text": "induced", "start": 1275, "end": 1282}, "arguments": [{"role": "Theme", "text": "binding", "start": 1322, "end": 1329}]}]}}, "schema": []}
{"input": "Anti-rheumatic compound aurothioglucose inhibits tumor necrosis factor-alpha-induced HIV-1 replication in latently infected OM10.1 and Ach2 cells. \nNF-kappaB is a potent cellular activator of HIV-1 gene expression. Down-regulation of NF-kappaB activation is known to inhibit HIV replication from the latently infected cells. Gold compounds have been effectively used for many decades in the treatment of rheumatoid arthritis. We previously reported that gold compounds, especially aurothioglucose (AuTG) containing monovalent gold ion, inhibited the DNA-binding of NF-kappaB in vitro. In this report we have examined the efficacy of the gold compound AuTG as an inhibitor of HIV replication in latently infected OM10.1 and Ach2 cells. Tumor necrosis factor (TNF)-alpha-induced HIV-1 replication in OM10.1 or Ach2 cells was significantly inhibited by non-cytotoxic doses of AuTG (>10 microM in OM10.1 cells and >25 F.M in Ach2 cells), while 25 microM of the counter-anion thioglucose (TG) or gold compound containing divalent gold ion, HAuCl3, had no effect. The effect of AuTG on NF-kappaB-dependent gene expression was confirmed by a transient CAT assay. Specific staining as well as electron microscopic examinations revealed the accumulation of metal gold in the cells, supporting our previous hypothesis that gold ions could block NF-kappaB-DNA binding by a redox mechanism. These observations indicate that the monovalent gold compound AuTG is a potentially useful drug for the treatment of patients infected with HIV. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Evidence for suppressed activity of the transcription factor NFAT1 at its proximal binding element P0 in the IL-4 promoter associated with enhanced IL-4 gene transcription in T cells of atopic patients. \nAllergen-specific T cells in atopic patients are polarized IL-4-producing Th2 cells, promoting IgE synthesis by B cells. The molecular basis for increased IL-4 gene expression in atopy is not fully understood. IL-4 gene regulation in general involves the nuclear factor of activated T cells (NFAT) family of transcription factors, of which NFAT1 and NFAT2 are most prominent in peripheral T cells. Recently, a unique inhibitory role of NFAT1 in IL-4 gene control was shown in the mouse. In a series of electrophoretic mobility shift assays with protein extracts of highly polarized Th2 clones from atopics and Th1 clones from controls we compared DNA-binding activities at the two NFAT-binding elements P0 and P1 of the crucial proximal human IL-4 promoter. At the most proximal P0 site, NFAT-containing complexes devoid of NFAT2 were readily inducible in the Th1 clones, but hardly or not in the Th2 clones. In contrast, both in Th1 and Th2 clones NFAT-containing complexes were strongly inducible at the P1 site, consisting of NFAT2 and a P0-compatible NFAT activity, without apparent differences between Th1 and Th2 clones. Like in Th2 clones, suppressed NFAT-P0 complex formation was observed also at the polyclonal level in peripheral blood mononuclear cells (PBMC) of three of five severe atopic dermatitis patients with strongly elevated serum IgE levels, but not in control PBMC. These findings suggest that high-level IL-4 production in atopic Th2 cells is associated with selective reduction of suppressive NFAT1 activity at the IL-4 P0 element and that some patients with this multifactorial disease may have a putative systemic disorder at this level. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 83, "end": 90}, "arguments": [{"role": "Theme", "text": "NFAT1", "start": 61, "end": 66}, {"role": "Site2", "text": "proximal binding element P0", "start": 74, "end": 101}, {"role": "Theme2", "text": "IL-4", "start": 109, "end": 113}]}, {"trigger": {"text": "complexes", "start": 1008, "end": 1017}, "arguments": [{"role": "Theme", "text": "NFAT2", "start": 1028, "end": 1033}]}, {"trigger": {"text": "complexes", "start": 1169, "end": 1178}, "arguments": [{"role": "Theme", "text": "NFAT2", "start": 1233, "end": 1238}]}], "gene expression": [{"trigger": {"text": "producing", "start": 268, "end": 277}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 263, "end": 267}]}, {"trigger": {"text": "synthesis", "start": 303, "end": 312}, "arguments": [{"role": "Theme", "text": "IgE", "start": 299, "end": 302}]}, {"trigger": {"text": "expression", "start": 369, "end": 379}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 359, "end": 363}]}, {"trigger": {"text": "levels", "start": 1559, "end": 1565}, "arguments": [{"role": "Theme", "text": "IgE", "start": 1555, "end": 1558}]}, {"trigger": {"text": "production", "start": 1636, "end": 1646}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1631, "end": 1635}]}], "negative regulation": [{"trigger": {"text": "suppressed", "start": 13, "end": 23}, "arguments": [{"role": "Theme", "text": "NFAT1", "start": 61, "end": 66}, {"role": "Cause", "text": "binding", "start": 83, "end": 90}]}, {"trigger": {"text": "inhibitory role", "start": 621, "end": 636}, "arguments": [{"role": "Cause", "text": "NFAT1", "start": 640, "end": 645}, {"role": "Theme", "text": "control", "start": 659, "end": 666}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 139, "end": 147}, "arguments": [{"role": "Theme", "text": "transcription", "start": 158, "end": 171}]}, {"trigger": {"text": "promoting", "start": 289, "end": 298}, "arguments": [{"role": "Cause", "text": "producing", "start": 268, "end": 277}, {"role": "Theme", "text": "synthesis", "start": 303, "end": 312}]}, {"trigger": {"text": "increased", "start": 349, "end": 358}, "arguments": [{"role": "Theme", "text": "expression", "start": 369, "end": 379}]}, {"trigger": {"text": "inducible", "start": 1193, "end": 1202}, "arguments": [{"role": "Theme", "text": "complexes", "start": 1169, "end": 1178}]}, {"trigger": {"text": "elevated", "start": 1540, "end": 1548}, "arguments": [{"role": "Theme", "text": "levels", "start": 1559, "end": 1565}]}, {"trigger": {"text": "high-level", "start": 1620, "end": 1630}, "arguments": [{"role": "Theme", "text": "production", "start": 1636, "end": 1646}]}], "regulation": [{"trigger": {"text": "regulation", "start": 424, "end": 434}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 414, "end": 418}]}, {"trigger": {"text": "involves", "start": 446, "end": 454}, "arguments": [{"role": "Theme", "text": "regulation", "start": 424, "end": 434}, {"role": "Cause", "text": "NFAT1", "start": 544, "end": 549}]}, {"trigger": {"text": "involves", "start": 446, "end": 454}, "arguments": [{"role": "Theme", "text": "regulation", "start": 424, "end": 434}, {"role": "Cause", "text": "NFAT2", "start": 554, "end": 559}]}, {"trigger": {"text": "control", "start": 659, "end": 666}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 649, "end": 653}]}], "transcription": [{"trigger": {"text": "transcription", "start": 158, "end": 171}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 148, "end": 152}]}]}}, "schema": []}
{"input": "Nuclear factor-kappa B activity in T cells from patients with rheumatic diseases: a preliminary report. \nOBJECTIVE: The NF-kappa B/Rel family of transcription factors regulates the expression of many genes involved in the immune or inflammatory response at the transcriptional level. The aim of this study was to determine whether distinctive patterns of NF-kappa B activation are seen in different forms of joint disease. METHODS: The DNA binding activity of these nucleoproteins was examined in purified synovial and peripheral T cells from patients with various chronic rheumatic diseases (12: four with rheumatoid arthritis; five with spondyloarthropathies; and three with osteoarthritis). RESULTS: Electrophoretic mobility shift assays disclosed two specific complexes bound to a NF-kappa B specific 32P-labelled oligonucleotide in nucleoproteins extracted from purified T cells isolated from synovial fluid and peripheral blood of patients with rheumatoid arthritis. The complexes consisted of p50/p50 homodimers and p50/p65 heterodimers. Increased NF-kappa B binding to DNA in synovial T cells was observed relative to peripheral T cells. In non-rheumatoid arthritis, binding of NF-kappa B in synovial T cells was exclusively mediated by p50/p50 homodimers. CONCLUSION: Overall, the results suggest that NF-kappa B may play a central part in the activation of infiltrating T cells in chronic rheumatoid arthritis. The activation of this nuclear factor is qualitatively different in rheumatoid synovial T cells to that in other forms of non-rheumatoid arthritis (for example, osteoarthritis, spondyloarthropathies). ", "output": {"json_structures": {}}, "schema": []}
{"input": "N-acetyl-L-cysteine inhibits primary human T cell responses at the dendritic cell level: association with NF-kappaB inhibition. \nN-acetyl-L-cysteine (NAC) is an antioxidant molecule endowed with immunomodulatory properties. To investigate the effect of NAC on the induction phase of T cell responses, we analyzed its action on human dendritic cells (DC) derived from adherent PBMC cultured with IL-4 and granulocyte-macrophage CSF. We first found that NAC inhibited the constitutive as well as the LPS-induced activity of the transcription factor NF-kappaB. In parallel, NAC was shown to down-regulate the production of cytokines by DC as well as their surface expression of HLA-DR, CD86 (B7-2), and CD40 molecules both at the basal state and upon LPS activation. NAC also inhibited DC responses induced by CD40 engagement. The inhibitory effects of NAC were not due to nonspecific toxicity as neither the viability of DC nor their mannose receptor-mediated endocytosis were modified by NAC. Finally, we found that the addition of NAC to MLR between naive T cells and allogeneic DC resulted in a profound inhibition of alloreactive responses, which could be attributed to a defect of DC as APC-independent T cell responses were not inhibited by NAC. Altogether, our results suggest that NAC might impair the generation of primary immune responses in humans through its inhibitory action on DC. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "engagement", "start": 812, "end": 822}, "arguments": [{"role": "Theme", "text": "CD40", "start": 807, "end": 811}]}], "gene expression": [{"trigger": {"text": "expression", "start": 661, "end": 671}, "arguments": [{"role": "Theme", "text": "CD86", "start": 683, "end": 687}]}, {"trigger": {"text": "expression", "start": 661, "end": 671}, "arguments": [{"role": "Theme", "text": "CD40", "start": 700, "end": 704}]}], "negative regulation": [{"trigger": {"text": "down-regulate", "start": 588, "end": 601}, "arguments": [{"role": "Theme", "text": "expression", "start": 661, "end": 671}]}, {"trigger": {"text": "down-regulate", "start": 588, "end": 601}, "arguments": [{"role": "Theme", "text": "activation", "start": 752, "end": 762}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 752, "end": 762}, "arguments": [{"role": "Theme", "text": "expression", "start": 661, "end": 671}]}]}}, "schema": []}
{"input": "Bacterial lipopolysaccharide activates nuclear factor-kappaB through interleukin-1 signaling mediators in cultured human dermal endothelial cells and mononuclear phagocytes. \nBacterial lipopolysaccharide (LPS)-mediated immune responses, including activation of monocytes, macrophages, and endothelial cells, play an important role in the pathogenesis of Gram-negative bacteria-induced sepsis syndrome. Activation of NF-kappaB is thought to be required for cytokine release from LPS-responsive cells, a critical step for endotoxic effects. Here we investigated the role and involvement of interleukin-1 (IL-1) and tumor necrosis factor (TNF-alpha) signal transducer molecules in LPS signaling in human dermal microvessel endothelial cells (HDMEC) and THP-1 monocytic cells. LPS stimulation of HDMEC and THP-1 cells initiated an IL-1 receptor-like NF-kappaB signaling cascade. In transient cotransfection experiments, dominant negative mutants of the IL-1 signaling pathway, including MyD88, IRAK, IRAK2, and TRAF6 inhibited both IL-1- and LPS-induced NF-kappaB-luciferase activity. LPS-induced NF-kappaB activation was not inhibited by a dominant negative mutant of TRAF2 that is involved in TNF signaling. LPS-induced activation of NF-kappaB-responsive reporter gene was not inhibited by IL-1 receptor antagonist. TLR2 and TLR4 were expressed on the cell surface of HDMEC and THP-1 cells. These findings suggest that a signal transduction molecule in the LPS receptor complex may belong to the IL-1 receptor/toll-like receptor (TLR) super family, and the LPS signaling cascade uses an analogous molecular framework for signaling as IL-1 in mononuclear phagocytes and endothelial cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 1333, "end": 1342}, "arguments": [{"role": "Theme", "text": "TLR2", "start": 1314, "end": 1318}]}, {"trigger": {"text": "expressed", "start": 1333, "end": 1342}, "arguments": [{"role": "Theme", "text": "TLR4", "start": 1323, "end": 1327}]}]}}, "schema": []}
{"input": "Selective activation and functional significance of p38alpha mitogen-activated protein kinase in lipopolysaccharide-stimulated neutrophils. \nActivation of leukocytes by proinflammatory stimuli selectively initiates intracellular signal transduction via sequential phosphorylation of kinases. Lipopolysaccharide (LPS) stimulation of human neutrophils is known to result in activation of p38 mitogen-activated protein kinase (MAPk); however, the upstream activator(s) of p38 MAPk is unknown, and consequences of p38 MAPk activation remain largely undefined. We investigated the MAPk kinase (MKK) that activates p38 MAPk in response to LPS, the p38 MAPk isoforms that are activated as part of this pathway, and the functional responses affected by p38 MAPk activation. Although MKK3, MKK4, and MKK6 all activated p38 MAPk in experimental models, only MKK3 was found to activate recombinant p38 MAPk in LPS-treated neutrophils. Of p38 MAPk isoforms studied, only p38alpha and p38delta were detected in neutrophils. LPS stimulation selectively activated p38alpha. Specific inhibitors of p38alpha MAPk blocked LPS-induced adhesion, nuclear factor-kappa B (NF-kappaB) activation, and synthesis of tumor necrosis factor-alpha (TNF-alpha). Inhibition of p38alpha MAPk resulted in a transient decrease in TNF-alpha mRNA accumulation but persistent loss of TNF-alpha synthesis. These findings support a pathway by which LPS stimulation of neutrophils results in activation of MKK3, which in turn activates p38alpha MAPk, ultimately regulating adhesion, NF-kappaB activation, enhanced gene expression of TNF-alpha, and regulation of TNF-alpha synthesis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "detected", "start": 986, "end": 994}, "arguments": [{"role": "Theme", "text": "p38alpha", "start": 959, "end": 967}]}, {"trigger": {"text": "detected", "start": 986, "end": 994}, "arguments": [{"role": "Theme", "text": "p38delta", "start": 972, "end": 980}]}, {"trigger": {"text": "synthesis", "start": 1177, "end": 1186}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1219, "end": 1228}]}, {"trigger": {"text": "synthesis", "start": 1356, "end": 1365}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1346, "end": 1355}]}, {"trigger": {"text": "expression", "start": 1578, "end": 1588}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1592, "end": 1601}]}, {"trigger": {"text": "synthesis", "start": 1631, "end": 1640}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1621, "end": 1630}]}], "negative regulation": [{"trigger": {"text": "inhibitors", "start": 1068, "end": 1078}, "arguments": [{"role": "Theme", "text": "p38alpha MAPk", "start": 1082, "end": 1095}]}, {"trigger": {"text": "blocked", "start": 1096, "end": 1103}, "arguments": [{"role": "Cause", "text": "inhibitors", "start": 1068, "end": 1078}, {"role": "Theme", "text": "synthesis", "start": 1177, "end": 1186}]}, {"trigger": {"text": "Inhibition", "start": 1231, "end": 1241}, "arguments": [{"role": "Theme", "text": "p38alpha MAPk", "start": 1245, "end": 1258}]}, {"trigger": {"text": "loss", "start": 1338, "end": 1342}, "arguments": [{"role": "Cause", "text": "Inhibition", "start": 1231, "end": 1241}, {"role": "Theme", "text": "synthesis", "start": 1356, "end": 1365}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 1039, "end": 1048}, "arguments": [{"role": "Theme", "text": "p38alpha", "start": 1049, "end": 1057}]}, {"trigger": {"text": "results", "start": 1440, "end": 1447}, "arguments": [{"role": "Theme", "text": "activation", "start": 1451, "end": 1461}]}, {"trigger": {"text": "activation", "start": 1451, "end": 1461}, "arguments": [{"role": "Theme", "text": "MKK3", "start": 1465, "end": 1469}]}, {"trigger": {"text": "activates", "start": 1485, "end": 1494}, "arguments": [{"role": "Cause", "text": "results", "start": 1440, "end": 1447}, {"role": "Theme", "text": "p38alpha MAPk", "start": 1495, "end": 1508}]}, {"trigger": {"text": "enhanced", "start": 1564, "end": 1572}, "arguments": [{"role": "Cause", "text": "activates", "start": 1485, "end": 1494}, {"role": "Theme", "text": "expression", "start": 1578, "end": 1588}]}], "regulation": [{"trigger": {"text": "regulation", "start": 1607, "end": 1617}, "arguments": [{"role": "Cause", "text": "activates", "start": 1485, "end": 1494}, {"role": "Theme", "text": "synthesis", "start": 1631, "end": 1640}]}]}}, "schema": []}
{"input": "Inhibition of IL-4-inducible gene expression in human monocytes by type I and type II interferons. \nThe Th2-type cytokines, interleukin-4 (IL-4) and interleukin-13 (IL-13), induce expression of a distinct subset of genes in human monocytes, including FcepsilonRIIb (CD23), 15-lipoxygenase, IL-1 receptor antagonist (IL-1ra), and type I and type II IL-1 receptors (IL-1R). Type I interferons (IFN-alpha and IFN-beta) and type II interferon (IFN-gamma) inhibit induction of these genes by IL-4 and IL-13. However, the mechanism by which IFNs mediate this inhibition has not been defined. In this overview, we discuss the role of the transcription factor, STAT6 (signal transducer and activator of transcription-6) in mediating IL-4- and IL-13-induced gene expression in monocytes. We also discuss our recent findings that type I and type II IFNs suppress IL-4/IL-13-inducible gene expression by inhibiting tyrosine phosphorylation and nuclear translocation of STAT6. The ability of type I and type II IFNs to inhibit IL-4/IL-13-induced STAT6 activity is dose- and time-dependent, and is not unique to monocytes because IFNs induce the same effects in fibroblasts. Inhibition of STAT6 activity is not evident unless cells are preincubated with IFN for at least 1 h before IL-4 stimulation. Furthermore, inhibition can be blocked by actinomycin D, indicating a requirement for de novo transcription. We propose a model in which stimulation of monocytes by IFN activates de novo synthesis of an inhibitory factor, possibly one or more members of the SOCS/ SSI/CIS gene family, capable of suppressing activation of STAT6 by IL-4 and IL-13. Because STAT6 activation plays an essential role in IL-4/IL-13-induced gene expression, the ability of IFN-beta and IFN-gamma to inhibit STAT6 activity provides an explanation for how IFNs can suppress IL-4/IL-13-inducible gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 180, "end": 190}, "arguments": [{"role": "Theme", "text": "CD23", "start": 266, "end": 270}]}, {"trigger": {"text": "expression", "start": 180, "end": 190}, "arguments": [{"role": "Theme", "text": "15-lipoxygenase", "start": 273, "end": 288}]}, {"trigger": {"text": "expression", "start": 180, "end": 190}, "arguments": [{"role": "Theme", "text": "IL-1ra", "start": 316, "end": 322}]}], "localization": [{"trigger": {"text": "translocation", "start": 941, "end": 954}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 933, "end": 940}, {"role": "Theme", "text": "STAT6", "start": 958, "end": 963}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 451, "end": 458}, "arguments": [{"role": "Cause", "text": "IFN-beta", "start": 406, "end": 414}, {"role": "Theme", "text": "induction", "start": 459, "end": 468}]}, {"trigger": {"text": "inhibit", "start": 451, "end": 458}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 440, "end": 449}, {"role": "Theme", "text": "induction", "start": 459, "end": 468}]}, {"trigger": {"text": "inhibit", "start": 451, "end": 458}, "arguments": [{"role": "Theme", "text": "induction", "start": 459, "end": 468}]}, {"trigger": {"text": "inhibiting", "start": 893, "end": 903}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 913, "end": 928}]}, {"trigger": {"text": "inhibit", "start": 1007, "end": 1014}, "arguments": [{"role": "Theme", "text": "induced", "start": 1026, "end": 1033}]}, {"trigger": {"text": "Inhibition", "start": 1162, "end": 1172}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1176, "end": 1181}]}, {"trigger": {"text": "blocked", "start": 1318, "end": 1325}, "arguments": [{"role": "Theme", "text": "Inhibition", "start": 1162, "end": 1172}]}, {"trigger": {"text": "suppressing", "start": 1583, "end": 1594}, "arguments": [{"role": "Theme", "text": "activation", "start": 1595, "end": 1605}]}, {"trigger": {"text": "inhibit", "start": 1763, "end": 1770}, "arguments": [{"role": "Cause", "text": "IFN-beta", "start": 1737, "end": 1745}, {"role": "Theme", "text": "STAT6", "start": 1771, "end": 1776}]}, {"trigger": {"text": "inhibit", "start": 1763, "end": 1770}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 1750, "end": 1759}, {"role": "Theme", "text": "STAT6", "start": 1771, "end": 1776}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 913, "end": 928}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 904, "end": 912}, {"role": "Theme", "text": "STAT6", "start": 958, "end": 963}]}], "positive regulation": [{"trigger": {"text": "induce", "start": 173, "end": 179}, "arguments": [{"role": "Cause", "text": "interleukin-4", "start": 124, "end": 137}, {"role": "Theme", "text": "expression", "start": 180, "end": 190}]}, {"trigger": {"text": "induce", "start": 173, "end": 179}, "arguments": [{"role": "Cause", "text": "interleukin-13", "start": 149, "end": 163}, {"role": "Theme", "text": "expression", "start": 180, "end": 190}]}, {"trigger": {"text": "induction", "start": 459, "end": 468}, "arguments": [{"role": "Theme", "text": "CD23", "start": 266, "end": 270}, {"role": "Cause", "text": "IL-4", "start": 487, "end": 491}]}, {"trigger": {"text": "induction", "start": 459, "end": 468}, "arguments": [{"role": "Theme", "text": "15-lipoxygenase", "start": 273, "end": 288}, {"role": "Cause", "text": "IL-4", "start": 487, "end": 491}]}, {"trigger": {"text": "induction", "start": 459, "end": 468}, "arguments": [{"role": "Theme", "text": "IL-1ra", "start": 316, "end": 322}, {"role": "Cause", "text": "IL-4", "start": 487, "end": 491}]}, {"trigger": {"text": "induction", "start": 459, "end": 468}, "arguments": [{"role": "Theme", "text": "CD23", "start": 266, "end": 270}, {"role": "Cause", "text": "IL-13", "start": 496, "end": 501}]}, {"trigger": {"text": "induction", "start": 459, "end": 468}, "arguments": [{"role": "Theme", "text": "15-lipoxygenase", "start": 273, "end": 288}, {"role": "Cause", "text": "IL-13", "start": 496, "end": 501}]}, {"trigger": {"text": "induction", "start": 459, "end": 468}, "arguments": [{"role": "Theme", "text": "IL-1ra", "start": 316, "end": 322}, {"role": "Cause", "text": "IL-13", "start": 496, "end": 501}]}, {"trigger": {"text": "mediate", "start": 540, "end": 547}, "arguments": [{"role": "Theme", "text": "inhibit", "start": 451, "end": 458}]}, {"trigger": {"text": "induced", "start": 1026, "end": 1033}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1015, "end": 1019}, {"role": "Theme", "text": "STAT6", "start": 1034, "end": 1039}]}, {"trigger": {"text": "induced", "start": 1026, "end": 1033}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 1020, "end": 1025}, {"role": "Theme", "text": "STAT6", "start": 1034, "end": 1039}]}, {"trigger": {"text": "requirement", "start": 1357, "end": 1368}, "arguments": [{"role": "Theme", "text": "Inhibition", "start": 1162, "end": 1172}]}, {"trigger": {"text": "activation", "start": 1595, "end": 1605}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1609, "end": 1614}, {"role": "Cause", "text": "IL-4", "start": 1618, "end": 1622}]}, {"trigger": {"text": "activation", "start": 1595, "end": 1605}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1609, "end": 1614}, {"role": "Cause", "text": "IL-13", "start": 1627, "end": 1632}]}, {"trigger": {"text": "activation", "start": 1648, "end": 1658}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1642, "end": 1647}]}]}}, "schema": []}
{"input": "Involvement of NF-kappaB p50/p65 heterodimer in activation of the human pro-interleukin-1beta gene at two subregions of the upstream enhancer element. \nA region between-3134 and -2729 bp upstream from the transcription site of the human pro-interleukin 1beta (proIL-1beta) gene was identified as an LPS-responsive enhancer element. In this study, the influence of the sequences located between -3134 and -2987 on the transcriptional activity of the proIL-1beta gene in LPS-stimulated Raw 264.7 cells was examined in detail. The results obtained by transient transfection of fos -CAT constructs that contained serial 5'-deletion mutations showed that the region between -3134 and -3059 appears to be required for the induction of transcription by LPS. Gel shift assay studies with synthetic oligonucleotides corresponding to partial sequences of the latter region and nuclear extracts from stimulated cells revealed specific protein binding sites between -3110 and -3090 and between -3079 and -3059. These specific bindings were time and LPS dose dependent. The results of supershift analysis using specific antibodies against transcription factors suggested that both binding complexes contained the NF-kappaB components p50 and p65, and did not contain other NF-kappaB proteins (p52, c-Rel, Rel B), AP-1 proteins (c-Fos, C-Jun), CREB or C/EBPbeta (NF-IL6). Mutation of either of the putative NF-kappaB-binding sites in the enhancer element decreased the LPS-stimulated transcriptional activity. These data indicated that two NF-kappaB-binding sites, which are located between -3134 and -3059, are critical for the activation of proIL-1beta gene transcription. Copyright 1999 Academic Press. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "decreased", "start": 1441, "end": 1450}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 1459, "end": 1469}]}], "positive regulation": [{"trigger": {"text": "Involvement", "start": 0, "end": 11}, "arguments": [{"role": "Cause", "text": "p50", "start": 25, "end": 28}, {"role": "Theme", "text": "activation", "start": 48, "end": 58}]}, {"trigger": {"text": "Involvement", "start": 0, "end": 11}, "arguments": [{"role": "Cause", "text": "p65", "start": 29, "end": 32}, {"role": "Theme", "text": "activation", "start": 48, "end": 58}]}, {"trigger": {"text": "activation", "start": 48, "end": 58}, "arguments": [{"role": "Theme", "text": "pro-interleukin-1beta", "start": 72, "end": 93}]}, {"trigger": {"text": "induction", "start": 716, "end": 725}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 417, "end": 441}]}, {"trigger": {"text": "stimulated", "start": 1459, "end": 1469}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 417, "end": 441}]}, {"trigger": {"text": "critical", "start": 1598, "end": 1606}, "arguments": [{"role": "Theme", "text": "activation", "start": 1615, "end": 1625}]}, {"trigger": {"text": "activation", "start": 1615, "end": 1625}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1646, "end": 1659}]}], "regulation": [{"trigger": {"text": "influence", "start": 351, "end": 360}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 417, "end": 441}]}], "transcription": [{"trigger": {"text": "transcriptional activity", "start": 417, "end": 441}, "arguments": [{"role": "Theme", "text": "proIL-1beta", "start": 449, "end": 460}]}, {"trigger": {"text": "transcription", "start": 1646, "end": 1659}, "arguments": [{"role": "Theme", "text": "proIL-1beta", "start": 1629, "end": 1640}]}]}}, "schema": []}
{"input": "Phosphorylation of TRAF2 inhibits binding to the CD40 cytoplasmic domain. \nTRAF2 is a signal transducing adaptor molecule which binds to the CD40 cytoplasmic domain. We have found that it is phosphorylated, predominantly on serine residues, when transiently overexpressed in 293 cells. The phosphorylation appears to be related to the signaling events that are activated by TRAF2 under these circumstances, since two nonfunctional mutants were found to be phosphorylated significantly less than the wild-type protein. Furthermore, the phosphorylation status of TRAF2 had significant effects on the ability of the protein to bind to CD40, as evidenced by our observations that the CD40 cytoplasmic domain interacted preferentially with underphosphorylated TRAF2 and that phosphatase treatment significantly enhanced the binding of TRAF2 to CD40. We conclude from these studies that the phosphorylation of TRAF2 is likely to play an important role in regulating signaling by virtue of its ability to influence the CD40-TRAF2 interaction. Copyright 1999 Academic Press. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 34, "end": 41}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 19, "end": 24}, {"role": "Theme2", "text": "CD40", "start": 49, "end": 53}, {"role": "Site2", "text": "cytoplasmic domain", "start": 54, "end": 72}]}, {"trigger": {"text": "binds", "start": 128, "end": 133}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 75, "end": 80}, {"role": "Theme2", "text": "CD40", "start": 141, "end": 145}, {"role": "Site2", "text": "cytoplasmic domain", "start": 146, "end": 164}]}, {"trigger": {"text": "bind", "start": 624, "end": 628}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 561, "end": 566}, {"role": "Theme2", "text": "CD40", "start": 632, "end": 636}]}, {"trigger": {"text": "interacted", "start": 704, "end": 714}, "arguments": [{"role": "Theme", "text": "CD40", "start": 680, "end": 684}, {"role": "Site", "text": "cytoplasmic domain", "start": 685, "end": 703}, {"role": "Theme2", "text": "TRAF2", "start": 755, "end": 760}]}, {"trigger": {"text": "binding", "start": 819, "end": 826}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 830, "end": 835}, {"role": "Theme2", "text": "CD40", "start": 839, "end": 843}]}, {"trigger": {"text": "interaction", "start": 1023, "end": 1034}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1012, "end": 1016}, {"role": "Theme2", "text": "TRAF2", "start": 1017, "end": 1022}]}], "gene expression": [{"trigger": {"text": "overexpressed", "start": 258, "end": 271}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 75, "end": 80}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 25, "end": 33}, "arguments": [{"role": "Cause", "text": "Phosphorylation", "start": 0, "end": 15}, {"role": "Theme", "text": "binding", "start": 34, "end": 41}]}, {"trigger": {"text": "underphosphorylated", "start": 735, "end": 754}, "arguments": [{"role": "Theme", "text": "underphosphorylated", "start": 735, "end": 754}]}], "phosphorylation": [{"trigger": {"text": "Phosphorylation", "start": 0, "end": 15}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 19, "end": 24}]}, {"trigger": {"text": "phosphorylated", "start": 191, "end": 205}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 75, "end": 80}, {"role": "Site", "text": "serine residues", "start": 224, "end": 239}]}, {"trigger": {"text": "phosphorylation", "start": 535, "end": 550}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 561, "end": 566}]}, {"trigger": {"text": "underphosphorylated", "start": 735, "end": 754}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 755, "end": 760}]}, {"trigger": {"text": "phosphorylation", "start": 885, "end": 900}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 904, "end": 909}]}], "positive regulation": [{"trigger": {"text": "when", "start": 241, "end": 245}, "arguments": [{"role": "Theme", "text": "phosphorylated", "start": 191, "end": 205}, {"role": "Cause", "text": "overexpressed", "start": 258, "end": 271}]}, {"trigger": {"text": "overexpressed", "start": 258, "end": 271}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 258, "end": 271}]}, {"trigger": {"text": "enhanced", "start": 806, "end": 814}, "arguments": [{"role": "Theme", "text": "binding", "start": 819, "end": 826}]}], "regulation": [{"trigger": {"text": "effects", "start": 583, "end": 590}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 535, "end": 550}, {"role": "Theme", "text": "bind", "start": 624, "end": 628}]}, {"trigger": {"text": "influence", "start": 998, "end": 1007}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 885, "end": 900}, {"role": "Theme", "text": "interaction", "start": 1023, "end": 1034}]}]}}, "schema": []}
{"input": "Cobalt chloride-induced signaling in endothelium leading to the augmented adherence of sickle red blood cells and transendothelial migration of monocyte-like HL-60 cells is blocked by PAF-receptor antagonist. \nIn response to hypoxia, sickle red blood cells (SS RBC) and leukocytes exhibit increased adherence to the vascular endothelium, while diapedesis of leukocytes through the blood vessel increases. However, the cellular signaling pathway(s) caused by hypoxia is poorly understood. We utilized CoCl2 as a mimetic molecule for hypoxia to study cellular signaling pathways. We found that in human umbilical vein endothelial cells (HUVEC), CoCl2 at 2 mM concentration induced the surface expression of a subset of CAMs (VCAM-1) and activation of transcription factor NF-kappaB in the nuclear extracts of HUVEC. Furthermore, CoCl2 also caused time-dependent tyrosine phosphorylation of mitogen-activated protein (MAP) kinase isoform ERK2 without significantly affecting ERK1, indicating ERK2 is the preferred substrate for upstream kinase of the MAPK pathway. Inhibitors of MAP kinase (PD98059) or platelet-activating factor (PAF)- receptor antagonist (CV3988) inhibited the CoCl2-induced NF-kappaB activation and VCAM-1 expression. Augmented expression of VCAM-1 led to increased SS RBC adhesion, inhibitable by a VCAM-1 antibody. Additionally, CoCl2 caused a two- to threefold increase in the rate of transendothelial migration of monocyte-like HL-60 cells and a twentyfold increase in phosphorylation of platelet endothelial cell adhesion molecules (PECAM-1). The transendothelial migration of monocytes was inhibited by an antibody to PECAM-1. Both phosphorylation of PECAM-1 and transendothelial migration of monocytes in response to CoCl2 were inhibited by protein kinase inhibitor (GF109203X) and augmented by protein phosphatase inhibitor (Calyculin A). Our data suggests that CoCl2-induced cellular signals directing increased expression of VCAM-1 in HUVEC involve downstream activation of MAP kinase and NF-kappaB, while the phosphorylation of PECAM-1 occurs as a result of activation of PKC. We conclude that PAF-receptor antagonist inhibits the CoCl2- or hypoxia-induced increase in the adhesion of SS RBC, PECAM-1 phosphorylation, and the concomitant transendothelial migration of monocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 691, "end": 701}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 723, "end": 729}]}, {"trigger": {"text": "expression", "start": 1223, "end": 1233}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1216, "end": 1222}]}, {"trigger": {"text": "expression", "start": 1245, "end": 1255}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1259, "end": 1265}]}, {"trigger": {"text": "expression", "start": 1938, "end": 1948}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1952, "end": 1958}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1163, "end": 1172}, "arguments": [{"role": "Theme", "text": "induced", "start": 1183, "end": 1190}]}, {"trigger": {"text": "inhibited", "start": 1752, "end": 1761}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1655, "end": 1670}]}, {"trigger": {"text": "inhibits", "start": 2146, "end": 2154}, "arguments": [{"role": "Theme", "text": "increase", "start": 2185, "end": 2193}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 869, "end": 884}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 860, "end": 868}, {"role": "Theme", "text": "ERK2", "start": 935, "end": 939}]}, {"trigger": {"text": "phosphorylation", "start": 1490, "end": 1505}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 1555, "end": 1562}]}, {"trigger": {"text": "phosphorylation", "start": 1655, "end": 1670}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 1674, "end": 1681}]}, {"trigger": {"text": "phosphorylation", "start": 2037, "end": 2052}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 2056, "end": 2063}]}, {"trigger": {"text": "phosphorylation", "start": 2229, "end": 2244}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 2221, "end": 2228}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 671, "end": 678}, "arguments": [{"role": "Theme", "text": "expression", "start": 691, "end": 701}]}, {"trigger": {"text": "caused", "start": 838, "end": 844}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 869, "end": 884}]}, {"trigger": {"text": "for", "start": 1021, "end": 1024}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 869, "end": 884}]}, {"trigger": {"text": "induced", "start": 1183, "end": 1190}, "arguments": [{"role": "Theme", "text": "expression", "start": 1223, "end": 1233}]}, {"trigger": {"text": "Augmented", "start": 1235, "end": 1244}, "arguments": [{"role": "Theme", "text": "expression", "start": 1245, "end": 1255}]}, {"trigger": {"text": "caused", "start": 1354, "end": 1360}, "arguments": [{"role": "Theme", "text": "increase", "start": 1478, "end": 1486}]}, {"trigger": {"text": "increase", "start": 1478, "end": 1486}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1490, "end": 1505}]}, {"trigger": {"text": "in response", "start": 1726, "end": 1737}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1655, "end": 1670}]}, {"trigger": {"text": "augmented", "start": 1806, "end": 1815}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1655, "end": 1670}]}, {"trigger": {"text": "induced", "start": 1893, "end": 1900}, "arguments": [{"role": "Theme", "text": "directing", "start": 1918, "end": 1927}]}, {"trigger": {"text": "directing", "start": 1918, "end": 1927}, "arguments": [{"role": "Theme", "text": "increased", "start": 1928, "end": 1937}]}, {"trigger": {"text": "increased", "start": 1928, "end": 1937}, "arguments": [{"role": "Theme", "text": "expression", "start": 1938, "end": 1948}]}, {"trigger": {"text": "occurs", "start": 2064, "end": 2070}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 2037, "end": 2052}]}, {"trigger": {"text": "increase", "start": 2185, "end": 2193}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 2229, "end": 2244}]}], "regulation": [{"trigger": {"text": "affecting", "start": 962, "end": 971}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 972, "end": 976}]}]}}, "schema": []}
{"input": "Molecular mechanisms of neutrophil-endothelial cell adhesion induced by redox imbalance. \nPrevious studies have implicated a role for intracellular thiols in the activation of nuclear factor-kappaB and transcriptional regulation of endothelial cell adhesion molecules. This study was designed to determine whether changes in endothelial cell glutathione (GSH) or oxidized glutathione (GSSG) can alter neutrophil adhesivity and to define the molecular mechanism that underlies this GSSG/GSH-induced adhesion response. Treatment of human umbilical vein endothelial cell (HUVEC) monolayers for 6 hours with 0.2 mmol/L diamide and 1 mmol/L buthionine sulfoximine (BSO) decreased GSH levels and increased the ratio of GSSG to GSH without cell toxicity. These redox changes are similar to those observed with anoxia/reoxygenation. Diamide plus BSO-induced thiol/disulfide imbalance was associated with a biphasic increase in neutrophil adhesion to HUVECs with peak responses observed at 15 minutes (phase 1) and 240 minutes (phase 2). N-Acetylcysteine treatment attenuated neutrophil adhesion in both phases, which indicated a role for GSH in the adhesion responses. Interestingly, phase 1 adhesion was inversely correlated with GSH levels but not with the GSSG/GSH ratio, whereas phase 2 neutrophil adhesion was positively correlated with GSSG/GSH ratio but not with GSH levels. Intercellular adhesion molecule-1 and P-selectin-specific monoclonal antibodies attenuated the increased neutrophil adhesion during both phases, whereas an anti-E-selectin monoclonal antibody also attenuated the phase 2 response. Pretreatment with actinomycin D and cycloheximide or with competing ds-oligonucleotides that contained nuclear factor-kappaB or activator protein-1 cognate DNA sequences significantly attenuated the phase 2 response, which implicated a role for de novo protein synthesis. Surface expression of intercellular adhesion molecule-1, P-selectin, and E-selectin on HUVECs correlated with the phase 1 and 2 neutrophil adhesion responses. This study demonstrates that changes in endothelial cell GSSG/GSH cause transcription-independent and transcription-dependent surface expression of different endothelial cell adhesion molecules, which leads to a 2-phase neutrophil-endothelial adhesion response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1884, "end": 1894}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 1898, "end": 1931}]}, {"trigger": {"text": "expression", "start": 1884, "end": 1894}, "arguments": [{"role": "Theme", "text": "P-selectin", "start": 1933, "end": 1943}]}, {"trigger": {"text": "expression", "start": 1884, "end": 1894}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1949, "end": 1959}]}]}}, "schema": []}
{"input": "Decreased proteasome-mediated degradation in T cells from the elderly: A role in immune senescence. \nInduction of NFkappaB is a highly regulated process requiring phosphorylation, ubiquitination, and proteasome-mediated degradation of the cytosolic inhibitor IkappaBalpha. Analyses of the regulation of IkappaBalpha in TNF-alpha-treated T lymphocytes from young and elderly donors revealed severely compromised degradation of IkappaBalpha in T cells from the elderly. Examination of activation-induced phosphorylation and ubiquitination of IkappaBalpha did not demonstrate any significant age-related alterations. However, examination of proteasome activity in these T cells using fluorogenic peptide assays revealed a significant age-related decline in chymotryptic activity. These results suggest that a decline in proteasome activity results in a failure to fully degrade IkappaBalpha in the elderly. This failure to degrade IkappaBalpha may underlie both the observed decrease in NFkappaB induction and the IL-2 receptor expression in TNF-treated T cells during aging. Thus, decreased proteasome-mediated degradation may be central to immune dysfunction that accompanies aging. Copyright 1999 Academic Press. ", "output": {"json_structures": {"phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 502, "end": 517}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 540, "end": 552}]}], "positive regulation": [{"trigger": {"text": "mediated", "start": 211, "end": 219}, "arguments": [{"role": "Theme", "text": "degradation", "start": 220, "end": 231}]}, {"trigger": {"text": "induced", "start": 494, "end": 501}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 502, "end": 517}]}, {"trigger": {"text": "results", "start": 837, "end": 844}, "arguments": [{"role": "Theme", "text": "degrade", "start": 867, "end": 874}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 220, "end": 231}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 259, "end": 271}]}, {"trigger": {"text": "degradation", "start": 411, "end": 422}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 426, "end": 438}]}, {"trigger": {"text": "degrade", "start": 867, "end": 874}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 875, "end": 887}]}, {"trigger": {"text": "degrade", "start": 920, "end": 927}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 928, "end": 940}]}], "regulation": [{"trigger": {"text": "regulation", "start": 289, "end": 299}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 303, "end": 315}]}, {"trigger": {"text": "alterations", "start": 601, "end": 612}, "arguments": [{"role": "Theme", "text": "induced", "start": 494, "end": 501}]}]}}, "schema": []}
{"input": "Identification of upstream regulatory elements that repress expression of adult beta-like globin genes in a primitive erythroid environment. \nOur investigations have focused on localizing cis-elements responsible for the down regulation of the adult beta-like globin genes (delta and beta) in immature, or primitive erythroid tissues. We studied their activity after transfection into K562 cells, an erythroleukemia cell line with an embryonic-fetal phenotype. Analyzed DNA sequences included delta and beta 5' flanking regions extending from approximately -500 to +50bp (promoter regions), truncated delta and beta 5' flanking regions extending from approximately -250 to +50 bp, and chimeric promoter constructions, which consisted of a distal delta or beta fragment fused to a proximal beta or delta sequence. In CAT reporter constructions no appreciable level of CAT activity was supported by the beta globin promoter, and only low level activity by the delta promoter. Truncation of the beta globin promoter led to a 2-3 fold increase in promoter activity. In contrast, deletion of the upstream portion of the delta promoter led to a 10 fold decrease in expression. Coupling of the upstream beta globin sequence from approximately -500 to -250 bp to the truncated delta promoter fragment led to complete extinction of transcription activity, consistent with a negative regulatory effect of the beta globin gene upstream element(s). Fusion of the upstream portion of the delta promoter to the truncated beta globin promoter yielded a modest increase in promoter strength relative to the truncated beta gene promoter, indicating the presence of a positive transcriptional element(s) in the upstream delta globin regulatory region. Site-directed mutagenesis of binding sites for the repressor proteins BP1 and BP2 in the upstream portion of the beta globin gene flanking region led to a 4-6 fold increase in promoter activity. DNase I footprinting of the upstream delta-globin region revealed protected sequences corresponding to consensus binding sites for GATA-1 and BP2. These results confirm that sequences in the upstream promoter region of the adult beta globin gene contribute to its factor-mediated suppression early in development and then may modulate its expression at a later stage. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1159, "end": 1169}, "arguments": [{"role": "Theme", "text": "CAT", "start": 867, "end": 870}]}, {"trigger": {"text": "expression", "start": 2268, "end": 2278}, "arguments": [{"role": "Theme", "text": "beta globin", "start": 2158, "end": 2169}]}], "negative regulation": [{"trigger": {"text": "down regulation", "start": 221, "end": 236}, "arguments": [{"role": "Theme", "text": "delta", "start": 274, "end": 279}]}, {"trigger": {"text": "down regulation", "start": 221, "end": 236}, "arguments": [{"role": "Theme", "text": "beta", "start": 284, "end": 288}]}, {"trigger": {"text": "decrease", "start": 1147, "end": 1155}, "arguments": [{"role": "Theme", "text": "expression", "start": 1159, "end": 1169}]}, {"trigger": {"text": "suppression", "start": 2209, "end": 2220}, "arguments": [{"role": "Theme", "text": "beta globin", "start": 2158, "end": 2169}]}], "positive regulation": [{"trigger": {"text": "supported", "start": 884, "end": 893}, "arguments": [{"role": "Theme", "text": "CAT", "start": 867, "end": 870}, {"role": "Cause", "text": "beta globin", "start": 901, "end": 912}, {"role": "CSite", "text": "promoter", "start": 913, "end": 921}]}, {"trigger": {"text": "supported", "start": 884, "end": 893}, "arguments": [{"role": "Theme", "text": "CAT", "start": 867, "end": 870}, {"role": "Cause", "text": "delta", "start": 958, "end": 963}, {"role": "CSite", "text": "promoter", "start": 964, "end": 972}]}, {"trigger": {"text": "increase", "start": 1031, "end": 1039}, "arguments": [{"role": "Theme", "text": "beta globin", "start": 992, "end": 1003}, {"role": "Site", "text": "promoter", "start": 1004, "end": 1012}]}, {"trigger": {"text": "increase", "start": 1545, "end": 1553}, "arguments": [{"role": "Theme", "text": "beta globin", "start": 1507, "end": 1518}, {"role": "Site", "text": "promoter", "start": 1519, "end": 1527}]}, {"trigger": {"text": "contribute", "start": 2175, "end": 2185}, "arguments": [{"role": "CSite", "text": "upstream promoter region", "start": 2120, "end": 2144}, {"role": "Cause", "text": "beta globin", "start": 2158, "end": 2169}, {"role": "Theme", "text": "suppression", "start": 2209, "end": 2220}]}], "regulation": [{"trigger": {"text": "responsible", "start": 201, "end": 212}, "arguments": [{"role": "Theme", "text": "down regulation", "start": 221, "end": 236}]}, {"trigger": {"text": "modulate", "start": 2255, "end": 2263}, "arguments": [{"role": "Cause", "text": "contribute", "start": 2175, "end": 2185}, {"role": "Theme", "text": "expression", "start": 2268, "end": 2278}]}]}}, "schema": []}
{"input": "Reduction of tumour necrosis factor alpha expression and signalling in peripheral blood mononuclear cells from patients with thalassaemia or sickle cell anaemia upon treatment with desferrioxamine. \nRecent evidence indicates that the rate of progression of the HIV-1 disease is significantly reduced in thalassaemia major patients upon treatment with high doses of desferrioxamine (DFX). The authors have previously demonstrated that in vitro exposure of mononuclear cells to DFX decreases the bioavailability of tumour necrosis factor alpha (TNF-alpha) which has a stimulatory effect on HIV-1 replication. In this study, therefore, TNF-alpha bioavailability from mononuclear cells isolated from 10 patients with thalassaemia or sickle cell anaemia given DFX as compared to 10 untreated subjects has been evaluated. Evidence is presented showing that DFX treatment reduces TNF-alpha bioavailability (P<0.05) by inhibiting its steady state (P<0.05) and by enhancing its inactivation through binding to soluble TNF-alpha receptor type II (P<0.05). We also show that DFX treatment limits the in vivo activation of NF-kappaB, a transcription factor involved in both TNF-alpha gene transcription and TNF-alpha signalling (P<0.005). We conclude that TNF-alpha bioavailability and signalling are impaired in patients upon DFX treatment. This mechanism may contribute to delayed progression of the HIV-1 infection in vivo. Copyright 1999 Academic Press. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 990, "end": 997}, "arguments": [{"role": "Theme", "text": "TNF-alpha receptor type II", "start": 1009, "end": 1035}]}], "gene expression": [{"trigger": {"text": "expression", "start": 42, "end": 52}, "arguments": [{"role": "Theme", "text": "tumour necrosis factor alpha", "start": 13, "end": 41}]}], "negative regulation": [{"trigger": {"text": "Reduction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "expression", "start": 42, "end": 52}]}, {"trigger": {"text": "decreases", "start": 480, "end": 489}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 543, "end": 552}]}, {"trigger": {"text": "reduces", "start": 865, "end": 872}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 873, "end": 882}]}, {"trigger": {"text": "inactivation", "start": 969, "end": 981}, "arguments": [{"role": "Theme", "text": "TNF-alpha receptor type II", "start": 1009, "end": 1035}]}, {"trigger": {"text": "impaired", "start": 1289, "end": 1297}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1244, "end": 1253}]}], "positive regulation": [{"trigger": {"text": "enhancing", "start": 955, "end": 964}, "arguments": [{"role": "Theme", "text": "inactivation", "start": 969, "end": 981}, {"role": "Cause", "text": "binding", "start": 990, "end": 997}]}, {"trigger": {"text": "involved", "start": 1145, "end": 1153}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1177, "end": 1190}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1177, "end": 1190}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1162, "end": 1171}]}]}}, "schema": []}
{"input": "Inhibition of cyclooxygenase-2 expression by 4-trifluoromethyl derivatives of salicylate, triflusal, and its deacetylated metabolite, 2-hydroxy-4-trifluoromethylbenzoic acid. \nThe therapeutic potential of drugs that block the induction of cyclooxygenase-2 has been emphasized. When two 4-trifluoromethyl salicylate derivatives [2-acetoxy-4-trifluoromethyl-benzoic acid (triflusal) and its deacetylated metabolite 2-hydroxy-4-trifluoromethylbenzoic acid (HTB)] were compared with aspirin and sodium salicylate as cyclooxygenase-2 (COX-2) inhibitors, we observed that in bacterial lipopolysaccharide-activated human blood, triflusal, aspirin, and HTB, but not sodium salicylate, inhibited COX-2-mediated prostaglandin E2 (PGE2) production (IC50 = 0.16, 0.18, 0.39, and >10 mM, respectively). However, only triflusal and aspirin inhibited purified COX-2 enzyme. To test this apparent discrepancy, we realized that HTB and triflusal (but neither aspirin nor salicylate) produced a concentration-dependent inhibition of COX-2 protein expression in peripheral human mononuclear cells. This observation was further confirmed in a rat air pouch model in vivo, in which both aspirin and triflusal inhibited PGE2 production (ID50 = 18.9 and 11.4 mg/kg p.o., respectively) but only triflusal-treated animals showed a decrease in COX-2 expression. This different behavior may be, at least in part, due to the ability of HTB and triflusal to block the activation of the transcription factor nuclear factor-kappaB to a higher extent than aspirin and sodium salicylate. Thus, in addition to inhibiting the COX-2 activity at therapeutic concentrations, triflusal is able to block through its metabolite HTB the expression of new enzyme, and hence the resumption of PGE2 synthesis. Triflusal and HTB may exert beneficial effects in processes in which de novo COX-2 expression is involved and, in a broader sense, in pathological situations in which genes under nuclear factor-kappaB control are up-regulated. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 31, "end": 41}, "arguments": [{"role": "Theme", "text": "cyclooxygenase-2", "start": 14, "end": 30}]}, {"trigger": {"text": "expression", "start": 1029, "end": 1039}, "arguments": [{"role": "Theme", "text": "COX-2", "start": 1015, "end": 1020}]}, {"trigger": {"text": "expression", "start": 1324, "end": 1334}, "arguments": [{"role": "Theme", "text": "COX-2", "start": 1318, "end": 1323}]}, {"trigger": {"text": "expression", "start": 1695, "end": 1705}, "arguments": [{"role": "Theme", "text": "COX-2", "start": 1318, "end": 1323}]}, {"trigger": {"text": "expression", "start": 1848, "end": 1858}, "arguments": [{"role": "Theme", "text": "COX-2", "start": 1842, "end": 1847}]}], "negative regulation": [{"trigger": {"text": "Inhibition", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 31, "end": 41}]}, {"trigger": {"text": "inhibited", "start": 826, "end": 835}, "arguments": [{"role": "Theme", "text": "COX-2", "start": 845, "end": 850}]}, {"trigger": {"text": "inhibition", "start": 1001, "end": 1011}, "arguments": [{"role": "Theme", "text": "expression", "start": 1029, "end": 1039}]}, {"trigger": {"text": "decrease", "start": 1306, "end": 1314}, "arguments": [{"role": "Theme", "text": "expression", "start": 1324, "end": 1334}]}, {"trigger": {"text": "block", "start": 1658, "end": 1663}, "arguments": [{"role": "Theme", "text": "expression", "start": 1695, "end": 1705}]}], "positive regulation": [{"trigger": {"text": "produced", "start": 966, "end": 974}, "arguments": [{"role": "Theme", "text": "inhibition", "start": 1001, "end": 1011}]}]}}, "schema": []}
{"input": "Expression of IkappaBalpha in the nucleus of human peripheral blood T lymphocytes. \nAccording to current models the inhibitory capacity of I(kappa)B(alpha) would be mediated through the retention of Rel/NF-kappaB proteins in the cytosol. However, I(kappa)B(alpha) has also been detected in the nucleus of cell lines and when overexpressed by transient transfection. To gain better insight into the potential role of nuclear I(kappa)B(alpha) in a physiological context we have analysed its presence in the nucleus of human peripheral blood T lymphocytes (PBL). We demonstrate the nuclear localization of I(kappa)B(alpha) in PBL by different techniques: Western blot, indirect immunofluorescence and electron microscopy. Low levels of nuclear I(kappa)B(alpha) were detected in resting cells whereas a superinduction was obtained after PMA activation. The nuclear pool of I(kappa)B(alpha) showed a higher stability than cytosolic I(kappa)B(alpha) and was partially independent of the resynthesis of the protein. Unexpectedly, the presence of nuclear I(kappa)B(alpha) did not inhibit NF-kappaB binding to DNA and this phenomenon was not due to the presence of IkappaBbeta at the nuclear level. Immunoprecipitation experiments failed to demonstrate an association between nuclear I(kappa)B(alpha) and NF-kappaB proteins. Our results demonstrate that in resting and PMA-activated human PBL, I(kappa)B(alpha) is present in the nucleus in an apparently inactive form unable to disrupt NF-kappaB binding from DNA. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 14, "end": 26}]}, {"trigger": {"text": "detected", "start": 278, "end": 286}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 247, "end": 263}]}, {"trigger": {"text": "resynthesis", "start": 981, "end": 992}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 869, "end": 885}]}], "localization": [{"trigger": {"text": "localization", "start": 587, "end": 599}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 579, "end": 586}, {"role": "Theme", "text": "I(kappa)B(alpha)", "start": 603, "end": 619}]}, {"trigger": {"text": "presence", "start": 1027, "end": 1035}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 1039, "end": 1046}, {"role": "Theme", "text": "I(kappa)B(alpha)", "start": 1047, "end": 1063}]}, {"trigger": {"text": "presence", "start": 1144, "end": 1152}, "arguments": [{"role": "Theme", "text": "IkappaBbeta", "start": 1156, "end": 1167}, {"role": "AtLoc", "text": "nuclear", "start": 1175, "end": 1182}]}, {"trigger": {"text": "present", "start": 1405, "end": 1412}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 1385, "end": 1401}, {"role": "AtLoc", "text": "nucleus", "start": 1420, "end": 1427}]}], "negative regulation": [{"trigger": {"text": "inhibitory capacity", "start": 116, "end": 135}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 139, "end": 155}]}], "positive regulation": [{"trigger": {"text": "mediated", "start": 165, "end": 173}, "arguments": [{"role": "Theme", "text": "inhibitory capacity", "start": 116, "end": 135}]}, {"trigger": {"text": "detected", "start": 278, "end": 286}, "arguments": [{"role": "Theme", "text": "detected", "start": 278, "end": 286}, {"role": "Cause", "text": "overexpressed", "start": 325, "end": 338}]}, {"trigger": {"text": "overexpressed", "start": 325, "end": 338}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 247, "end": 263}]}, {"trigger": {"text": "detected", "start": 763, "end": 771}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 741, "end": 757}]}, {"trigger": {"text": "super", "start": 799, "end": 804}, "arguments": [{"role": "Theme", "text": "induction", "start": 804, "end": 813}]}, {"trigger": {"text": "induction", "start": 804, "end": 813}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 741, "end": 757}]}, {"trigger": {"text": "higher stability", "start": 895, "end": 911}, "arguments": [{"role": "Theme", "text": "I(kappa)B(alpha)", "start": 869, "end": 885}]}], "regulation": [{"trigger": {"text": "presence", "start": 1144, "end": 1152}, "arguments": [{"role": "Theme", "text": "presence", "start": 1027, "end": 1035}, {"role": "Cause", "text": "presence", "start": 1144, "end": 1152}]}]}}, "schema": []}
{"input": "PGG-glucan, a soluble beta-(1,3)-glucan, enhances the oxidative burst response, microbicidal activity, and activates an NF-kappa B-like factor in human PMN: evidence for a glycosphingolipid beta-(1,3)-glucan receptor. \nPGG-Glucan, a soluble beta-(1,6)-branched beta-(1,3)-linked glucose homopolymer derived from the cell wall of the yeast Saccharomyces cerevisiae, is an immunomodulator which enhances leukocyte anti-infective activity and enhances myeloid and megakaryocyte progenitor proliferation. Incubation of human whole blood with PGG-Glucan significantly enhanced the oxidative burst response of subsequently isolated blood leukocytes to both soluble and particulate activators in a dose-dependent manner, and increased leukocyte microbicidal activity. No evidence for inflammatory cytokine production was obtained under these conditions. Electrophoretic mobility shift assays demonstrated that PGG-Glucan induced the activation of an NF-kappaB-like nuclear transcription factor in purified human neutrophils. The binding of 3H-PGG-Glucan to human leukocyte membranes was specific, concentration-dependent, saturable, and high affinity (Kd approximately 6 nM). A monoclonal antibody specific to the glycosphingolipid lactosylceramide was able to inhibit activation of the NF-kappaB-like factor by PGG-Glucan, and ligand binding data, including polysaccharide specificity, suggested that the PGG-Glucan binding moiety was lactosylceramide. These results indicate that PGG-Glucan enhances neutrophil anti-microbial functions and that interaction between this beta-glucan and human neutrophils is mediated by the glycosphingolipid lactosylceramide present at the cell surface. ", "output": {"json_structures": {}}, "schema": []}
{"input": "[Corticoids and allergy] \nInflammation is constantly observed in allergic reactions. Corticosteroids are most effective in preventing the late phase of allergic reaction. The action of glucocorticosteroids is mediated through glucocorticoid receptors present in the cellular cytoplasm. When activated, glucocorticoid receptors form a dimer and bind to DNA after migration into the nucleus. Interaction to DNA induces changes in the transcription rate, leading to either gene induction or gene repression. Glucocorticoid receptors are also able to interact with transcriptional factors such as AP-1 (activator protein-1) of NF-kappa B (nuclear factor-kappa B). Through these actions glucocorticosteroids are susceptible to modify functions of cells involved in the allergic inflammatory response. They are in particular able to inhibit most of the pro-inflammatory functions of the eosinophils. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Activation of NF-kappaB in Mycobacterium tuberculosis- induced interleukin-2 receptor expression in mononuclear phagocytes. \nSoluble interleukin-2 receptor-alpha (IL-2Ralpha) has been reported to be increased in the sera of patients with advanced tuberculosis, and levels decline after therapy in accordance with improvement of radiologic findings. We investigated expression of the IL-2Ralpha in bronchoalveolar lavage (BAL) cells in active pulmonary tuberculosis, and evaluated the mechanism Mycobacterium tuberculosis induces in the IL-2Ralpha using the THP-1 mononuclear phagocyte cell line. We found IL-2Ralpha expression to be increased in BAL cells from involved sites of active pulmonary tuberculosis. Expression of the alpha-chain of IL-2Ralpha on peripheral blood monocytes (PBM) was induced by M. tuberculosis by flow cytometry evaluation. Northern analysis demonstrated increased IL-2Ralpha gene expression after stimulation with M. tuberculosis which was further induced by interferon-gamma (IFN-gamma). The IL-2Ralpha promoter containing the nuclear factor kappa B (NF-kappaB) site was transcriptionally induced by M. tuberculosis and this NF-kappaB site could confer inducibility to a heterologous herpes thymidine kinase (TK) promoter by M. tuberculosis. Electrophoretic mobility shift assays (EMSAs) revealed specific binding of nuclear protein to the NF-kappaB site upon induction with M. tuberculosis. Using antibodies against the p50 and p65 subunits of NF-kappaB in EMSAs, the involvement of both p50 and p65 proteins was further demonstrated. Functional expression of the IL-2Ralpha on mononuclear phagocytes in M. tuberculosis infection may play an important immunomodulatory role in the host response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 365, "end": 375}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 383, "end": 393}]}, {"trigger": {"text": "expression", "start": 616, "end": 626}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 605, "end": 615}]}, {"trigger": {"text": "Expression", "start": 710, "end": 720}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 743, "end": 753}]}, {"trigger": {"text": "expression", "start": 908, "end": 918}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 892, "end": 902}]}, {"trigger": {"text": "expression", "start": 1576, "end": 1586}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 1594, "end": 1604}]}], "negative regulation": [{"trigger": {"text": "decline", "start": 272, "end": 279}, "arguments": [{"role": "Theme", "text": "increased", "start": 199, "end": 208}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 199, "end": 208}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 163, "end": 173}]}, {"trigger": {"text": "induces", "start": 521, "end": 528}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 536, "end": 546}]}, {"trigger": {"text": "increased", "start": 633, "end": 642}, "arguments": [{"role": "Theme", "text": "expression", "start": 616, "end": 626}]}, {"trigger": {"text": "induced", "start": 794, "end": 801}, "arguments": [{"role": "Theme", "text": "Expression", "start": 710, "end": 720}]}, {"trigger": {"text": "increased", "start": 882, "end": 891}, "arguments": [{"role": "Theme", "text": "expression", "start": 908, "end": 918}]}, {"trigger": {"text": "induced", "start": 976, "end": 983}, "arguments": [{"role": "Theme", "text": "expression", "start": 908, "end": 918}, {"role": "Cause", "text": "IFN-gamma", "start": 1005, "end": 1014}]}, {"trigger": {"text": "induced", "start": 1118, "end": 1125}, "arguments": [{"role": "Theme", "text": "IL-2Ralpha", "start": 1021, "end": 1031}, {"role": "Site", "text": "promoter", "start": 1032, "end": 1040}]}]}}, "schema": []}
{"input": "Regulation of the megakaryocytic glycoprotein IX promoter by the oncogenic Ets transcription factor Fli-1. \nGlycoprotein (GP) IX is a subunit of the von Willebrand receptor, GPIb-V-IX, which mediates adhesion of platelets to the subendothelium of damaged blood vessels. Previous characterization of the GPIX promoter identified a functional Ets site that, when disrupted, reduced promoter activity. However, the Ets protein(s) that regulated GPIX promoter expression was unknown. In this study, transient cotransfection of several GPIX promoter/reporter constructs into 293T kidney fibroblasts with a Fli-1 expression vector shows that the oncogenic protein Fli-1 can transactivate the GPIX promoter when an intact GPIX Ets site is present. In addition, Fli-1 binding of the GPIX Ets site was identified in antibody supershift experiments in nuclear extracts derived from hematopoietic human erythroleukemia cells. Comparative studies showed that Fli-1 was also able to transactivate the GPIbalpha and, to a lesser extent, the GPIIb promoter. Immunoblot analysis identified Fli-1 protein in lysates derived from platelets. In addition, expression of Fli-1 was identified immunohistochemically in megakaryocytes derived from CD34(+) cells treated with the megakaryocyte differentiation and proliferation factor, thrombopoietin. These results suggest that Fli-1 is likely to regulate lineage-specific genes during megakaryocytopoiesis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 760, "end": 767}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 754, "end": 759}]}], "gene expression": [{"trigger": {"text": "expression", "start": 456, "end": 466}, "arguments": [{"role": "Theme", "text": "GPIX", "start": 442, "end": 446}]}, {"trigger": {"text": "identified", "start": 1063, "end": 1073}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 1074, "end": 1079}]}, {"trigger": {"text": "expression", "start": 1136, "end": 1146}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 1150, "end": 1155}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 372, "end": 379}, "arguments": [{"role": "Theme", "text": "GPIX", "start": 303, "end": 307}, {"role": "Site", "text": "promoter", "start": 308, "end": 316}]}], "positive regulation": [{"trigger": {"text": "transactivate", "start": 668, "end": 681}, "arguments": [{"role": "Cause", "text": "Fli-1", "start": 658, "end": 663}, {"role": "Theme", "text": "GPIX", "start": 686, "end": 690}, {"role": "Site", "text": "promoter", "start": 691, "end": 699}]}, {"trigger": {"text": "transactivate", "start": 970, "end": 983}, "arguments": [{"role": "Cause", "text": "Fli-1", "start": 947, "end": 952}, {"role": "Theme", "text": "GPIIb", "start": 1027, "end": 1032}, {"role": "Site", "text": "promoter", "start": 1033, "end": 1041}]}, {"trigger": {"text": "transactivate", "start": 970, "end": 983}, "arguments": [{"role": "Cause", "text": "Fli-1", "start": 947, "end": 952}, {"role": "Theme", "text": "GPIbalpha", "start": 988, "end": 997}, {"role": "Site", "text": "promoter", "start": 1033, "end": 1041}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "glycoprotein IX", "start": 33, "end": 48}, {"role": "Cause", "text": "Fli-1", "start": 100, "end": 105}]}, {"trigger": {"text": "regulated", "start": 432, "end": 441}, "arguments": [{"role": "Theme", "text": "expression", "start": 456, "end": 466}]}]}}, "schema": []}
{"input": "Studies into the effect of tyrosine phosphatase inhibitor phenylarsine oxide on NFkappaB activation in T lymphocytes during aging: evidence for altered IkappaB-alpha phosphorylation and degradation. \nNuclear Factor kappa B (NFkappaB) is a critical regulator of several genes involved in immune and inflammatory responses. Treatment of T cells with a variety of stimuli, including TNF-alpha, leads to the translocation of the active p65-50 heterodimer to the nucleus, albeit at a lower level in T cells from the elderly. We demonstrate here that pretreatment with PAO results in the inhibition of NFkappaB induction in TNF-alpha treated T cells, suggesting a role for PAO-sensitive phosphatase in the activation of the NFkappaB via this pathway in human T cells. Furthermore, it demonstrates that aging does not influence the sensitivity of this phosphatase. Treatment with DMP prior to treatment with PAO and TNF abolishes the inhibition induced by PAO, in T cells from both young and old donors, alike. Finally, we demonstrate that a failure to degrade IkappaB-alpha in cytosols of TNF-treated T cells pretreated with PAO is due to its interference with the phosphorylation of IkappaB-alpha and not due to its inhibitory effect on proteasomal degradation. These data collectively suggest that PAO interferes with the phosphorylation and the regulated degradation of IkappaB-alpha, induced by TNF, without affecting the chymotryptic activity of the proteasome, independent of age. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "interference", "start": 1137, "end": 1149}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1159, "end": 1174}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 166, "end": 181}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 152, "end": 165}]}, {"trigger": {"text": "phosphorylation", "start": 1159, "end": 1174}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1178, "end": 1191}]}, {"trigger": {"text": "phosphorylation", "start": 1318, "end": 1333}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1367, "end": 1380}]}], "positive regulation": [{"trigger": {"text": "due", "start": 1126, "end": 1129}, "arguments": [{"role": "Theme", "text": "degrade", "start": 1046, "end": 1053}, {"role": "Cause", "text": "interference", "start": 1137, "end": 1149}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 186, "end": 197}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 152, "end": 165}]}, {"trigger": {"text": "degrade", "start": 1046, "end": 1053}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1054, "end": 1067}]}, {"trigger": {"text": "degradation", "start": 1352, "end": 1363}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1367, "end": 1380}]}], "regulation": [{"trigger": {"text": "altered", "start": 144, "end": 151}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 166, "end": 181}]}, {"trigger": {"text": "altered", "start": 144, "end": 151}, "arguments": [{"role": "Theme", "text": "degradation", "start": 186, "end": 197}]}, {"trigger": {"text": "due", "start": 1200, "end": 1203}, "arguments": [{"role": "Theme", "text": "degrade", "start": 1046, "end": 1053}]}]}}, "schema": []}
{"input": "A novel lipopolysaccharide-induced transcription factor regulating tumor necrosis factor alpha gene expression: molecular cloning, sequencing, characterization, and chromosomal assignment. \nLipopolysaccharide (LPS) is a potent stimulator of monocytes and macrophages, causing secretion of tumor necrosis factor alpha (TNF-alpha) and other inflammatory mediators. Given the deleterious effects to the host of TNF-alpha, it has been postulated that TNF-alpha gene expression must be tightly regulated. The nature of the nuclear factor(s) that control TNF-alpha gene transcription in humans remains obscure, although NF-kappaB has been suggested. Our previous studies pertaining to macrophage response to LPS identified a novel DNA-binding domain located from -550 to -487 in the human TNF-alpha promoter that contains transcriptional activity, but lacks any known NF-kappaB-binding sites. We have used this DNA fragment to isolate and purify a 60-kDa protein binding to this fragment and obtained its amino-terminal sequence, which was used to design degenerate probes to screen a cDNA library from THP-1 cells. A novel cDNA clone (1.8 kb) was isolated and fully sequenced. Characterization of this cDNA clone revealed that its induction was dependent on LPS activation of THP-1 cells; hence, the name LPS-induced TNF-alpha factor (LITAF). Inhibition of LITAF mRNA expression in THP-1 cells resulted in a reduction of TNF-alpha transcripts. In addition, high level of expression of LITAF mRNA was observed predominantly in the placenta, peripheral blood leukocytes, lymph nodes, and the spleen. Finally, chromosomal localization using fluorescence in situ hybridization revealed that LITAF mapped to chromosome 16p12-16p13.3. Together, these findings suggest that LITAF plays an important role in the activation of the human TNF-alpha gene and proposes a new mechanism to control TNF-alpha gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 957, "end": 964}, "arguments": [{"role": "Site", "text": "DNA-binding domain", "start": 725, "end": 743}, {"role": "Theme", "text": "TNF-alpha", "start": 783, "end": 792}]}], "gene expression": [{"trigger": {"text": "gene expression", "start": 95, "end": 110}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 67, "end": 94}]}, {"trigger": {"text": "gene expression", "start": 457, "end": 472}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 447, "end": 456}]}, {"trigger": {"text": "gene expression", "start": 1888, "end": 1903}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1878, "end": 1887}]}], "localization": [{"trigger": {"text": "secretion", "start": 276, "end": 285}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 318, "end": 327}]}], "negative regulation": [{"trigger": {"text": "Inhibition", "start": 1338, "end": 1348}, "arguments": [{"role": "Theme", "text": "expression", "start": 1363, "end": 1373}]}, {"trigger": {"text": "resulted in a reduction", "start": 1389, "end": 1412}, "arguments": [{"role": "Cause", "text": "Inhibition", "start": 1338, "end": 1348}, {"role": "Theme", "text": "transcripts", "start": 1426, "end": 1437}]}], "positive regulation": [{"trigger": {"text": "causing", "start": 268, "end": 275}, "arguments": [{"role": "Theme", "text": "secretion", "start": 276, "end": 285}]}, {"trigger": {"text": "induction", "start": 1226, "end": 1235}, "arguments": [{"role": "Theme", "text": "LITAF", "start": 1330, "end": 1335}]}, {"trigger": {"text": "high level", "start": 1452, "end": 1462}, "arguments": [{"role": "Theme", "text": "expression", "start": 1466, "end": 1476}]}, {"trigger": {"text": "activation", "start": 1799, "end": 1809}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1823, "end": 1832}]}], "regulation": [{"trigger": {"text": "regulating", "start": 56, "end": 66}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 95, "end": 110}]}, {"trigger": {"text": "regulated", "start": 489, "end": 498}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 457, "end": 472}]}, {"trigger": {"text": "control", "start": 541, "end": 548}, "arguments": [{"role": "Theme", "text": "gene transcription", "start": 559, "end": 577}]}, {"trigger": {"text": "dependent", "start": 1240, "end": 1249}, "arguments": [{"role": "Theme", "text": "induction", "start": 1226, "end": 1235}]}, {"trigger": {"text": "role", "start": 1787, "end": 1791}, "arguments": [{"role": "Cause", "text": "LITAF", "start": 1762, "end": 1767}, {"role": "Theme", "text": "activation", "start": 1799, "end": 1809}]}, {"trigger": {"text": "control", "start": 1870, "end": 1877}, "arguments": [{"role": "Cause", "text": "LITAF", "start": 1762, "end": 1767}, {"role": "Theme", "text": "gene expression", "start": 1888, "end": 1903}]}], "transcription": [{"trigger": {"text": "gene transcription", "start": 559, "end": 577}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 549, "end": 558}]}, {"trigger": {"text": "expression", "start": 1363, "end": 1373}, "arguments": [{"role": "Theme", "text": "LITAF", "start": 1352, "end": 1357}]}, {"trigger": {"text": "transcripts", "start": 1426, "end": 1437}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1416, "end": 1425}]}, {"trigger": {"text": "expression", "start": 1466, "end": 1476}, "arguments": [{"role": "Theme", "text": "LITAF", "start": 1480, "end": 1485}]}]}}, "schema": []}
{"input": "Engagement of natural cytotoxicity programs regulates AP-1 expression in the NKL human NK cell line. \nNK cell cytotoxicity is a fast and efficient mechanism of target cell lysis. Using transcription analysis, such as multiplex messenger assays, we show here that natural cytotoxicity exerted by the human NKL cell line correlates with mRNA accumulation of very early activator protein (AP)-1 transcription factor genes such as JunB, FosB and c-Fos. In addition, DNA-binding activities of Jun-Fos heterodimers were observed by electrophoretic mobility shift assays during the course of natural cytotoxicity. Interaction between immunoglobulin-like transcript-2/leukocyte Ig-like receptor 1 on NKL cells and HLA-B27 on target cells leads to an impairment of NKL natural cytotoxicity, which correlates with an absence of JunB, FosB, and c-Fos transcription, as well as an absence of their DNA-binding activity. Our studies thus indicate that, despite the rapidity of NK cell-mediated lysis, AP-1 transcription factor is activated during the early stage of NK cell cytolytic programs and that engagement of NK cell inhibitory receptors for MHC class I molecules impairs the very early activation of AP-1. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Interaction", "start": 607, "end": 618}, "arguments": [{"role": "Theme", "text": "immunoglobulin-like transcript-2", "start": 627, "end": 659}, {"role": "Theme2", "text": "HLA-B27", "start": 706, "end": 713}]}, {"trigger": {"text": "binding activity", "start": 890, "end": 906}, "arguments": [{"role": "Theme", "text": "JunB", "start": 818, "end": 822}]}, {"trigger": {"text": "binding activity", "start": 890, "end": 906}, "arguments": [{"role": "Theme", "text": "FosB", "start": 824, "end": 828}]}, {"trigger": {"text": "binding activity", "start": 890, "end": 906}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 834, "end": 839}]}], "negative regulation": [{"trigger": {"text": "absence", "start": 807, "end": 814}, "arguments": [{"role": "Theme", "text": "transcription", "start": 840, "end": 853}]}, {"trigger": {"text": "absence", "start": 869, "end": 876}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 890, "end": 906}]}], "positive regulation": [{"trigger": {"text": "mRNA accumulation", "start": 335, "end": 352}, "arguments": [{"role": "Theme", "text": "JunB", "start": 427, "end": 431}]}, {"trigger": {"text": "mRNA accumulation", "start": 335, "end": 352}, "arguments": [{"role": "Theme", "text": "FosB", "start": 433, "end": 437}]}, {"trigger": {"text": "mRNA accumulation", "start": 335, "end": 352}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 442, "end": 447}]}], "transcription": [{"trigger": {"text": "transcription", "start": 840, "end": 853}, "arguments": [{"role": "Theme", "text": "JunB", "start": 818, "end": 822}]}, {"trigger": {"text": "transcription", "start": 840, "end": 853}, "arguments": [{"role": "Theme", "text": "FosB", "start": 824, "end": 828}]}, {"trigger": {"text": "transcription", "start": 840, "end": 853}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 834, "end": 839}]}]}}, "schema": []}
{"input": "Human cytomegalovirus binding to human monocytes induces immunoregulatory gene expression. \nTo continue our investigation of the cellular events that occur following human CMV (HCMV) infection, we focused on the regulation of cellular activation following viral binding to human monocytes. First, we showed that viral binding induced a number of immunoregulatory genes (IL-1beta, A20, NF-kappaB-p105/p50, and IkappaBalpha) in unactivated monocytes and that neutralizing Abs to the major HCMV glycoproteins, gB (UL55) and gH (UL75), inhibited the induction of these genes. Next, we demonstrated that these viral ligands directly up-regulated monocyte gene expression upon their binding to their appropriate cellular receptors. We then investigated if HCMV binding also resulted in the translation and secretion of cytokines. Our results showed that HCMV binding to monocytes resulted in the production and release of IL-1beta protein. Because these induced gene products have NF-kappaB sites in their promoter regions, we next examined whether there was an up-regulation of nuclear NF-kappaB levels. These experiments showed that, in fact, NF-kappaB was translocated to the nucleus following viral binding or purified viral ligand binding. Changes in IkappaBalpha levels correlated with the changes in NF-kappaB translocation. Lastly, we demonstrated that p38 kinase activity played a central role in IL-1beta production and that it was rapidly up-regulated following infection. These results support our hypothesis that HCMV initiates a signal transduction pathway that leads to monocyte activation and pinpoints a potential mechanism whereby HCMV infection of monocytes can result in profound pathogenesis, especially in chronic inflammatory-type conditions. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 890, "end": 900}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 916, "end": 924}]}, {"trigger": {"text": "production", "start": 1409, "end": 1419}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1400, "end": 1408}]}], "localization": [{"trigger": {"text": "release", "start": 905, "end": 912}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 916, "end": 924}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 532, "end": 541}, "arguments": [{"role": "Theme", "text": "induction", "start": 546, "end": 555}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 326, "end": 333}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 370, "end": 378}]}, {"trigger": {"text": "induced", "start": 326, "end": 333}, "arguments": [{"role": "Theme", "text": "A20", "start": 380, "end": 383}]}, {"trigger": {"text": "induced", "start": 326, "end": 333}, "arguments": [{"role": "Theme", "text": "p105", "start": 395, "end": 399}]}, {"trigger": {"text": "induced", "start": 326, "end": 333}, "arguments": [{"role": "Theme", "text": "p50", "start": 400, "end": 403}]}, {"trigger": {"text": "induced", "start": 326, "end": 333}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 409, "end": 421}]}, {"trigger": {"text": "induction", "start": 546, "end": 555}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 370, "end": 378}]}, {"trigger": {"text": "induction", "start": 546, "end": 555}, "arguments": [{"role": "Theme", "text": "A20", "start": 380, "end": 383}]}, {"trigger": {"text": "induction", "start": 546, "end": 555}, "arguments": [{"role": "Theme", "text": "p105", "start": 395, "end": 399}]}, {"trigger": {"text": "induction", "start": 546, "end": 555}, "arguments": [{"role": "Theme", "text": "p50", "start": 400, "end": 403}]}, {"trigger": {"text": "induction", "start": 546, "end": 555}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 409, "end": 421}]}, {"trigger": {"text": "resulted", "start": 874, "end": 882}, "arguments": [{"role": "Theme", "text": "production", "start": 890, "end": 900}]}, {"trigger": {"text": "resulted", "start": 874, "end": 882}, "arguments": [{"role": "Theme", "text": "release", "start": 905, "end": 912}]}, {"trigger": {"text": "role", "start": 1392, "end": 1396}, "arguments": [{"role": "Theme", "text": "production", "start": 1409, "end": 1419}]}], "regulation": [{"trigger": {"text": "Changes", "start": 1239, "end": 1246}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1250, "end": 1262}]}]}}, "schema": []}
{"input": "Signal transduction pathways activated in endothelial cells following infection with Chlamydia pneumoniae. \nChlamydia pneumoniae is an important respiratory pathogen. Recently, its presence has been demonstrated in atherosclerotic lesions. In this study, we characterized C. pneumoniae-mediated activation of endothelial cells and demonstrated an enhanced expression of endothelial adhesion molecules followed by subsequent rolling, adhesion, and transmigration of leukocytes (monocytes, granulocytes). These effects were blocked by mAbs against endothelial and/or leukocyte adhesion molecules (beta1 and beta2 integrins). Additionally, activation of different signal transduction pathways in C. pneumoniae-infected endothelial cells was shown: protein tyrosine phosphorylation, up-regulation of phosphorylated p42/p44 mitogen-activated protein kinase, and NF-kappaB activation/translocation occurred within 10-15 min. Increased mRNA and surface expression of E-selectin, ICAM-1, and VCAM-1 were noted within hours. Thus, C. pneumoniae triggers a cascade of events that could lead to endothelial activation, inflammation, and thrombosis, which in turn may result in or may promote atherosclerosis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 960, "end": 970}]}, {"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 972, "end": 978}]}, {"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 984, "end": 990}]}], "positive regulation": [{"trigger": {"text": "up-regulation", "start": 779, "end": 792}, "arguments": [{"role": "Theme", "text": "p42", "start": 811, "end": 814}]}, {"trigger": {"text": "up-regulation", "start": 779, "end": 792}, "arguments": [{"role": "Theme", "text": "p44 mitogen-activated protein kinase", "start": 815, "end": 851}]}, {"trigger": {"text": "occurred", "start": 892, "end": 900}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 779, "end": 792}]}, {"trigger": {"text": "Increased", "start": 919, "end": 928}, "arguments": [{"role": "Theme", "text": "expression", "start": 946, "end": 956}]}], "transcription": [{"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 960, "end": 970}]}, {"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 972, "end": 978}]}, {"trigger": {"text": "expression", "start": 946, "end": 956}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 984, "end": 990}]}]}}, "schema": []}
{"input": "Extracellular-regulated kinase 1/2, Jun N-terminal kinase, and c-Jun are involved in NF-kappa B-dependent IL-6 expression in human monocytes. \nIn the present study we investigated the possible involvement of the mitogen-activated protein kinase family members extracellular-regulated kinase 1/2 (ERK1/2) and c-Jun N-terminal kinase (JNK) in mediating IL-6 gene expression in human monocytes, in particular their role in enhancing NF-kappa B activity. Freshly isolated monocytes treated with the protein phosphatase inhibitor okadaic acid secreted high levels of IL-6 protein, which coincided with enhanced binding activity of NF-kappa B as well as with phosphorylation and activation of the ERK1/2 and JNK proteins. The ERK pathway-specific inhibitor PD98059 inhibited IL-6 secretion from monocytes. Transient overexpression of inactive mutants of either Raf-1 or JNK1 showed that both pathways were involved in kappa B-dependent IL-6 promoter activity. By using PD98059, we demonstrated that the Raf1/MEK1/ERK1/2 pathway did not affect the DNA binding of NF-kappa B but, rather, acted at the level of transcriptional activity of NF-kappa B. Interestingly, it was shown that NF-kappa B-mediated gene transcription, both in the context of the IL-6 promoter as well as on its own, was dependent on both serine kinase activity and interaction with c-Jun protein. We conclude that okadaic acid-induced IL-6 gene expression is at least partly mediated through the ERK1/2 and JNK pathway-dependent activation of NF-kappa B transcriptional capacity. Our results suggest that the JNK pathway may regulate NF-kappa B-mediated gene transcription through its phosphorylation and activation of c-Jun. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 1328, "end": 1339}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 1345, "end": 1350}]}], "gene expression": [{"trigger": {"text": "expression", "start": 111, "end": 121}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 106, "end": 110}]}, {"trigger": {"text": "expression", "start": 361, "end": 371}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 351, "end": 355}]}, {"trigger": {"text": "secreted", "start": 538, "end": 546}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 562, "end": 566}]}, {"trigger": {"text": "expression", "start": 1408, "end": 1418}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1398, "end": 1402}]}], "localization": [{"trigger": {"text": "secretion", "start": 774, "end": 783}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 769, "end": 773}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 759, "end": 768}, "arguments": [{"role": "Theme", "text": "secretion", "start": 774, "end": 783}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 653, "end": 668}, "arguments": [{"role": "Theme", "text": "JNK", "start": 702, "end": 705}]}, {"trigger": {"text": "phosphorylation", "start": 1648, "end": 1663}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 1682, "end": 1687}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 96, "end": 105}, "arguments": [{"role": "Theme", "text": "expression", "start": 111, "end": 121}]}, {"trigger": {"text": "mediating", "start": 341, "end": 350}, "arguments": [{"role": "Theme", "text": "expression", "start": 361, "end": 371}]}, {"trigger": {"text": "high levels", "start": 547, "end": 558}, "arguments": [{"role": "Theme", "text": "secreted", "start": 538, "end": 546}]}, {"trigger": {"text": "activation", "start": 673, "end": 683}, "arguments": [{"role": "Theme", "text": "JNK", "start": 702, "end": 705}]}, {"trigger": {"text": "dependent", "start": 1283, "end": 1292}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1200, "end": 1213}, {"role": "Cause", "text": "interaction", "start": 1328, "end": 1339}]}, {"trigger": {"text": "dependent", "start": 1283, "end": 1292}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1200, "end": 1213}]}, {"trigger": {"text": "induced", "start": 1390, "end": 1397}, "arguments": [{"role": "Theme", "text": "expression", "start": 1408, "end": 1418}]}, {"trigger": {"text": "mediated", "start": 1438, "end": 1446}, "arguments": [{"role": "Theme", "text": "induced", "start": 1390, "end": 1397}]}, {"trigger": {"text": "phosphorylation", "start": 1648, "end": 1663}, "arguments": [{"role": "Cause", "text": "JNK", "start": 1572, "end": 1575}, {"role": "Theme", "text": "phosphorylation", "start": 1648, "end": 1663}]}, {"trigger": {"text": "activation", "start": 1668, "end": 1678}, "arguments": [{"role": "Cause", "text": "JNK", "start": 1572, "end": 1575}, {"role": "Theme", "text": "c-Jun", "start": 1682, "end": 1687}]}], "regulation": [{"trigger": {"text": "dependent", "start": 920, "end": 929}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 930, "end": 934}, {"role": "Site", "text": "promoter", "start": 935, "end": 943}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1200, "end": 1213}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1242, "end": 1246}]}]}}, "schema": []}
{"input": "Differential induction of interferon (IFN)-inducible protein 10 following differentiation of a monocyte, macrophage cell lineage is related to the changes of nuclear proteins bound to IFN stimulus response element and kappaB sites. \nWe examined chemokine gene expression following the differentiation of a monocyte, macrophage cell lineage. The human monoblastic cell line, U937 was differentiated to macrophages by the treatment with either phorbol 12-myristate 13-acetate (PMA), retinoic acid (RA), or vitamin D3 (VitD3). The gene expression of interferon (IFN)-inducible protein 10 (IP-10) (a CXC chemokine) was markedly augmented by the IFNgamma treatment in PMA- or RA-differentiated U937 cells, but only marginally in undifferentiated or VitD3-treated cells. In contrast, another inducible gene expression of monocyte chemotactic protein-1 (a CC chemokine) and the activation of the transcriptional factor (FcRFgamma) bound to the gamma response region were similarly or less abundantly induced by IFNgamma treatment in PMA- or RA-differentiated U937 cells, indicating that increased IP-10 mRNA induction was not due to the augmented ability of the cells to respond to the presence of IFNgamma. Increased expression of IFNgamma-induced IP-10 mRNA following the differentiation of U937 cells was mediated largely by augmented transcriptional activity of the gene and was related to differentiation-dependent changes of the proteins bound to IFN stimulus response element (ISRE) and kB sites, suggesting that these nuclear proteins may determine the IP-10 mRNA inducibility by IFNgamma. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "gene expression", "start": 528, "end": 543}, "arguments": [{"role": "Theme", "text": "IP-10", "start": 586, "end": 591}]}, {"trigger": {"text": "expression", "start": 801, "end": 811}, "arguments": [{"role": "Theme", "text": "monocyte chemotactic protein-1", "start": 815, "end": 845}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 13, "end": 22}, "arguments": [{"role": "Theme", "text": "interferon (IFN)-inducible protein 10", "start": 26, "end": 63}]}, {"trigger": {"text": "following", "start": 64, "end": 73}, "arguments": [{"role": "Theme", "text": "induction", "start": 13, "end": 22}]}, {"trigger": {"text": "augmented", "start": 624, "end": 633}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 528, "end": 543}, {"role": "Cause", "text": "IFNgamma", "start": 641, "end": 649}]}, {"trigger": {"text": "induced", "start": 993, "end": 1000}, "arguments": [{"role": "Theme", "text": "expression", "start": 801, "end": 811}, {"role": "Cause", "text": "IFNgamma", "start": 1004, "end": 1012}]}, {"trigger": {"text": "increased", "start": 1080, "end": 1089}, "arguments": [{"role": "Theme", "text": "induction", "start": 1101, "end": 1110}]}, {"trigger": {"text": "induction", "start": 1101, "end": 1110}, "arguments": [{"role": "Theme", "text": "IP-10", "start": 1090, "end": 1095}]}, {"trigger": {"text": "due", "start": 1119, "end": 1122}, "arguments": [{"role": "Theme", "text": "increased", "start": 1080, "end": 1089}]}, {"trigger": {"text": "Increased", "start": 1201, "end": 1210}, "arguments": [{"role": "Theme", "text": "induced", "start": 1234, "end": 1241}]}, {"trigger": {"text": "induced", "start": 1234, "end": 1241}, "arguments": [{"role": "Theme", "text": "expression", "start": 1211, "end": 1221}, {"role": "Cause", "text": "IFNgamma", "start": 1225, "end": 1233}]}, {"trigger": {"text": "mediated", "start": 1301, "end": 1309}, "arguments": [{"role": "Theme", "text": "Increased", "start": 1201, "end": 1210}, {"role": "Cause", "text": "augmented", "start": 1321, "end": 1330}]}, {"trigger": {"text": "augmented", "start": 1321, "end": 1330}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 1331, "end": 1355}]}, {"trigger": {"text": "transcriptional activity", "start": 1331, "end": 1355}, "arguments": [{"role": "Theme", "text": "IP-10", "start": 1242, "end": 1247}]}, {"trigger": {"text": "inducibility", "start": 1565, "end": 1577}, "arguments": [{"role": "Cause", "text": "IP-10", "start": 1554, "end": 1559}, {"role": "Theme", "text": "IFNgamma", "start": 1581, "end": 1589}]}], "regulation": [{"trigger": {"text": "determine", "start": 1540, "end": 1549}, "arguments": [{"role": "Theme", "text": "inducibility", "start": 1565, "end": 1577}]}], "transcription": [{"trigger": {"text": "expression", "start": 1211, "end": 1221}, "arguments": [{"role": "Theme", "text": "IP-10", "start": 1242, "end": 1247}]}]}}, "schema": []}
{"input": "Fludarabine-induced immunosuppression is associated with inhibition of STAT1 signaling. \nFludarabine is a nucleoside analog used in the treatment of hematologic malignancies that can induce severe and prolonged immunosuppression. Although it can be incorporated into the DNA of dividing cells, fludarabine is also a potent inhibitor of cells with a low growth fraction, thus it must have other mechanisms of action. STAT1, which is activated in response to many lymphocyte-activating cytokines including the interferons, is essential for cell-mediated immunity, as the absence of this protein is associated with prominent defects in the ability to control viral infections. Here we show that fludarabine, but not the immunosuppressant cyclosporine A, inhibits the cytokine-induced activation of STAT1 and STAT1-dependent gene transcription in normal resting or activated lymphocytes. Fludarabine caused a specific depletion of STAT1 protein (and mRNA) but not of other STATs. This loss of STAT1 was also seen in cells from patients treated with fludarabine in vivo. Brief exposure to fludarabine led to a sustained loss of STAT1, analogous to the prolonged period of immunosuppression induced by exposure to the drug in vivo. Thus, STAT1 may be a useful target in the development of new immunosuppressive and antineoplastic agents. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "absence", "start": 569, "end": 576}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 416, "end": 421}]}, {"trigger": {"text": "inhibits", "start": 751, "end": 759}, "arguments": [{"role": "Theme", "text": "activation", "start": 781, "end": 791}]}, {"trigger": {"text": "depletion", "start": 914, "end": 923}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 927, "end": 932}]}, {"trigger": {"text": "loss", "start": 981, "end": 985}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 989, "end": 994}]}, {"trigger": {"text": "loss", "start": 1115, "end": 1119}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1123, "end": 1128}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 432, "end": 441}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 416, "end": 421}]}, {"trigger": {"text": "activation", "start": 781, "end": 791}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 795, "end": 800}]}, {"trigger": {"text": "caused", "start": 896, "end": 902}, "arguments": [{"role": "Theme", "text": "depletion", "start": 914, "end": 923}]}, {"trigger": {"text": "led", "start": 1096, "end": 1099}, "arguments": [{"role": "Theme", "text": "loss", "start": 1115, "end": 1119}]}]}}, "schema": []}
{"input": "Suppressive effects of anti-inflammatory agents on human endothelial cell activation and induction of heat shock proteins. \nBACKGROUND: Studies from our laboratory have shown that the earliest stages of atherosclerosis may be mediated by an autoimmune reaction against heat shock protein 60 (Hsp60). The interactions of Hsp60-specific T cells with arterial endothelial cells (EC) require expression of both Hsp60 and certain adhesion molecules shown to be induced simultaneously in EC by mechanical and other types of stress. Recently, it was shown that suppression of T cell-mediated immune responses by cyclosporin A (CyA) enhanced atherosclerotic lesion formation in mice. In contrast, aspirin was found to lower the risk of myocardial infarction in men. These conflicting observations may be due to different effects of anti-inflammatory agents on adhesion molecule and Hsp expression in EC, respectively. MATERIAL AND METHODS: In the present study, we analyzed the effects of CyA, aspirin, and indomethacin on T cell proliferation using a proliferation assay. To explore the expression of adhesion molecules, monocyte chemoattractant protein-1 (MCP-1), and Hsp60 in human umbilical vein endothelial cells (HUVECs), Northern blot analyses were used. To examine the activation status of the transcription factors nuclear factor kappaB (NF-kappaB) and heat shock factor-1 (HSF-1), electrophoretic mobility shift assays were performed. RESULTS: With the exception of indomethacin, the used immunosuppressive and anti-inflammatory agents significantly inhibited T cell proliferation in response to influenza virus antigen in a dose-dependent manner. Interestingly, CyA and indomethacin did not suppress tumor necrosis factor-alpha (TNF-alpha)-induced adhesion molecule expression on HUVECs, whereas aspirin had an inhibitory effect. These observations correlated with the modulation of NF-kappaB activity in EC. All agents tested induced expression of Hsp60 6 hr after application. In addition, aspirin and indomethacin, but not CyA, induced Hsp70 expression in HUVECs that correlated with induction of HSF-1 activity. CONCLUSION: Our results show that the tested agents (except indomethacin) are inhibitors of the T cell-mediated immune response, as expected, that aspirin is an effective suppressor of adhesion molecule expression, and that all three agents can induce Hsp60 in HUVECs. These data provide the molecular basis for the notion that (1) part of the anti-atherogenic effect of aspirin may be due to the prevention of the adhesion of sensitized T cells to stressed EC; (2) that part of the atherosclerosis-promoting effect of CyA may be due to its potential as an inducer of Hsp60 expression and its inability to down-regulate adhesion molecule expression on EC; and (3) that down-regulation of MCP-1 expression by aspirin may result in decreased recruitment of monocytes into the arterial intima beneath stressed EC. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 388, "end": 398}, "arguments": [{"role": "Theme", "text": "Hsp60", "start": 407, "end": 412}]}, {"trigger": {"text": "expression", "start": 1080, "end": 1090}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 1150, "end": 1155}]}, {"trigger": {"text": "expression", "start": 1080, "end": 1090}, "arguments": [{"role": "Theme", "text": "Hsp60", "start": 1162, "end": 1167}]}, {"trigger": {"text": "expression", "start": 1938, "end": 1948}, "arguments": [{"role": "Theme", "text": "Hsp60", "start": 1952, "end": 1957}]}, {"trigger": {"text": "expression", "start": 2048, "end": 2058}, "arguments": [{"role": "Theme", "text": "Hsp70", "start": 2042, "end": 2047}]}, {"trigger": {"text": "expression", "start": 2693, "end": 2703}, "arguments": [{"role": "Theme", "text": "Hsp60", "start": 2687, "end": 2692}]}, {"trigger": {"text": "expression", "start": 2813, "end": 2823}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 2807, "end": 2812}]}], "negative regulation": [{"trigger": {"text": "down-regulation", "start": 2788, "end": 2803}, "arguments": [{"role": "Theme", "text": "expression", "start": 2813, "end": 2823}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 1269, "end": 1279}, "arguments": [{"role": "Theme", "text": "HSF-1", "start": 1375, "end": 1380}]}, {"trigger": {"text": "induced", "start": 1930, "end": 1937}, "arguments": [{"role": "Theme", "text": "expression", "start": 1938, "end": 1948}]}, {"trigger": {"text": "induced", "start": 2034, "end": 2041}, "arguments": [{"role": "Theme", "text": "expression", "start": 2048, "end": 2058}]}, {"trigger": {"text": "induction", "start": 2090, "end": 2099}, "arguments": [{"role": "Theme", "text": "HSF-1", "start": 2103, "end": 2108}]}, {"trigger": {"text": "induce", "start": 2364, "end": 2370}, "arguments": [{"role": "Theme", "text": "Hsp60", "start": 2371, "end": 2376}]}, {"trigger": {"text": "inducer", "start": 2676, "end": 2683}, "arguments": [{"role": "Theme", "text": "expression", "start": 2693, "end": 2703}]}]}}, "schema": []}
{"input": "Amelioration of rat cerulein pancreatitis by guamerin-derived peptide, a novel elastase inhibitor. \nIncreased activity of various proteases is observed in both human and experimental pancreatitis; however, the information on the effects of specific protease inhibitors on the disease is limited. In this study we show that a novel elastase inhibitor, guamerin-derived synthetic peptide (GDSP), improves the parameters of cerulein-induced acute pancreatitis in the rat. The effects of GDSP on pancreatic weight, serum amylase and lipase, morphologic changes in the pancreas, neutrophil infiltration, and nuclear factor KB (NF-KB) activation were measured in rats infused with supramaximal dose of cerulein (5 (g/kg/h) for 6 h. The effects of GDSP were also measured on superoxide formation by activated human neutrophils. The effects of GDSP were compared with those of another elastase inhibitor, elastatinal. GDSP significantly inhibited edema formation, neutrophil infiltration, acinar cell damage, and plasma lipase and amylase increases caused by cerulein. GDSP also completely inhibited superoxide formation in the human neutrophils stimulated by N-formyl-methionine-leucine-phenyl-alanine (fMLP) or 12-O-tetradecanoylphorbol-13-acetate (TPA). Elastatinal had some of the same effects as GDSP but was less potent and effective. These results demonstrate a beneficial effect of GDSP, a novel specific elastase inhibitor, on the development of rat cerulein pancreatitis. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Inhibition of T cell signaling by mitogen-activated protein kinase-targeted hematopoietic tyrosine phosphatase (HePTP). \nActivation of T lymphocytes to produce cytokines is regulated by the counterbalance of protein-tyrosine kinases and protein-tyrosine phosphatases, many of which have a high degree of substrate specificity because of physical association with their targets. Overexpression of hematopoietic protein-tyrosine phosphatase (HePTP) results in suppression of T lymphocyte activation as measured by T cell antigen receptor-induced activation of transcription factors binding to the 5' promoter of the interleukin-2 gene. Efforts to pinpoint the exact site of action and specificity of HePTP in the signaling cascade revealed that HePTP acts directly on the mitogen-activated protein (MAP) kinases Erk1 and 2 and consequently reduces the magnitude and duration of their catalytic activation in intact T cells. In contrast, HePTP had no effects on N-terminal c-Jun kinase or on events upstream of the MAP kinases. The specificity of HePTP correlated with its physical association through its noncatalytic N terminus with Erk and another MAP kinase, p38, but not Jnk or other proteins. We propose that HePTP plays a negative role in antigen receptor signaling by specifically regulating MAP kinases in the cytosol and at early time points of T cell activation before the activation-induced expression of nuclear dual-specific MAP kinase phosphatases. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 580, "end": 587}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 614, "end": 627}]}, {"trigger": {"text": "physical association", "start": 1070, "end": 1090}, "arguments": [{"role": "Theme", "text": "HePTP", "start": 1044, "end": 1049}]}], "gene expression": [{"trigger": {"text": "Overexpression", "start": 378, "end": 392}, "arguments": [{"role": "Theme", "text": "HePTP", "start": 440, "end": 445}]}], "negative regulation": [{"trigger": {"text": "reduces", "start": 838, "end": 845}, "arguments": [{"role": "Cause", "text": "HePTP", "start": 743, "end": 748}, {"role": "Theme", "text": "catalytic activation", "start": 882, "end": 902}]}], "positive regulation": [{"trigger": {"text": "Overexpression", "start": 378, "end": 392}, "arguments": [{"role": "Theme", "text": "HePTP", "start": 440, "end": 445}]}, {"trigger": {"text": "activation", "start": 544, "end": 554}, "arguments": [{"role": "Theme", "text": "binding", "start": 580, "end": 587}]}, {"trigger": {"text": "catalytic activation", "start": 882, "end": 902}, "arguments": [{"role": "Theme", "text": "Erk1", "start": 810, "end": 814}]}, {"trigger": {"text": "catalytic activation", "start": 882, "end": 902}, "arguments": [{"role": "Theme", "text": "2", "start": 819, "end": 820}]}], "regulation": [{"trigger": {"text": "acts", "start": 749, "end": 753}, "arguments": [{"role": "Cause", "text": "HePTP", "start": 743, "end": 748}, {"role": "Theme", "text": "Erk1", "start": 810, "end": 814}]}, {"trigger": {"text": "acts", "start": 749, "end": 753}, "arguments": [{"role": "Cause", "text": "HePTP", "start": 743, "end": 748}, {"role": "Theme", "text": "2", "start": 819, "end": 820}]}]}}, "schema": []}
{"input": "Angiotensin II activates the proinflammatory transcription factor nuclear factor-kappaB in human monocytes. \nThe renin-angiotensin system may contribute to the pathogenesis of atherosclerosis. A common feature of all stages of atherosclerosis is inflammation of the vessel wall. The transcription factor nuclear factor-kappaB (NF-kappaB) participates in most signaling pathways involved in inflammation. This study therefore examined the effect of angiotensin (ANG) II on NF-kappaB activation in monocytic cells, a major cellular component of human atheroma, by electrophoretic mobility shift assay. ANG II, like TNFalpha, caused rapid activation of NF-kappaB in human mononuclear cells isolated from peripheral blood by Ficoll density gradient. This ANG II effect was blocked by the angiotensin AT1 receptor antagonist losartan. Specificity of ANG II-induced NF-kappaB activation was ascertained by supershift and competition experiments. Moreover, ANG II stimulated NF-kappaB activation in human monocytes, but not in lymphocytes from the same preparation. Together, the data demonstrate the ability of the vasoactive peptide ANG II to activate inflammatory pathways in human monocytes. Copyright 1999 Academic Press. ", "output": {"json_structures": {}}, "schema": []}
{"input": "SHP2-interacting transmembrane adaptor protein (SIT), a novel disulfide-linked dimer regulating human T cell activation. \nT lymphocytes express several low molecular weight transmembrane adaptor proteins that recruit src homology (SH)2 domain-containing intracellular molecules to the cell membrane via tyrosine-based signaling motifs. We describe here a novel molecule of this group termed SIT (SHP2 interacting transmembrane adaptor protein). SIT is a disulfide-linked homodimeric glycoprotein that is expressed in lymphocytes. After tyrosine phosphorylation by src and possibly syk protein tyrosine kinases SIT recruits the SH2 domain-containing tyrosine phosphatase SHP2 via an immunoreceptor tyrosine-based inhibition motif. Overexpression of SIT in Jurkat cells downmodulates T cell receptor- and phytohemagglutinin-mediated activation of the nuclear factor of activated T cells (NF-AT) by interfering with signaling processes that are probably located upstream of activation of phospholipase C. However, binding of SHP2 to SIT is not required for inhibition of NF-AT induction, suggesting that SIT not only regulates NF-AT activity but also controls NF-AT unrelated pathways of T cell activation involving SHP2. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1011, "end": 1018}, "arguments": [{"role": "Theme", "text": "SHP2", "start": 1022, "end": 1026}, {"role": "Theme2", "text": "SIT", "start": 1030, "end": 1033}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 504, "end": 513}, "arguments": [{"role": "Theme", "text": "SIT", "start": 445, "end": 448}]}, {"trigger": {"text": "Overexpression", "start": 730, "end": 744}, "arguments": [{"role": "Theme", "text": "SIT", "start": 748, "end": 751}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 545, "end": 560}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 536, "end": 544}, {"role": "Theme", "text": "SIT", "start": 610, "end": 613}]}], "positive regulation": [{"trigger": {"text": "by", "start": 561, "end": 563}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 545, "end": 560}, {"role": "Cause", "text": "src", "start": 564, "end": 567}]}, {"trigger": {"text": "by", "start": 561, "end": 563}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 545, "end": 560}, {"role": "Cause", "text": "syk", "start": 581, "end": 584}]}]}}, "schema": []}
{"input": "GrpL, a Grb2-related adaptor protein, interacts with SLP-76 to regulate nuclear factor of activated T cell activation. \nPropagation of signals from the T cell antigen receptor (TCR) involves a number of adaptor molecules. SH2 domain-containing protein 76 (SLP-76) interacts with the guanine nucleotide exchange factor Vav to activate the nuclear factor of activated cells (NF-AT), and its expression is required for normal T cell development. We report the cloning and characterization of a novel Grb2-like adaptor molecule designated as Grb2-related protein of the lymphoid system (GrpL). Expression of GrpL is restricted to hematopoietic tissues, and it is distinguished from Grb2 by having a proline-rich region. GrpL can be coimmunoprecipitated with SLP-76 but not with Sos1 or Sos2 from Jurkat cell lysates. In contrast, Grb2 can be coimmunoprecipitated with Sos1 and Sos2 but not with SLP-76. Moreover, tyrosine-phosphorylated LAT/pp36/38 in detergent lysates prepared from anti-CD3 stimulated T cells associated with Grb2 but not GrpL. These data reveal the presence of distinct complexes involving GrpL and Grb2 in T cells. A functional role of the GrpL-SLP-76 complex is suggested by the ability of GrpL to act alone or in concert with SLP-76 to augment NF-AT activation in Jurkat T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 38, "end": 47}, "arguments": [{"role": "Theme", "text": "GrpL", "start": 0, "end": 4}, {"role": "Theme2", "text": "SLP-76", "start": 53, "end": 59}]}, {"trigger": {"text": "interacts", "start": 264, "end": 273}, "arguments": [{"role": "Theme", "text": "SLP-76", "start": 256, "end": 262}, {"role": "Theme2", "text": "Vav", "start": 318, "end": 321}]}, {"trigger": {"text": "coimmunoprecipitated", "start": 728, "end": 748}, "arguments": [{"role": "Theme", "text": "GrpL", "start": 716, "end": 720}, {"role": "Theme2", "text": "SLP-76", "start": 754, "end": 760}]}, {"trigger": {"text": "coimmunoprecipitated", "start": 728, "end": 748}, "arguments": [{"role": "Theme", "text": "GrpL", "start": 716, "end": 720}, {"role": "Theme2", "text": "Sos1", "start": 774, "end": 778}]}, {"trigger": {"text": "coimmunoprecipitated", "start": 728, "end": 748}, "arguments": [{"role": "Theme", "text": "GrpL", "start": 716, "end": 720}, {"role": "Theme2", "text": "Sos2", "start": 782, "end": 786}]}, {"trigger": {"text": "coimmunoprecipitated", "start": 838, "end": 858}, "arguments": [{"role": "Theme", "text": "Grb2", "start": 826, "end": 830}, {"role": "Theme2", "text": "Sos1", "start": 864, "end": 868}]}, {"trigger": {"text": "coimmunoprecipitated", "start": 838, "end": 858}, "arguments": [{"role": "Theme", "text": "Grb2", "start": 826, "end": 830}, {"role": "Theme2", "text": "Sos2", "start": 873, "end": 877}]}, {"trigger": {"text": "coimmunoprecipitated", "start": 838, "end": 858}, "arguments": [{"role": "Theme", "text": "Grb2", "start": 826, "end": 830}, {"role": "Theme2", "text": "SLP-76", "start": 891, "end": 897}]}, {"trigger": {"text": "associated", "start": 1008, "end": 1018}, "arguments": [{"role": "Theme", "text": "LAT", "start": 933, "end": 936}, {"role": "Theme2", "text": "Grb2", "start": 1024, "end": 1028}]}, {"trigger": {"text": "associated", "start": 1008, "end": 1018}, "arguments": [{"role": "Theme", "text": "LAT", "start": 933, "end": 936}, {"role": "Theme2", "text": "GrpL", "start": 1037, "end": 1041}]}], "gene expression": [{"trigger": {"text": "expression", "start": 389, "end": 399}, "arguments": [{"role": "Theme", "text": "SLP-76", "start": 256, "end": 262}]}, {"trigger": {"text": "Expression", "start": 590, "end": 600}, "arguments": [{"role": "Theme", "text": "GrpL", "start": 604, "end": 608}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 918, "end": 932}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 909, "end": 917}, {"role": "Theme", "text": "LAT", "start": 933, "end": 936}]}]}}, "schema": []}
{"input": "Unexpected and coordinated expression of Spi-1, Fli-1, and megakaryocytic genes in four Epo-dependent cell lines established from transgenic mice displaying erythroid-specific expression of a thermosensitive SV40 T antigen. \nMost erythroleukemic cell lines established in vitro coexpress erythrocytic and megakaryocytic markers that often are associated with expression of Spi-1 and/or Fli-1 transcription factors known as transactivators of megakaryocyte-specific promoters. In the present study, we examined the possibility of establishing new cell lines keeping strictly erythroid-specific properties in vitro through the targeted and conditional immortalization of erythrocytic progenitors. For that purpose, we established several lines of transgenic mice displaying erythroid-specific expression of a thermosensitive SV40 T antigen. As expected, these transgenic mice developed splenomegaly due to the massive amplification of Ter 119 positive erythroid nucleated cells expressing T antigen. Despite this drastic effect in vivo, the in vitro immortalization of erythropoietin-dependent erythroid progenitors unexpectedly occurred at low frequency, and all four cell lines established expressed both erythrocytic (globins) and megakaryocytic markers (glycoprotein IIb, platelet factor 4) as well as Spi-1 and Fli-1 transcripts at permissive temperature. Switching the cells to the nonpermissive temperature led to a marked increase in globin gene expression and concomitant decrease in expression of Spi-1, Fli-1, and megakaryocytic genes in an erythropoietin-dependent manner. Interestingly, enhanced expression of Spi-1 and Fli-1 genes already was detected in the Ter 119 positive cell population of transgenic mice spleen in vivo. However, like normal Ter 119 erythroid cells, these Ter 119 positive cells from transgenic mice still expressed high levels of beta-globin and very low or undetectable glycoprotein IIb and platelet factor 4 megakaryocytic transcripts. Taken together, these data indicate that the unexpected expression of megakaryocytic genes is a specific property of immortalized cells that cannot be explained only by enhanced expression of Spi-1 and/or Fli-1 genes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 27, "end": 37}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 41, "end": 46}]}, {"trigger": {"text": "expression", "start": 27, "end": 37}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 48, "end": 53}]}, {"trigger": {"text": "expression", "start": 359, "end": 369}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 373, "end": 378}]}, {"trigger": {"text": "expression", "start": 359, "end": 369}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 386, "end": 391}]}, {"trigger": {"text": "expressed", "start": 1190, "end": 1199}, "arguments": [{"role": "Theme", "text": "glycoprotein IIb", "start": 1256, "end": 1272}]}, {"trigger": {"text": "expressed", "start": 1190, "end": 1199}, "arguments": [{"role": "Theme", "text": "platelet factor 4", "start": 1274, "end": 1291}]}, {"trigger": {"text": "expression", "start": 1491, "end": 1501}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 1505, "end": 1510}]}, {"trigger": {"text": "expression", "start": 1491, "end": 1501}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 1512, "end": 1517}]}, {"trigger": {"text": "expression", "start": 1607, "end": 1617}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 1621, "end": 1626}]}, {"trigger": {"text": "expression", "start": 1607, "end": 1617}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 1631, "end": 1636}]}, {"trigger": {"text": "expression", "start": 2152, "end": 2162}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 2166, "end": 2171}]}, {"trigger": {"text": "expression", "start": 2152, "end": 2162}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 2179, "end": 2184}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 1479, "end": 1487}, "arguments": [{"role": "Theme", "text": "expression", "start": 1491, "end": 1501}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 1565, "end": 1574}, "arguments": [{"role": "Theme", "text": "decrease", "start": 1479, "end": 1487}, {"role": "Cause", "text": "erythropoietin", "start": 1550, "end": 1564}]}, {"trigger": {"text": "enhanced", "start": 2143, "end": 2151}, "arguments": [{"role": "Theme", "text": "expression", "start": 2152, "end": 2162}]}], "transcription": [{"trigger": {"text": "expressed", "start": 1190, "end": 1199}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 1304, "end": 1309}]}, {"trigger": {"text": "expressed", "start": 1190, "end": 1199}, "arguments": [{"role": "Theme", "text": "Fli-1", "start": 1314, "end": 1319}]}, {"trigger": {"text": "expressed", "start": 1841, "end": 1850}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 1866, "end": 1877}]}, {"trigger": {"text": "expressed", "start": 1841, "end": 1850}, "arguments": [{"role": "Theme", "text": "glycoprotein IIb", "start": 1907, "end": 1923}]}, {"trigger": {"text": "expressed", "start": 1841, "end": 1850}, "arguments": [{"role": "Theme", "text": "platelet factor 4", "start": 1928, "end": 1945}]}]}}, "schema": []}
{"input": "LPS-Induced NF-kappaB activation and TNF-alpha release in human monocytes are protein tyrosine kinase dependent and protein kinase C independent. \nBACKGROUND: Tumor necrosis factor alpha (TNF-alpha) is an important mediator of septic shock. Endotoxin (LPS) signal transduction in human monocytes leads to activation of nuclear factor-kappa B (NF-kappaB) and TNF-alpha release. Previous studies have implicated activation of both protein kinase C (PKC) and protein tyrosine kinases (PTK) in LPS-induced NF-kappaB activation and TNF-alpha production. We hypothesized that inhibition of either PKC or PTK would decrease LPS-induced NF-kappaB DNA binding and TNF-alpha release in human monocytes. MATERIALS AND METHODS: Human monocytes were stimulated with PMA (50 ng/ml) alone or LPS (100 ng/ml) with and without a nonspecific serine/threonine protein kinase inhibitor staurosporine (Stauro), a specific pan-PKC inhibitor bisindolylmaleimide (Bis), or an inhibitor of PTK genistein (Gen). TNF-alpha release in culture supernatants was measured by an ELISA. NF-kappaB DNA binding was evaluated by electrophoretic mobility shift assay. RESULTS: LPS increased NF-kappaB DNA binding and TNF-alpha release in human monocytes. Nonspecific protein kinase inhibition inhibited NF-kappaB activation and TNF-alpha release, while specific PKC inhibition with Bis had no effect on LPS-induced NF-kappaB DNA binding or TNF-alpha release. PTK inhibition with Gen attenuated both LPS-induced NF-kappaB DNA binding and TNF-alpha production in human monocytes. Direct activation of PKC with PMA induced both NF-kappaB activation and TNF-alpha production by human monocytes. CONCLUSIONS: These results suggest that LPS-induced NF-kappaB activation and TNF-alpha release in human monocytes are independent of PKC activity. Furthermore, our results provide evidence that PTK plays a role in LPS-induced NF-kappaB activation and TNF-alpha release in human monocytes and thus could be a potential therapeutic target in inflammatory states. Copyright 1999 Academic Press. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 537, "end": 547}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 527, "end": 536}]}, {"trigger": {"text": "production", "start": 1510, "end": 1520}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1500, "end": 1509}]}, {"trigger": {"text": "production", "start": 1623, "end": 1633}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1613, "end": 1622}]}], "localization": [{"trigger": {"text": "release", "start": 47, "end": 54}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 37, "end": 46}]}, {"trigger": {"text": "release", "start": 368, "end": 375}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 358, "end": 367}]}, {"trigger": {"text": "release", "start": 1190, "end": 1197}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1180, "end": 1189}]}, {"trigger": {"text": "release", "start": 1301, "end": 1308}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1291, "end": 1300}]}, {"trigger": {"text": "release", "start": 1413, "end": 1420}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1403, "end": 1412}]}, {"trigger": {"text": "release", "start": 1741, "end": 1748}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1731, "end": 1740}]}, {"trigger": {"text": "release", "start": 1915, "end": 1922}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1905, "end": 1914}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1256, "end": 1265}, "arguments": [{"role": "Theme", "text": "release", "start": 1301, "end": 1308}]}, {"trigger": {"text": "attenuated", "start": 1446, "end": 1456}, "arguments": [{"role": "Theme", "text": "induced", "start": 1466, "end": 1473}]}], "positive regulation": [{"trigger": {"text": "Induced", "start": 4, "end": 11}, "arguments": [{"role": "Theme", "text": "release", "start": 47, "end": 54}]}, {"trigger": {"text": "leads", "start": 296, "end": 301}, "arguments": [{"role": "Theme", "text": "release", "start": 368, "end": 375}]}, {"trigger": {"text": "induced", "start": 494, "end": 501}, "arguments": [{"role": "Theme", "text": "production", "start": 537, "end": 547}]}, {"trigger": {"text": "increased", "start": 1144, "end": 1153}, "arguments": [{"role": "Theme", "text": "release", "start": 1190, "end": 1197}]}, {"trigger": {"text": "induced", "start": 1370, "end": 1377}, "arguments": [{"role": "Theme", "text": "release", "start": 1413, "end": 1420}]}, {"trigger": {"text": "induced", "start": 1466, "end": 1473}, "arguments": [{"role": "Theme", "text": "production", "start": 1510, "end": 1520}]}, {"trigger": {"text": "induced", "start": 1575, "end": 1582}, "arguments": [{"role": "Theme", "text": "production", "start": 1623, "end": 1633}]}, {"trigger": {"text": "induced", "start": 1698, "end": 1705}, "arguments": [{"role": "Theme", "text": "release", "start": 1741, "end": 1748}]}, {"trigger": {"text": "induced", "start": 1872, "end": 1879}, "arguments": [{"role": "Theme", "text": "release", "start": 1915, "end": 1922}]}], "regulation": [{"trigger": {"text": "effect", "start": 1356, "end": 1362}, "arguments": [{"role": "Theme", "text": "induced", "start": 1370, "end": 1377}]}]}}, "schema": []}
{"input": "Cellular disposition of sulphamethoxazole and its metabolites: implications for hypersensitivity. \n1. Bioactivation of sulphamethoxazole (SMX) to chemically-reactive metabolites and subsequent protein conjugation is thought to be involved in SMX hypersensitivity. We have therefore examined the cellular metabolism, disposition and conjugation of SMX and its metabolites in vitro. 2. Flow cytometry revealed binding of N-hydroxy (SMX-NHOH) and nitroso (SMX-NO) metabolites of SMX, but not of SMX itself, to the surface of viable white blood cells. Cellular haptenation by SMX-NO was reduced by exogenous glutathione (GSH). 3. SMX-NHOH and SMX-NO were rapidly reduced back to the parent compound by cysteine (CYS), GSH, human peripheral blood cells and plasma, suggesting that this is an important and ubiquitous bioinactivation mechanism. 4. Fluorescence HPLC showed that SMX-NHOH and SMX-NO depleted CYS and GSH in buffer, and to a lesser extent, in cells and plasma. 5. Neutrophil apoptosis and inhibition of neutrophil function were induced at lower concentrations of SMX-NHOH and SMX-NO than those inducing loss of membrane viability, with SMX having no effect. Lymphocytes were significantly (P<0.05) more sensitive to the direct cytotoxic effects of SMX-NO than neutrophils. 6. Partitioning of SMX-NHOH into red blood cells was significantly (P<0.05) lower than with the hydroxylamine of dapsone. 7. Our results suggest that the balance between oxidation of SMX to its toxic metabolites and their reduction is an important protective cellular mechanism. If an imbalance exists, haptenation of the toxic metabolites to bodily proteins including the surface of viable cells can occur, and may result in drug hypersensitivity. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Tcf-1-mediated transcription in T lymphocytes: differential role for glycogen synthase kinase-3 in fibroblasts and T cells. \nBeta-catenin is the vertebrate homolog of the Drosophila segment polarity gene Armadillo and plays roles in both cell-cell adhesion and transduction of the Wnt signaling cascade. Recently, members of the Lef/Tcf transcription factor family have been identified as protein partners of beta-catenin, explaining how beta-catenin alters gene expression. Here we report that in T cells, Tcf-1 also becomes transcriptionally active through interaction with beta-catenin, suggesting that the Wnt signal transduction pathway is operational in T lymphocytes as well. However, although Wnt signals are known to inhibit the activity of the negative regulatory protein kinase glycogen synthase kinase-3beta (GSK-3beta), resulting in increased levels of beta-catenin, we find no evidence for involvement of GSK-3beta in Tcf-mediated transcription in T cells. That is, a dominant negative GSK-3beta does not specifically activate Tcf transcription and stimuli (lithium or phytohemagglutinin) that inhibit GSK-3beta activity also do not activate Tcf reporter genes. Thus, inhibition of GSK-3beta is insufficient to activate Tcf-dependent transcription in T lymphocytes. In contrast, in C57MG fibroblast cells, lithium inactivates GSK-3beta and induces Tcf-controlled transcription. This is the first demonstration that lithium can alter gene expression of Tcf-responsive genes, and points to a difference in regulation of Wnt signaling between fibroblasts and lymphocytes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 559, "end": 570}, "arguments": [{"role": "Theme", "text": "Tcf-1", "start": 507, "end": 512}, {"role": "Theme2", "text": "beta-catenin", "start": 576, "end": 588}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 726, "end": 733}, "arguments": [{"role": "Theme", "text": "GSK-3beta", "start": 821, "end": 830}]}, {"trigger": {"text": "inhibit", "start": 1108, "end": 1115}, "arguments": [{"role": "Cause", "text": "phytohemagglutinin", "start": 1083, "end": 1101}, {"role": "Theme", "text": "GSK-3beta", "start": 1116, "end": 1125}]}, {"trigger": {"text": "inhibit", "start": 1108, "end": 1115}, "arguments": [{"role": "Theme", "text": "GSK-3beta", "start": 1116, "end": 1125}]}, {"trigger": {"text": "inhibition", "start": 1182, "end": 1192}, "arguments": [{"role": "Theme", "text": "GSK-3beta", "start": 1196, "end": 1205}]}, {"trigger": {"text": "inactivates", "start": 1328, "end": 1339}, "arguments": [{"role": "Theme", "text": "GSK-3beta", "start": 1340, "end": 1349}]}], "positive regulation": [{"trigger": {"text": "becomes transcriptionally active", "start": 518, "end": 550}, "arguments": [{"role": "Theme", "text": "Tcf-1", "start": 507, "end": 512}, {"role": "Cause", "text": "interaction", "start": 559, "end": 570}]}, {"trigger": {"text": "increased levels", "start": 846, "end": 862}, "arguments": [{"role": "Cause", "text": "inhibit", "start": 726, "end": 733}, {"role": "Theme", "text": "beta-catenin", "start": 866, "end": 878}]}]}}, "schema": []}
{"input": "CIITA-induced occupation of MHC class II promoters is independent of the cooperative stabilization of the promoter-bound multi-protein complexes. \nPrecise regulation of MHC class II expression plays a crucial role in the control of the immune response. The transactivator CIITA behaves as a master controller of constitutive and inducible MHC class II gene activation, but its exact mechanism of action is not known. Activation of MHC class II promoters requires binding of at least three distinct multi-protein complexes (RFX, X2BP and NF-Y). It is known that the stability of this binding results from cooperative interactions between these proteins. We show here that expression of CIITA in MHC class II- cells triggers occupation of the promoters by these complexes. This observation raised the possibility that the effect of CIITA on promoter occupation is mediated by an effect on the cooperative stabilization of the DNA-bound multi-protein complexes. We show, however, that the presence of CIITA does not affect the stability of the higher-order protein complex formed on DNA by RFX, X2BP and NF-Y. This suggests other mechanisms for CIITA-induced promoter occupancy, such as an effect on chromatin structure leading to increased accessibility of MHC class II promoters. This ability of CIITA to facilitate promoter occupation is undissociable from its transactivation potential. Finally, we conclude that this effect of CIITA is cell-type specific, since expression of CIITA is not required for normal occupation of MHC class II promoters in B lymphocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 671, "end": 681}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 685, "end": 690}]}, {"trigger": {"text": "expression", "start": 1464, "end": 1474}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 1478, "end": 1483}]}]}}, "schema": []}
{"input": "Immunosuppressant PG490 (triptolide) inhibits T-cell interleukin-2 expression at the level of purine-box/nuclear factor of activated T-cells and NF-kappaB transcriptional activation. \nPG490 (triptolide) is a diterpene triepoxide with potent immunosuppressive and antiinflammatory properties. PG490 inhibits interleukin(IL)-2 expression by normal human peripheral blood lymphocytes stimulated with phorbol 12-myristate 13-acetate (PMA) and antibody to CD3 (IC50 of 10 ng/ml), and with PMA and ionomycin (Iono, IC50 of 40 ng/ml). In Jurkat T-cells, PG490 inhibits PMA/Iono-stimulated IL-2 transcription. PG490 inhibits the induction of DNA binding activity at the purine-box/antigen receptor response element (ARRE)/nuclear factor of activated T-cells (NF-AT) target sequence but not at the NF-kappaB site. PG490 can completely inhibit transcriptional activation at the purine-box/ARRE/NF-AT and NF-kappaB target DNA sequences triggered by all stimuli examined (PMA, PMA/Iono, tumor necrosis factor-alpha). PG490 also inhibits PMA-stimulated activation of a chimeric transcription factor in which the C-terminal TA1 transactivation domain of NF-kappaB p65 is fused to the DNA binding domain of GAL4. In 16HBE human bronchial epithelial cells, IL-8 expression is regulated predominantly by NF-kappaB, and PG490 but not cyclosporin A can completely inhibit expression of IL-8. The mechanism of PG490 inhibition of cytokine gene expression differs from cyclosporin A and involves nuclear inhibition of transcriptional activation of NF-kappaB and the purine-box regulator operating at the ARRE/NF-AT site at a step after specific DNA binding. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 67, "end": 77}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 53, "end": 66}]}, {"trigger": {"text": "expression", "start": 325, "end": 335}, "arguments": [{"role": "Theme", "text": "interleukin(IL)-2", "start": 307, "end": 324}]}, {"trigger": {"text": "expression", "start": 1246, "end": 1256}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1241, "end": 1245}]}, {"trigger": {"text": "expression", "start": 1353, "end": 1363}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1367, "end": 1371}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 37, "end": 45}, "arguments": [{"role": "Theme", "text": "expression", "start": 67, "end": 77}]}, {"trigger": {"text": "inhibits", "start": 298, "end": 306}, "arguments": [{"role": "Theme", "text": "expression", "start": 325, "end": 335}]}, {"trigger": {"text": "PG490", "start": 547, "end": 552}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 571, "end": 581}]}, {"trigger": {"text": "inhibit", "start": 1345, "end": 1352}, "arguments": [{"role": "Theme", "text": "expression", "start": 1353, "end": 1363}]}], "positive regulation": [{"trigger": {"text": "stimulated", "start": 571, "end": 581}, "arguments": [{"role": "Theme", "text": "transcription", "start": 587, "end": 600}]}], "regulation": [{"trigger": {"text": "regulated", "start": 1260, "end": 1269}, "arguments": [{"role": "Theme", "text": "expression", "start": 1246, "end": 1256}]}], "transcription": [{"trigger": {"text": "transcription", "start": 587, "end": 600}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 582, "end": 586}]}]}}, "schema": []}
{"input": "Activation of nuclear factor-kappaB by lipopolysaccharide in mononuclear leukocytes is prevented by inhibitors of cytosolic phospholipase A2. \nIn monocytes, lipopolysaccharide induces synthesis and activity of the 85-kDa cytosolic phospholipase A2. This enzyme releases arachidonic acid and lyso-phospholipids from membranes which are metabolized to eicosanoids and platelet-activating-factor. These lipid mediators increase activity of transcription factors and expression of cytokine genes indicating a function for cytosolic phospholipase A2 in signal transduction and inflammation. We have shown previously that trifluoromethylketone inhibitors of cytosolic phospholipase A2 suppressed interleukin-1beta protein and steady-state mRNA levels in human lipopolysaccharide-stimulated peripheral blood mononuclear leukocytes. In this study, the subcellular mechanisms were analyzed by which trifluoromethylketones interfere with gene expression. We found that they reduced the initial interleukin-1beta mRNA transcription rate through prevention of degradation of inhibitor-kappaB alpha. Consequently, cytosolic activation, nuclear translocation and DNA-binding of nuclear factor-kappaB were decreased. Trifluoromethylketones ameliorate chronic inflammation in vivo. Thus, this therapeutic potency may reside in retention of inactive nuclear factor-kappaB in the cytosol thereby abrogating interleukin-1beta gene transcription. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "suppressed", "start": 679, "end": 689}, "arguments": [{"role": "Theme", "text": "interleukin-1beta", "start": 690, "end": 707}]}, {"trigger": {"text": "reduced", "start": 964, "end": 971}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1007, "end": 1020}]}, {"trigger": {"text": "abrogating", "start": 1378, "end": 1388}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1412, "end": 1425}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 1048, "end": 1059}, "arguments": [{"role": "Theme", "text": "inhibitor-kappaB alpha", "start": 1063, "end": 1085}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1007, "end": 1020}, "arguments": [{"role": "Theme", "text": "interleukin-1beta", "start": 984, "end": 1001}]}, {"trigger": {"text": "transcription", "start": 1412, "end": 1425}, "arguments": [{"role": "Theme", "text": "interleukin-1beta", "start": 1389, "end": 1406}]}]}}, "schema": []}
{"input": "Molecular regulation of cytokine gene expression during the immune response. \nCytokine expression by immune system cells plays an important role in the regulation of the immune response. On first encounter with antigen, naive CD4+ T helper (Th) cells differentiate into cytokine-producing effector cells. Two types of effector cells characterized by their distinct expression of cytokine profiles have been described. Th1 cells produce IL-2 and IFN-gamma, whereas Th2 cells produce IL-4, IL-5, IL-6, IL-10, and IL-13. In many pathological situations, the balance between Th1 and Th2 immune responses determines the outcome of diverse immunologically mediated clinical syndromes including infectious, autoimmune, and allergic diseases. However, the molecular basis for the tissue-specific expression of Th1/Th2-like cytokines has remained elusive. In this review we evaluate the possible in vivo role of different transcription factors and transcriptional mechanisms in T cell differentiation and the immune response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "produce", "start": 428, "end": 435}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 436, "end": 440}]}, {"trigger": {"text": "produce", "start": 428, "end": 435}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 445, "end": 454}]}, {"trigger": {"text": "produce", "start": 474, "end": 481}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 482, "end": 486}]}, {"trigger": {"text": "produce", "start": 474, "end": 481}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 488, "end": 492}]}, {"trigger": {"text": "produce", "start": 474, "end": 481}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 494, "end": 498}]}, {"trigger": {"text": "produce", "start": 474, "end": 481}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 500, "end": 505}]}, {"trigger": {"text": "produce", "start": 474, "end": 481}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 511, "end": 516}]}]}}, "schema": []}
{"input": "The evolutionarily conserved sequence upstream of the human Ig heavy chain S gamma 3 region is an inducible promoter: synergistic activation by CD40 ligand and IL-4 via cooperative NF-kappa B and STAT-6 binding sites. \nGermline C gamma gene transcription is a crucial event in the process that leads to switch DNA recombination to IgG, but its regulation in the human is poorly understood. We took advantage of our monoclonal model of germinal center B cell differentiation, IgM+ IgD+ CL-01 cells, to define the role of the I gamma 3 evolutionarily conserved sequence (ECS) in the germline transcriptional activation of the human C gamma 3 gene. The I gamma 3 ECS lies upstream of the major I gamma 3 transcription initiation site and displays more than 90% identity with the corresponding human I gamma 1, I gamma 2, and I gamma 4 regions. Reporter luciferase gene vectors containing the human gamma 3 ECS were used to transfect CL-01 cells, which have been shown to undergo Smu-->S gamma 3 DNA recombination, upon engagement of CD40 by CD40 ligand (CD40L) and exposure to IL-4. In these transfected CL-01 cells, CD40:CD40L engagement and exposure to IL-4 synergistically induced gamma 3 ECS-dependent luciferase reporter gene activation. Targeted mutational analysis demonstrated that a tandem NF-kappa B/Rel binding motif is critical for the gamma 3 ECS responsiveness to both CD40L and IL-4, while a STAT-6-binding site is additionally required for IL-4 inducibility. Electrophoretic mobility shift assays showed that p50/p65/c-Rel and STAT-6 are effectively induced by CD40L and IL-4, respectively, and bind to specific DNA motifs within the ECS. These partially overlapping CD40L and IL-4 responsive elements are functionally cooperative as the disruption of one of them prevents synergistic promoter activation. Thus, the gamma 3 ECS is an inducible promoter containing cis elements that critically mediate CD40L and IL-4-triggered transcriptional activation of the human C gamma 3 gene. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "engagement", "start": 1016, "end": 1026}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1030, "end": 1034}, {"role": "Theme2", "text": "CD40 ligand", "start": 1038, "end": 1049}]}, {"trigger": {"text": "engagement", "start": 1125, "end": 1135}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1114, "end": 1118}, {"role": "Theme2", "text": "CD40L", "start": 1119, "end": 1124}]}, {"trigger": {"text": "bind", "start": 1608, "end": 1612}, "arguments": [{"role": "Theme", "text": "p50", "start": 1522, "end": 1525}]}, {"trigger": {"text": "bind", "start": 1608, "end": 1612}, "arguments": [{"role": "Theme", "text": "p65", "start": 1526, "end": 1529}]}, {"trigger": {"text": "bind", "start": 1608, "end": 1612}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1530, "end": 1535}]}, {"trigger": {"text": "bind", "start": 1608, "end": 1612}, "arguments": [{"role": "Theme", "text": "STAT-6", "start": 1540, "end": 1546}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 606, "end": 616}, "arguments": [{"role": "Theme", "text": "C gamma 3", "start": 630, "end": 639}]}, {"trigger": {"text": "inducibility", "start": 1458, "end": 1470}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1453, "end": 1457}]}, {"trigger": {"text": "induced", "start": 1563, "end": 1570}, "arguments": [{"role": "Theme", "text": "p50", "start": 1522, "end": 1525}, {"role": "Cause", "text": "CD40L", "start": 1574, "end": 1579}]}, {"trigger": {"text": "induced", "start": 1563, "end": 1570}, "arguments": [{"role": "Theme", "text": "p65", "start": 1526, "end": 1529}, {"role": "Cause", "text": "CD40L", "start": 1574, "end": 1579}]}, {"trigger": {"text": "induced", "start": 1563, "end": 1570}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1530, "end": 1535}, {"role": "Cause", "text": "CD40L", "start": 1574, "end": 1579}]}, {"trigger": {"text": "induced", "start": 1563, "end": 1570}, "arguments": [{"role": "Theme", "text": "STAT-6", "start": 1540, "end": 1546}, {"role": "Cause", "text": "IL-4", "start": 1584, "end": 1588}]}], "regulation": [{"trigger": {"text": "role", "start": 512, "end": 516}, "arguments": [{"role": "Theme", "text": "activation", "start": 606, "end": 616}]}]}}, "schema": []}
{"input": "Thrombin-induced p65 homodimer binding to downstream NF-kappa B site of the promoter mediates endothelial ICAM-1 expression and neutrophil adhesion. \nWe investigated the mechanisms by which proinflammatory mediator, thrombin, released during intravascular coagulation and tissue injury, induces ICAM-1 (CD54) expression in endothelial cells. Stimulation of HUVEC with thrombin resulted in dose- and time-dependent increases in ICAM-1 mRNA and cell surface expression and in ICAM-1-dependent endothelial adhesivity toward polymorphonuclear leukocytes. Transient transfection of endothelial cells with ICAM-1 promoter luciferase reporter gene (ICAM-1LUC) constructs indicated that deletion of upstream NF-kappa B site (-533 bases from translation start site) had no effect on thrombin responsiveness, whereas mutation/deletion of downstream NF-kappa B site (-223 bases from the translation start site) prevented the activation of ICAM-1 promoter, indicating that the downstream NF-kappa B site is critical for thrombin inducibility. NF-kappa B-directed luciferase activity increased approximately 3-fold when cells transfected with the plasmid pNF-kappa BLUC containing five copies of consensus NF-kappa B site linked to a minimal adenovirus E1B promoter-luciferase gene were exposed to thrombin, indicating that activation of NF-kappa B was essential for thrombin response. Gel supershift assays demonstrated that thrombin induced binding of NF-kappa Bp65 (Rel A) to downstream NF-kappa B site of the ICAM-1 promoter. Thrombin receptor activation peptide, a 14-amino-acid peptide representing the new NH2 terminus of proteolytically activated receptor-1, mimicked thrombin's action in inducing ICAM-1 expression. These data indicate that thrombin activates endothelial ICAM-1 expression and polymorphonuclear leukocyte adhesion by NF-kappa Bp65 binding to the downstream NF-kappa B site of ICAM-1 promoter after proteolytically activated receptor-1 activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 31, "end": 38}, "arguments": [{"role": "Theme", "text": "p65", "start": 17, "end": 20}]}, {"trigger": {"text": "binding", "start": 1430, "end": 1437}, "arguments": [{"role": "Theme", "text": "Rel A", "start": 1456, "end": 1461}, {"role": "Site2", "text": "downstream NF-kappa B site", "start": 1466, "end": 1492}, {"role": "Theme2", "text": "ICAM-1", "start": 1500, "end": 1506}]}, {"trigger": {"text": "binding", "start": 1844, "end": 1851}, "arguments": [{"role": "Theme", "text": "p65", "start": 1840, "end": 1843}, {"role": "Theme2", "text": "ICAM-1", "start": 1889, "end": 1895}, {"role": "Site2", "text": "promoter", "start": 1896, "end": 1904}]}], "gene expression": [{"trigger": {"text": "expression", "start": 113, "end": 123}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 106, "end": 112}]}, {"trigger": {"text": "expression", "start": 309, "end": 319}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 295, "end": 301}]}, {"trigger": {"text": "expression", "start": 456, "end": 466}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 427, "end": 433}]}, {"trigger": {"text": "expression", "start": 1700, "end": 1710}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1693, "end": 1699}]}, {"trigger": {"text": "expression", "start": 1775, "end": 1785}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1768, "end": 1774}]}], "localization": [{"trigger": {"text": "released", "start": 226, "end": 234}, "arguments": [{"role": "Theme", "text": "thrombin", "start": 216, "end": 224}]}], "negative regulation": [{"trigger": {"text": "prevented", "start": 900, "end": 909}, "arguments": [{"role": "Theme", "text": "activation", "start": 914, "end": 924}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 9, "end": 16}, "arguments": [{"role": "Cause", "text": "Thrombin", "start": 0, "end": 8}, {"role": "Theme", "text": "binding", "start": 31, "end": 38}]}, {"trigger": {"text": "mediates", "start": 85, "end": 93}, "arguments": [{"role": "Cause", "text": "induced", "start": 9, "end": 16}, {"role": "Theme", "text": "expression", "start": 113, "end": 123}]}, {"trigger": {"text": "induces", "start": 287, "end": 294}, "arguments": [{"role": "Cause", "text": "thrombin", "start": 216, "end": 224}, {"role": "Theme", "text": "expression", "start": 309, "end": 319}]}, {"trigger": {"text": "increases", "start": 414, "end": 423}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 427, "end": 433}]}, {"trigger": {"text": "increases", "start": 414, "end": 423}, "arguments": [{"role": "Theme", "text": "expression", "start": 456, "end": 466}]}, {"trigger": {"text": "activation", "start": 914, "end": 924}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 928, "end": 934}, {"role": "Site", "text": "promoter", "start": 935, "end": 943}]}, {"trigger": {"text": "induced", "start": 1422, "end": 1429}, "arguments": [{"role": "Cause", "text": "thrombin", "start": 1413, "end": 1421}, {"role": "Theme", "text": "binding", "start": 1430, "end": 1437}]}, {"trigger": {"text": "inducing", "start": 1684, "end": 1692}, "arguments": [{"role": "Cause", "text": "thrombin", "start": 1663, "end": 1671}, {"role": "Theme", "text": "expression", "start": 1700, "end": 1710}]}, {"trigger": {"text": "inducing", "start": 1684, "end": 1692}, "arguments": [{"role": "Theme", "text": "expression", "start": 1700, "end": 1710}]}, {"trigger": {"text": "activates", "start": 1746, "end": 1755}, "arguments": [{"role": "Cause", "text": "thrombin", "start": 1737, "end": 1745}, {"role": "Theme", "text": "expression", "start": 1775, "end": 1785}]}, {"trigger": {"text": "after", "start": 1905, "end": 1910}, "arguments": [{"role": "Theme", "text": "binding", "start": 1844, "end": 1851}, {"role": "Cause", "text": "activation", "start": 1948, "end": 1958}]}, {"trigger": {"text": "activation", "start": 1948, "end": 1958}, "arguments": [{"role": "Theme", "text": "proteolytically activated receptor-1", "start": 1911, "end": 1947}]}]}}, "schema": []}
{"input": "CTLA-4-Mediated inhibition of early events of T cell proliferation. \nCTLA-4 engagement by mAbs inhibits, while CD28 enhances, IL-2 production and proliferation upon T cell activation. Here, we have analyzed the mechanisms involved in CTLA-4-mediated inhibition of T cell activation of naive CD4+ T cells using Ab cross-linking. CTLA-4 ligation inhibited CD3/CD28-induced IL-2 mRNA accumulation by inhibiting IL-2 transcription, which appears to be mediated in part through decreasing NF-AT accumulation in the nuclei. However, CTLA-4 ligation did not appear to affect the CD28-mediated stabilization of IL-2 mRNA. Further, CTLA-4 engagement inhibited progression through the cell cycle by inhibiting the production of cyclin D3, cyclin-dependent kinase (cdk)4, and cdk6 when the T cells were stimulated with anti-CD3/CD28 and with anti-CD3 alone. These results indicate that CTLA-4 signaling inhibits events early in T cell activation both at IL-2 transcription and at the level of IL-2-independent events of the cell cycle, and does not simply oppose CD28-mediated costimulation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "engagement", "start": 76, "end": 86}, "arguments": [{"role": "Theme", "text": "CTLA-4", "start": 69, "end": 75}]}, {"trigger": {"text": "ligation", "start": 335, "end": 343}, "arguments": [{"role": "Theme", "text": "CTLA-4", "start": 328, "end": 334}]}, {"trigger": {"text": "ligation", "start": 534, "end": 542}, "arguments": [{"role": "Theme", "text": "CTLA-4", "start": 527, "end": 533}]}, {"trigger": {"text": "engagement", "start": 630, "end": 640}, "arguments": [{"role": "Theme", "text": "CTLA-4", "start": 623, "end": 629}]}], "gene expression": [{"trigger": {"text": "production", "start": 131, "end": 141}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 126, "end": 130}]}, {"trigger": {"text": "production", "start": 704, "end": 714}, "arguments": [{"role": "Theme", "text": "cyclin D3", "start": 718, "end": 727}]}, {"trigger": {"text": "production", "start": 704, "end": 714}, "arguments": [{"role": "Theme", "text": "(cdk)4", "start": 753, "end": 759}]}, {"trigger": {"text": "production", "start": 704, "end": 714}, "arguments": [{"role": "Theme", "text": "cdk6", "start": 765, "end": 769}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 95, "end": 103}, "arguments": [{"role": "Cause", "text": "engagement", "start": 76, "end": 86}, {"role": "Theme", "text": "upon", "start": 160, "end": 164}]}, {"trigger": {"text": "inhibited", "start": 344, "end": 353}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 381, "end": 393}, {"role": "Cause", "text": "inhibiting", "start": 397, "end": 407}]}, {"trigger": {"text": "inhibiting", "start": 397, "end": 407}, "arguments": [{"role": "Cause", "text": "ligation", "start": 335, "end": 343}, {"role": "Theme", "text": "transcription", "start": 413, "end": 426}]}, {"trigger": {"text": "inhibiting", "start": 689, "end": 699}, "arguments": [{"role": "Cause", "text": "engagement", "start": 630, "end": 640}, {"role": "Theme", "text": "production", "start": 704, "end": 714}]}, {"trigger": {"text": "inhibits", "start": 892, "end": 900}, "arguments": [{"role": "Theme", "text": "transcription", "start": 948, "end": 961}]}], "positive regulation": [{"trigger": {"text": "enhances", "start": 116, "end": 124}, "arguments": [{"role": "Cause", "text": "CD28", "start": 111, "end": 115}, {"role": "Theme", "text": "upon", "start": 160, "end": 164}]}, {"trigger": {"text": "upon", "start": 160, "end": 164}, "arguments": [{"role": "Theme", "text": "production", "start": 131, "end": 141}]}, {"trigger": {"text": "accumulation", "start": 381, "end": 393}, "arguments": [{"role": "Cause", "text": "CD28", "start": 358, "end": 362}, {"role": "Theme", "text": "IL-2", "start": 371, "end": 375}]}, {"trigger": {"text": "mediated", "start": 448, "end": 456}, "arguments": [{"role": "Theme", "text": "inhibiting", "start": 397, "end": 407}]}, {"trigger": {"text": "mediated", "start": 577, "end": 585}, "arguments": [{"role": "Cause", "text": "CD28", "start": 572, "end": 576}, {"role": "Theme", "text": "stabilization", "start": 586, "end": 599}]}, {"trigger": {"text": "stabilization", "start": 586, "end": 599}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 603, "end": 607}]}, {"trigger": {"text": "when", "start": 770, "end": 774}, "arguments": [{"role": "Theme", "text": "production", "start": 704, "end": 714}]}], "regulation": [{"trigger": {"text": "affect", "start": 561, "end": 567}, "arguments": [{"role": "Cause", "text": "ligation", "start": 534, "end": 542}, {"role": "Theme", "text": "mediated", "start": 577, "end": 585}]}], "transcription": [{"trigger": {"text": "transcription", "start": 413, "end": 426}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 408, "end": 412}]}, {"trigger": {"text": "transcription", "start": 948, "end": 961}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 943, "end": 947}]}]}}, "schema": []}
{"input": "Fibroblast growth factor-1 (FGF-1) enhances IL-2 production and nuclear translocation of NF-kappaB in FGF receptor-bearing Jurkat T cells. \nFibroblast growth factors (FGFs) are heparin-binding proteins crucial to embryogenesis, angiogenesis, and wound healing. FGF-1 is abundantly expressed in the synovium in rheumatoid arthritis and in rejecting allografts, sites of chronic immune-mediated inflammation. The frequency of FGF-1-responsive T cells is increased in the peripheral blood of these disorders, and a high percentage of infiltrating T cells in rheumatoid arthritis synovium express receptors for FGF-1. To understand the action of FGF-1 in T cells, studies were initiated in Jurkat T cells that express the signaling isoform of FGF receptor-1. These experiments show that FGF-1 stimulation of Jurkat T cells provides a second signal that augments TCR-mediated IL-2 production. Analogous to costimulation via CD28, this activity is mediated through activation of Rel/kappaB, a family of transcription factors known to regulate IL-2 and other activation-inducible proteins. FGF-1 alone induces modest nuclear translocation of kappaB-binding proteins, and this translocation is enhanced by the combination of anti-CD3 and FGF-1. This NF-kappaB binding complex is composed of transcriptionally active p65(RelA)/p50 heterodimers and results primarily from the targeted degradation of IkappaB-alpha, an inhibitor that sequesters Rel/kappaB in the cytoplasm. These data are the first to show a connection between FGF-1 signaling and NF-kappaB activation outside of embryonic development. The signaling events that link FGF receptor-1 engagement and NF-kappaB activation in Jurkat are probably distinct from the CD28 costimulation pathway, since FGF-1-induced Rel/kappaB binding proteins do not contain significant levels of c-Rel and are not identical with the CD28 response complex. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "engagement", "start": 1638, "end": 1648}, "arguments": [{"role": "Theme", "text": "FGF receptor-1", "start": 1623, "end": 1637}]}], "gene expression": [{"trigger": {"text": "production", "start": 49, "end": 59}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 44, "end": 48}]}, {"trigger": {"text": "expressed", "start": 281, "end": 290}, "arguments": [{"role": "Theme", "text": "FGF-1", "start": 261, "end": 266}]}, {"trigger": {"text": "express", "start": 706, "end": 713}, "arguments": [{"role": "Theme", "text": "FGF receptor-1", "start": 739, "end": 753}]}, {"trigger": {"text": "production", "start": 876, "end": 886}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 871, "end": 875}]}], "positive regulation": [{"trigger": {"text": "enhances", "start": 35, "end": 43}, "arguments": [{"role": "Cause", "text": "FGF-1", "start": 28, "end": 33}, {"role": "Theme", "text": "production", "start": 49, "end": 59}]}, {"trigger": {"text": "provides", "start": 819, "end": 827}, "arguments": [{"role": "Theme", "text": "augments", "start": 849, "end": 857}]}, {"trigger": {"text": "augments", "start": 849, "end": 857}, "arguments": [{"role": "Theme", "text": "mediated", "start": 862, "end": 870}]}, {"trigger": {"text": "mediated", "start": 862, "end": 870}, "arguments": [{"role": "Theme", "text": "production", "start": 876, "end": 886}]}, {"trigger": {"text": "mediated", "start": 942, "end": 950}, "arguments": [{"role": "Theme", "text": "provides", "start": 819, "end": 827}]}, {"trigger": {"text": "composed", "start": 1271, "end": 1279}, "arguments": [{"role": "Theme", "text": "p65", "start": 1308, "end": 1311}]}, {"trigger": {"text": "composed", "start": 1271, "end": 1279}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1312, "end": 1316}]}, {"trigger": {"text": "composed", "start": 1271, "end": 1279}, "arguments": [{"role": "Theme", "text": "p50", "start": 1318, "end": 1321}]}, {"trigger": {"text": "results", "start": 1339, "end": 1346}, "arguments": [{"role": "Theme", "text": "composed", "start": 1271, "end": 1279}, {"role": "Cause", "text": "degradation", "start": 1375, "end": 1386}]}, {"trigger": {"text": "induced", "start": 1755, "end": 1762}, "arguments": [{"role": "Cause", "text": "FGF-1", "start": 1749, "end": 1754}, {"role": "Theme", "text": "c-Rel", "start": 1828, "end": 1833}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 1375, "end": 1386}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1390, "end": 1403}]}], "regulation": [{"trigger": {"text": "regulate", "start": 1028, "end": 1036}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1037, "end": 1041}]}]}}, "schema": []}
{"input": "Signaling through the lymphotoxin-beta receptor stimulates HIV-1 replication alone and in cooperation with soluble or membrane-bound TNF-alpha. \nThe level of ongoing HIV-1 replication within an individual is critical to HIV-1 pathogenesis. Among host immune factors, the cytokine TNF-alpha has previously been shown to increase HIV-1 replication in various monocyte and T cell model systems. Here, we demonstrate that signaling through the TNF receptor family member, the lymphotoxin-beta (LT-beta) receptor (LT-betaR), also regulates HIV-1 replication. Furthermore, HIV-1 replication is cooperatively stimulated when the distinct LT-betaR and TNF receptor systems are simultaneously engaged by their specific ligands. Moreover, in a physiological coculture cellular assay system, we show that membrane-bound TNF-alpha and LT-alpha1beta2 act virtually identically to their soluble forms in the regulation of HIV-1 replication. Thus, cosignaling via the LT-beta and TNF-alpha receptors is probably involved in the modulation of HIV-1 replication and the subsequent determination of HIV-1 viral burden in monocytes. Intriguingly, surface expression of LT-alpha1beta2 is up-regulated on a T cell line acutely infected with HIV-1, suggesting a positive feedback loop between HIV-1 infection, LT-alpha1beta2 expression, and HIV-1 replication. Given the critical role that LT-alpha1beta2 plays in lymphoid architecture, we speculate that LT-alpha1beta2 may be involved in HIV-associated abnormalities of the lymphoid organs. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "simultaneously engaged", "start": 669, "end": 691}, "arguments": [{"role": "Theme", "text": "LT-betaR", "start": 631, "end": 639}]}]}}, "schema": []}
{"input": "Resistance to tumor necrosis factor induced apoptosis in vitro correlates with high metastatic capacity of cells in vivo. \nTNF is one of the cytokines secreted by the cells of the immune system. Our data demonstrate that those cell lines lacking capability to form metastatic tumors in vivo are susceptible to TNF induced apoptosis in vitro. However, cell lines with high metastatic potential are resistant to TNF in vitro. Furthermore, the same cell lines were resistant to cytolytic action of other cytotoxic proteins secreted by LAK cells. Our data showed that TNF resistance in vitro correlates with the increased level of transcription factor NF-kappaB. This finding may provide a tool to improve current protocols of immunotherapy and insights to how tumor cells are or are not killed by LAK cells. ", "output": {"json_structures": {}}, "schema": []}
{"input": "NF-kappaB activation is required for C5a-induced interleukin-8 gene expression in mononuclear cells. \nC5a, a potent peptide chemoattractant, stimulates interleukin-8 (IL-8) secretion from peripheral blood mononuclear cells (PBMC). Experiments were conducted to understand the mechanisms for C5a-induced IL-8 production, which was 14-fold greater than that in unstimulated cells by 2 hours. IL-8 secretion was accompanied by accumulation of IL-8 mRNA in the cytosol and by nuclear expression of a kappaB DNA binding activity within 30 minutes. AP-1 but not NF-IL-6 DNA binding activity was also detected in C5a-stimulated PBMC; however, its delayed expression (maximal at 4 hours) suggested a less important role in the rapid production of IL-8. The correlation between C5a-induced kappaB binding activity and IL-8 gene expression was examined in the RAW264.7 macrophage cells using reporter genes directed by the kappaB sequence from IkappaBalpha and IL-8 promoter regions. C5a-induced reporter gene expression was abolished by introducing mutations into the kappaB sites and by coexpression of a dominant negative IkappaBalpha construct resistant to agonist-induced phosphorylation. Pertussis toxin, which ADP-ribosylates the Gi proteins known to couple to the C5a receptor, produced minimal inhibition of C5a-induced IL-8 expression and had little effect on C5a-induced calcium mobilization in RAW264.7 cells. These results suggest that NF-kappaB activation is required for C5a-induced IL-8 gene expression and that this response is mediated primarily through a pertussis toxin-insensitive pathway. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 568, "end": 575}, "arguments": [{"role": "Theme", "text": "NF-IL-6", "start": 556, "end": 563}]}, {"trigger": {"text": "couple", "start": 1248, "end": 1254}, "arguments": [{"role": "Theme", "text": "C5a receptor", "start": 1262, "end": 1274}]}], "gene expression": [{"trigger": {"text": "expression", "start": 68, "end": 78}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 49, "end": 62}]}, {"trigger": {"text": "production", "start": 308, "end": 318}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 303, "end": 307}]}, {"trigger": {"text": "production", "start": 725, "end": 735}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 739, "end": 743}]}, {"trigger": {"text": "expression", "start": 819, "end": 829}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 809, "end": 813}]}, {"trigger": {"text": "coexpression", "start": 1079, "end": 1091}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1115, "end": 1127}]}, {"trigger": {"text": "expression", "start": 1324, "end": 1334}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1319, "end": 1323}]}, {"trigger": {"text": "expression", "start": 1498, "end": 1508}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1488, "end": 1492}]}], "localization": [{"trigger": {"text": "secretion", "start": 173, "end": 182}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 167, "end": 171}]}, {"trigger": {"text": "secretion", "start": 395, "end": 404}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 390, "end": 394}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 1293, "end": 1303}, "arguments": [{"role": "Theme", "text": "induced", "start": 1311, "end": 1318}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 41, "end": 48}, "arguments": [{"role": "Theme", "text": "expression", "start": 68, "end": 78}]}, {"trigger": {"text": "stimulates", "start": 141, "end": 151}, "arguments": [{"role": "Theme", "text": "secretion", "start": 173, "end": 182}]}, {"trigger": {"text": "induced", "start": 295, "end": 302}, "arguments": [{"role": "Theme", "text": "production", "start": 308, "end": 318}]}, {"trigger": {"text": "detected", "start": 594, "end": 602}, "arguments": [{"role": "Theme", "text": "binding", "start": 568, "end": 575}]}, {"trigger": {"text": "induced", "start": 1311, "end": 1318}, "arguments": [{"role": "Theme", "text": "expression", "start": 1324, "end": 1334}]}, {"trigger": {"text": "induced", "start": 1480, "end": 1487}, "arguments": [{"role": "Theme", "text": "expression", "start": 1498, "end": 1508}]}], "regulation": [{"trigger": {"text": "role", "start": 707, "end": 711}, "arguments": [{"role": "Theme", "text": "production", "start": 725, "end": 735}]}]}}, "schema": []}
{"input": "Transcriptional targeting of retroviral vectors to the erythroblastic progeny of transduced hematopoietic stem cells. \nTargeted expression to specific tissues or cell lineages is a necessary feature of a gene therapy vector for many clinical applications, such as correction of hemoglobinopathies or thalassemias by transplantation of genetically modified hematopoietic stem cells. We developed retroviral vectors in which the constitutive viral enhancer in the U3 region of the 3' LTR is replaced by an autoregulatory enhancer of the erythroid-specific GATA-1 transcription factor gene. The replaced enhancer is propagated to the 5' LTR upon integration into the target cell genome. The modified vectors were used to transduce human hematopoietic cell lines, cord blood-derived CD34(+) stem/progenitor cells, and murine bone marrow repopulating stem cells. The expression of appropriate reporter genes (triangle upLNGFR, EGFP) was analyzed in the differentiated progeny of transduced stem cells in vitro, in liquid culture as well as in clonogenic assay, and in vivo, after bone marrow transplantation in lethally irradiated mice. The GATA-1 autoregulatory enhancer effectively restricts the expression of the LTR-driven proviral transcription unit to the erythroblastic progeny of both human progenitors and mouse-repopulating stem cells. Packaging of viral particles, integration into the target genome, and stability of the integrated provirus are not affected by the LTR modification. Enhancer replacement is therefore an effective strategy to target expression of a retroviral transgene to a specific progeny of transduced hematopoietic stem cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 862, "end": 872}, "arguments": [{"role": "Theme", "text": "EGFP", "start": 922, "end": 926}]}]}}, "schema": []}
{"input": "An essential role for NF-kappaB in human CD34(+) bone marrow cell survival. \nThe transcription factor, NF-kappaB, is important for T-cell activation, B-cell maturation, and human immunodeficiency virus transcription and plays a role in alternatively mediating and protecting against apoptosis in a variety of cell types. However, a role for NF-kappaB in human CD34(+) bone marrow cells has not been described. We provide evidence here that virtually all human CD34(+) bone marrow cells express NF-kappaB that can be activated by exposure to phorbol 12-myristate 13-acetate and a variety of cytokines, eg, tumor necrosis factor alpha, interleukin-3, and granulocyte-macrophage colony-stimulating factor. In addition, we demonstrate that NF-kappaB may be required for human CD34(+) bone marrow cell clonogenic function and survival. These results offer insight into a new role for NF-kappaB in maintaining survival and function in hematopoietic stem and progenitor cells and suggest that proposed strategies involving inhibition of NF-kappaB activation as an adjunct to cancer chemotherapy should be approached with caution. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "express", "start": 486, "end": 493}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 605, "end": 632}]}, {"trigger": {"text": "express", "start": 486, "end": 493}, "arguments": [{"role": "Theme", "text": "interleukin-3", "start": 634, "end": 647}]}, {"trigger": {"text": "express", "start": 486, "end": 493}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 653, "end": 701}]}]}}, "schema": []}
{"input": "Unicellular-unilineage erythropoietic cultures: molecular analysis of regulatory gene expression at sibling cell level. \nIn vitro studies on hematopoietic control mechanisms have been hampered by the heterogeneity of the analyzed cell populations, ie, lack of lineage specificity and developmental stage homogeneity of progenitor/precursor cells growing in culture. We developed unicellular culture systems for unilineage differentiation of purified hematopoietic progenitor cells followed by daughter cell analysis at cellular and molecular level. In the culture system reported here, (1) the growth factor (GF) stimulus induces cord blood (CB) progenitor cells to proliferate and differentiate/mature exclusively along the erythroid lineage; (2) this erythropoietic wave is characterized by less than 4% apoptotic cells; (3) asymmetric divisions are virtually absent, ie, nonresponsive hematopoietic progenitors with no erythropoietic potential are forced into apoptosis; (4) the system is cell division controlled (cdc), ie, the number of divisions performed by each cell is monitored. Single-cell reverse transcriptase-polymerase chain reaction (RT-PCR) analysis was applied to this culture system to investigate gene expression of diverse receptors, markers of differentiation, and transcription factors (EKLF, GATA-1, GATA-2, p45 NF-E2, PU.1, and SCL/Tal1) at discrete stages of erythropoietic development. Freshly isolated CD34(+) cells expressed CD34, c-kit, PU.1, and GATA-2 but did not express CD36, erythropoietin receptor (EpoR), SCL/Tal1, EKLF, NF-E2, GATA-1, or glyocophorin A (GPA). In early to intermediate stages of erythroid differentiation we monitored the induction of CD36, Tal1, EKLF, NF-E2, and GATA-1 that preceeded expression of EpoR. In late stages of erythroid maturation, GPA was upregulated, whereas CD34, c-kit, PU.1, and GATA-2 were barely or not detected. In addition, competitive single-cell RT-PCR was used to assay CD34 mRNA transcripts in sibling CD34(+) CD38(-) cells differentiating in unilineage erythroid cultures: this analysis allowed us to semiquantitate the gradual downmodulation of CD34 mRNA from progenitor cells through their differentiating erythroid progeny. It is concluded that this novel culture system, coupled with single-cell RT-PCR analysis, may eliminate the ambiguities intrinsic to molecular studies on heterogeneous populations of hematopoietic progenitors/precursors growing in culture, particularly in the initial stages of development. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "gene expression", "start": 1217, "end": 1232}, "arguments": [{"role": "Theme", "text": "EKLF", "start": 1310, "end": 1314}]}, {"trigger": {"text": "gene expression", "start": 1217, "end": 1232}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1316, "end": 1322}]}, {"trigger": {"text": "gene expression", "start": 1217, "end": 1232}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 1324, "end": 1330}]}, {"trigger": {"text": "gene expression", "start": 1217, "end": 1232}, "arguments": [{"role": "Theme", "text": "p45 NF-E2", "start": 1332, "end": 1341}]}, {"trigger": {"text": "gene expression", "start": 1217, "end": 1232}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1343, "end": 1347}]}, {"trigger": {"text": "gene expression", "start": 1217, "end": 1232}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1353, "end": 1356}]}, {"trigger": {"text": "expressed", "start": 1444, "end": 1453}, "arguments": [{"role": "Theme", "text": "CD34", "start": 1454, "end": 1458}]}, {"trigger": {"text": "expressed", "start": 1444, "end": 1453}, "arguments": [{"role": "Theme", "text": "c-kit", "start": 1460, "end": 1465}]}, {"trigger": {"text": "expressed", "start": 1444, "end": 1453}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1467, "end": 1471}]}, {"trigger": {"text": "expressed", "start": 1444, "end": 1453}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 1477, "end": 1483}]}, {"trigger": {"text": "express", "start": 1496, "end": 1503}, "arguments": [{"role": "Theme", "text": "CD36", "start": 1504, "end": 1508}]}, {"trigger": {"text": "express", "start": 1496, "end": 1503}, "arguments": [{"role": "Theme", "text": "EpoR", "start": 1535, "end": 1539}]}, {"trigger": {"text": "express", "start": 1496, "end": 1503}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1542, "end": 1545}]}, {"trigger": {"text": "express", "start": 1496, "end": 1503}, "arguments": [{"role": "Theme", "text": "EKLF", "start": 1552, "end": 1556}]}, {"trigger": {"text": "express", "start": 1496, "end": 1503}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1565, "end": 1571}]}, {"trigger": {"text": "express", "start": 1496, "end": 1503}, "arguments": [{"role": "Theme", "text": "GPA", "start": 1592, "end": 1595}]}, {"trigger": {"text": "induction", "start": 1676, "end": 1685}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1718, "end": 1724}]}, {"trigger": {"text": "expression", "start": 1740, "end": 1750}, "arguments": [{"role": "Theme", "text": "EpoR", "start": 1754, "end": 1758}]}, {"trigger": {"text": "detected", "start": 1878, "end": 1886}, "arguments": [{"role": "Theme", "text": "CD34", "start": 1829, "end": 1833}]}, {"trigger": {"text": "detected", "start": 1878, "end": 1886}, "arguments": [{"role": "Theme", "text": "c-kit", "start": 1835, "end": 1840}]}, {"trigger": {"text": "detected", "start": 1878, "end": 1886}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1842, "end": 1846}]}, {"trigger": {"text": "detected", "start": 1878, "end": 1886}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 1852, "end": 1858}]}], "negative regulation": [{"trigger": {"text": "downmodulation", "start": 2110, "end": 2124}, "arguments": [{"role": "Theme", "text": "CD34", "start": 2128, "end": 2132}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 1676, "end": 1685}, "arguments": [{"role": "Theme", "text": "CD36", "start": 1689, "end": 1693}]}, {"trigger": {"text": "induction", "start": 1676, "end": 1685}, "arguments": [{"role": "Theme", "text": "Tal1", "start": 1695, "end": 1699}]}, {"trigger": {"text": "induction", "start": 1676, "end": 1685}, "arguments": [{"role": "Theme", "text": "EKLF", "start": 1701, "end": 1705}]}, {"trigger": {"text": "upregulated", "start": 1808, "end": 1819}, "arguments": [{"role": "Theme", "text": "GPA", "start": 1800, "end": 1803}]}], "transcription": [{"trigger": {"text": "mRNA transcripts", "start": 1955, "end": 1971}, "arguments": [{"role": "Theme", "text": "CD34", "start": 1950, "end": 1954}]}]}}, "schema": []}
{"input": "Control of cell cycle entry and apoptosis in B lymphocytes infected by Epstein-Barr virus. \nInfection of human B cells with Epstein-Barr virus (EBV) results in activation of the cell cycle and cell growth. To interpret the mechanisms by which EBV activates the cell, we have assayed many proteins involved in control of the G0 and G1 phases of the cell cycle and regulation of apoptosis. In EBV infection most of the changes, including the early induction of cyclin D2, are dependent on expression of EBV genes, but an alteration in the E2F-4 profile was partly independent of viral gene expression, presumably occurring in response to signal transduction activated when the virus binds to its receptor, CD21. By comparing the expression of genes controlling apoptosis, including those encoding several members of the BCL-2 family of proteins, the known relative resistance of EBV-immortalized B-cell lines to apoptosis induced by low serum was found to correlate with expression of both BCL-2 and A20. A20 can be regulated by the NF-kappaB transcription factor, which is known to be activated by the EBV LMP-1 protein. Quantitative assays demonstrated a direct temporal relationship between LMP-1 protein levels and active NF-kappaB during the time course of infection. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 681, "end": 686}, "arguments": [{"role": "Theme", "text": "CD21", "start": 704, "end": 708}]}], "gene expression": [{"trigger": {"text": "expression", "start": 969, "end": 979}, "arguments": [{"role": "Theme", "text": "BCL-2", "start": 988, "end": 993}]}, {"trigger": {"text": "expression", "start": 969, "end": 979}, "arguments": [{"role": "Theme", "text": "A20", "start": 998, "end": 1001}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 446, "end": 455}, "arguments": [{"role": "Theme", "text": "cyclin D2", "start": 459, "end": 468}]}, {"trigger": {"text": "dependent", "start": 474, "end": 483}, "arguments": [{"role": "Theme", "text": "induction", "start": 446, "end": 455}]}, {"trigger": {"text": "occurring", "start": 611, "end": 620}, "arguments": [{"role": "Theme", "text": "alteration", "start": 519, "end": 529}]}], "regulation": [{"trigger": {"text": "alteration", "start": 519, "end": 529}, "arguments": [{"role": "Theme", "text": "E2F-4", "start": 537, "end": 542}]}, {"trigger": {"text": "independent", "start": 562, "end": 573}, "arguments": [{"role": "Theme", "text": "alteration", "start": 519, "end": 529}]}, {"trigger": {"text": "regulated", "start": 1014, "end": 1023}, "arguments": [{"role": "Theme", "text": "A20", "start": 1003, "end": 1006}]}]}}, "schema": []}
{"input": "Immortalization of CD4(+) and CD8(+) T lymphocytes by human T-cell leukemia virus type 1 Tax mutants expressed in a functional molecular clone. \nThe human T-cell leukemia virus type 1 (HTLV-1) transcriptional trans-activator Tax has been demonstrated to have transforming activity in multiple cell culture and transgenic-mouse models. In addition to activating transcription from the viral long terminal repeat (LTR) through the cyclic AMP response element binding protein/activating transcription factor (CREB/ATF) family of transcription factors, Tax activates the expression of multiple cellular promoters through the NF-kappaB pathway of transcriptional activation. The Tax mutants M22 and M47 have previously been demonstrated to selectively abrogate the ability of Tax to activate transcription through the NF-kappaB or CREB/ATF pathway, respectively. These mutations were introduced in the tax gene of the ACH functional molecular clone of HTLV-1, and virus produced from the mutant ACH clones was examined for the ability to replicate and immortalize primary human lymphocytes. While virus derived from the clone containing the M47 mutation retained the ability to immortalize T lymphocytes, the M22 mutant lost the ability to immortalize infected cells. These results indicate that activation of the CREB/ATF pathway by Tax is dispensable for the immortalization of T cells by HTLV-1, whereas activation of the NF-kappaB pathway may be critical. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 101, "end": 110}, "arguments": [{"role": "Theme", "text": "Tax", "start": 89, "end": 92}]}]}}, "schema": []}
{"input": "HIV-1 reactivation in resting peripheral blood mononuclear cells of infected adults upon in vitro CD4 cross-linking by ligands of the CDR2-loop in extracellular domain 1. \nHIV-1 infects resting peripheral blood mononuclear cells (PBMCs) but remains inactive state until subsequent cell activation. We have demonstrated that the cross-linking of cell surface CD4 by gp120-anti-gp120 immune complexes or heat-inactivated HIV-1 (iHIV-1) is sufficient to trigger activation signals leading to virus reactivation (9). In this study, we demonstrate that NF-kappaB nuclear translocation and stimulation of virus production by iHIV-1 were strictly linked to the concentrations of viral proteins used as exogenous stimuli. Moreover, we further investigated the physiologic relevance of these observations. When submitted to an in vitro CD4 cross-linking by iHIV-1, PBMCs from HIV-1-infected patients were found to produce virus. This viral reactivation was associated with increased NF-kappaB nuclear translocation in patients' PBMCs. Additionally, virus reactivation in resting PBMCs infected in vitro with HIV-1 was found to be specifically induced by ligands of the CDR2-loop in domain 1 (D1) of CD4 (virus envelope and anti-CD4 monoclonal antibodies). In contrast, virus reactivation was not observed following CD4 oligomerization by antibodies that bind other epitopes in D1, including the D1/CDR3-loop. Finally, soluble CD4 (sCD4) prevented virus reactivation by D1/CDR2-loop ligands. Our results indicate that the signaling events initiated in PBMCs by oligomerization of CD4 at the D1/CDR2-loop can trigger HIV-1 upregulation in infected individuals. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 102, "end": 115}, "arguments": [{"role": "Theme", "text": "CD4", "start": 98, "end": 101}]}, {"trigger": {"text": "cross-linking", "start": 328, "end": 341}, "arguments": [{"role": "Theme", "text": "CD4", "start": 358, "end": 361}]}, {"trigger": {"text": "cross-linking", "start": 831, "end": 844}, "arguments": [{"role": "Theme", "text": "CD4", "start": 827, "end": 830}]}, {"trigger": {"text": "oligomerization", "start": 1310, "end": 1325}, "arguments": [{"role": "Theme", "text": "CD4", "start": 1306, "end": 1309}]}, {"trigger": {"text": "oligomerization", "start": 1551, "end": 1566}, "arguments": [{"role": "Theme", "text": "CD4", "start": 1570, "end": 1573}]}]}}, "schema": []}
{"input": "Defining therapeutic targets by using adenovirus: blocking NF-kappaB inhibits both inflammatory and destructive mechanisms in rheumatoid synovium but spares anti-inflammatory mediators. \nThe role of the transcription factor NF-kappaB in the pathogenesis of rheumatoid arthritis has long been a subject of controversy. We used an adenoviral technique of blocking NF-kappaB through overexpression of the inhibitory subunit IkappaBalpha, which has the advantage that it can be used in the diseased tissue itself, with >90% of the synovial macrophages, fibroblasts, and T cells infected. We found that the spontaneous production of tumor necrosis factor alpha and other pro-inflammatory cytokines is NF-kappaB-dependent in rheumatoid synovial tissue, in contrast to the main anti-inflammatory mediators, like IL-10 and -11, and the IL-1 receptor antagonist. Of even more interest, IkappaBalpha overexpression inhibited the production of matrix metalloproteinases 1 and 3 while not affecting their tissue inhibitor. Blocking NF-kappaB in the rheumatoid joint thus has a very beneficial profile, reducing both the inflammatory response and the tissue destruction. The adenoviral technique described here has widespread applicability, allowing rapid testing of the effects of blocking a potential therapeutic target in either cultures of normal cells or in the diseased tissue itself. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 614, "end": 624}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 628, "end": 655}]}, {"trigger": {"text": "overexpression", "start": 890, "end": 904}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 877, "end": 889}]}, {"trigger": {"text": "production", "start": 919, "end": 929}, "arguments": [{"role": "Theme", "text": "matrix metalloproteinases 1", "start": 933, "end": 960}]}, {"trigger": {"text": "production", "start": 919, "end": 929}, "arguments": [{"role": "Theme", "text": "3", "start": 965, "end": 966}]}], "negative regulation": [{"trigger": {"text": "overexpression", "start": 380, "end": 394}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 421, "end": 433}]}, {"trigger": {"text": "inhibited", "start": 905, "end": 914}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 890, "end": 904}, {"role": "Theme", "text": "production", "start": 919, "end": 929}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 380, "end": 394}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 380, "end": 394}]}, {"trigger": {"text": "overexpression", "start": 890, "end": 904}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 890, "end": 904}]}], "regulation": [{"trigger": {"text": "dependent", "start": 706, "end": 715}, "arguments": [{"role": "Theme", "text": "production", "start": 614, "end": 624}]}, {"trigger": {"text": "dependent", "start": 706, "end": 715}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 805, "end": 810}]}, {"trigger": {"text": "dependent", "start": 706, "end": 715}, "arguments": [{"role": "Theme", "text": "-11", "start": 815, "end": 818}]}, {"trigger": {"text": "affecting", "start": 977, "end": 986}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 890, "end": 904}, {"role": "Theme", "text": "matrix metalloproteinases 1", "start": 933, "end": 960}]}, {"trigger": {"text": "affecting", "start": 977, "end": 986}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 890, "end": 904}, {"role": "Theme", "text": "3", "start": 965, "end": 966}]}]}}, "schema": []}
{"input": "Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F. \nInitiation of DNA replication requires the function of MCM gene products, which participate in ensuring that DNA replication occurs only once in the cell cycle. Expression of all mammalian genes of the MCM family is induced by growth stimulation, unlike yeast, and the mRNA levels peak at G1/S boundary. In this study, we examined the transcriptional activities of isolated human MCM gene promoters. Human MCM5 and MCM6 promoters with mutation in the E2F sites failed in promoter regulation following serum stimulation and exogenous E2F expression. In addition, we identified a novel E2F-like sequence in human MCM6 promoter which cooperates with the authentic E2F sites in E2F-dependent regulation. Forced expression of E2F1 could induce expression of all members of the endogenous MCM genes in rat embryonal fibroblast REF52 cells. Our results demonstrated that the growth-regulated expression of mammalian MCM5 and MCM6 genes, and presumably other MCM members, is primarily regulated by E2F through binding to multiple E2F sites in the promoters. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1111, "end": 1118}, "arguments": [{"role": "Theme", "text": "MCM5", "start": 1018, "end": 1022}]}, {"trigger": {"text": "binding", "start": 1111, "end": 1118}, "arguments": [{"role": "Theme", "text": "MCM6", "start": 1027, "end": 1031}]}], "gene expression": [{"trigger": {"text": "expression", "start": 22, "end": 32}, "arguments": [{"role": "Theme", "text": "MCM5", "start": 46, "end": 50}]}, {"trigger": {"text": "expression", "start": 22, "end": 32}, "arguments": [{"role": "Theme", "text": "MCM6", "start": 55, "end": 59}]}, {"trigger": {"text": "expression", "start": 816, "end": 826}, "arguments": [{"role": "Theme", "text": "E2F1", "start": 830, "end": 834}]}, {"trigger": {"text": "expression", "start": 994, "end": 1004}, "arguments": [{"role": "Theme", "text": "MCM5", "start": 1018, "end": 1022}]}, {"trigger": {"text": "expression", "start": 994, "end": 1004}, "arguments": [{"role": "Theme", "text": "MCM6", "start": 1027, "end": 1031}]}], "negative regulation": [{"trigger": {"text": "failed", "start": 570, "end": 576}, "arguments": [{"role": "Theme", "text": "regulation", "start": 589, "end": 599}]}], "positive regulation": [{"trigger": {"text": "mediated", "start": 66, "end": 74}, "arguments": [{"role": "Theme", "text": "expression", "start": 22, "end": 32}]}], "regulation": [{"trigger": {"text": "regulated", "start": 12, "end": 21}, "arguments": [{"role": "Theme", "text": "expression", "start": 22, "end": 32}]}, {"trigger": {"text": "regulation", "start": 589, "end": 599}, "arguments": [{"role": "Theme", "text": "MCM5", "start": 515, "end": 519}, {"role": "Site", "text": "promoters", "start": 529, "end": 538}]}, {"trigger": {"text": "regulation", "start": 589, "end": 599}, "arguments": [{"role": "Theme", "text": "MCM6", "start": 524, "end": 528}, {"role": "Site", "text": "promoters", "start": 529, "end": 538}]}, {"trigger": {"text": "cooperates", "start": 740, "end": 750}, "arguments": [{"role": "Theme", "text": "regulation", "start": 589, "end": 599}, {"role": "CSite", "text": "E2F-like sequence", "start": 693, "end": 710}, {"role": "Cause", "text": "MCM6", "start": 720, "end": 724}]}, {"trigger": {"text": "regulated", "start": 984, "end": 993}, "arguments": [{"role": "Theme", "text": "expression", "start": 994, "end": 1004}]}, {"trigger": {"text": "regulated", "start": 1086, "end": 1095}, "arguments": [{"role": "Theme", "text": "expression", "start": 994, "end": 1004}, {"role": "Cause", "text": "binding", "start": 1111, "end": 1118}]}]}}, "schema": []}
{"input": "Non-steroidal anti-inflammatory drugs inhibit the expression of cytokines and induce HSP70 in human monocytes. \nRecent studies have shown that the non-steroidal anti-inflammatory drugs (NSAIDs) activate heat shock transcription factor (HSF1) from a latent cytoplasmic form to a nuclear, DNA binding state. As HSF1 can function as both an activator of heat shock genes and a repressor of non-heat shock genes such as IL1B and c- fos, we have examined the potential role of HSF1 in the effects of NSAIDs on gene expression in a human monocytic cell line THP-1. We found that two members of the NSAIDs, sodium salicylate and sulindac repress the IL1B promoter to similar degree to heat shock or HSF1 overexpression. In addition, sodium salicylate and additional NSAIDs used at concentrations that activate HSF1 also inhibited the expression of other monocytic genes (TNF-alpha, IL-1beta, IL-6, IL-8, IL-10, ICAM-1) activated by exposure to a pro-inflammatory stimulus (lipopolysaccharide, LPS). At least in the case of the IL1B promoter, repression did not seem to involve another factor whose activity is affected by the NSAIDs, NFkappaB as the IL1B promoter fragment used in our studies is not NFkappaB responsive and binds specifically to HSF1. Exposure to NSAIDs had a complex effect on HSP gene expression and while sulindac activated the stress responsive HSP70B promoter, sodium salicylate did not. In addition, only a subset of the NSAIDs induced HSP70 mRNA species. These findings reflect the properties of HSF1 which can be activated to at least two DNA binding forms only one of which activates heat shock promoters and suggest that individual NSAID family members may differentially induce one or other of these forms. Overall therefore, exposure to NSAIDs leads to a profound switch in gene expression in monocytic cells, with suppression of genes involved in macrophage activation and induction of stress genes and HSF1 appears to play a regulatory role in these effects. Copyright 1999 Academic Press. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 291, "end": 298}, "arguments": [{"role": "Theme", "text": "HSF1", "start": 236, "end": 240}]}, {"trigger": {"text": "binds", "start": 1217, "end": 1222}, "arguments": [{"role": "Theme", "text": "IL1B", "start": 1143, "end": 1147}, {"role": "Site", "text": "promoter", "start": 1148, "end": 1156}, {"role": "Theme2", "text": "HSF1", "start": 1239, "end": 1243}]}, {"trigger": {"text": "binding", "start": 1561, "end": 1568}, "arguments": [{"role": "Theme", "text": "HSF1", "start": 1513, "end": 1517}]}], "gene expression": [{"trigger": {"text": "expression", "start": 701, "end": 711}, "arguments": [{"role": "Theme", "text": "IL1B", "start": 416, "end": 420}]}, {"trigger": {"text": "expression", "start": 701, "end": 711}, "arguments": [{"role": "Theme", "text": "c- fos", "start": 425, "end": 431}]}, {"trigger": {"text": "expression", "start": 701, "end": 711}, "arguments": [{"role": "Theme", "text": "HSF1", "start": 692, "end": 696}]}, {"trigger": {"text": "expression", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 864, "end": 873}]}, {"trigger": {"text": "expression", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 875, "end": 883}]}, {"trigger": {"text": "expression", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 885, "end": 889}]}, {"trigger": {"text": "expression", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 891, "end": 895}]}, {"trigger": {"text": "expression", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 897, "end": 902}]}, {"trigger": {"text": "expression", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 904, "end": 910}]}], "negative regulation": [{"trigger": {"text": "repressor", "start": 374, "end": 383}, "arguments": [{"role": "Cause", "text": "HSF1", "start": 309, "end": 313}, {"role": "Theme", "text": "IL1B", "start": 416, "end": 420}]}, {"trigger": {"text": "repressor", "start": 374, "end": 383}, "arguments": [{"role": "Cause", "text": "HSF1", "start": 309, "end": 313}, {"role": "Theme", "text": "c- fos", "start": 425, "end": 431}]}, {"trigger": {"text": "repress", "start": 631, "end": 638}, "arguments": [{"role": "Theme", "text": "IL1B", "start": 643, "end": 647}, {"role": "Site", "text": "promoter", "start": 648, "end": 656}]}, {"trigger": {"text": "repress", "start": 631, "end": 638}, "arguments": [{"role": "Theme", "text": "over", "start": 697, "end": 701}]}, {"trigger": {"text": "inhibited", "start": 813, "end": 822}, "arguments": [{"role": "Theme", "text": "activated", "start": 912, "end": 921}]}, {"trigger": {"text": "repression", "start": 1035, "end": 1045}, "arguments": [{"role": "Theme", "text": "IL1B", "start": 1020, "end": 1024}, {"role": "Site", "text": "promoter", "start": 1025, "end": 1033}]}], "positive regulation": [{"trigger": {"text": "activate", "start": 194, "end": 202}, "arguments": [{"role": "Theme", "text": "binding", "start": 291, "end": 298}]}, {"trigger": {"text": "activator", "start": 338, "end": 347}, "arguments": [{"role": "Cause", "text": "HSF1", "start": 309, "end": 313}, {"role": "Theme", "text": "IL1B", "start": 416, "end": 420}]}, {"trigger": {"text": "activator", "start": 338, "end": 347}, "arguments": [{"role": "Cause", "text": "HSF1", "start": 309, "end": 313}, {"role": "Theme", "text": "c- fos", "start": 425, "end": 431}]}, {"trigger": {"text": "over", "start": 697, "end": 701}, "arguments": [{"role": "Theme", "text": "expression", "start": 701, "end": 711}]}, {"trigger": {"text": "activate", "start": 794, "end": 802}, "arguments": [{"role": "Theme", "text": "HSF1", "start": 803, "end": 807}]}, {"trigger": {"text": "activated", "start": 912, "end": 921}, "arguments": [{"role": "Theme", "text": "expression", "start": 827, "end": 837}]}, {"trigger": {"text": "activated", "start": 1327, "end": 1336}, "arguments": [{"role": "Theme", "text": "HSP70B", "start": 1359, "end": 1365}, {"role": "Site", "text": "promoter", "start": 1366, "end": 1374}]}, {"trigger": {"text": "responsive", "start": 1348, "end": 1358}, "arguments": [{"role": "Theme", "text": "HSP70B", "start": 1359, "end": 1365}, {"role": "Site", "text": "promoter", "start": 1366, "end": 1374}]}, {"trigger": {"text": "induced", "start": 1444, "end": 1451}, "arguments": [{"role": "Theme", "text": "HSP70", "start": 1452, "end": 1457}]}, {"trigger": {"text": "activated", "start": 1531, "end": 1540}, "arguments": [{"role": "Theme", "text": "binding", "start": 1561, "end": 1568}]}], "regulation": [{"trigger": {"text": "responsive", "start": 1202, "end": 1212}, "arguments": [{"role": "Theme", "text": "IL1B", "start": 1143, "end": 1147}, {"role": "Site", "text": "promoter", "start": 1148, "end": 1156}]}]}}, "schema": []}
{"input": "Disruption of alpha beta but not of gamma delta T cell development by overexpression of the helix-loop-helix protein Id3 in committed T cell progenitors. \nEnforced expression of Id3, which has the capacity to inhibit many basic helix-loop-helix (bHLH) transcription factors, in human CD34(+) hematopoietic progenitor cells that have not undergone T cell receptor (TCR) gene rearrangements inhibits development of the transduced cells into TCRalpha beta and gamma delta cells in a fetal thymic organ culture (FTOC). Here we document that overexpression of Id3, in progenitors that have initiated TCR gene rearrangements (pre-T cells), inhibits development into TCRalpha beta but not into TCRgamma delta T cells. Furthermore, Id3 impedes expression of recombination activating genes and downregulates pre-Talpha mRNA. These observations suggest possible mechanisms by which Id3 overexpression can differentially affect development of pre-T cells into TCRalpha beta and gamma delta cells. We also observed that cell surface CD4(-)CD8(-)CD3(-) cells with rearranged TCR genes developed from Id3-transduced but not from control-transduced pre-T cells in an FTOC. These cells had properties of both natural killer (NK) and pre-T cells. These findings suggest that bHLH factors are required to control T cell development after the T/NK developmental checkpoint. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "overexpression", "start": 70, "end": 84}, "arguments": [{"role": "Theme", "text": "Id3", "start": 117, "end": 120}]}, {"trigger": {"text": "expression", "start": 164, "end": 174}, "arguments": [{"role": "Theme", "text": "Id3", "start": 178, "end": 181}]}, {"trigger": {"text": "overexpression", "start": 537, "end": 551}, "arguments": [{"role": "Theme", "text": "Id3", "start": 555, "end": 558}]}, {"trigger": {"text": "overexpression", "start": 876, "end": 890}, "arguments": [{"role": "Theme", "text": "Id3", "start": 872, "end": 875}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 70, "end": 84}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 70, "end": 84}]}, {"trigger": {"text": "Enforced", "start": 155, "end": 163}, "arguments": [{"role": "Theme", "text": "expression", "start": 164, "end": 174}]}, {"trigger": {"text": "overexpression", "start": 876, "end": 890}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 876, "end": 890}]}]}}, "schema": []}
{"input": "Rel/NF-kappaB can trigger the Notch signaling pathway by inducing the expression of Jagged1, a ligand for Notch receptors. \nJagged1 belongs to the DSL family of ligands for Notch receptors that control the proliferation and differentiation of various cell lineages. However, little is known about the transcription factors that regulate its expression. Here, we show that Jagged1 is a Rel/NF-kappaB-responsive gene. Both c-Rel and RelA induced jagged1 gene expression, whereas a mutant defective for transactivation did not. Importantly, jagged1 transcripts were also upregulated by endogenous NF-kappaB activation and this effect was inhibited by a dominant mutant of IkappaBalpha, a physiological inhibitor of NF-kappaB. Cell surface expression of Jagged1 in c-Rel-expressing cell monolayers led to a functional interaction with lymphocytes expressing the Notch1/TAN-1 receptor. This correlated with the initiation of signaling downstream of Notch, as evidenced by increased levels of HES-1 transcripts in co-cultivated T cells and of CD23 transcripts in co-cultivated B cells. Consistent with its Rel/NF-kappaB-dependent induction, Jagged1 was found to be highly expressed in splenic B cells where c-Rel is expressed constitutively. These results demonstrate that c-Rel can trigger the Notch signaling pathway in neighboring cells by inducing jagged1 gene expression, and suggest a role for Jagged1 in B-cell activation, differentiation or function. These findings also highlight the potential for an interplay between the Notch and NF-kappaB signaling pathways in the immune system. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 70, "end": 80}, "arguments": [{"role": "Theme", "text": "Jagged1", "start": 84, "end": 91}]}, {"trigger": {"text": "expression", "start": 341, "end": 351}, "arguments": [{"role": "Theme", "text": "Jagged1", "start": 124, "end": 131}]}, {"trigger": {"text": "expression", "start": 457, "end": 467}, "arguments": [{"role": "Theme", "text": "jagged1", "start": 444, "end": 451}]}, {"trigger": {"text": "expression", "start": 736, "end": 746}, "arguments": [{"role": "Theme", "text": "Jagged1", "start": 750, "end": 757}]}, {"trigger": {"text": "expressing", "start": 767, "end": 777}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 761, "end": 766}]}, {"trigger": {"text": "expressing", "start": 843, "end": 853}, "arguments": [{"role": "Theme", "text": "Notch1", "start": 858, "end": 864}]}, {"trigger": {"text": "expressed", "start": 1166, "end": 1175}, "arguments": [{"role": "Theme", "text": "Jagged1", "start": 1135, "end": 1142}]}, {"trigger": {"text": "expressed", "start": 1210, "end": 1219}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1201, "end": 1206}]}, {"trigger": {"text": "expression", "start": 1359, "end": 1369}, "arguments": [{"role": "Theme", "text": "jagged1", "start": 1346, "end": 1353}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 635, "end": 644}, "arguments": [{"role": "Theme", "text": "upregulated", "start": 568, "end": 579}, {"role": "Cause", "text": "IkappaBalpha", "start": 669, "end": 681}]}], "positive regulation": [{"trigger": {"text": "inducing", "start": 57, "end": 65}, "arguments": [{"role": "Theme", "text": "expression", "start": 70, "end": 80}]}, {"trigger": {"text": "induced", "start": 436, "end": 443}, "arguments": [{"role": "Cause", "text": "c-Rel", "start": 421, "end": 426}, {"role": "Theme", "text": "expression", "start": 457, "end": 467}]}, {"trigger": {"text": "induced", "start": 436, "end": 443}, "arguments": [{"role": "Cause", "text": "RelA", "start": 431, "end": 435}, {"role": "Theme", "text": "expression", "start": 457, "end": 467}]}, {"trigger": {"text": "induced", "start": 436, "end": 443}, "arguments": [{"role": "Theme", "text": "expression", "start": 457, "end": 467}]}, {"trigger": {"text": "upregulated", "start": 568, "end": 579}, "arguments": [{"role": "Theme", "text": "jagged1", "start": 538, "end": 545}]}, {"trigger": {"text": "increased levels", "start": 967, "end": 983}, "arguments": [{"role": "Theme", "text": "CD23", "start": 1037, "end": 1041}]}, {"trigger": {"text": "increased levels", "start": 967, "end": 983}, "arguments": [{"role": "Theme", "text": "HES-1", "start": 987, "end": 992}]}, {"trigger": {"text": "induction", "start": 1124, "end": 1133}, "arguments": [{"role": "Theme", "text": "Jagged1", "start": 1135, "end": 1142}]}, {"trigger": {"text": "highly", "start": 1159, "end": 1165}, "arguments": [{"role": "Theme", "text": "expressed", "start": 1166, "end": 1175}]}, {"trigger": {"text": "inducing", "start": 1337, "end": 1345}, "arguments": [{"role": "Cause", "text": "c-Rel", "start": 1267, "end": 1272}, {"role": "Theme", "text": "expression", "start": 1359, "end": 1369}]}], "regulation": [{"trigger": {"text": "regulate", "start": 328, "end": 336}, "arguments": [{"role": "Theme", "text": "expression", "start": 341, "end": 351}]}, {"trigger": {"text": "responsive", "start": 399, "end": 409}, "arguments": [{"role": "Theme", "text": "Jagged1", "start": 372, "end": 379}]}]}}, "schema": []}
{"input": "Transcriptional control of the IL-5 gene by human helper T cells: IL-5 synthesis is regulated independently from IL-2 or IL-4 synthesis. \nBACKGROUND: IL-5 is fundamentally involved in eosinophilic inflammation. Control of IL-5 production may be effective for the management of allergic diseases. OBJECTIVE: We aimed to find the transcriptional mechanisms that regulate the IL-5 gene to selectively control IL-5 synthesis. METHODS: Allergen-specific T-cell clones and T-cell hybridomas were established from the peripheral blood lymphocytes of patients with asthma, and the transcriptional regulation of the IL-5 gene was investigated with transient transfection and electrophoretic mobility shift analysis. RESULTS: A human IL-5 promoter/enhancer-luciferase gene construct, pIL-5(-511)Luc, was transcribed on activation of IL-5-producing T-cell clones, but not IL-5-nonproducing clones. pIL-5(-511)Luc was transcribed by T-cell hybridomas derived from fusion between IL-5-producing T-cell clones and an IL-5 gene-nonexpressing T-cell line, but not by hybridomas derived from IL-5-nonproducing T-cell clones. IL-5 synthesis was not only induced by T-cell receptor stimulation but also by IL-2 receptor stimulation. Binding of NF-AT, NF-kappaB, and AP-1 was induced by T-cell receptor (TcR) stimulation, although there was no significant upregulation of binding by IL-2 stimulation. CONCLUSION: IL-5 synthesis by human helper T cells is regulated at the transcriptional level. A unique transcriptional mechanism distinct from those regulating the IL-2 or IL-4 genes seems to control the IL-5 gene. Selective regulation of IL-5 gene transcription may be useful for treating eosinophlic inflammation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "synthesis", "start": 71, "end": 80}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 66, "end": 70}]}, {"trigger": {"text": "synthesis", "start": 126, "end": 135}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 113, "end": 117}]}, {"trigger": {"text": "synthesis", "start": 126, "end": 135}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 121, "end": 125}]}, {"trigger": {"text": "production", "start": 227, "end": 237}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 222, "end": 226}]}, {"trigger": {"text": "synthesis", "start": 411, "end": 420}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 406, "end": 410}]}, {"trigger": {"text": "producing", "start": 828, "end": 837}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 823, "end": 827}]}, {"trigger": {"text": "nonproducing", "start": 866, "end": 878}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 861, "end": 865}]}, {"trigger": {"text": "producing", "start": 972, "end": 981}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 967, "end": 971}]}, {"trigger": {"text": "nonexpressing", "start": 1013, "end": 1026}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1003, "end": 1007}]}, {"trigger": {"text": "nonproducing", "start": 1080, "end": 1092}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1075, "end": 1079}]}, {"trigger": {"text": "synthesis", "start": 1113, "end": 1122}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1108, "end": 1112}]}, {"trigger": {"text": "synthesis", "start": 1398, "end": 1407}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1393, "end": 1397}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1136, "end": 1143}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1113, "end": 1122}]}], "regulation": [{"trigger": {"text": "Transcriptional control", "start": 0, "end": 23}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 31, "end": 35}]}, {"trigger": {"text": "regulated", "start": 84, "end": 93}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 71, "end": 80}]}, {"trigger": {"text": "Control", "start": 211, "end": 218}, "arguments": [{"role": "Theme", "text": "production", "start": 227, "end": 237}]}, {"trigger": {"text": "regulate", "start": 360, "end": 368}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 328, "end": 343}]}, {"trigger": {"text": "control", "start": 398, "end": 405}, "arguments": [{"role": "Cause", "text": "regulate", "start": 360, "end": 368}, {"role": "Theme", "text": "synthesis", "start": 411, "end": 420}]}, {"trigger": {"text": "regulated", "start": 1435, "end": 1444}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1398, "end": 1407}]}, {"trigger": {"text": "regulating", "start": 1530, "end": 1540}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1545, "end": 1549}]}, {"trigger": {"text": "regulating", "start": 1530, "end": 1540}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1553, "end": 1557}]}, {"trigger": {"text": "control", "start": 1573, "end": 1580}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 31, "end": 35}]}, {"trigger": {"text": "regulation", "start": 1606, "end": 1616}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1630, "end": 1643}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 328, "end": 343}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 373, "end": 377}]}, {"trigger": {"text": "transcriptional regulation", "start": 573, "end": 599}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 607, "end": 611}]}, {"trigger": {"text": "transcription", "start": 1630, "end": 1643}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 31, "end": 35}]}]}}, "schema": []}
{"input": "Regulation of low shear flow-induced HAEC VCAM-1 expression and monocyte adhesion. \nWe recently reported that prolonged exposure of human aortic endothelial cells (HAEC) to low shear stress flow patterns is associated with a sustained increase in the activated form of the transcriptional regulator nuclear factor-kappaB (NF-kappaB). Here we investigate the hypothesis that low shear-induced activation of NF-kappaB is responsible for enhanced expression of vascular cell adhesion molecule (VCAM-1) resulting in augmented endothelial cell-monocyte (EC-Mn) adhesion and that this activation is dependent on intracellular oxidant activity. Before exposure to low shear (2 dyn/cm2) for 6 h, HAEC were preincubated with or without the antioxidants pyrrolidine dithiocarbamate (PDTC) or N-acetyl-L-cysteine (NAC). PDTC strongly inhibited low shear-induced activation of NF-kappaB, expression of VCAM-1, and EC-Mn adhesion. Paradoxically, NAC exerted a positive effect on low shear-induced VCAM-1 expression and EC-Mn adhesion and only slightly downregulated NF-kappaB activation. However, cytokine-induced NF-kappaB activation and VCAM-1 expression are blocked by both PDTC and NAC. These data suggest that NF-kappaB plays a key role in low shear-induced VCAM-1 expression and that pathways mediating low shear- and cytokine-induced EC-Mn adhesion may be differentially regulated. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 49, "end": 59}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 42, "end": 48}]}, {"trigger": {"text": "expression", "start": 444, "end": 454}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 491, "end": 497}]}, {"trigger": {"text": "expression", "start": 876, "end": 886}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 890, "end": 896}]}, {"trigger": {"text": "expression", "start": 991, "end": 1001}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 984, "end": 990}]}, {"trigger": {"text": "expression", "start": 1133, "end": 1143}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1126, "end": 1132}]}, {"trigger": {"text": "expression", "start": 1257, "end": 1267}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1250, "end": 1256}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 823, "end": 832}, "arguments": [{"role": "Theme", "text": "induced", "start": 843, "end": 850}]}, {"trigger": {"text": "blocked", "start": 1148, "end": 1155}, "arguments": [{"role": "Theme", "text": "induced", "start": 1093, "end": 1100}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 29, "end": 36}, "arguments": [{"role": "Theme", "text": "expression", "start": 49, "end": 59}]}, {"trigger": {"text": "responsible for enhanced", "start": 419, "end": 443}, "arguments": [{"role": "Theme", "text": "expression", "start": 444, "end": 454}]}, {"trigger": {"text": "induced", "start": 843, "end": 850}, "arguments": [{"role": "Theme", "text": "expression", "start": 876, "end": 886}]}, {"trigger": {"text": "exerted a positive effect", "start": 937, "end": 962}, "arguments": [{"role": "Theme", "text": "induced", "start": 976, "end": 983}]}, {"trigger": {"text": "induced", "start": 976, "end": 983}, "arguments": [{"role": "Theme", "text": "expression", "start": 991, "end": 1001}]}, {"trigger": {"text": "induced", "start": 1093, "end": 1100}, "arguments": [{"role": "Theme", "text": "expression", "start": 1133, "end": 1143}]}, {"trigger": {"text": "induced", "start": 1242, "end": 1249}, "arguments": [{"role": "Theme", "text": "expression", "start": 1257, "end": 1267}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "induced", "start": 29, "end": 36}]}]}}, "schema": []}
{"input": "Nuclear localization and formation of beta-catenin-lymphoid enhancer factor 1 complexes are not sufficient for activation of gene expression. \nIn response to activation of the Wnt signaling pathway, beta-catenin accumulates in the nucleus, where it cooperates with LEF/TCF (for lymphoid enhancer factor and T-cell factor) transcription factors to activate gene expression. The mechanisms by which beta-catenin undergoes this shift in location and participates in activation of gene transcription are unknown. We demonstrate here that beta-catenin can be imported into the nucleus independently of LEF/TCF binding, and it may also be exported from nuclei. We have introduced a small deletion within beta-catenin (Delta19) that disrupts binding to LEF-1, E-cadherin, and APC but not axin. This Delta19 beta-catenin mutant localizes to the nucleus because it may not be efficiently sequestered in the cytoplasm. The nuclear localization of Delta19 definitively demonstrates that the mechanisms by which beta-catenin localizes in the nucleus are completely independent of LEF/TCF factors. beta-Catenin and LEF-1 complexes can activate reporter gene expression in a transformed T-lymphocyte cell line (Jurkat) but not in normal T lymphocytes, even though both factors are nuclear. Thus, localization of both factors to the nucleus is not sufficient for activation of gene expression. Excess beta-catenin can squelch reporter gene activation by LEF-1-beta-catenin complexes but not activation by the transcription factor VP16. Taken together, these data suggest that a third component is necessary for gene activation and that this third component may vary with cell type. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complexes", "start": 78, "end": 87}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 38, "end": 50}, {"role": "Theme2", "text": "lymphoid enhancer factor 1", "start": 51, "end": 77}]}, {"trigger": {"text": "binding", "start": 605, "end": 612}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 534, "end": 546}]}, {"trigger": {"text": "binding", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 698, "end": 710}, {"role": "Theme2", "text": "LEF-1", "start": 746, "end": 751}]}, {"trigger": {"text": "binding", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 698, "end": 710}, {"role": "Theme2", "text": "E-cadherin", "start": 753, "end": 763}]}, {"trigger": {"text": "binding", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 698, "end": 710}, {"role": "Theme2", "text": "APC", "start": 769, "end": 772}]}, {"trigger": {"text": "binding", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 698, "end": 710}, {"role": "Theme2", "text": "axin", "start": 781, "end": 785}]}], "localization": [{"trigger": {"text": "localization", "start": 8, "end": 20}, "arguments": [{"role": "AtLoc", "text": "Nuclear", "start": 0, "end": 7}, {"role": "Theme", "text": "beta-catenin", "start": 38, "end": 50}]}, {"trigger": {"text": "localization", "start": 8, "end": 20}, "arguments": [{"role": "AtLoc", "text": "Nuclear", "start": 0, "end": 7}, {"role": "Theme", "text": "lymphoid enhancer factor 1", "start": 51, "end": 77}]}, {"trigger": {"text": "accumulates", "start": 212, "end": 223}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 199, "end": 211}, {"role": "AtLoc", "text": "nucleus", "start": 231, "end": 238}]}, {"trigger": {"text": "imported", "start": 554, "end": 562}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 534, "end": 546}, {"role": "ToLoc", "text": "nucleus", "start": 572, "end": 579}]}, {"trigger": {"text": "exported", "start": 633, "end": 641}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 534, "end": 546}]}, {"trigger": {"text": "localizes", "start": 1013, "end": 1022}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 1000, "end": 1012}, {"role": "AtLoc", "text": "nucleus", "start": 1030, "end": 1037}]}, {"trigger": {"text": "are", "start": 1263, "end": 1266}, "arguments": [{"role": "Theme", "text": "beta-Catenin", "start": 1085, "end": 1097}, {"role": "AtLoc", "text": "nuclear", "start": 1267, "end": 1274}]}, {"trigger": {"text": "are", "start": 1263, "end": 1266}, "arguments": [{"role": "Theme", "text": "LEF-1", "start": 1102, "end": 1107}, {"role": "AtLoc", "text": "nuclear", "start": 1267, "end": 1274}]}, {"trigger": {"text": "localization", "start": 1282, "end": 1294}, "arguments": [{"role": "Theme", "text": "beta-Catenin", "start": 1085, "end": 1097}, {"role": "ToLoc", "text": "nucleus", "start": 1318, "end": 1325}]}, {"trigger": {"text": "localization", "start": 1282, "end": 1294}, "arguments": [{"role": "Theme", "text": "LEF-1", "start": 1102, "end": 1107}, {"role": "ToLoc", "text": "nucleus", "start": 1318, "end": 1325}]}], "negative regulation": [{"trigger": {"text": "disrupts", "start": 726, "end": 734}, "arguments": [{"role": "Theme", "text": "binding", "start": 735, "end": 742}]}], "positive regulation": [{"trigger": {"text": "In response to", "start": 143, "end": 157}, "arguments": [{"role": "Theme", "text": "accumulates", "start": 212, "end": 223}]}, {"trigger": {"text": "undergoes", "start": 410, "end": 419}, "arguments": [{"role": "Theme", "text": "In response to", "start": 143, "end": 157}]}, {"trigger": {"text": "Excess", "start": 1379, "end": 1385}, "arguments": [{"role": "Theme", "text": "beta-catenin", "start": 1386, "end": 1398}]}]}}, "schema": []}
{"input": "Paradoxical priming effects of IL-10 on cytokine production. \nIL-10 is a well-known immunosuppressive and/or anti-inflammatory cytokine. However, we report in vitro experimental studies in which IL-10 primed leukocytes and led to an enhanced production of tumor necrosis factor (TNF) upon further stimulation by lipopolysaccharide (LPS). Monocytes and peripheral blood mononuclear cells (PBMC) prepared from whole blood maintained for 20 h at 37 degrees C in the presence of recombinant human IL-10 had an enhanced capacity to produce TNF in response to LPS. In addition to TNF, LPS-induced IL-6 and spontaneous IL-1ra production were also enhanced. When isolated PBMC were first cultured for 20 h in the presence of IL-10 on Teflon to prevent adherence, washed to remove IL-10 and then further cultured in plastic dishes for an additional 20 h in the presence of LPS or IL-1beta, an enhanced release of TNF was observed. This was not the case when PBMC were pre-cultured in plastic multidishes in the presence of IL-10. TNF mRNA expression induced by LPS was decreased when the pre-treatment of PBMC with IL-10 was performed on plastic, whereas this was not the case when cells were pre-cultured with IL-10 on Teflon. Furthermore, NFkappaB translocation following LPS activation was higher after IL-10 pre-treatment on Teflon than on plastic. Interestingly, an enhanced frequency of CD16 and CD68(+) cells among the CD14(+) cells was observed in the presence of IL-10, independently of the pre-culture conditions of the PBMC. Altogether, these results indicate that the IL-10-induced up-regulation of cytokine production depends on the prevention of monocyte adherence by red cells in the whole blood assays or by cultures of PBMC on Teflon. In contrast, the adherence parameter has no effect on the IL-10-induced modulation of some monocyte surface markers. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 242, "end": 252}, "arguments": [{"role": "Theme", "text": "TNF", "start": 279, "end": 282}]}, {"trigger": {"text": "produce", "start": 527, "end": 534}, "arguments": [{"role": "Theme", "text": "TNF", "start": 535, "end": 538}]}, {"trigger": {"text": "production", "start": 619, "end": 629}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 591, "end": 595}]}, {"trigger": {"text": "production", "start": 619, "end": 629}, "arguments": [{"role": "Theme", "text": "IL-1ra", "start": 612, "end": 618}]}], "localization": [{"trigger": {"text": "release", "start": 893, "end": 900}, "arguments": [{"role": "Theme", "text": "TNF", "start": 904, "end": 907}]}], "positive regulation": [{"trigger": {"text": "led to an enhanced", "start": 223, "end": 241}, "arguments": [{"role": "Theme", "text": "upon", "start": 284, "end": 288}]}, {"trigger": {"text": "upon", "start": 284, "end": 288}, "arguments": [{"role": "Theme", "text": "production", "start": 242, "end": 252}]}, {"trigger": {"text": "enhanced", "start": 506, "end": 514}, "arguments": [{"role": "Theme", "text": "in response to", "start": 539, "end": 553}]}, {"trigger": {"text": "in response to", "start": 539, "end": 553}, "arguments": [{"role": "Theme", "text": "produce", "start": 527, "end": 534}]}, {"trigger": {"text": "induced", "start": 583, "end": 590}, "arguments": [{"role": "Theme", "text": "production", "start": 619, "end": 629}]}, {"trigger": {"text": "enhanced", "start": 640, "end": 648}, "arguments": [{"role": "Theme", "text": "induced", "start": 583, "end": 590}]}, {"trigger": {"text": "enhanced", "start": 640, "end": 648}, "arguments": [{"role": "Theme", "text": "production", "start": 619, "end": 629}]}, {"trigger": {"text": "enhanced", "start": 884, "end": 892}, "arguments": [{"role": "Theme", "text": "release", "start": 893, "end": 900}]}, {"trigger": {"text": "not", "start": 931, "end": 934}, "arguments": [{"role": "Theme", "text": "release", "start": 893, "end": 900}]}]}}, "schema": []}
{"input": "Different sequence requirements for expression in erythroid and megakaryocytic cells within a regulatory element upstream of the GATA-1 gene. \nThe lineage-restricted transcription factor GATA-1 is required for differentiation of erythroid and megakaryocytic cells. We have localized a 317 base pair cis-acting regulatory element, HS I, associated with a hematopoietic-specific DNase I hypersensitive site, which lies approx. 3.7 kilobases upstream of the murine hematopoietic-specific GATA-1 IE promoter. HS I directs high-level expression of reporter GATA-1/lacZ genes to primitive and definitive erythroid cells and megakaryocytes in transgenic mice. Comparative sequence analysis of HS I between human and mouse shows approx. 63% nucleotide identity with a more conserved core of 169 base pairs (86% identity). This core contains a GATA site separated by 10 base pairs from an E-box motif. The composite motif binds a multi-protein hematopoietic-specific transcription factor complex which includes GATA-1, SCL/tal-1, E2A, Lmo2 and Ldb-1. Point mutations of the GATA site abolishes HS I function, whereas mutation of the E-box motif still allows reporter gene expression in both lineages. Strict dependence of HS I activity on a GATA site implies that assembly of a protein complex containing a GATA-factor, presumably GATA-1 or GATA-2, is critical to activating or maintaining its function. Further dissection of the 317 base pair region demonstrates that, whereas all 317 base pairs are required for expression in megakaryocytes, only the 5' 62 base pairs are needed for erythroid-specific reporter expression. These findings demonstrate differential lineage requirements for expression within the HS I element. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 913, "end": 918}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1002, "end": 1008}]}, {"trigger": {"text": "binds", "start": 913, "end": 918}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1010, "end": 1013}]}, {"trigger": {"text": "binds", "start": 913, "end": 918}, "arguments": [{"role": "Theme", "text": "E2A", "start": 1021, "end": 1024}]}, {"trigger": {"text": "binds", "start": 913, "end": 918}, "arguments": [{"role": "Theme", "text": "Lmo2", "start": 1026, "end": 1030}]}, {"trigger": {"text": "binds", "start": 913, "end": 918}, "arguments": [{"role": "Theme", "text": "Ldb-1", "start": 1035, "end": 1040}]}, {"trigger": {"text": "assembly of a protein complex", "start": 1255, "end": 1284}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1322, "end": 1328}]}, {"trigger": {"text": "assembly of a protein complex", "start": 1255, "end": 1284}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 1332, "end": 1338}]}], "gene expression": [{"trigger": {"text": "expression", "start": 36, "end": 46}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 129, "end": 135}]}, {"trigger": {"text": "expression", "start": 529, "end": 539}, "arguments": [{"role": "Theme", "text": "lacZ", "start": 559, "end": 563}]}], "positive regulation": [{"trigger": {"text": "requirements", "start": 19, "end": 31}, "arguments": [{"role": "Theme", "text": "expression", "start": 36, "end": 46}]}, {"trigger": {"text": "directs", "start": 510, "end": 517}, "arguments": [{"role": "Theme", "text": "expression", "start": 529, "end": 539}]}]}}, "schema": []}
{"input": "Monocyte arrest and transmigration on inflamed endothelium in shear flow is inhibited by adenovirus-mediated gene transfer of IkappaB-alpha. \nMobilization of nuclear factor-kappaB (NF-kappaB) activates transcription of genes encoding endothelial adhesion molecules and chemokines that contribute to monocyte infiltration critical in atherogenesis. Inhibition of NF-kappaB has been achieved by pharmacological and genetic approaches; however, monocyte interactions with activated endothelium in shear flow following gene transfer of the NF-kappaB inhibitor IkappaB-alpha have not been studied. We found that overexpression of IkappaB-alpha in endothelial cells using a recombinant adenovirus prevented tumor necrosis factor-alpha (TNF-alpha)-induced degradation of IkappaB-alpha and suppressed the upregulation of vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), and E-selectin mRNA and surface protein expression and the upregulation of transcripts for the chemokines monocyte chemoattractant protein 1 (MCP-1) and growth-related activity-alpha (GRO-alpha) by TNF-alpha. This was associated with a reduction in endothelial MCP-1 secretion and GRO-alpha immobilization. Adhesion assays under physiological shear flow conditions showed that firm arrest, spreading, and transmigration of monocytes on TNF-alpha-activated endothelium was markedly inhibited by IkappaB-alpha overexpression. Inhibition with monoclonal antibodies and peptide antagonists inferred that this was due to reduced expression of Ig integrin ligand as well as of chemokines specifically involved in these events. In contrast, rolling of monocytes was increased by IkappaB-alpha transfer and was partly mediated by P-selectin; however, it appeared to be unaffected by the inhibition of E-selectin induction. Thus, our data provide novel evidence that selective modulation of NF-kappaB by adenoviral transfer of IkappaB-alpha impairs the expression of multiple endothelial gene products required for subsequent monocyte arrest and emigration in shear flow and thus for monocyte infiltration in atherosclerotic plaques. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "gene transfer", "start": 109, "end": 122}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 126, "end": 139}]}, {"trigger": {"text": "gene transfer", "start": 515, "end": 528}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 556, "end": 569}]}, {"trigger": {"text": "overexpression", "start": 607, "end": 621}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 625, "end": 638}]}, {"trigger": {"text": "expression", "start": 941, "end": 951}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 848, "end": 854}]}, {"trigger": {"text": "expression", "start": 941, "end": 951}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 892, "end": 898}]}, {"trigger": {"text": "expression", "start": 941, "end": 951}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 905, "end": 915}]}, {"trigger": {"text": "overexpression", "start": 1409, "end": 1423}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1395, "end": 1408}]}, {"trigger": {"text": "transfer", "start": 1687, "end": 1695}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1673, "end": 1686}]}, {"trigger": {"text": "transfer", "start": 1907, "end": 1915}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1919, "end": 1932}]}], "localization": [{"trigger": {"text": "secretion", "start": 1168, "end": 1177}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 1162, "end": 1167}]}, {"trigger": {"text": "immobilization", "start": 1192, "end": 1206}, "arguments": [{"role": "Theme", "text": "GRO-alpha", "start": 1182, "end": 1191}]}], "negative regulation": [{"trigger": {"text": "prevented", "start": 691, "end": 700}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 607, "end": 621}, {"role": "Theme", "text": "degradation", "start": 749, "end": 760}]}, {"trigger": {"text": "suppressed", "start": 782, "end": 792}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 607, "end": 621}, {"role": "Theme", "text": "upregulation", "start": 797, "end": 809}]}, {"trigger": {"text": "suppressed", "start": 782, "end": 792}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 607, "end": 621}, {"role": "Theme", "text": "upregulation", "start": 960, "end": 972}]}, {"trigger": {"text": "reduction", "start": 1137, "end": 1146}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1168, "end": 1177}]}, {"trigger": {"text": "inhibition", "start": 1780, "end": 1790}, "arguments": [{"role": "Theme", "text": "induction", "start": 1805, "end": 1814}]}], "positive regulation": [{"trigger": {"text": "gene transfer", "start": 109, "end": 122}, "arguments": [{"role": "Theme", "text": "gene transfer", "start": 109, "end": 122}]}, {"trigger": {"text": "following", "start": 505, "end": 514}, "arguments": [{"role": "Theme", "text": "gene transfer", "start": 515, "end": 528}]}, {"trigger": {"text": "gene transfer", "start": 515, "end": 528}, "arguments": [{"role": "Theme", "text": "gene transfer", "start": 515, "end": 528}]}, {"trigger": {"text": "overexpression", "start": 607, "end": 621}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 607, "end": 621}]}, {"trigger": {"text": "induced", "start": 741, "end": 748}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 730, "end": 739}, {"role": "Theme", "text": "degradation", "start": 749, "end": 760}]}, {"trigger": {"text": "upregulation", "start": 797, "end": 809}, "arguments": [{"role": "Theme", "text": "expression", "start": 941, "end": 951}]}, {"trigger": {"text": "upregulation", "start": 960, "end": 972}, "arguments": [{"role": "Theme", "text": "transcripts", "start": 976, "end": 987}, {"role": "Cause", "text": "TNF-alpha", "start": 1099, "end": 1108}]}, {"trigger": {"text": "overexpression", "start": 1409, "end": 1423}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1409, "end": 1423}]}, {"trigger": {"text": "transfer", "start": 1687, "end": 1695}, "arguments": [{"role": "Theme", "text": "transfer", "start": 1687, "end": 1695}]}, {"trigger": {"text": "induction", "start": 1805, "end": 1814}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1794, "end": 1804}]}, {"trigger": {"text": "transfer", "start": 1907, "end": 1915}, "arguments": [{"role": "Theme", "text": "transfer", "start": 1907, "end": 1915}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 749, "end": 760}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 764, "end": 777}]}], "transcription": [{"trigger": {"text": "expression", "start": 941, "end": 951}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 848, "end": 854}]}, {"trigger": {"text": "expression", "start": 941, "end": 951}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 892, "end": 898}]}, {"trigger": {"text": "expression", "start": 941, "end": 951}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 905, "end": 915}]}, {"trigger": {"text": "transcripts", "start": 976, "end": 987}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 1043, "end": 1048}]}, {"trigger": {"text": "transcripts", "start": 976, "end": 987}, "arguments": [{"role": "Theme", "text": "GRO-alpha", "start": 1085, "end": 1094}]}]}}, "schema": []}
{"input": "SLP-76 and Vav function in separate, but overlapping pathways to augment interleukin-2 promoter activity. \nSLP-76 and Vav, two hematopoietic cell specific molecules, are critical for T cell development and activation. Following T cell antigen receptor stimulation, SLP-76 and Vav both undergo tyrosine phosphorylation and associate with each other via the SH2 domain of Vav and phosphorylated tyrosines of SLP-76. Furthermore, SLP-76 and Vav have a synergistic effect on interleukin (IL)-2 promoter activity in T cells. In this report, we show that two tyrosines, Tyr-113 and Tyr-128, of SLP-76 are required for its binding to Vav, both in vitro and in intact cells. Surprisingly, we find also that the interaction between SLP-76 and Vav is not required for their cooperation in augmenting IL-2 promoter activity, as the two molecules appear to function in different signaling pathways upstream of IL-2 gene expression. Overexpression of SLP-76 in the Jurkat T cell line potentiates the activities of both nuclear factor of activated T cells and AP-1 transcription factors. In contrast, overexpression of Vav leads to enhanced nuclear factor of activated T cells activity without affecting AP-1. Additionally, overexpression of Vav, but not SLP-76, augments CD28-induced IL-2 promoter activity. These findings suggest that the synergy between SLP-76 and Vav in regulating IL-2 gene expression reflects the cooperation between different signaling pathways. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associate", "start": 322, "end": 331}, "arguments": [{"role": "Site", "text": "SH2 domain", "start": 356, "end": 366}, {"role": "Theme", "text": "Vav", "start": 370, "end": 373}, {"role": "Theme2", "text": "SLP-76", "start": 406, "end": 412}]}, {"trigger": {"text": "binding", "start": 616, "end": 623}, "arguments": [{"role": "Theme", "text": "SLP-76", "start": 588, "end": 594}, {"role": "Theme2", "text": "Vav", "start": 627, "end": 630}]}, {"trigger": {"text": "interaction", "start": 703, "end": 714}, "arguments": [{"role": "Theme", "text": "SLP-76", "start": 723, "end": 729}, {"role": "Theme2", "text": "Vav", "start": 734, "end": 737}]}], "gene expression": [{"trigger": {"text": "gene expression", "start": 903, "end": 918}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 898, "end": 902}]}, {"trigger": {"text": "Overexpression", "start": 920, "end": 934}, "arguments": [{"role": "Theme", "text": "SLP-76", "start": 938, "end": 944}]}, {"trigger": {"text": "overexpression", "start": 1087, "end": 1101}, "arguments": [{"role": "Theme", "text": "Vav", "start": 1105, "end": 1108}]}, {"trigger": {"text": "overexpression", "start": 1210, "end": 1224}, "arguments": [{"role": "Theme", "text": "Vav", "start": 1228, "end": 1231}]}, {"trigger": {"text": "overexpression", "start": 1210, "end": 1224}, "arguments": [{"role": "Theme", "text": "SLP-76", "start": 1241, "end": 1247}]}, {"trigger": {"text": "gene expression", "start": 1377, "end": 1392}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1372, "end": 1376}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 302, "end": 317}, "arguments": [{"role": "Theme", "text": "SLP-76", "start": 265, "end": 271}, {"role": "Site", "text": "tyrosine", "start": 293, "end": 301}]}, {"trigger": {"text": "phosphorylation", "start": 302, "end": 317}, "arguments": [{"role": "Theme", "text": "Vav", "start": 276, "end": 279}, {"role": "Site", "text": "tyrosine", "start": 293, "end": 301}]}, {"trigger": {"text": "phosphorylated", "start": 378, "end": 392}, "arguments": [{"role": "Site", "text": "tyrosines", "start": 393, "end": 402}, {"role": "Theme", "text": "SLP-76", "start": 406, "end": 412}]}], "positive regulation": [{"trigger": {"text": "augment", "start": 65, "end": 72}, "arguments": [{"role": "Cause", "text": "SLP-76", "start": 0, "end": 6}, {"role": "Theme", "text": "interleukin-2", "start": 73, "end": 86}, {"role": "Site", "text": "promoter", "start": 87, "end": 95}]}, {"trigger": {"text": "augment", "start": 65, "end": 72}, "arguments": [{"role": "Cause", "text": "Vav", "start": 11, "end": 14}, {"role": "Theme", "text": "interleukin-2", "start": 73, "end": 86}, {"role": "Site", "text": "promoter", "start": 87, "end": 95}]}, {"trigger": {"text": "Following", "start": 218, "end": 227}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 302, "end": 317}]}, {"trigger": {"text": "effect", "start": 461, "end": 467}, "arguments": [{"role": "Cause", "text": "SLP-76", "start": 427, "end": 433}, {"role": "Theme", "text": "interleukin (IL)-2", "start": 471, "end": 489}, {"role": "Site", "text": "promoter", "start": 490, "end": 498}]}, {"trigger": {"text": "effect", "start": 461, "end": 467}, "arguments": [{"role": "Cause", "text": "Vav", "start": 438, "end": 441}, {"role": "Theme", "text": "interleukin (IL)-2", "start": 471, "end": 489}, {"role": "Site", "text": "promoter", "start": 490, "end": 498}]}, {"trigger": {"text": "required", "start": 745, "end": 753}, "arguments": [{"role": "Cause", "text": "interaction", "start": 703, "end": 714}, {"role": "Theme", "text": "augmenting", "start": 779, "end": 789}]}, {"trigger": {"text": "augmenting", "start": 779, "end": 789}, "arguments": [{"role": "Cause", "text": "SLP-76", "start": 723, "end": 729}, {"role": "Theme", "text": "IL-2", "start": 790, "end": 794}, {"role": "Site", "text": "promoter", "start": 795, "end": 803}]}, {"trigger": {"text": "augmenting", "start": 779, "end": 789}, "arguments": [{"role": "Cause", "text": "Vav", "start": 734, "end": 737}, {"role": "Theme", "text": "IL-2", "start": 790, "end": 794}, {"role": "Site", "text": "promoter", "start": 795, "end": 803}]}, {"trigger": {"text": "upstream", "start": 886, "end": 894}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 903, "end": 918}]}, {"trigger": {"text": "Overexpression", "start": 920, "end": 934}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 920, "end": 934}]}, {"trigger": {"text": "overexpression", "start": 1087, "end": 1101}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1087, "end": 1101}]}, {"trigger": {"text": "overexpression", "start": 1210, "end": 1224}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1210, "end": 1224}]}, {"trigger": {"text": "augments", "start": 1249, "end": 1257}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 1210, "end": 1224}, {"role": "Theme", "text": "induced", "start": 1263, "end": 1270}]}, {"trigger": {"text": "induced", "start": 1263, "end": 1270}, "arguments": [{"role": "Cause", "text": "CD28", "start": 1258, "end": 1262}, {"role": "Theme", "text": "IL-2", "start": 1271, "end": 1275}, {"role": "Site", "text": "promoter", "start": 1276, "end": 1284}]}], "regulation": [{"trigger": {"text": "required", "start": 599, "end": 607}, "arguments": [{"role": "Theme", "text": "binding", "start": 616, "end": 623}]}, {"trigger": {"text": "regulating", "start": 1361, "end": 1371}, "arguments": [{"role": "Cause", "text": "SLP-76", "start": 1343, "end": 1349}, {"role": "Theme", "text": "gene expression", "start": 1377, "end": 1392}]}, {"trigger": {"text": "regulating", "start": 1361, "end": 1371}, "arguments": [{"role": "Cause", "text": "Vav", "start": 1354, "end": 1357}, {"role": "Theme", "text": "gene expression", "start": 1377, "end": 1392}]}]}}, "schema": []}
{"input": "Targeted remodeling of human beta-globin promoter chromatin structure produces increased expression and decreased silencing. \nThe chromatin structure of the human beta-globin gene locus assumes a transcriptionally-active conformation in erythroid cells. One feature of this chromatin reorganization is the formation of DNase 1 hypersensitive sites in the regions of active globin gene promoters. This reorganization requires the globin locus control region and is associated with normal expression of the beta-like globin genes. To determine whether it is possible to artificially enhance the opening of the chromatin structure of a minimal beta-globin promoter, we placed a 101bp, erythroid-specific DNase 1 hypersensitive site-forming element (HSFE) immediately upstream of the beta-globin promoter and gene. This element includes binding sites for NF-E2, AP-1, GATA-1 and Sp-1. Constructs were stably transfected into murine erythroleukemia cells and promoter chromatin structure and gene expression were analyzed. The HSFE induced an area of enhanced DNase 1 hypersensitivity extending from the transcriptional start site to -300bp of the artificial promoter and significantly increased the proportion of beta-globin promoters in an open chromatin configuration. This remodeling of promoter chromatin structure resulted in 3-fold increases in beta-globin gene transcription and induction, and inhibited long-term beta-globin gene silencing. These results indicate that a relatively small cis-acting element is able to enhance remodeling of promoter chromatin structure resulting in increased beta-globin gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 89, "end": 99}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 29, "end": 40}]}, {"trigger": {"text": "expression", "start": 1613, "end": 1623}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 1596, "end": 1607}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 79, "end": 88}, "arguments": [{"role": "Theme", "text": "expression", "start": 89, "end": 99}]}, {"trigger": {"text": "increased the proportion", "start": 1181, "end": 1205}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 1209, "end": 1220}, {"role": "Site", "text": "promoters", "start": 1221, "end": 1230}]}, {"trigger": {"text": "increases", "start": 1334, "end": 1343}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1364, "end": 1377}]}, {"trigger": {"text": "increases", "start": 1334, "end": 1343}, "arguments": [{"role": "Theme", "text": "induction", "start": 1382, "end": 1391}]}, {"trigger": {"text": "induction", "start": 1382, "end": 1391}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 1347, "end": 1358}]}, {"trigger": {"text": "increased", "start": 1586, "end": 1595}, "arguments": [{"role": "Theme", "text": "expression", "start": 1613, "end": 1623}]}], "transcription": [{"trigger": {"text": "transcriptionally-active", "start": 196, "end": 220}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 163, "end": 174}]}, {"trigger": {"text": "transcription", "start": 1364, "end": 1377}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 1347, "end": 1358}]}]}}, "schema": []}
{"input": "In vivo inhibition of NF-kappa B in T-lineage cells leads to a dramatic decrease in cell proliferation and cytokine production and to increased cell apoptosis in response to mitogenic stimuli, but not to abnormal thymopoiesis. \nTo understand the role of NF-kappa B complexes in T cell development and activation, we have generated transgenic mice in which RelA and c-Rel complexes were selectively inhibited in the T-lineage cells by specific expression of a trans-dominant form of I kappa B alpha. Transgene expression did not affect the thymic development, but led to lowered numbers of splenic T cells and to a dramatic decrease in the ex vivo proliferative response of splenic T lymphocytes. Analysis of IL-2 and IL-2R alpha expression demonstrated that the perturbation of the proliferation response was not attributable to an abnormal expression of these genes. In contrast, expression of IL-4, IL-10, and IFN-gamma was strongly inhibited in the transgenic T cells. The proliferative deficiency of the transgenic T cells was associated with an increased apoptosis. These results point out the involvement of NF-kappa B/Rel family proteins in growth signaling pathways by either regulating proteins involved in the IL-2 signaling or by functionally interfering with the cell cycle progression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 443, "end": 453}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 482, "end": 497}]}, {"trigger": {"text": "expression", "start": 509, "end": 519}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 482, "end": 497}]}, {"trigger": {"text": "expression", "start": 729, "end": 739}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 708, "end": 712}]}, {"trigger": {"text": "expression", "start": 729, "end": 739}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 717, "end": 728}]}, {"trigger": {"text": "expression", "start": 841, "end": 851}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 708, "end": 712}]}, {"trigger": {"text": "expression", "start": 841, "end": 851}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 717, "end": 728}]}, {"trigger": {"text": "expression", "start": 881, "end": 891}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 895, "end": 899}]}, {"trigger": {"text": "expression", "start": 881, "end": 891}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 901, "end": 906}]}, {"trigger": {"text": "expression", "start": 881, "end": 891}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 912, "end": 921}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 398, "end": 407}, "arguments": [{"role": "Theme", "text": "RelA", "start": 356, "end": 360}, {"role": "Cause", "text": "expression", "start": 443, "end": 453}]}, {"trigger": {"text": "inhibited", "start": 398, "end": 407}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 365, "end": 370}, {"role": "Cause", "text": "expression", "start": 443, "end": 453}]}, {"trigger": {"text": "abnormal", "start": 832, "end": 840}, "arguments": [{"role": "Theme", "text": "expression", "start": 841, "end": 851}]}, {"trigger": {"text": "inhibited", "start": 935, "end": 944}, "arguments": [{"role": "Theme", "text": "expression", "start": 881, "end": 891}]}]}}, "schema": []}
{"input": "CD28 costimulation augments IL-2 secretion of activated lamina propria T cells by increasing mRNA stability without enhancing IL-2 gene transactivation. \nThe pathways leading to activation in lamina propria (LP) T cells are different from peripheral T cells. LP T cells exhibit enhanced IL-2 secretion when activated through the CD2 pathway. Coligation of CD28 leads to synergistic enhancement of IL-2 secretion. Previous studies have characterized the CD28 augmentation of TCR-mediated signaling in peripheral blood T cells through transcriptional activation of an IL-2 promoter CD28 response element (CD28RE), along with enhanced mRNA stability. This study characterized molecular events involved in CD28 costimulation of IL-2 production in LP mononuclear cells (LPMC). LPMC exhibited increased IL-2 production in response to CD28 costimulation, compared with cells activated through CD2 alone. IL-2 secretion was paralleled by increased expression of IL-2 mRNA, resulting from enhanced IL-2 mRNA stability. In contrast to transcriptional activation in PBMC, EMSA revealed that CD28 coligation of CD2-activated LPMC does not result in increased binding of trans-factors to the CD28RE, nor did Western blots detect changes in I-kappaBalpha or I-kappaBbeta levels following CD28 coligation. Furthermore, CD28 coligation fails to enhance IL-2 promoter-reporter or RE/AP construct expression in CD2-activated LPMC. The results reported herein indicate that the molecular mechanisms involved in CD28 cosignaling and regulation of IL-2 secretion in LP T cells are unique to that compartment and differ from those seen in peripheral blood T cells. These observations suggest a biological significance for different mechanisms of IL-2 activation in initiation and maintenance of the cytokine repertoire found in the mucosa. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Coligation", "start": 342, "end": 352}, "arguments": [{"role": "Theme", "text": "CD28", "start": 356, "end": 360}]}, {"trigger": {"text": "coligation", "start": 1085, "end": 1095}, "arguments": [{"role": "Theme", "text": "CD28", "start": 1080, "end": 1084}]}, {"trigger": {"text": "coligation", "start": 1279, "end": 1289}, "arguments": [{"role": "Theme", "text": "CD28", "start": 1274, "end": 1278}]}, {"trigger": {"text": "coligation", "start": 1309, "end": 1319}, "arguments": [{"role": "Theme", "text": "CD28", "start": 1304, "end": 1308}]}], "gene expression": [{"trigger": {"text": "production", "start": 729, "end": 739}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 724, "end": 728}]}, {"trigger": {"text": "production", "start": 802, "end": 812}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 797, "end": 801}]}, {"trigger": {"text": "levels", "start": 1257, "end": 1263}, "arguments": [{"role": "Theme", "text": "I-kappaBalpha", "start": 1227, "end": 1240}]}, {"trigger": {"text": "levels", "start": 1257, "end": 1263}, "arguments": [{"role": "Theme", "text": "I-kappaBbeta", "start": 1244, "end": 1256}]}], "localization": [{"trigger": {"text": "secretion", "start": 33, "end": 42}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 28, "end": 32}]}, {"trigger": {"text": "secretion", "start": 292, "end": 301}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 287, "end": 291}]}, {"trigger": {"text": "secretion", "start": 402, "end": 411}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 397, "end": 401}]}, {"trigger": {"text": "secretion", "start": 902, "end": 911}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 897, "end": 901}]}, {"trigger": {"text": "secretion", "start": 1532, "end": 1541}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1527, "end": 1531}]}], "positive regulation": [{"trigger": {"text": "costimulation", "start": 5, "end": 18}, "arguments": [{"role": "Theme", "text": "CD28", "start": 0, "end": 4}]}, {"trigger": {"text": "augments", "start": 19, "end": 27}, "arguments": [{"role": "Theme", "text": "secretion", "start": 33, "end": 42}, {"role": "Cause", "text": "increasing", "start": 82, "end": 92}]}, {"trigger": {"text": "increasing", "start": 82, "end": 92}, "arguments": [{"role": "Cause", "text": "costimulation", "start": 5, "end": 18}, {"role": "Theme", "text": "IL-2", "start": 126, "end": 130}]}, {"trigger": {"text": "enhancing", "start": 116, "end": 125}, "arguments": [{"role": "Cause", "text": "costimulation", "start": 5, "end": 18}, {"role": "Theme", "text": "transactivation", "start": 136, "end": 151}]}, {"trigger": {"text": "transactivation", "start": 136, "end": 151}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 126, "end": 130}]}, {"trigger": {"text": "enhanced", "start": 278, "end": 286}, "arguments": [{"role": "Theme", "text": "secretion", "start": 292, "end": 301}]}, {"trigger": {"text": "leads to synergistic enhancement", "start": 361, "end": 393}, "arguments": [{"role": "Cause", "text": "Coligation", "start": 342, "end": 352}, {"role": "Theme", "text": "secretion", "start": 402, "end": 411}]}, {"trigger": {"text": "enhanced", "start": 623, "end": 631}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 566, "end": 570}]}, {"trigger": {"text": "costimulation", "start": 707, "end": 720}, "arguments": [{"role": "Cause", "text": "CD28", "start": 702, "end": 706}, {"role": "Theme", "text": "production", "start": 729, "end": 739}]}, {"trigger": {"text": "in response to", "start": 813, "end": 827}, "arguments": [{"role": "Theme", "text": "production", "start": 802, "end": 812}]}, {"trigger": {"text": "increased", "start": 930, "end": 939}, "arguments": [{"role": "Theme", "text": "expression", "start": 940, "end": 950}]}, {"trigger": {"text": "resulting", "start": 965, "end": 974}, "arguments": [{"role": "Theme", "text": "increased", "start": 930, "end": 939}, {"role": "Cause", "text": "enhanced", "start": 980, "end": 988}]}, {"trigger": {"text": "enhanced", "start": 980, "end": 988}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 989, "end": 993}]}], "regulation": [{"trigger": {"text": "involved", "start": 690, "end": 698}, "arguments": [{"role": "Theme", "text": "costimulation", "start": 707, "end": 720}]}, {"trigger": {"text": "changes", "start": 1216, "end": 1223}, "arguments": [{"role": "Theme", "text": "levels", "start": 1257, "end": 1263}, {"role": "Cause", "text": "coligation", "start": 1279, "end": 1289}]}, {"trigger": {"text": "involved", "start": 1480, "end": 1488}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1513, "end": 1523}]}, {"trigger": {"text": "regulation", "start": 1513, "end": 1523}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1532, "end": 1541}]}], "transcription": [{"trigger": {"text": "expression", "start": 940, "end": 950}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 954, "end": 958}]}]}}, "schema": []}
{"input": "Repression by Ikaros and Aiolos is mediated through histone deacetylase complexes. \nHere we show that the lymphoid lineage-determining factors Ikaros and Aiolos can function as strong transcriptional repressors. This function is mediated through two repression domains and is dependent upon the promoter context and cell type. Repression by Ikaros proteins correlates with hypo-acetylation of core histones at promoter sites and is relieved by histone deacetylase inhibitors. Consistent with these findings, Ikaros and its repression domains can interact in vivo and in vitro with the mSin3 family of co-repressors which bind to histone deacetylases. Based on these and our recent findings of associations between Ikaros and Mi-2-HDAC, we propose that Ikaros family members modulate gene expression during lymphocyte development by recruiting distinct histone deacetylase complexes to specific promoters. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 546, "end": 554}, "arguments": [{"role": "Theme", "text": "Ikaros", "start": 508, "end": 514}]}, {"trigger": {"text": "associations", "start": 693, "end": 705}, "arguments": [{"role": "Theme", "text": "Ikaros", "start": 714, "end": 720}, {"role": "Theme2", "text": "Mi-2-HDAC", "start": 725, "end": 734}]}]}}, "schema": []}
{"input": "New immunosuppressive drug PNU156804 blocks IL-2-dependent proliferation and NF-kappa B and AP-1 activation. \nWe had previously shown that the drug undecylprodigiosin (UP) blocks human lymphocyte proliferation in vitro. We have now investigated the mechanism of action of a new analogue of UP, PNU156804, which shows a more favorable activity profile than UP in mice. We demonstrate here that the biological effect of PNU156804 in vitro is indistinguishable from UP: PNU156804 blocks human T cell proliferation in mid-late G1, as determined by cell cycle analysis, expression of cyclins, and cyclin-dependent kinases and retinoblastoma phosphorylation. In addition, we show that PNU156804 does not block significantly the induction of either IL-2 or IL-2R alpha- and gamma-chains but inhibits IL-2-dependent T cell proliferation. We have investigated several molecular pathways that are known to be activated by IL-2 in T cells. We show that PNU156804 does not inhibit c-myc and bcl-2 mRNA induction. On the other hand, PNU156804 efficiently inhibits the activation of the NF-kappa B and AP-1 transcription factors. PNU156804 inhibition of NF-kappa B activation is due to the inhibition of the degradation of I kappa B-alpha and I kappa B-beta. PNU156804 action is restricted to some signaling pathways; it does not affect NF-kappa B activation by PMA in T cells but blocks that induced by CD40 cross-linking in B lymphocytes. We conclude that the prodigiosin family of immunosuppressants is a new family of molecules that show a novel target specificity clearly distinct from that of other immunosuppressive drugs such as cyclosporin A, FK506, and rapamycin. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 1395, "end": 1408}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1390, "end": 1394}]}], "negative regulation": [{"trigger": {"text": "block", "start": 698, "end": 703}, "arguments": [{"role": "Theme", "text": "induction", "start": 722, "end": 731}]}, {"trigger": {"text": "inhibit", "start": 961, "end": 968}, "arguments": [{"role": "Theme", "text": "induction", "start": 990, "end": 999}]}, {"trigger": {"text": "inhibition", "start": 1176, "end": 1186}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1194, "end": 1205}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 722, "end": 731}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 742, "end": 746}]}, {"trigger": {"text": "induction", "start": 990, "end": 999}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 969, "end": 974}]}, {"trigger": {"text": "induction", "start": 990, "end": 999}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 979, "end": 984}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 1194, "end": 1205}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 1209, "end": 1224}]}, {"trigger": {"text": "degradation", "start": 1194, "end": 1205}, "arguments": [{"role": "Theme", "text": "I kappa B-beta", "start": 1229, "end": 1243}]}]}}, "schema": []}
{"input": "IL-12 induces IFN regulating factor-1 (IRF-1) gene expression in human NK and T cells. \nIL-12 is a critical immunoregulatory cytokine that promotes cell-mediated immune responses and the differentiation of naive CD4+ cells to Th1 cells; however, relatively few IL-12 target genes have been identified. To better clarify the molecular basis of IL-12 action, we set out to characterize genes up-regulated by IL-12, first by contrasting IL-12- and IFN-alpha-inducible genes. We identified several genes up-regulated by IL-12, namely, MIP-1alpha, MIP-1beta, IL-1RA, and IFN regulatory factor-1 (IRF-1). IRF-1 is a transcription factor regulated by IFNs that is also essential for Th1 responses. We demonstrated that IL-12 directly up-regulates IRF-1 to the same extent as IFN-alpha in normal human T cells and in NK cells. We showed that IL-12 had a direct effect on IRF-1, an effect not mediated indirectly by the induction of IFN-gamma production. Furthermore, IL-2 and IL-12 synergistically induced IRF-1, whereas IFN-alpha and IL-12 did not. The participation of STAT4 in the regulation of IRF-1 was demonstrated in two ways. First, STAT4 was required for the IL-12-dependent transactivation of an IRF-1 reporter construct, and second, STAT4 binding to the IRF-1 promoter was shown using EMSA. In contrast to IL-12, no up-regulation of IRF-1 was found in IL-4-stimulated cells, and IL-4 did not block IL-12-dependent up-regulation of IRF-1. Therefore, IRF-1 may be an important contributor to IL-12 signaling, and we speculate that the defective IL-12 responses seen in IRF-1-/- mice might be attributable, in part, to the absence of this transcription factor. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1242, "end": 1249}, "arguments": [{"role": "Theme", "text": "STAT4", "start": 1236, "end": 1241}, {"role": "Theme2", "text": "IRF-1", "start": 1257, "end": 1262}, {"role": "Site2", "text": "promoter", "start": 1263, "end": 1271}]}], "gene expression": [{"trigger": {"text": "expression", "start": 51, "end": 61}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 39, "end": 44}]}, {"trigger": {"text": "production", "start": 934, "end": 944}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 924, "end": 933}]}], "negative regulation": [{"trigger": {"text": "block", "start": 1395, "end": 1400}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1382, "end": 1386}, {"role": "Theme", "text": "up-regulation", "start": 1417, "end": 1430}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 6, "end": 13}, "arguments": [{"role": "Theme", "text": "expression", "start": 51, "end": 61}]}, {"trigger": {"text": "up-regulated", "start": 500, "end": 512}, "arguments": [{"role": "Theme", "text": "MIP-1alpha", "start": 531, "end": 541}]}, {"trigger": {"text": "up-regulated", "start": 500, "end": 512}, "arguments": [{"role": "Theme", "text": "MIP-1beta", "start": 543, "end": 552}]}, {"trigger": {"text": "up-regulated", "start": 500, "end": 512}, "arguments": [{"role": "Theme", "text": "IL-1RA", "start": 554, "end": 560}]}, {"trigger": {"text": "up-regulated", "start": 500, "end": 512}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 591, "end": 596}]}, {"trigger": {"text": "up-regulates", "start": 727, "end": 739}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 740, "end": 745}]}, {"trigger": {"text": "mediated", "start": 884, "end": 892}, "arguments": [{"role": "Theme", "text": "effect", "start": 853, "end": 859}, {"role": "Cause", "text": "induction", "start": 911, "end": 920}]}, {"trigger": {"text": "induction", "start": 911, "end": 920}, "arguments": [{"role": "Theme", "text": "production", "start": 934, "end": 944}]}, {"trigger": {"text": "synergistically induced", "start": 974, "end": 997}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 998, "end": 1003}]}, {"trigger": {"text": "up-regulation", "start": 1319, "end": 1332}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1336, "end": 1341}]}, {"trigger": {"text": "up-regulation", "start": 1417, "end": 1430}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1434, "end": 1439}]}, {"trigger": {"text": "absence", "start": 1623, "end": 1630}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1452, "end": 1457}]}], "regulation": [{"trigger": {"text": "regulated", "start": 631, "end": 640}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 599, "end": 604}]}, {"trigger": {"text": "effect", "start": 853, "end": 859}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 863, "end": 868}]}, {"trigger": {"text": "participation", "start": 1046, "end": 1059}, "arguments": [{"role": "Cause", "text": "STAT4", "start": 1063, "end": 1068}, {"role": "Theme", "text": "regulation", "start": 1076, "end": 1086}]}, {"trigger": {"text": "regulation", "start": 1076, "end": 1086}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1090, "end": 1095}]}]}}, "schema": []}
{"input": "Transcriptional regulation of T lymphocyte development and function. \nThe development and function of T lymphocytes are regulated tightly by signal transduction pathways that include specific cell-surface receptors, intracellular signaling molecules, and nuclear transcription factors. Since 1988, several families of functionally important T cell transcription factors have been identified. These include the Ikaros, LKLF, and GATA3 zinc-finger proteins; the Ets, CREB/ATF, and NF-kappa B/Rel/NFAT transcription factors; the Stat proteins; and HMG box transcription factors such as LEF1, TCF1, and Sox4. In this review, we summarize our current understanding of the transcriptional regulation of T cell development and function with particular emphasis on the results of recent gene targeting and transgenic experiments. In addition to increasing our understanding of the molecular pathways that regulate T cell development and function, these results have suggested novel targets for genetic and pharmacological manipulation of T cell immunity. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Binding of YY1 and Oct1 to a novel element that downregulates expression of IL-5 in human T cells. \nBACKGROUND: IL-5 controls development of eosinophilia and has been shown to be involved in the pathogenesis of allergic diseases. In both atopic and nonatopic asthma, elevated IL-5 has been detected in peripheral blood and the airways. IL-5 is produced mainly by activated T cells, and its expression is regulated at the transcriptional level. OBJECTIVE: This study focuses on the functional analysis of the human IL-5 (hIL-5) promoter and characterization of cis -regulatory elements and transcription factors involved in the suppression of IL-5 transcription in T cells. METHODS: Methods used in this study include DNase I footprint assays, electrophoretic mobility shift assays, and functional analysis by mammalian cell transfection involving deletion analysis and site-directed mutagenesis. RESULTS: We identified 5 protein binding regions (BRs) located within the proximal hIL-5 promoter. Functional analysis indicates that the BRs are involved in control of hIL-5 promoter activity. Two of these regions, BR3 and BR4 located at positions -102 to -73, have not previously been described as regulators of IL-5 expression in T cells. We show that the BR3 sequence contains a novel negative regulatory element located at positions -90 to -79 of the hIL-5 promoter, which binds Oct1, octamer-like, and YY1 nuclear factors. Substitution mutations, which abolished binding of these proteins to the BR3 sequence, significantly increased hIL-5 promoter activity in activated T cells. CONCLUSION: We suggest that Oct1, YY1, and octamer-like factors binding to the -90/-79 sequence within the proximal IL-5 promoter are involved in suppression of IL-5 transcription in T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Binding", "start": 0, "end": 7}, "arguments": [{"role": "Theme", "text": "YY1", "start": 11, "end": 14}]}, {"trigger": {"text": "Binding", "start": 0, "end": 7}, "arguments": [{"role": "Theme", "text": "Oct1", "start": 19, "end": 23}]}, {"trigger": {"text": "binds", "start": 1374, "end": 1379}, "arguments": [{"role": "Theme", "text": "Oct1", "start": 1380, "end": 1384}]}, {"trigger": {"text": "binds", "start": 1374, "end": 1379}, "arguments": [{"role": "Theme", "text": "YY1", "start": 1404, "end": 1407}]}, {"trigger": {"text": "binding", "start": 1465, "end": 1472}, "arguments": [{"role": "Theme", "text": "Oct1", "start": 1380, "end": 1384}]}, {"trigger": {"text": "binding", "start": 1465, "end": 1472}, "arguments": [{"role": "Theme", "text": "YY1", "start": 1404, "end": 1407}]}, {"trigger": {"text": "binding", "start": 1646, "end": 1653}, "arguments": [{"role": "Theme", "text": "Oct1", "start": 1610, "end": 1614}, {"role": "Theme2", "text": "IL-5", "start": 1698, "end": 1702}, {"role": "Site2", "text": "promoter", "start": 1703, "end": 1711}]}, {"trigger": {"text": "binding", "start": 1646, "end": 1653}, "arguments": [{"role": "Theme", "text": "YY1", "start": 1616, "end": 1619}, {"role": "Theme2", "text": "IL-5", "start": 1698, "end": 1702}, {"role": "Site2", "text": "promoter", "start": 1703, "end": 1711}]}, {"trigger": {"text": "binding", "start": 1646, "end": 1653}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1698, "end": 1702}, {"role": "Site", "text": "promoter", "start": 1703, "end": 1711}]}], "gene expression": [{"trigger": {"text": "expression", "start": 62, "end": 72}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 76, "end": 80}]}, {"trigger": {"text": "produced", "start": 344, "end": 352}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 336, "end": 340}]}, {"trigger": {"text": "expression", "start": 1215, "end": 1225}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1210, "end": 1214}]}], "negative regulation": [{"trigger": {"text": "downregulates", "start": 48, "end": 61}, "arguments": [{"role": "Theme", "text": "expression", "start": 62, "end": 72}]}, {"trigger": {"text": "suppression", "start": 627, "end": 638}, "arguments": [{"role": "Theme", "text": "transcription", "start": 647, "end": 660}]}, {"trigger": {"text": "negative regulatory", "start": 1285, "end": 1304}, "arguments": [{"role": "Theme", "text": "hIL-5", "start": 1352, "end": 1357}, {"role": "Site", "text": "promoter", "start": 1358, "end": 1366}]}, {"trigger": {"text": "abolished", "start": 1455, "end": 1464}, "arguments": [{"role": "Theme", "text": "binding", "start": 1465, "end": 1472}]}, {"trigger": {"text": "suppression", "start": 1728, "end": 1739}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1748, "end": 1761}]}], "positive regulation": [{"trigger": {"text": "elevated", "start": 267, "end": 275}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 276, "end": 280}]}, {"trigger": {"text": "increased", "start": 1526, "end": 1535}, "arguments": [{"role": "Theme", "text": "hIL-5", "start": 1536, "end": 1541}, {"role": "Site", "text": "promoter", "start": 1542, "end": 1550}]}], "regulation": [{"trigger": {"text": "regulated", "start": 404, "end": 413}, "arguments": [{"role": "Theme", "text": "produced", "start": 344, "end": 352}]}, {"trigger": {"text": "involved", "start": 611, "end": 619}, "arguments": [{"role": "Theme", "text": "suppression", "start": 627, "end": 638}]}, {"trigger": {"text": "control", "start": 1054, "end": 1061}, "arguments": [{"role": "Theme", "text": "hIL-5", "start": 1065, "end": 1070}, {"role": "Site", "text": "promoter", "start": 1071, "end": 1079}]}, {"trigger": {"text": "regulators", "start": 1196, "end": 1206}, "arguments": [{"role": "Theme", "text": "expression", "start": 1215, "end": 1225}]}, {"trigger": {"text": "involved", "start": 1716, "end": 1724}, "arguments": [{"role": "Cause", "text": "binding", "start": 1646, "end": 1653}, {"role": "Theme", "text": "suppression", "start": 1728, "end": 1739}]}], "transcription": [{"trigger": {"text": "transcription", "start": 647, "end": 660}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 642, "end": 646}]}, {"trigger": {"text": "transcription", "start": 1748, "end": 1761}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1743, "end": 1747}]}]}}, "schema": []}
{"input": "Direct interaction of hematopoietic transcription factors PU.1 and GATA-1: functional antagonism in erythroid cells. \nMalignant transformation usually inhibits terminal cell differentiation but the precise mechanisms involved are not understood. PU.1 is a hematopoietic-specific Ets family transcription factor that is required for development of some lymphoid and myeloid lineages. PU.1 can also act as an oncoprotein as activation of its expression in erythroid precursors by proviral insertion or transgenesis causes erythroleukemias in mice. Restoration of terminal differentiation in the mouse erythroleukemia (MEL) cells requires a decline in the level of PU.1, indicating that PU.1 can block erythroid differentiation. Here we investigate the mechanism by which PU.1 interferes with erythroid differentiation. We find that PU.1 interacts directly with GATA-1, a zinc finger transcription factor required for erythroid differentiation. Interaction between PU.1 and GATA-1 requires intact DNA-binding domains in both proteins. PU.1 represses GATA-1-mediated transcriptional activation. Both the DNA binding and transactivation domains of PU.1 are required for repression and both domains are also needed to block terminal differentiation in MEL cells. We also show that ectopic expression of PU.1 in Xenopus embryos is sufficient to block erythropoiesis during normal development. Furthermore, introduction of exogenous GATA-1 in both MEL cells and Xenopus embryos and explants relieves the block to erythroid differentiation imposed by PU.1. Our results indicate that the stoichiometry of directly interacting but opposing transcription factors may be a crucial determinant governing processes of normal differentiation and malignant transformation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 7, "end": 18}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 58, "end": 62}, {"role": "Theme2", "text": "GATA-1", "start": 67, "end": 73}]}, {"trigger": {"text": "interacts", "start": 835, "end": 844}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 830, "end": 834}, {"role": "Theme2", "text": "GATA-1", "start": 859, "end": 865}]}, {"trigger": {"text": "Interaction", "start": 942, "end": 953}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 962, "end": 966}, {"role": "Theme2", "text": "GATA-1", "start": 971, "end": 977}]}, {"trigger": {"text": "interacting", "start": 1604, "end": 1615}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1425, "end": 1431}, {"role": "Theme2", "text": "PU.1", "start": 1542, "end": 1546}]}], "gene expression": [{"trigger": {"text": "expression", "start": 440, "end": 450}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 383, "end": 387}]}, {"trigger": {"text": "expression", "start": 1283, "end": 1293}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1297, "end": 1301}]}], "negative regulation": [{"trigger": {"text": "decline in the level", "start": 638, "end": 658}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 662, "end": 666}]}, {"trigger": {"text": "opposing", "start": 1620, "end": 1628}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 1425, "end": 1431}, {"role": "Theme", "text": "PU.1", "start": 1542, "end": 1546}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 422, "end": 432}, "arguments": [{"role": "Theme", "text": "expression", "start": 440, "end": 450}]}, {"trigger": {"text": "requires", "start": 978, "end": 986}, "arguments": [{"role": "Theme", "text": "Interaction", "start": 942, "end": 953}]}]}}, "schema": []}
{"input": "Potent and stable attenuation of live-HIV-1 by gain of a proteolysis-resistant inhibitor of NF-kappaB (IkappaB-alphaS32/36A) and the implications for vaccine development. \nLive-attenuated human immunodeficiency viruses (HIVs) are candidates for Acquired Immunodeficiency Syndrome (AIDS) vaccine. Based on the simian immunodeficiency virus (SIV) model for AIDS, loss-of-function (e.g. deletion of accessory genes such as nef) has been forwarded as a primary approach for creating enfeebled, but replication-competent, HIV-1/SIV. Regrettably, recent evidence suggests that loss-of-function alone is not always sufficient to prevent the emergence of virulent mutants. New strategies that attenuate via mechanisms distinct from loss-of-function are needed for enhancing the safety phenotype of viral genome. Here, we propose gain-of-function to be used simultaneously with loss-of-function as a novel approach for attenuating HIV-1. We have constructed an HIV-1 genome carrying the cDNA of a proteolysis-resistant nuclear factor-kappaB inhibitor (IkappaB-alphaS32/36A) in the nef region. HIV-1 expressing IkappaB-alphaS32/36A down-regulates viral expression and is highly attenuated in both Jurkat and peripheral blood mononuclear cells. We provide formal proof that the phenotypic and attenuating characteristics of IkappaB-alphaS32/36A permit its stable maintenance in a live, replicating HIV-1 despite 180 days of forced ex vivo passaging in tissue culture. As compared with other open-reading frames embedded into HIV/SIV genome, this degree of stability is unprecedented. Thus, IkappaB-alphaS32/36A offers proof-of-principle that artifactually gained functions, when used to attenuate the replication of live HIV-1, can be stable. These findings illustrate gain-of-function as a feasible strategy for developing safer live-attenuated HIVs to be tested as candidates for AIDS vaccine. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 1090, "end": 1100}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1101, "end": 1114}]}], "negative regulation": [{"trigger": {"text": "resistant", "start": 1000, "end": 1009}, "arguments": [{"role": "Theme", "text": "proteolysis", "start": 988, "end": 999}]}, {"trigger": {"text": "attenuated", "start": 1168, "end": 1178}, "arguments": [{"role": "Theme", "text": "expressing", "start": 1090, "end": 1100}]}], "positive regulation": [{"trigger": {"text": "maintenance", "start": 1352, "end": 1363}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1313, "end": 1326}]}], "protein catabolism": [{"trigger": {"text": "proteolysis", "start": 57, "end": 68}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 103, "end": 116}]}, {"trigger": {"text": "proteolysis", "start": 988, "end": 999}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1043, "end": 1056}]}]}}, "schema": []}
{"input": "Human alveolar macrophages are markedly deficient in REF-1 and AP-1 DNA binding activity. \nAlthough many functions of human alveolar macrophages are altered compared with their precursor cell, the blood monocyte (monocyte), the reason(s) for these functional changes have not been determined. We recently reported that human alveolar macrophages do not express AP-1 DNA binding activity (Monick, M. M., Carter, A. B., Gudmundsson, G., Geist, L. J., and Hunninghake, G. W. (1998) Am. J. Physiol. 275, L389-L397). To determine why alveolar macrophages do not express AP-1 DNA binding activity, we first showed that there was not a decrease in expression of the FOS and JUN proteins that make up the AP-1 complex. There was, however, a significant difference in the amounts of the nuclear protein, REF-1 (which regulates AP-1 DNA binding by altering the redox status of FOS and JUN proteins), in alveolar macrophages compared with monocytes. In addition, in vitro differentiation of monocytes to a macrophage-like cell resulted in decreased amounts of REF-1. Finally, addition of REF-1 from activated monocytes to alveolar macrophage nuclear proteins resulted in a marked increase in AP-1 DNA binding. These studies strongly suggest that the process of differentiation of monocytes into alveolar macrophages is associated with a loss of REF-1 and AP-1 activity. This observation may explain, in part, some of the functional differences observed for alveolar macrophages compared with monocytes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 72, "end": 88}, "arguments": [{"role": "Theme", "text": "REF-1", "start": 53, "end": 58}]}], "gene expression": [{"trigger": {"text": "in the amounts", "start": 756, "end": 770}, "arguments": [{"role": "Theme", "text": "REF-1", "start": 795, "end": 800}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 40, "end": 49}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 72, "end": 88}]}, {"trigger": {"text": "decreased", "start": 1028, "end": 1037}, "arguments": [{"role": "Theme", "text": "REF-1", "start": 1049, "end": 1054}]}, {"trigger": {"text": "loss", "start": 1326, "end": 1330}, "arguments": [{"role": "Theme", "text": "REF-1", "start": 1334, "end": 1339}]}]}}, "schema": []}
{"input": "A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria [see comments] \nGenetic variation in cytokine promoter regions is postulated to influence susceptibility to infection, but the molecular mechanisms by which such polymorphisms might affect gene regulation are unknown. Through systematic DNA footprinting of the TNF (encoding tumour necrosis factor, TNF) promoter region, we have identified a single nucleotide polymorphism (SNP) that causes the helix-turn-helix transcription factor OCT-1 to bind to a novel region of complex protein-DNA interactions and alters gene expression in human monocytes. The OCT-1-binding genotype, found in approximately 5% of Africans, is associated with fourfold increased susceptibility to cerebral malaria in large case-control studies of West African and East African populations, after correction for other known TNF polymorphisms and linked HLA alleles. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 34, "end": 41}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 28, "end": 33}, {"role": "Theme2", "text": "TNF", "start": 49, "end": 52}, {"role": "Site2", "text": "promoter region", "start": 53, "end": 68}]}, {"trigger": {"text": "bind", "start": 545, "end": 549}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 536, "end": 541}]}, {"trigger": {"text": "binding genotype", "start": 661, "end": 677}, "arguments": [{"role": "Theme", "text": "TNF", "start": 49, "end": 52}, {"role": "Site", "text": "promoter region", "start": 53, "end": 68}, {"role": "Theme2", "text": "OCT-1", "start": 655, "end": 660}]}], "gene expression": [{"trigger": {"text": "expression", "start": 620, "end": 630}, "arguments": [{"role": "Theme", "text": "TNF", "start": 402, "end": 405}]}], "positive regulation": [{"trigger": {"text": "causes", "start": 487, "end": 493}, "arguments": [{"role": "Theme", "text": "bind", "start": 545, "end": 549}]}], "regulation": [{"trigger": {"text": "affects", "start": 20, "end": 27}, "arguments": [{"role": "Theme", "text": "binding", "start": 34, "end": 41}]}, {"trigger": {"text": "alters", "start": 608, "end": 614}, "arguments": [{"role": "Theme", "text": "expression", "start": 620, "end": 630}]}]}}, "schema": []}
{"input": "Novel therapies for inflammatory bowel disease. \nLooking back at successes and failures in newer approaches to treating IBD, it is tempting--although still difficult--to draw conclusions about pathogenesis. When a therapy proves effective, do clinicians truly know how it works? Even with a therapy as specific as anti-TNF antibody, it is not clear if the benefit is attributable to simple binding and clearance of TNF-alpha or to binding on the cell surface and subsequent deletion of the activated macrophage. When a drug appears to be less effective than preclinical models suggest, can failures in effectiveness from delivery or dosing be differentiated? The disappointing results of clinical trials with IL-10--so at odds with the prediction of benefit from animal models--bring into question the validity of those models as well as the soundness of design of the clinical trials on which efficacy of IL-10 is judged. The variability of response even to the most narrowly targeted agents suggests that these diseases are far more heterogeneous in humans than in their murine counterparts. Clinicians are only just beginning to recognize subclinical markers of response, and it may soon be possible to predict response on the basis of genetic composition. For the moment, however, the field of pharmacogenetics is embryonic. Challenges in developing new therapeutic strategies include not only identifying novel agents, but also improving the definitions of clinical endpoints and defining efficacy at the biologic level. Only through considered evaluation of clinical evidence may clinicians determine which therapies should remain novelties and which should become an accepted part of the armamentarium. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 390, "end": 397}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 415, "end": 424}]}]}}, "schema": []}
{"input": "PPARalpha activators inhibit cytokine-induced vascular cell adhesion molecule-1 expression in human endothelial cells. \nBACKGROUND: Adhesion molecule expression on the endothelial cell (EC) surface is critical for leukocyte recruitment to atherosclerotic lesions. Better understanding of transcriptional regulation of adhesion molecules in ECs may provide important insight into plaque formation. Peroxisome proliferator-activated receptor-alpha (PPARalpha), a member of the nuclear receptor family, regulates gene expression in response to certain fatty acids and fibric acid derivatives. The present study investigated PPARalpha expression in human ECs and their regulation of vascular cell adhesion molecule-1 (VCAM-1). METHODS AND RESULTS: Immunohistochemistry revealed that human carotid artery ECs express PPARalpha. Pretreatment of cultured human ECs with the PPARalpha activators fenofibrate or WY14643 inhibited TNF-alpha-induced VCAM-1 in a time- and concentration-dependent manner, an effect not seen with PPARgamma activators. Both PPARalpha activators decreased cytokine-induced VCAM-1 mRNA expression without altering its mRNA half-life. Transient transfection of deletional VCAM-1 promoter constructs and electrophoretic mobility shift assays suggest that fenofibrate inhibits VCAM-1 transcription in part by inhibiting NF-kappaB. Finally, PPARalpha activators significantly reduced adhesion of U937 cells to cultured human ECs. CONCLUSIONS: Human ECs express PPARalpha, a potentially important regulator of atherogenesis through its transcriptional control of VCAM-1 gene expression. Such findings also have implications regarding the clinical use of lipid-lowering agents, like fibric acids, which can activate PPARalpha. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 80, "end": 90}, "arguments": [{"role": "Theme", "text": "vascular cell adhesion molecule-1", "start": 46, "end": 79}]}, {"trigger": {"text": "expression", "start": 631, "end": 641}, "arguments": [{"role": "Theme", "text": "PPARalpha", "start": 621, "end": 630}]}, {"trigger": {"text": "express", "start": 804, "end": 811}, "arguments": [{"role": "Theme", "text": "PPARalpha", "start": 812, "end": 821}]}, {"trigger": {"text": "express", "start": 1467, "end": 1474}, "arguments": [{"role": "Theme", "text": "PPARalpha", "start": 1475, "end": 1484}]}, {"trigger": {"text": "expression", "start": 1588, "end": 1598}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1576, "end": 1582}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 21, "end": 28}, "arguments": [{"role": "Theme", "text": "induced", "start": 38, "end": 45}]}, {"trigger": {"text": "inhibited", "start": 911, "end": 920}, "arguments": [{"role": "Theme", "text": "induced", "start": 931, "end": 938}]}, {"trigger": {"text": "decreased", "start": 1065, "end": 1074}, "arguments": [{"role": "Theme", "text": "induced", "start": 1084, "end": 1091}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 38, "end": 45}, "arguments": [{"role": "Theme", "text": "expression", "start": 80, "end": 90}]}, {"trigger": {"text": "activators", "start": 877, "end": 887}, "arguments": [{"role": "Theme", "text": "PPARalpha", "start": 867, "end": 876}]}, {"trigger": {"text": "induced", "start": 931, "end": 938}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 921, "end": 930}, {"role": "Theme", "text": "VCAM-1", "start": 939, "end": 945}]}, {"trigger": {"text": "induced", "start": 1084, "end": 1091}, "arguments": [{"role": "Theme", "text": "mRNA expression", "start": 1099, "end": 1114}]}, {"trigger": {"text": "activate", "start": 1719, "end": 1727}, "arguments": [{"role": "Theme", "text": "PPARalpha", "start": 1728, "end": 1737}]}], "regulation": [{"trigger": {"text": "in response to", "start": 526, "end": 540}, "arguments": [{"role": "Theme", "text": "PPARalpha", "start": 447, "end": 456}]}, {"trigger": {"text": "regulation", "start": 665, "end": 675}, "arguments": [{"role": "Cause", "text": "PPARalpha", "start": 621, "end": 630}, {"role": "Theme", "text": "VCAM-1", "start": 714, "end": 720}]}, {"trigger": {"text": "altering", "start": 1123, "end": 1131}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1092, "end": 1098}]}, {"trigger": {"text": "transcriptional control", "start": 1549, "end": 1572}, "arguments": [{"role": "Cause", "text": "PPARalpha", "start": 1475, "end": 1484}, {"role": "Theme", "text": "expression", "start": 1588, "end": 1598}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 1099, "end": 1114}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1092, "end": 1098}]}, {"trigger": {"text": "transcription", "start": 1299, "end": 1312}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1292, "end": 1298}]}]}}, "schema": []}
{"input": "The intracellular parasite Theileria parva protects infected T cells from apoptosis. \nParasites have evolved a plethora of strategies to ensure their survival. The intracellular parasite Theileria parva secures its propagation and spreads through the infected animal by infecting and transforming T cells, inducing their continuous proliferation and rendering them metastatic. In previous work, we have shown that the parasite induces constitutive activation of the transcription factor NF-kappaB, by inducing the constitutive degradation of its cytoplasmic inhibitors. The biological significance of NF-kappaB activation in T. parva-infected cells, however, has not yet been defined. Cells that have been transformed by viruses or oncogenes can persist only if they manage to avoid destruction by the apoptotic mechanisms that are activated on transformation and that contribute to maintain cellular homeostasis. We now demonstrate that parasite-induced NF-kappaB activation plays a crucial role in the survival of T. parva-transformed T cells by conveying protection against an apoptotic signal that accompanies parasite-mediated transformation. Consequently, inhibition of NF-kappaB nuclear translocation and the expression of dominant negative mutant forms of components of the NF-kappaB activation pathway, such as IkappaBalpha or p65, prompt rapid apoptosis of T. parva-transformed T cells. Our findings offer important insights into parasite survival strategies and demonstrate that parasite-induced constitutive NF-kappaB activation is an essential step in maintaining the transformed phenotype of the infected cells. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Downregulation of Wilms' tumor gene (WT1) is not a prerequisite for erythroid or megakaryocytic differentiation of the leukemic cell line K562. \nThe Wilms' tumor gene (WT1) encodes a transcription factor of the zinc finger type. A high expression of WT1 has been detected in a range of acute leukemias, and WT1 is downregulated during induced differentiation of some leukemic cell lines. Overexpression of WT1 in some myeloid cell lines confers resistance to differentiation induction. These observations suggest that a high WT1 expression in hematopoietic cells is incompatible with differentiation. In this study, each of the four different isoforms of WT1 was constitutively overexpressed in the leukemic cell line K562. K562 cells express endogenous WT1, which is downregulated as a response to induced differentiation along the erythroid and megakaryocytic pathways. We now demonstrate that a forced exogenous expression of the four different isoforms of WT1 in K562 does not affect the differentiation response, as judged by accumulation of hemoglobin in response to hemin or the expression of megakaryocytic cell surface markers in response to 12-O-tetradecanoylphorbol-13-acetate (TPA). We conclude that downregulation of WT1 during induced differentiation of K562 cells is not a prerequisite for erythroid or megakaryocytic differentiation of these cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 236, "end": 246}, "arguments": [{"role": "Theme", "text": "WT1", "start": 250, "end": 253}]}, {"trigger": {"text": "Overexpression", "start": 388, "end": 402}, "arguments": [{"role": "Theme", "text": "WT1", "start": 406, "end": 409}]}, {"trigger": {"text": "expression", "start": 529, "end": 539}, "arguments": [{"role": "Theme", "text": "WT1", "start": 525, "end": 528}]}, {"trigger": {"text": "overexpressed", "start": 678, "end": 691}, "arguments": [{"role": "Theme", "text": "WT1", "start": 655, "end": 658}]}, {"trigger": {"text": "express", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "WT1", "start": 754, "end": 757}]}, {"trigger": {"text": "expression", "start": 915, "end": 925}, "arguments": [{"role": "Theme", "text": "WT1", "start": 960, "end": 963}]}], "negative regulation": [{"trigger": {"text": "Downregulation", "start": 0, "end": 14}, "arguments": [{"role": "Theme", "text": "WT1", "start": 37, "end": 40}]}, {"trigger": {"text": "downregulated", "start": 314, "end": 327}, "arguments": [{"role": "Theme", "text": "WT1", "start": 307, "end": 310}]}, {"trigger": {"text": "downregulated", "start": 768, "end": 781}, "arguments": [{"role": "Theme", "text": "express", "start": 735, "end": 742}]}, {"trigger": {"text": "downregulation", "start": 1212, "end": 1226}, "arguments": [{"role": "Theme", "text": "WT1", "start": 1230, "end": 1233}]}], "positive regulation": [{"trigger": {"text": "high expression", "start": 231, "end": 246}, "arguments": [{"role": "Theme", "text": "expression", "start": 236, "end": 246}]}, {"trigger": {"text": "Overexpression", "start": 388, "end": 402}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 388, "end": 402}]}, {"trigger": {"text": "high", "start": 520, "end": 524}, "arguments": [{"role": "Theme", "text": "expression", "start": 529, "end": 539}]}, {"trigger": {"text": "overexpressed", "start": 678, "end": 691}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 678, "end": 691}]}, {"trigger": {"text": "forced", "start": 898, "end": 904}, "arguments": [{"role": "Theme", "text": "expression", "start": 915, "end": 925}]}]}}, "schema": []}
{"input": "GATA-1 and erythropoietin cooperate to promote erythroid cell survival by regulating bcl-xL expression. \nThe transcription factor GATA-1 is essential for normal erythropoiesis. By examining in vitro-differentiated embryonic stem cells, we showed previously that in the absence of GATA-1, committed erythroid precursors fail to complete maturation and instead undergo apoptosis. The mechanisms by which GATA-1 controls cell survival are unknown. Here we report that in erythroid cells, GATA-1 strongly induces the expression of the anti-apoptotic protein bcl-xL, but not the related proteins bcl-2 and mcl-1. Consistent with a role for bcl-xL in mediating GATA-1-induced erythroid cell survival, in vitro-differentiated bcl-xL-/- embryonic stem cells fail to generate viable mature definitive erythroid cells, a phenotype resembling that of GATA-1 gene disruption. In addition, we show that erythropoietin, which is also required for erythroid cell survival, cooperates with GATA-1 to stimulate bcl-xL gene expression and to maintain erythroid cell viability during terminal maturation. Together, our data show that bcl-xL is essential for normal erythroid development and suggest a regulatory hierarchy in which bcl-xL is a critical downstream effector of GATA-1 and erythropoietin-mediated signals. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 92, "end": 102}, "arguments": [{"role": "Theme", "text": "bcl-xL", "start": 85, "end": 91}]}, {"trigger": {"text": "expression", "start": 513, "end": 523}, "arguments": [{"role": "Theme", "text": "bcl-xL", "start": 554, "end": 560}]}, {"trigger": {"text": "expression", "start": 513, "end": 523}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 591, "end": 596}]}, {"trigger": {"text": "expression", "start": 513, "end": 523}, "arguments": [{"role": "Theme", "text": "mcl-1", "start": 601, "end": 606}]}, {"trigger": {"text": "expression", "start": 1006, "end": 1016}, "arguments": [{"role": "Theme", "text": "bcl-xL", "start": 994, "end": 1000}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 501, "end": 508}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 485, "end": 491}, {"role": "Theme", "text": "expression", "start": 513, "end": 523}]}, {"trigger": {"text": "stimulate", "start": 984, "end": 993}, "arguments": [{"role": "Cause", "text": "erythropoietin", "start": 890, "end": 904}, {"role": "Theme", "text": "expression", "start": 1006, "end": 1016}]}, {"trigger": {"text": "stimulate", "start": 984, "end": 993}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 974, "end": 980}, {"role": "Theme", "text": "expression", "start": 1006, "end": 1016}]}], "regulation": [{"trigger": {"text": "regulating", "start": 74, "end": 84}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 0, "end": 6}, {"role": "Theme", "text": "expression", "start": 92, "end": 102}]}, {"trigger": {"text": "regulating", "start": 74, "end": 84}, "arguments": [{"role": "Cause", "text": "erythropoietin", "start": 11, "end": 25}, {"role": "Theme", "text": "expression", "start": 92, "end": 102}]}, {"trigger": {"text": "downstream effector", "start": 1233, "end": 1252}, "arguments": [{"role": "Theme", "text": "bcl-xL", "start": 1212, "end": 1218}, {"role": "Cause", "text": "GATA-1", "start": 1256, "end": 1262}]}, {"trigger": {"text": "downstream effector", "start": 1233, "end": 1252}, "arguments": [{"role": "Theme", "text": "bcl-xL", "start": 1212, "end": 1218}, {"role": "Cause", "text": "erythropoietin", "start": 1267, "end": 1281}]}]}}, "schema": []}
{"input": "NF-kappaB functions as both a proapoptotic and antiapoptotic regulatory factor within a single cell type. \nRecently NF-kappaB has been shown to have both proapoptotic and antiapoptotic functions. In T cell hybridomas, both T cell activators and glucocorticoids induce apoptosis. Here we show that blockade of NF-kappaB activity, using a dominant negative IkappaBalpha, has opposite effects on these two apoptotic signals. Treatment with PMA plus ionomycin (P/I) results in the upregulation of Fas Ligand (FasL) and induction of apoptosis. Inhibition of NF-kappaB activity inhibits the P/I mediated induction of FasL mRNA and decreases the level of apoptosis in these cultures, thus establishing NF-kappaB as a proapoptotic factor in this context. Conversely, inhibition of NF-kappaB confers a tenfold increase in glucocorticoid mediated apoptosis, establishing that NF-kappaB also functions as an antiapoptotic factor. We conclude that NF-kappaB is a context-dependent apoptosis regulator. Our data suggests that NF-kappaB may function as an antiapoptotic factor in thymocytes while functioning as a proapoptotic factor in mature peripheral T cells. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibits", "start": 572, "end": 580}, "arguments": [{"role": "Theme", "text": "induction", "start": 598, "end": 607}]}], "positive regulation": [{"trigger": {"text": "upregulation", "start": 477, "end": 489}, "arguments": [{"role": "Theme", "text": "FasL", "start": 505, "end": 509}]}, {"trigger": {"text": "mediated", "start": 589, "end": 597}, "arguments": [{"role": "Theme", "text": "induction", "start": 598, "end": 607}]}], "transcription": [{"trigger": {"text": "induction", "start": 598, "end": 607}, "arguments": [{"role": "Theme", "text": "FasL", "start": 611, "end": 615}]}]}}, "schema": []}
{"input": "3-deazaadenosine, a S-adenosylhomocysteine hydrolase inhibitor, has dual effects on NF-kappaB regulation. Inhibition of NF-kappaB transcriptional activity and promotion of IkappaBalpha degradation. \nPreviously we reported that 3-deazaadenosine (DZA), a potent inhibitor and substrate for S-adenosylhomocysteine hydrolase inhibits bacterial lipopolysaccharide-induced transcription of tumor necrosis factor-alpha and interleukin-1beta in mouse macrophage RAW 264.7 cells. In this study, we demonstrate the effects of DZA on nuclear factor-kappaB (NF-kappaB) regulation. DZA inhibits the transcriptional activity of NF-kappaB through the hindrance of p65 (Rel-A) phosphorylation without reduction of its nuclear translocation and DNA binding activity. The inhibitory effect of DZA on NF-kappaB transcriptional activity is potentiated by the addition of homocysteine. Taken together, DZA promotes the proteolytic degradation of IkappaBalpha, but not IkappaBbeta, resulting in an increase of DNA binding activity of NF-kappaB in the nucleus in the absence of its transcriptional activity in RAW 264.7 cells. The reduction of IkappaBalpha by DZA is neither involved in IkappaB kinase complex activation nor modulated by the addition of homocysteine. This study strongly suggests that DZA may be a potent drug for the treatment of diseases in which NF-kappaB plays a central pathogenic role, as well as a useful tool for studying the regulation and physiological functions of NF-kappaB. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitor", "start": 53, "end": 62}, "arguments": [{"role": "Theme", "text": "S-adenosylhomocysteine hydrolase", "start": 20, "end": 52}]}, {"trigger": {"text": "inhibits", "start": 321, "end": 329}, "arguments": [{"role": "Theme", "text": "induced", "start": 359, "end": 366}]}, {"trigger": {"text": "hindrance", "start": 636, "end": 645}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 661, "end": 676}]}, {"trigger": {"text": "reduction", "start": 1108, "end": 1117}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1121, "end": 1133}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 661, "end": 676}, "arguments": [{"role": "Theme", "text": "Rel-A", "start": 654, "end": 659}]}], "positive regulation": [{"trigger": {"text": "promotion", "start": 159, "end": 168}, "arguments": [{"role": "Theme", "text": "degradation", "start": 185, "end": 196}]}, {"trigger": {"text": "induced", "start": 359, "end": 366}, "arguments": [{"role": "Theme", "text": "transcription", "start": 367, "end": 380}]}, {"trigger": {"text": "promotes", "start": 885, "end": 893}, "arguments": [{"role": "Theme", "text": "proteolytic degradation", "start": 898, "end": 921}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 185, "end": 196}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 172, "end": 184}]}, {"trigger": {"text": "proteolytic degradation", "start": 898, "end": 921}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 925, "end": 937}]}, {"trigger": {"text": "proteolytic degradation", "start": 898, "end": 921}, "arguments": [{"role": "Theme", "text": "IkappaBbeta", "start": 947, "end": 958}]}], "regulation": [{"trigger": {"text": "modulated", "start": 1202, "end": 1211}, "arguments": [{"role": "Theme", "text": "reduction", "start": 1108, "end": 1117}]}], "transcription": [{"trigger": {"text": "transcription", "start": 367, "end": 380}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 384, "end": 411}]}, {"trigger": {"text": "transcription", "start": 367, "end": 380}, "arguments": [{"role": "Theme", "text": "interleukin-1beta", "start": 416, "end": 433}]}]}}, "schema": []}
{"input": "STAT1 activation during monocyte to macrophage maturation: role of adhesion molecules. \nHuman monocytes isolated from peripheral blood of healthy donors show a time-dependent differentiation into macrophages upon in vitro cultivation, closely mimicking their in vivo migration and maturation into extravascular tissues. The mediator(s) of this maturation process has not been yet defined. We investigated the involvement of signal transducers and activators of transcription (STAT) factors in this phenomenon and reported the specific, time-dependent, activation of STAT1 protein starting at day 0/1 of cultivation and maximally expressed at day 5. STAT1 activity was evident on the STAT binding sequences (SBE) present in the promoters of genes which are up-regulated during monocyte to macrophage maturation such as FcgammaRI and ICAM-1, and in the promoter of the transcription factor IFN regulatory factor-1. Moreover, the effect of cell adhesion to fibronectin or laminin was studied to investigate mechanisms involved in STAT1 activation. Compared with monocytes adherent on plastic surfaces, freshly isolated cells allowed to adhere either to fibronectin- or laminin-coated flasks exhibited an increased STAT1 binding activity both in control and in IFN-gamma-treated cells. The molecular events leading to enhanced STAT1 activation and cytokine responsiveness concerned both Y701 and S727 STAT1 phosphorylation. Exogenous addition of transforming growth factor-beta, which exerts an inhibitory effect on some monocytic differentiation markers, inhibited macrophage maturation, integrin expression and STAT1 binding activity. Taken together these results indicate that STAT1 plays a pivotal role in the differentiation/maturation process of monocytes as an early transcription factor initially activated by adherence and then able to modulate the expression of functional genes, such as ICAM-1 and FcgammaRI. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 688, "end": 695}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 649, "end": 654}]}, {"trigger": {"text": "binding activity", "start": 1217, "end": 1233}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1211, "end": 1216}]}, {"trigger": {"text": "binding activity", "start": 1615, "end": 1631}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1609, "end": 1614}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1854, "end": 1864}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1894, "end": 1900}]}, {"trigger": {"text": "expression", "start": 1854, "end": 1864}, "arguments": [{"role": "Theme", "text": "FcgammaRI", "start": 1905, "end": 1914}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1552, "end": 1561}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 1615, "end": 1631}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1403, "end": 1418}, "arguments": [{"role": "Site", "text": "Y701", "start": 1383, "end": 1387}, {"role": "Theme", "text": "STAT1", "start": 1397, "end": 1402}]}, {"trigger": {"text": "phosphorylation", "start": 1403, "end": 1418}, "arguments": [{"role": "Site", "text": "S727", "start": 1392, "end": 1396}, {"role": "Theme", "text": "STAT1", "start": 1397, "end": 1402}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 6, "end": 16}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 0, "end": 5}]}, {"trigger": {"text": "role", "start": 59, "end": 63}, "arguments": [{"role": "Theme", "text": "activation", "start": 6, "end": 16}]}, {"trigger": {"text": "activation", "start": 552, "end": 562}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 566, "end": 571}]}, {"trigger": {"text": "maximally expressed", "start": 619, "end": 638}, "arguments": [{"role": "Theme", "text": "activation", "start": 552, "end": 562}]}, {"trigger": {"text": "up-regulated", "start": 756, "end": 768}, "arguments": [{"role": "Theme", "text": "FcgammaRI", "start": 818, "end": 827}]}, {"trigger": {"text": "up-regulated", "start": 756, "end": 768}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 832, "end": 838}]}, {"trigger": {"text": "activation", "start": 1033, "end": 1043}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1027, "end": 1032}]}, {"trigger": {"text": "increased", "start": 1201, "end": 1210}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 1217, "end": 1233}]}, {"trigger": {"text": "enhanced", "start": 1314, "end": 1322}, "arguments": [{"role": "Theme", "text": "activation", "start": 1329, "end": 1339}]}, {"trigger": {"text": "activation", "start": 1329, "end": 1339}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1323, "end": 1328}]}, {"trigger": {"text": "activated", "start": 1801, "end": 1810}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1676, "end": 1681}]}], "regulation": [{"trigger": {"text": "modulate", "start": 1841, "end": 1849}, "arguments": [{"role": "Cause", "text": "activated", "start": 1801, "end": 1810}, {"role": "Theme", "text": "expression", "start": 1854, "end": 1864}]}]}}, "schema": []}
{"input": "Stimulation of neutrophil interleukin-8 production by eosinophil granule major basic protein. \nWe evaluated the ability of eosinophil granule major basic protein (MBP) to stimulate interleukin (IL)-8 production by neutrophils. MBP over the concentration range of 0.1 to 10 microM stimulated the release of up to approximately 8 ng/ml IL-8. Incubation with 2 microM MBP showed that, after a 1 h lag, the level of IL-8 release increased with time for approximately 10 h. At the 2 microM concentration, eosinophil cationic protein, eosinophil-derived neurotoxin, and eosinophil peroxidase did not stimulate significant levels of IL-8 production. MBP stimulated 2-fold increases in IL-8 messenger RNA (mRNA) after 1 and 3 h of incubation, which were blocked by pretreatment with actinomycin D. However, stimulation with MBP did not produce an increase in the binding activity of nuclear factor (NF)-kappaB or activator protein-1. No NF-IL-6 binding activity was detected in the same nuclear extracts. In addition, stimulation with MBP prolonged the stability of IL-8 mRNA. MBP also induced transient increases in mRNA for macrophage inflammatory protein (MIP)-1alpha and MIP-1beta, but did not stimulate the release of either chemokine. These findings indicate that MBP is selective among the eosinophil granule proteins as a stimulus for neutrophil IL-8 release and, further, that stimulation of neutrophil IL-8 release by MBP involves both transcriptional and posttranscriptional regulation. We postulate that MBP-induced release of IL-8 by neutrophils may contribute to the pathophysiology of acute asthma and other inflammatory lung diseases. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 40, "end": 50}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 26, "end": 39}]}, {"trigger": {"text": "production", "start": 200, "end": 210}, "arguments": [{"role": "Theme", "text": "interleukin (IL)-8", "start": 181, "end": 199}]}, {"trigger": {"text": "production", "start": 631, "end": 641}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 626, "end": 630}]}], "localization": [{"trigger": {"text": "release", "start": 295, "end": 302}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 334, "end": 338}]}, {"trigger": {"text": "release", "start": 417, "end": 424}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 412, "end": 416}]}, {"trigger": {"text": "release", "start": 1204, "end": 1211}, "arguments": [{"role": "Theme", "text": "macrophage inflammatory protein (MIP)-1alpha", "start": 1118, "end": 1162}]}, {"trigger": {"text": "release", "start": 1204, "end": 1211}, "arguments": [{"role": "Theme", "text": "MIP-1beta", "start": 1167, "end": 1176}]}, {"trigger": {"text": "release", "start": 1351, "end": 1358}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1346, "end": 1350}]}, {"trigger": {"text": "release", "start": 1409, "end": 1416}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1404, "end": 1408}]}, {"trigger": {"text": "release", "start": 1520, "end": 1527}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1531, "end": 1535}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 746, "end": 753}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 647, "end": 657}]}], "positive regulation": [{"trigger": {"text": "stimulate", "start": 171, "end": 180}, "arguments": [{"role": "Cause", "text": "MBP", "start": 163, "end": 166}, {"role": "Theme", "text": "production", "start": 200, "end": 210}]}, {"trigger": {"text": "stimulated", "start": 280, "end": 290}, "arguments": [{"role": "Cause", "text": "MBP", "start": 227, "end": 230}, {"role": "Theme", "text": "release", "start": 295, "end": 302}]}, {"trigger": {"text": "increased", "start": 425, "end": 434}, "arguments": [{"role": "Cause", "text": "MBP", "start": 365, "end": 368}, {"role": "Theme", "text": "release", "start": 417, "end": 424}]}, {"trigger": {"text": "stimulated", "start": 647, "end": 657}, "arguments": [{"role": "Cause", "text": "MBP", "start": 643, "end": 646}, {"role": "Theme", "text": "increases", "start": 665, "end": 674}]}, {"trigger": {"text": "increases", "start": 665, "end": 674}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 678, "end": 682}]}, {"trigger": {"text": "prolonged the stability", "start": 1031, "end": 1054}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1058, "end": 1062}]}, {"trigger": {"text": "increases", "start": 1096, "end": 1105}, "arguments": [{"role": "Cause", "text": "MBP", "start": 1069, "end": 1072}, {"role": "Theme", "text": "macrophage inflammatory protein (MIP)-1alpha", "start": 1118, "end": 1162}]}, {"trigger": {"text": "increases", "start": 1096, "end": 1105}, "arguments": [{"role": "Cause", "text": "MBP", "start": 1069, "end": 1072}, {"role": "Theme", "text": "MIP-1beta", "start": 1167, "end": 1176}]}, {"trigger": {"text": "stimulate", "start": 1190, "end": 1199}, "arguments": [{"role": "Cause", "text": "MBP", "start": 1069, "end": 1072}, {"role": "Theme", "text": "release", "start": 1204, "end": 1211}]}, {"trigger": {"text": "induced", "start": 1512, "end": 1519}, "arguments": [{"role": "Cause", "text": "MBP", "start": 1508, "end": 1511}, {"role": "Theme", "text": "release", "start": 1520, "end": 1527}]}]}}, "schema": []}
{"input": "PPARgamma activation induces the expression of the adipocyte fatty acid binding protein gene in human monocytes. \nThe peroxisome-proliferator activated receptor gamma (PPARgamma), a member of the nuclear receptor superfamily of ligand activated transcription factors, plays a key role in the anti-diabetic actions of the thiazolidinediones (TZDs). PPARgamma induces the expression of many genes involved in lipid anabolism, including the adipocyte fatty acid binding protein (aP2), and is a key regulator of adipocyte differentiation. PPARgamma is also expressed in hematopoietic cells and is up-regulated in activated monocytes/macrophages. Activation of PPARgamma may play a role in the induction of differentiation of macrophages to foam cells that are associated with atherosclerotic lesions. We report that both natural and synthetic PPARgamma agonists induce time- and dose-dependent increases in aP2 mRNA in both primary human monocytes and the monocytic cell line, THP-1. These data suggest that PPARgamma activation may play a role in monocyte differentiation and function analogous to its well-characterized role in adipocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 33, "end": 43}, "arguments": [{"role": "Theme", "text": "adipocyte fatty acid binding protein", "start": 51, "end": 87}]}, {"trigger": {"text": "expression", "start": 370, "end": 380}, "arguments": [{"role": "Theme", "text": "aP2", "start": 476, "end": 479}]}, {"trigger": {"text": "expressed", "start": 553, "end": 562}, "arguments": [{"role": "Theme", "text": "PPARgamma", "start": 535, "end": 544}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 10, "end": 20}, "arguments": [{"role": "Theme", "text": "PPARgamma", "start": 0, "end": 9}]}, {"trigger": {"text": "induces", "start": 21, "end": 28}, "arguments": [{"role": "Cause", "text": "activation", "start": 10, "end": 20}, {"role": "Theme", "text": "expression", "start": 33, "end": 43}]}, {"trigger": {"text": "induces", "start": 358, "end": 365}, "arguments": [{"role": "Cause", "text": "PPARgamma", "start": 348, "end": 357}, {"role": "Theme", "text": "expression", "start": 370, "end": 380}]}, {"trigger": {"text": "up-regulated", "start": 593, "end": 605}, "arguments": [{"role": "Theme", "text": "PPARgamma", "start": 535, "end": 544}]}, {"trigger": {"text": "Activation", "start": 642, "end": 652}, "arguments": [{"role": "Theme", "text": "PPARgamma", "start": 656, "end": 665}]}, {"trigger": {"text": "induce", "start": 858, "end": 864}, "arguments": [{"role": "Theme", "text": "increases", "start": 890, "end": 899}]}, {"trigger": {"text": "increases", "start": 890, "end": 899}, "arguments": [{"role": "Theme", "text": "aP2", "start": 903, "end": 906}]}, {"trigger": {"text": "activation", "start": 1014, "end": 1024}, "arguments": [{"role": "Theme", "text": "PPARgamma", "start": 1004, "end": 1013}]}]}}, "schema": []}
{"input": "Reactive oxygen intermediate-release of fibre-exposed monocytes increases inflammatory cytokine-mRNA level, protein tyrosine kinase and NF-kappaB activity in co-cultured bronchial epithelial cells (BEAS-2B). \nSome pulmonary diseases like bronchitis or asthma bronchiale are mediated by inflammatory mechanisms in bronchial epithelial cells. Alveolar macrophages are located directly in the surrounding of these cells, so that we suppose an interaction between epithelial cells and macrophages regarding to the release of inflammatory mediators. For measuring the contribution of macrophages to the release of inflammatory mediators by bronchial epithelial cells, we established an in vitro model of co-cultured blood monocytes (BM) and BEAS-2B cells in a transwell system (Costar). BM were exposed to Chrysotile B and soot particle FR 101 in a concentration of 100 microg/10(6) cells. After up to 90 min exposure time ELISA, EMSA (electromobility shift assay) and RT-PCR were used to measure protein tyrosine kinase activity, protein activity of NF-kappaB and cytokine (IL-1beta, IL-6, TNF-alpha) specific mRNA levels in BEAS-2B cells. We observed an increase in protein tyrosine kinase activity (up to 1.8 +/- 0.5-fold) and NF-kappaB protein activity in BEAS-2B cells after particle or fibre exposure of co-cultured BM. Consecutive IL-1beta-, IL-6- and TNF-alpha-mRNA were elevated (up to 1.9 +/- 0.58-fold). Protein tyrosine kinase activity, NF-kappaB activity, and the synthesis of cytokine-specific mRNA were inhibited by antioxidants. These data suggest a ROI-dependent NF-kappaB mediated transcription of inflammatory cytokines in bronchial epithelial cells. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "elevated", "start": 1374, "end": 1382}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1333, "end": 1341}]}, {"trigger": {"text": "elevated", "start": 1374, "end": 1382}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1344, "end": 1348}]}, {"trigger": {"text": "elevated", "start": 1374, "end": 1382}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1354, "end": 1363}]}]}}, "schema": []}
{"input": "Host defense mechanisms triggered by microbial lipoproteins through toll-like receptors. \nThe generation of cell-mediated immunity against many infectious pathogens involves the production of interleukin-12 (IL-12), a key signal of the innate immune system. Yet, for many pathogens, the molecules that induce IL-12 production by macrophages and the mechanisms by which they do so remain undefined. Here it is shown that microbial lipoproteins are potent stimulators of IL-12 production by human macrophages, and that induction is mediated by Toll-like receptors (TLRs). Several lipoproteins stimulated TLR-dependent transcription of inducible nitric oxide synthase and the production of nitric oxide, a powerful microbicidal pathway. Activation of TLRs by microbial lipoproteins may initiate innate defense mechanisms against infectious pathogens. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 178, "end": 188}, "arguments": [{"role": "Theme", "text": "IL-12", "start": 208, "end": 213}]}, {"trigger": {"text": "production", "start": 315, "end": 325}, "arguments": [{"role": "Theme", "text": "IL-12", "start": 309, "end": 314}]}, {"trigger": {"text": "production", "start": 475, "end": 485}, "arguments": [{"role": "Theme", "text": "IL-12", "start": 469, "end": 474}]}], "positive regulation": [{"trigger": {"text": "induce", "start": 302, "end": 308}, "arguments": [{"role": "Theme", "text": "production", "start": 315, "end": 325}]}, {"trigger": {"text": "stimulated", "start": 591, "end": 601}, "arguments": [{"role": "Theme", "text": "transcription", "start": 616, "end": 629}]}, {"trigger": {"text": "inducible", "start": 633, "end": 642}, "arguments": [{"role": "Theme", "text": "nitric oxide synthase", "start": 643, "end": 664}]}], "regulation": [{"trigger": {"text": "dependent", "start": 606, "end": 615}, "arguments": [{"role": "Theme", "text": "transcription", "start": 616, "end": 629}]}], "transcription": [{"trigger": {"text": "transcription", "start": 616, "end": 629}, "arguments": [{"role": "Theme", "text": "nitric oxide synthase", "start": 643, "end": 664}]}]}}, "schema": []}
{"input": "Cell activation and apoptosis by bacterial lipoproteins through toll-like receptor-2. \nApoptosis is implicated in the generation and resolution of inflammation in response to bacterial pathogens. All bacterial pathogens produce lipoproteins (BLPs), which trigger the innate immune response. BLPs were found to induce apoptosis in THP-1 monocytic cells through human Toll-like receptor-2 (hTLR2). BLPs also initiated apoptosis in an epithelial cell line transfected with hTLR2. In addition, BLPs stimulated nuclear factor-kappaB, a transcriptional activator of multiple host defense genes, and activated the respiratory burst through hTLR2. Thus, hTLR2 is a molecular link between microbial products, apoptosis, and host defense mechanisms. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "transfected", "start": 453, "end": 464}, "arguments": [{"role": "Theme", "text": "hTLR2", "start": 470, "end": 475}]}], "positive regulation": [{"trigger": {"text": "transfected", "start": 453, "end": 464}, "arguments": [{"role": "Theme", "text": "transfected", "start": 453, "end": 464}]}]}}, "schema": []}
{"input": "Tissue-specific regulation of the ecto-5'-nucleotidase promoter. Role of the camp response element site in mediating repression by the upstream regulatory region. \nWe have isolated the 5' region of the ecto-5'-nucleotidase (low K(m) 5'-NT) gene and established that a 969-base pair (bp) fragment confers cell-specific expression of a CAT reporter gene that correlates with the expression of endogenous ecto-5'-NT mRNA and enzymatic activity. A 768-bp upstream negative regulatory region has been identified that conferred lymphocyte-specific negative regulation in a heterologous system with a 244-bp deoxycytidine kinase core promoter. DNase I footprinting identified several protected areas including Sp1, Sp1/AP-2, and cAMP response element (CRE) binding sites within the 201-bp core promoter region and Sp1, NRE-2a, TCF-1/LEF-1, and Sp1/NF-AT binding sites in the upstream regulatory region. Whereas the CRE site was essential in mediating the negative activity of the upstream regulatory region in Jurkat but not in HeLa cells, mutation of the Sp1/AP-2 site decreased promoter activity in both cell lines. Electrophoretic mobility shift assay analysis of proteins binding to the CRE site identified both ATF-1 and ATF-2 in Jurkat cells. Finally, phorbol 12-myristate 13-acetate increased the activity of both the core and the 969-bp promoter fragments, and this increase was abrogated by mutations at the CRE site. In summary, we have identified a tissue-specific regulatory region 5' of the ecto-5'-NT core promoter that requires the presence of a functional CRE site within the basal promoter for its suppressive activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1169, "end": 1176}, "arguments": [{"role": "Theme", "text": "ATF-1", "start": 1209, "end": 1214}]}, {"trigger": {"text": "binding", "start": 1169, "end": 1176}, "arguments": [{"role": "Theme", "text": "ATF-2", "start": 1219, "end": 1224}]}], "negative regulation": [{"trigger": {"text": "repression", "start": 117, "end": 127}, "arguments": [{"role": "Theme", "text": "ecto-5'-nucleotidase", "start": 34, "end": 54}, {"role": "Site", "text": "promoter", "start": 55, "end": 63}]}], "positive regulation": [{"trigger": {"text": "mediating", "start": 107, "end": 116}, "arguments": [{"role": "Theme", "text": "repression", "start": 117, "end": 127}]}], "regulation": [{"trigger": {"text": "regulation", "start": 16, "end": 26}, "arguments": [{"role": "Theme", "text": "ecto-5'-nucleotidase", "start": 34, "end": 54}, {"role": "Site", "text": "promoter", "start": 55, "end": 63}]}, {"trigger": {"text": "Role", "start": 65, "end": 69}, "arguments": [{"role": "Theme", "text": "mediating", "start": 107, "end": 116}]}], "transcription": [{"trigger": {"text": "expression", "start": 377, "end": 387}, "arguments": [{"role": "Theme", "text": "ecto-5'-NT", "start": 402, "end": 412}]}]}}, "schema": []}
{"input": "NF-kappaB-mediated up-regulation of Bcl-x and Bfl-1/A1 is required for CD40 survival signaling in B lymphocytes. \nActivation of CD40 is essential for thymus-dependent humoral immune responses and rescuing B cells from apoptosis. Many of the effects of CD40 are believed to be achieved through altered gene expression. In addition to Bcl-x, a known CD40-regulated antiapoptotic molecule, we identified a related antiapoptotic molecule, A1/Bfl-1, as a CD40-inducible gene. Inhibition of the NF-kappaB pathway by overexpression of a dominant-active inhibitor of NF-kappaB abolished CD40-induced up-regulation of both the Bfl-1 and Bcl-x genes and also eliminated the ability of CD40 to rescue Fas-induced cell death. Within the upstream promoter region of Bcl-x, a potential NF-kappaB-binding sequence was found to support NF-kappaB-dependent transcriptional activation. Furthermore, expression of physiological levels of Bcl-x protected B cells from Fas-mediated apoptosis in the absence of NF-kappaB signaling. Thus, our results suggest that CD40-mediated cell survival proceeds through NF-kappaB-dependent up-regulation of Bcl-2 family members. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 881, "end": 891}, "arguments": [{"role": "Theme", "text": "Bcl-x", "start": 919, "end": 924}]}], "negative regulation": [{"trigger": {"text": "abolished", "start": 569, "end": 578}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 592, "end": 605}]}], "positive regulation": [{"trigger": {"text": "up-regulation", "start": 19, "end": 32}, "arguments": [{"role": "Theme", "text": "Bcl-x", "start": 36, "end": 41}]}, {"trigger": {"text": "up-regulation", "start": 19, "end": 32}, "arguments": [{"role": "Theme", "text": "Bfl-1/A1", "start": 46, "end": 54}]}, {"trigger": {"text": "Activation", "start": 114, "end": 124}, "arguments": [{"role": "Theme", "text": "CD40", "start": 128, "end": 132}]}, {"trigger": {"text": "inducible", "start": 455, "end": 464}, "arguments": [{"role": "Theme", "text": "A1/Bfl-1", "start": 435, "end": 443}, {"role": "Cause", "text": "CD40", "start": 450, "end": 454}]}, {"trigger": {"text": "up-regulation", "start": 592, "end": 605}, "arguments": [{"role": "Cause", "text": "CD40", "start": 579, "end": 583}, {"role": "Theme", "text": "Bfl-1", "start": 618, "end": 623}]}, {"trigger": {"text": "up-regulation", "start": 592, "end": 605}, "arguments": [{"role": "Cause", "text": "CD40", "start": 579, "end": 583}, {"role": "Theme", "text": "Bcl-x", "start": 628, "end": 633}]}], "regulation": [{"trigger": {"text": "regulated", "start": 353, "end": 362}, "arguments": [{"role": "Theme", "text": "Bcl-x", "start": 333, "end": 338}, {"role": "Cause", "text": "CD40", "start": 348, "end": 352}]}]}}, "schema": []}
{"input": "Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. \ncDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of coexpressed genes identified through manipulations of mammary epithelial cells in vitro also showed consistent patterns of variation in expression among breast tumor samples. By using immunohistochemistry with antibodies against proteins encoded by a particular gene in a cluster, the identity of the cell type within the tumor specimen that contributed the observed gene expression pattern could be determined. Clusters of genes with coherent expression patterns in cultured cells and in the breast tumors samples could be related to specific features of biological variation among the samples. Two such clusters were found to have patterns that correlated with variation in cell proliferation rates and with activation of the IFN-regulated signal transduction pathway, respectively. Clusters of genes expressed by stromal cells and lymphocytes in the breast tumors also were identified in this analysis. These results support the feasibility and usefulness of this systematic approach to studying variation in gene expression patterns in human cancers as a means to dissect and classify solid tumors. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Bcl-2-mediated drug resistance: inhibition of apoptosis by blocking nuclear factor of activated T lymphocytes (NFAT)-induced Fas ligand transcription. \nBcl-2 inhibits apoptosis induced by a variety of stimuli, including chemotherapy drugs and glucocorticoids. It is generally accepted that Bcl-2 exerts its antiapoptotic effects mainly by dimerizing with proapoptotic members of the Bcl-2 family such as Bax and Bad. However, the mechanism of the antiapoptotic effects is unclear. Paclitaxel and other drugs that disturb microtubule dynamics kill cells in a Fas/Fas ligand (FasL)-dependent manner; antibody to FasL inhibits paclitaxel-induced apoptosis. We have found that Bcl-2 overexpression leads to the prevention of chemotherapy (paclitaxel)-induced expression of FasL and blocks paclitaxel-induced apoptosis. The mechanism of this effect is that Bcl-2 prevents the nuclear translocation of NFAT (nuclear factor of activated T lymphocytes, a transcription factor activated by microtubule damage) by binding and sequestering calcineurin, a calcium-dependent phosphatase that must dephosphorylate NFAT to move to the nucleus. Without NFAT nuclear translocation, the FasL gene is not transcribed. Thus, it appears that paclitaxel and other drugs that disturb microtubule function kill cells at least in part through the induction of FasL. Furthermore, Bcl-2 antagonizes drug-induced apoptosis by inhibiting calcineurin activation, blocking NFAT nuclear translocation, and preventing FasL expression. The effects of Bcl-2 can be overcome, at least partially, through phosphorylation of Bcl-2. Phosphorylated Bcl-2 cannot bind calcineurin, and NFAT activation, FasL expression, and apoptosis can occur after Bcl-2 phosphorylation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "dimerizing", "start": 339, "end": 349}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 290, "end": 295}, {"role": "Theme2", "text": "Bax", "start": 404, "end": 407}]}, {"trigger": {"text": "dimerizing", "start": 339, "end": 349}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 290, "end": 295}, {"role": "Theme2", "text": "Bad", "start": 412, "end": 415}]}, {"trigger": {"text": "binding", "start": 1004, "end": 1011}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 852, "end": 857}]}, {"trigger": {"text": "bind", "start": 1622, "end": 1626}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1609, "end": 1614}, {"role": "Theme2", "text": "calcineurin", "start": 1627, "end": 1638}]}], "gene expression": [{"trigger": {"text": "overexpression", "start": 679, "end": 693}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 673, "end": 678}]}, {"trigger": {"text": "expression", "start": 755, "end": 765}, "arguments": [{"role": "Theme", "text": "FasL", "start": 769, "end": 773}]}, {"trigger": {"text": "expression", "start": 1490, "end": 1500}, "arguments": [{"role": "Theme", "text": "FasL", "start": 1485, "end": 1489}]}, {"trigger": {"text": "expression", "start": 1666, "end": 1676}, "arguments": [{"role": "Theme", "text": "FasL", "start": 1661, "end": 1665}]}], "negative regulation": [{"trigger": {"text": "blocking", "start": 59, "end": 67}, "arguments": [{"role": "Cause", "text": "Bcl-2", "start": 0, "end": 5}, {"role": "Theme", "text": "induced", "start": 117, "end": 124}]}, {"trigger": {"text": "leads to the prevention", "start": 694, "end": 717}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 679, "end": 693}, {"role": "Theme", "text": "induced", "start": 747, "end": 754}]}, {"trigger": {"text": "preventing", "start": 1474, "end": 1484}, "arguments": [{"role": "Theme", "text": "expression", "start": 1490, "end": 1500}]}, {"trigger": {"text": "cannot", "start": 1615, "end": 1621}, "arguments": [{"role": "Cause", "text": "Phosphorylated", "start": 1594, "end": 1608}, {"role": "Theme", "text": "bind", "start": 1622, "end": 1626}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1568, "end": 1583}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1587, "end": 1592}]}, {"trigger": {"text": "Phosphorylated", "start": 1594, "end": 1608}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1609, "end": 1614}]}, {"trigger": {"text": "phosphorylation", "start": 1714, "end": 1729}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1708, "end": 1713}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 117, "end": 124}, "arguments": [{"role": "Theme", "text": "transcription", "start": 136, "end": 149}]}, {"trigger": {"text": "overexpression", "start": 679, "end": 693}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 679, "end": 693}]}, {"trigger": {"text": "induced", "start": 747, "end": 754}, "arguments": [{"role": "Theme", "text": "expression", "start": 755, "end": 765}]}, {"trigger": {"text": "Without", "start": 1129, "end": 1136}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 1186, "end": 1197}]}, {"trigger": {"text": "induction", "start": 1322, "end": 1331}, "arguments": [{"role": "Theme", "text": "FasL", "start": 1335, "end": 1339}]}, {"trigger": {"text": "after", "start": 1702, "end": 1707}, "arguments": [{"role": "Theme", "text": "expression", "start": 1666, "end": 1676}, {"role": "Cause", "text": "phosphorylation", "start": 1714, "end": 1729}]}], "transcription": [{"trigger": {"text": "transcription", "start": 136, "end": 149}, "arguments": [{"role": "Theme", "text": "Fas ligand", "start": 125, "end": 135}]}, {"trigger": {"text": "transcribed", "start": 1186, "end": 1197}, "arguments": [{"role": "Theme", "text": "FasL", "start": 1169, "end": 1173}]}]}}, "schema": []}
{"input": "Retinoblastoma protein expression leads to reduced Oct-1 DNA binding activity and enhances interleukin-8 expression. \nTumor cell lines with a defective retinoblastoma gene are unable to transcribe the HLA class II genes in response to IFN-gamma treatment, and reconstitution of functional Rb rescues IFN-gamma-induced class II gene expression. However, the molecular mechanism of Rb rescue of the class II genes is unknown. We have examined the effect of Rb expression on the activation of the promoter for HLA-DRA, the prototype class II gene. Oct-1, a POU domain transcription factor, was identified as a repressor of HLA-DRA promoter activity in the Rb-defective cells. Rb expression led to phosphorylation of Oct-1, thus relieving its repressive effect. Oct-1 has also been shown to repress interleukin 8 promoter activity. Consistent with reduced levels of Oct-1 DNA binding activity in the Rb-transformed cell lines, interleukin 8 expression is higher in these cell lines. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 61, "end": 77}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 51, "end": 56}]}, {"trigger": {"text": "binding activity", "start": 872, "end": 888}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 862, "end": 867}]}], "gene expression": [{"trigger": {"text": "expression", "start": 23, "end": 33}, "arguments": [{"role": "Theme", "text": "Retinoblastoma", "start": 0, "end": 14}]}, {"trigger": {"text": "expression", "start": 105, "end": 115}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 91, "end": 104}]}, {"trigger": {"text": "expression", "start": 458, "end": 468}, "arguments": [{"role": "Theme", "text": "Rb", "start": 455, "end": 457}]}, {"trigger": {"text": "expression", "start": 676, "end": 686}, "arguments": [{"role": "Theme", "text": "Rb", "start": 673, "end": 675}]}, {"trigger": {"text": "expression", "start": 937, "end": 947}, "arguments": [{"role": "Theme", "text": "interleukin 8", "start": 923, "end": 936}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 43, "end": 50}, "arguments": [{"role": "Cause", "text": "expression", "start": 23, "end": 33}, {"role": "Theme", "text": "binding activity", "start": 61, "end": 77}]}, {"trigger": {"text": "defective", "start": 142, "end": 151}, "arguments": [{"role": "Theme", "text": "retinoblastoma", "start": 152, "end": 166}]}, {"trigger": {"text": "defective", "start": 656, "end": 665}, "arguments": [{"role": "Theme", "text": "Rb", "start": 653, "end": 655}]}, {"trigger": {"text": "repress", "start": 787, "end": 794}, "arguments": [{"role": "Cause", "text": "Oct-1", "start": 758, "end": 763}, {"role": "Theme", "text": "interleukin 8", "start": 795, "end": 808}, {"role": "Site", "text": "promoter", "start": 809, "end": 817}]}, {"trigger": {"text": "reduced levels", "start": 844, "end": 858}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 872, "end": 888}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 694, "end": 709}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 713, "end": 718}]}], "positive regulation": [{"trigger": {"text": "enhances", "start": 82, "end": 90}, "arguments": [{"role": "Cause", "text": "expression", "start": 23, "end": 33}, {"role": "Theme", "text": "expression", "start": 105, "end": 115}]}, {"trigger": {"text": "led", "start": 687, "end": 690}, "arguments": [{"role": "Cause", "text": "expression", "start": 676, "end": 686}, {"role": "Theme", "text": "phosphorylation", "start": 694, "end": 709}]}, {"trigger": {"text": "higher", "start": 951, "end": 957}, "arguments": [{"role": "Theme", "text": "expression", "start": 937, "end": 947}]}]}}, "schema": []}
{"input": "Protein kinase C and calcineurin synergize to activate IkappaB kinase and NF-kappaB in T lymphocytes. \nThe nuclear factor of kappaB (NF-kappaB) is a ubiquitous transcription factor that is key in the regulation of the immune response and inflammation. T cell receptor (TCR) cross-linking is in part required for activation of NF-kappaB, which is dependent on the phosphorylation and degradation of IkappaBalpha. By using Jurkat and primary human T lymphocytes, we demonstrate that the simultaneous activation of two second messengers of the TCR-initiated signal transduction, protein kinase C (PKC) and calcineurin, results in the synergistic activation of the IkappaBalpha kinase (IKK) complex but not of another putative IkappaBalpha kinase, p90(rsk). We also demonstrate that the IKK complex, but not p90(rsk), is responsible for the in vivo phosphorylation of IkappaBalpha mediated by the co-activation of PKC and calcineurin. Each second messenger is necessary, as inhibition of either one reverses the activation of the IKK complex and IkappaBalpha phosphorylation in vivo. Overexpression of dominant negative forms of IKKalpha and -beta demonstrates that only IKKbeta is the target for PKC and calcineurin. These results indicate that within the TCR/CD3 signal transduction pathway both PKC and calcineurin are required for the effective activation of the IKK complex and NF-kappaB in T lymphocytes. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "reverses", "start": 995, "end": 1003}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1055, "end": 1070}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 363, "end": 378}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 398, "end": 410}]}, {"trigger": {"text": "phosphorylation", "start": 845, "end": 860}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 864, "end": 876}]}, {"trigger": {"text": "phosphorylation", "start": 1055, "end": 1070}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1042, "end": 1054}]}], "positive regulation": [{"trigger": {"text": "synergistic activation", "start": 631, "end": 653}, "arguments": [{"role": "Theme", "text": "p90(rsk)", "start": 744, "end": 752}]}, {"trigger": {"text": "mediated", "start": 877, "end": 885}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 845, "end": 860}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 383, "end": 394}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 398, "end": 410}]}], "regulation": [{"trigger": {"text": "responsible", "start": 817, "end": 828}, "arguments": [{"role": "Cause", "text": "p90(rsk)", "start": 804, "end": 812}, {"role": "Theme", "text": "phosphorylation", "start": 845, "end": 860}]}, {"trigger": {"text": "responsible", "start": 817, "end": 828}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 845, "end": 860}]}, {"trigger": {"text": "target", "start": 1182, "end": 1188}, "arguments": [{"role": "Theme", "text": "IKKbeta", "start": 1167, "end": 1174}]}]}}, "schema": []}
{"input": "C/EBPbeta and GATA-1 synergistically regulate activity of the eosinophil granule major basic protein promoter: implication for C/EBPbeta activity in eosinophil gene expression. \nEosinophil granule major basic protein (MBP) is expressed exclusively in eosinophils and basophils in hematopoietic cells. In our previous study, we demonstrated a major positive regulatory role for GATA-1 and a negative regulatory role for GATA-2 in MBP gene transcription. Further analysis of the MBP promoter region identified a C/EBP (CCAAT/enhancer-binding protein) consensus binding site 6 bp upstream of the functional GATA-binding site in the MBP gene. In the cell line HT93A, which is capable of differentiating towards both the eosinophil and neutrophil lineages in response to retinoic acid (RA), C/EBPalpha mRNA expression decreased significantly concomitant with eosinophilic and neutrophilic differentiation, whereas C/EBPbeta expression was markedly increased. Electrophoretic mobility shift assays (EMSAs) showed that recombinant C/EBPbeta protein could bind to the potential C/EBP-binding site (bp -90 to -82) in the MBP promoter. Furthermore, we have demonstrated that both C/EBPbeta and GATA-1 can bind simultaneously to the C/EBP- and GATA-binding sites in the MBP promoter. To determine the functionality of both the C/EBP- and GATA- binding sites, we analyzed whether C/EBPbeta and GATA-1 can stimulate the MBP promoter in the C/EBPbeta and GATA-1 negative Jurkat T-cell line. Cotransfection with C/EBPbeta and GATA-1 expression vectors produced a 5-fold increase compared with cotransfection with the C/EBPbeta or GATA-1 expression vectors individually. In addition, GST pull-down experiments demonstrated a physical interaction between human GATA-1 and C/EBPbeta. Expression of FOG (riend ATA), which binds to GATA-1 and acts as a cofactor for GATA-binding proteins, decreased transactivation activity of GATA-1 for the MBP promoter in a dose-dependent manner. Our results provide the first evidence that both GATA-1 and C/EBPbeta synergistically transactivate the promoter of an eosinophil-specific granule protein gene and that FOG may act as a negative cofactor for the eosinophil lineage, unlike its positively regulatory function for the erythroid and megakaryocyte lineages. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 1048, "end": 1052}, "arguments": [{"role": "Theme", "text": "C/EBPbeta", "start": 1024, "end": 1033}, {"role": "Theme2", "text": "MBP", "start": 1112, "end": 1115}, {"role": "Site2", "text": "promoter", "start": 1116, "end": 1124}]}, {"trigger": {"text": "bind", "start": 1195, "end": 1199}, "arguments": [{"role": "Theme", "text": "C/EBPbeta", "start": 1170, "end": 1179}, {"role": "Theme2", "text": "MBP", "start": 1259, "end": 1262}, {"role": "Site2", "text": "promoter", "start": 1263, "end": 1271}]}, {"trigger": {"text": "bind", "start": 1195, "end": 1199}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1184, "end": 1190}, {"role": "Theme2", "text": "MBP", "start": 1259, "end": 1262}, {"role": "Site2", "text": "promoter", "start": 1263, "end": 1271}]}, {"trigger": {"text": "physical interaction", "start": 1709, "end": 1729}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1744, "end": 1750}, {"role": "Theme2", "text": "C/EBPbeta", "start": 1755, "end": 1764}]}, {"trigger": {"text": "binds", "start": 1803, "end": 1808}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1812, "end": 1818}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 226, "end": 235}, "arguments": [{"role": "Theme", "text": "MBP", "start": 218, "end": 221}]}, {"trigger": {"text": "expression", "start": 919, "end": 929}, "arguments": [{"role": "Theme", "text": "C/EBPbeta", "start": 909, "end": 918}]}, {"trigger": {"text": "negative", "start": 1448, "end": 1456}, "arguments": [{"role": "Theme", "text": "C/EBPbeta", "start": 1427, "end": 1436}]}, {"trigger": {"text": "negative", "start": 1448, "end": 1456}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1441, "end": 1447}]}, {"trigger": {"text": "Cotransfection", "start": 1477, "end": 1491}, "arguments": [{"role": "Theme", "text": "C/EBPbeta", "start": 1497, "end": 1506}]}, {"trigger": {"text": "Cotransfection", "start": 1477, "end": 1491}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1511, "end": 1517}]}, {"trigger": {"text": "cotransfection", "start": 1578, "end": 1592}, "arguments": [{"role": "Theme", "text": "C/EBPbeta", "start": 1602, "end": 1611}]}, {"trigger": {"text": "cotransfection", "start": 1578, "end": 1592}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1615, "end": 1621}]}], "negative regulation": [{"trigger": {"text": "negative regulatory role", "start": 390, "end": 414}, "arguments": [{"role": "Cause", "text": "GATA-2", "start": 419, "end": 425}, {"role": "Theme", "text": "transcription", "start": 438, "end": 451}]}, {"trigger": {"text": "decreased", "start": 813, "end": 822}, "arguments": [{"role": "Theme", "text": "expression", "start": 802, "end": 812}]}, {"trigger": {"text": "decreased", "start": 1869, "end": 1878}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 1879, "end": 1894}]}], "positive regulation": [{"trigger": {"text": "positive regulatory role", "start": 348, "end": 372}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 377, "end": 383}, {"role": "Theme", "text": "transcription", "start": 438, "end": 451}]}, {"trigger": {"text": "increased", "start": 943, "end": 952}, "arguments": [{"role": "Theme", "text": "expression", "start": 919, "end": 929}]}, {"trigger": {"text": "stimulate", "start": 1393, "end": 1402}, "arguments": [{"role": "Cause", "text": "C/EBPbeta", "start": 1368, "end": 1377}, {"role": "Theme", "text": "MBP", "start": 1407, "end": 1410}, {"role": "Site", "text": "promoter", "start": 1411, "end": 1419}]}, {"trigger": {"text": "stimulate", "start": 1393, "end": 1402}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 1382, "end": 1388}, {"role": "Theme", "text": "MBP", "start": 1407, "end": 1410}, {"role": "Site", "text": "promoter", "start": 1411, "end": 1419}]}, {"trigger": {"text": "Cotransfection", "start": 1477, "end": 1491}, "arguments": [{"role": "Theme", "text": "Cotransfection", "start": 1477, "end": 1491}]}, {"trigger": {"text": "increase", "start": 1555, "end": 1563}, "arguments": [{"role": "Theme", "text": "MBP", "start": 1407, "end": 1410}, {"role": "Site", "text": "promoter", "start": 1411, "end": 1419}, {"role": "Cause", "text": "Cotransfection", "start": 1477, "end": 1491}]}, {"trigger": {"text": "increase", "start": 1555, "end": 1563}, "arguments": [{"role": "Theme", "text": "MBP", "start": 1407, "end": 1410}, {"role": "Site", "text": "promoter", "start": 1411, "end": 1419}, {"role": "Cause", "text": "cotransfection", "start": 1578, "end": 1592}]}, {"trigger": {"text": "cotransfection", "start": 1578, "end": 1592}, "arguments": [{"role": "Theme", "text": "cotransfection", "start": 1578, "end": 1592}]}, {"trigger": {"text": "transactivation", "start": 1879, "end": 1894}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 1907, "end": 1913}, {"role": "Theme", "text": "MBP", "start": 1922, "end": 1925}, {"role": "Site", "text": "promoter", "start": 1926, "end": 1934}]}], "regulation": [{"trigger": {"text": "regulate", "start": 37, "end": 45}, "arguments": [{"role": "Cause", "text": "C/EBPbeta", "start": 0, "end": 9}, {"role": "Theme", "text": "eosinophil granule major basic protein", "start": 62, "end": 100}, {"role": "Site", "text": "promoter", "start": 101, "end": 109}]}, {"trigger": {"text": "regulate", "start": 37, "end": 45}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 14, "end": 20}, {"role": "Theme", "text": "eosinophil granule major basic protein", "start": 62, "end": 100}, {"role": "Site", "text": "promoter", "start": 101, "end": 109}]}], "transcription": [{"trigger": {"text": "transcription", "start": 438, "end": 451}, "arguments": [{"role": "Theme", "text": "MBP", "start": 429, "end": 432}]}, {"trigger": {"text": "expression", "start": 802, "end": 812}, "arguments": [{"role": "Theme", "text": "C/EBPalpha", "start": 786, "end": 796}]}]}}, "schema": []}
{"input": "Thymocyte-thymic epithelial cell interaction leads to high-level replication of human immunodeficiency virus exclusively in mature CD4(+) CD8(-) CD3(+) thymocytes: a critical role for tumor necrosis factor and interleukin-7. \nThis work aims at identifying the thymocyte subpopulation able to support human immunodeficiency virus (HIV) replication under the biological stimuli of the thymic microenvironment. In this report we demonstrate that interaction with thymic epithelial cells (TEC) induces a high-level replication of the T-tropic primary isolate HIV-1(B-LAIp) exclusively in the mature CD4(+) CD8(-) CD3(+) thymocytes. Tumor necrosis factor (TNF) and interleukin-7 (IL-7), secreted during this interaction, are critical cytokines for HIV long terminal repeat transactivation through NF-kappaB-dependent activation. TNF is the major inducer of NF-kappaB and particularly of the p50-p65 complex, whereas IL-7 acts as a cofactor by sustaining the expression of the p75 TNF receptor. The requirement for TNF is further confirmed by the observation that the inability of the intermediate CD4(+) CD8(-) CD3(-) thymocytes to replicate the virus is associated with a defect in TNF production during their interaction with TEC and correlates with the absence of nuclear NF-kappaB activity in these freshly isolated thymocytes. Addition of exogenous TNF to the intermediate thymocyte cultures induces NF-kappaB activity and is sufficient to promote HIV replication in the cocultures with TEC. The other major subpopulation expressing the CD4 receptor, namely, the double-positive (DP) CD4(+) CD8(+) CD3(+/-) thymocytes, despite the entry of the virus, do not produce a significant level of virus, presumably because they are unresponsive to TNF and IL-7. Together, these data suggest that in vivo, despite an efficient entry of the virus in all the CD4(+) subpopulations, a high viral load may be generated exclusively within the mature CD4(+) CD8(-) CD3(+) subset of thymocytes. However, under conditions of inflammatory response after infection, TNF might also be present in the intermediate thymocyte compartment, leading to efficient HIV replication in these cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 953, "end": 963}, "arguments": [{"role": "Theme", "text": "p75 TNF receptor", "start": 971, "end": 987}]}, {"trigger": {"text": "production", "start": 1182, "end": 1192}, "arguments": [{"role": "Theme", "text": "TNF", "start": 1178, "end": 1181}]}, {"trigger": {"text": "expressing", "start": 1522, "end": 1532}, "arguments": [{"role": "Theme", "text": "CD4", "start": 1537, "end": 1540}]}, {"trigger": {"text": "present", "start": 2065, "end": 2072}, "arguments": [{"role": "Theme", "text": "TNF", "start": 2047, "end": 2050}]}], "localization": [{"trigger": {"text": "secreted", "start": 682, "end": 690}, "arguments": [{"role": "Theme", "text": "TNF", "start": 651, "end": 654}]}, {"trigger": {"text": "secreted", "start": 682, "end": 690}, "arguments": [{"role": "Theme", "text": "IL-7", "start": 675, "end": 679}]}], "positive regulation": [{"trigger": {"text": "inducer", "start": 841, "end": 848}, "arguments": [{"role": "Cause", "text": "TNF", "start": 824, "end": 827}, {"role": "Theme", "text": "p50", "start": 886, "end": 889}]}, {"trigger": {"text": "inducer", "start": 841, "end": 848}, "arguments": [{"role": "Cause", "text": "TNF", "start": 824, "end": 827}, {"role": "Theme", "text": "p65", "start": 890, "end": 893}]}, {"trigger": {"text": "acts as a cofactor by sustaining", "start": 916, "end": 948}, "arguments": [{"role": "Cause", "text": "IL-7", "start": 911, "end": 915}, {"role": "Theme", "text": "expression", "start": 953, "end": 963}]}]}}, "schema": []}
{"input": "IL-2-independent activation and proliferation in human T cells induced by CD28. \nAlthough the role of CD28 in T cell costimulation is firmly established, the mechanisms by which it exerts its costimulatory actions are less clear. In many circumstances it is difficult to distinguish the effects of CD28 from subsequent actions of cytokines, such as IL-2, on T cell proliferation. Here, we report a model of CD28 costimulation using PMA plus the natural ligand CD80 that resulted in very limited stimulation of IL-2, as evidenced by both cytokine production and IL-2 promoter stimulation. Promoter assays revealed CD28-dependent effects on both NF-kappaB and AP-1, but not on NF-AT or the intact IL-2 promoter. In addition, T cell proliferation was completely resistant to the actions of the immunosuppressant cyclosporin A (CsA). Moreover T cell proliferation was unaffected by the addition of blocking Abs to both IL-2 and the IL-2 receptor, demonstrating that this form of costimulation by CD28 was independent of IL-2. We also investigated the effects of stimulating T cell blasts with CD80 alone and found that there was a limited requirement for IL-2 in this system. We conclude that CD28 costimulation can cause substantial T cell proliferation in the absence of IL-2, which is driven by a soluble factor independent of NF-AT transactivation. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "resulted in very limited", "start": 470, "end": 494}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 495, "end": 506}]}, {"trigger": {"text": "blocking", "start": 894, "end": 902}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 915, "end": 919}]}], "positive regulation": [{"trigger": {"text": "resulted", "start": 470, "end": 478}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 575, "end": 586}]}, {"trigger": {"text": "stimulation", "start": 495, "end": 506}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 510, "end": 514}]}, {"trigger": {"text": "stimulation", "start": 575, "end": 586}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 561, "end": 565}, {"role": "Site", "text": "promoter", "start": 566, "end": 574}]}], "regulation": [{"trigger": {"text": "effects", "start": 628, "end": 635}, "arguments": [{"role": "Cause", "text": "CD28", "start": 613, "end": 617}, {"role": "Theme", "text": "IL-2", "start": 695, "end": 699}, {"role": "Site", "text": "promoter", "start": 700, "end": 708}]}]}}, "schema": []}
{"input": "Suppression of TNFalpha-mediated NFkappaB activity by myricetin and other flavonoids through downregulating the activity of IKK in ECV304 cells. \nFlavonoids are a group of naturally-occurring phenolic compounds in the plant kingdom, and many flavonoids are found with vascular protective properties. Nevertheless how the protective response is exerted by flavonoids is not well characterized. In view of the nuclear factor-kappaB (NFkappaB) may play a central role in the initiation of atherosclerosis, prevention of the activation of NFkappaB represents an important role in protecting vascular injury. In this study, the effects of flavonoids on NFkappaB/inhibitor-kappaB (IkappaB) system in ECV304 cells activated with tumor necrosis factor-alpha (TNFalpha) were examined. We investigated the inhibitory action of six flavonoids on IkappaB kinase (IKK) activity, an enzyme recently found to phosphorylate critical serine residues of IkappaB for degradation. Of six flavonoids tested, myricetin was found to strongly inhibit IKK kinase activity, and prevent the degradation of IkappaBalpha and IkappaBbeta in activated endothelial cells. Furthermore, myricetin was also found to inhibit NFkappaB activity correlated with suppression of monocyte adhesion to ECV304 cells. Therefore we conclude that flavonoids may be of therapeutic value for vascular disease through down regulation of NFkappaB/IkappaB system. Copyright 1999 Wiley-Liss, Inc. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "prevent", "start": 1052, "end": 1059}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1064, "end": 1075}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 1064, "end": 1075}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1079, "end": 1091}]}, {"trigger": {"text": "degradation", "start": 1064, "end": 1075}, "arguments": [{"role": "Theme", "text": "IkappaBbeta", "start": 1096, "end": 1107}]}]}}, "schema": []}
{"input": "Induction of a functional vitamin D receptor in all-trans-retinoic acid-induced monocytic differentiation of M2-type leukemic blast cells. \nDifferent types of acute myeloid leukemia blast cells were induced to differentiate in vitro with all-trans-retinoic acid (ATRA) and vitamin D3 (VD). M0/M1 leukemic cells are not sensitive to differentiating agents, whereas M3 leukemic cells are induced to undergo granulocytic differentiation after ATRA treatment but are not sensitive to VD. M2 leukemic blast cells behave differently because they undergo monocytic differentiation with both the differentiation inducers. To gain some insight into the maturation of M2-type leukemic cells, we studied the molecular mechanisms underlying monocytic differentiation induced by ATRA and VD in spontaneous M2 blast cells as well as in Kasumi-1 cells (an acute myeloid leukemia M2-type cell line). Our results indicate that ATRA as well as VD efficiently increases the nuclear abundance of VD receptor (VDR) and promotes monocytic differentiation. VDR is functionally active in ATRA-treated Kasumi-1 cells because it efficiently heterodimerizes with retinoid X receptor, binds to a DR3-type vitamin D-responsive element, and activates the transcription of a vitamin D-responsive element-regulated reporter gene. Consistent with these findings, VD-responsive genes are induced by ATRA treatment of Kasumi-1 cells, suggesting that the genetic program underlying monocytic differentiation is activated. The molecular mechanism by which ATRA increases the nuclear abundance of a functional VDR is still unknown, but our data clearly indicate that the M2 leukemic cell context is only permissive of monocytic differentiation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "heterodimerizes", "start": 1115, "end": 1130}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1034, "end": 1037}, {"role": "Theme2", "text": "retinoid X receptor", "start": 1136, "end": 1155}]}, {"trigger": {"text": "binds", "start": 1157, "end": 1162}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1034, "end": 1037}]}], "localization": [{"trigger": {"text": "abundance", "start": 963, "end": 972}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 955, "end": 962}, {"role": "Theme", "text": "VDR", "start": 989, "end": 992}]}, {"trigger": {"text": "abundance", "start": 1546, "end": 1555}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 1538, "end": 1545}, {"role": "Theme", "text": "VDR", "start": 1572, "end": 1575}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "vitamin D receptor", "start": 26, "end": 44}]}, {"trigger": {"text": "increases", "start": 941, "end": 950}, "arguments": [{"role": "Theme", "text": "abundance", "start": 963, "end": 972}]}, {"trigger": {"text": "active", "start": 1054, "end": 1060}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1034, "end": 1037}]}, {"trigger": {"text": "increases", "start": 1524, "end": 1533}, "arguments": [{"role": "Theme", "text": "abundance", "start": 1546, "end": 1555}]}]}}, "schema": []}
{"input": "Signal transduction pathways triggered by the FcepsilonRIIb receptor (CD23) in human monocytes lead to nuclear factor-kappaB activation. \nBACKGROUND: Alveolar macrophages play a key role in the initiation of the inflammatory reaction of allergic asthma. Alveolar macrophages and peripheral blood monocytes are activated when IgE/allergen immune complexes bind to the CD23 receptor, which leads to the production of inflammatory cytokines. OBJECTIVE: We sought to investigate the molecular mechanisms regulating this early inflammatory response. We have focused on the study of the signal transduction pathways triggered by CD23 in human monocytes and the promonocytic cell line U937. METHODS: CD23 was cross-linked in human monocytes and U937 cells with IgE immune complexes. Surface expression of CD23 was determined by FACS analysis. Transcription factor activation and gene transcription were studied by gel-shift assays and Northern blot analysis, respectively. IkappaBalpha phosphorylation and degradation was analyzed by Western blot. RESULTS: Nuclear factor (NF)-kappaB is the main transcription factor involved in the gene activation that follows CD23 cross-linking in monocytes. CD23-induced NF-kappaB is a heterodimer composed of p65/p50 subunits. NF-kappaB nuclear translocation is secondary to the phosphorylation and subsequent degradation of the NF-kappaB inhibitory molecule IkappaBalpha. Tyrosine kinase-dependent, and not protein kinase C-dependent, pathways mediate CD23-triggered NF-kappaB activation but do not participate in the direct phosphorylation of IkappaBalpha. IkappaBalpha degradation and NF-kappaB nuclear translocation correlate with transcriptional activation of the inflammatory cytokines TNF-alpha and IL-1beta. CONCLUSIONS: NF-kappaB is the main transcription factor involved in the signal transduction pathway of CD23 in monocytes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 355, "end": 359}, "arguments": [{"role": "Theme", "text": "CD23 receptor", "start": 367, "end": 380}]}, {"trigger": {"text": "cross-linked", "start": 702, "end": 714}, "arguments": [{"role": "Theme", "text": "CD23", "start": 693, "end": 697}]}, {"trigger": {"text": "cross-linking", "start": 1160, "end": 1173}, "arguments": [{"role": "Theme", "text": "CD23", "start": 1155, "end": 1159}]}], "gene expression": [{"trigger": {"text": "expression", "start": 784, "end": 794}, "arguments": [{"role": "Theme", "text": "CD23", "start": 798, "end": 802}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 979, "end": 994}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 966, "end": 978}]}, {"trigger": {"text": "phosphorylation", "start": 1310, "end": 1325}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1390, "end": 1402}]}, {"trigger": {"text": "phosphorylation", "start": 1557, "end": 1572}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1576, "end": 1588}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1193, "end": 1200}, "arguments": [{"role": "Cause", "text": "CD23", "start": 1188, "end": 1192}, {"role": "Theme", "text": "p65", "start": 1240, "end": 1243}]}, {"trigger": {"text": "induced", "start": 1193, "end": 1200}, "arguments": [{"role": "Cause", "text": "CD23", "start": 1188, "end": 1192}, {"role": "Theme", "text": "p50", "start": 1244, "end": 1247}]}, {"trigger": {"text": "transcriptional activation", "start": 1666, "end": 1692}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1723, "end": 1732}]}, {"trigger": {"text": "transcriptional activation", "start": 1666, "end": 1692}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1737, "end": 1745}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 999, "end": 1010}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 966, "end": 978}]}, {"trigger": {"text": "degradation", "start": 1341, "end": 1352}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1390, "end": 1402}]}, {"trigger": {"text": "degradation", "start": 1603, "end": 1614}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1590, "end": 1602}]}], "regulation": [{"trigger": {"text": "participate", "start": 1531, "end": 1542}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1557, "end": 1572}]}]}}, "schema": []}
{"input": "Dopamine stimulates expression of the human immunodeficiency virus type 1 via NF-kappaB in cells of the immune system. \nRecent studies have reported that lymphocytes produce, transport and bind dopamine present in plasma. However, the action of dopamine on HIV-1 gene expression in cells of the immune system has not yet been examined. Here, we have investigated the regulation of HIV-1 expression by dopamine in Jurkat T cells and in primary blood mononuclear cells (PBMC). HIV-1 replication was increased by dopamine, which correlated with the increased levels of HIV-1 transactivation. Our transient expression data revealed that dopamine stimulated transcription through the NF-kappaB element present in the long terminal repeat. The importance of NF-kappaB sites was confirmed by using vectors containing wild-type or mutant kappaB sites in a heterologous promoter. Consistent with the role of NF-kappaB in mediating dopamine responsiveness, the proteasome inhibitor MG132 abolished dopamine-induced transcriptional activation. We further explored the effect of dopamine in the presence of phorbol esters or tumor necrosis factor-alpha (TNF-alpha) known to activate NF-kappaB. The combination of dopamine and TNF-alpha led to a stimulation of HIV-1 transcription and replication. However, in contrast with TNF-alpha, dopamine treatment did not affect NF-kappaB DNA binding activity nor the concentrations of p50, p65 and IkappaB-alpha proteins, which suggests a distinct NF-kappaB activation mechanism. These results reveal a new link between the dopamine system, cytokine signaling pathway and regulation of gene expression via the involvement of NF-kappaB in T cells and PBMC. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "affect", "start": 1349, "end": 1355}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1311, "end": 1320}, {"role": "Theme", "text": "concentrations", "start": 1395, "end": 1409}]}, {"trigger": {"text": "affect", "start": 1349, "end": 1355}, "arguments": [{"role": "Theme", "text": "concentrations", "start": 1395, "end": 1409}]}, {"trigger": {"text": "concentrations", "start": 1395, "end": 1409}, "arguments": [{"role": "Theme", "text": "p50", "start": 1413, "end": 1416}]}, {"trigger": {"text": "concentrations", "start": 1395, "end": 1409}, "arguments": [{"role": "Theme", "text": "p65", "start": 1418, "end": 1421}]}, {"trigger": {"text": "concentrations", "start": 1395, "end": 1409}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1426, "end": 1439}]}]}}, "schema": []}
{"input": "AML1 (CBFalpha2) cooperates with B cell-specific activating protein (BSAP/PAX5) in activation of the B cell-specific BLK gene promoter. \nAML1 plays a critical role during hematopoiesis and chromosomal translocations involving AML1 are commonly associated with different forms of leukemia, including pre-B acute lymphoblastic leukemia. To understand the function of AML1 during B cell differentiation, we analyzed regulatory regions of B cell-specific genes for potential AML1-binding sites and have identified a putative AML1-binding site in the promoter of the B cell-specific tyrosine kinase gene, blk. Gel mobility shift assays and transient transfection assays demonstrate that AML1 binds specifically to this site in the blk promoter and this binding site is important for blk promoter activity. Furthermore, in vitro binding analysis revealed that the AML1 runt DNA-binding domain physically interacts with the paired DNA-binding domain of BSAP, a B cell-specific transcription factor. BSAP has been shown previously to be important for B cell-specific regulation of the blk gene. Physical interaction of AML1 with BSAP correlates with functional cooperativity in transfection studies where AML1 and BSAP synergistically activate blk promoter transcription by more than 50-fold. These results demonstrate physical and functional interactions between AML1 and BSAP and suggest that AML1 is an important factor for regulating a critical B cell-specific gene, blk. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding sites", "start": 476, "end": 489}, "arguments": [{"role": "Theme", "text": "AML1", "start": 471, "end": 475}]}, {"trigger": {"text": "binds", "start": 687, "end": 692}, "arguments": [{"role": "Theme", "text": "AML1", "start": 682, "end": 686}, {"role": "Theme2", "text": "blk", "start": 726, "end": 729}, {"role": "Site2", "text": "promoter", "start": 730, "end": 738}]}, {"trigger": {"text": "physically interacts", "start": 887, "end": 907}, "arguments": [{"role": "Site", "text": "paired DNA-binding domain", "start": 917, "end": 942}, {"role": "Theme", "text": "BSAP", "start": 946, "end": 950}]}, {"trigger": {"text": "Physical interaction", "start": 1087, "end": 1107}, "arguments": [{"role": "Theme", "text": "AML1", "start": 1111, "end": 1115}, {"role": "Theme2", "text": "BSAP", "start": 1121, "end": 1125}]}, {"trigger": {"text": "interactions", "start": 1335, "end": 1347}, "arguments": [{"role": "Theme", "text": "AML1", "start": 1356, "end": 1360}, {"role": "Theme2", "text": "BSAP", "start": 1365, "end": 1369}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 83, "end": 93}, "arguments": [{"role": "Cause", "text": "AML1", "start": 0, "end": 4}, {"role": "Theme", "text": "BLK", "start": 117, "end": 120}, {"role": "Site", "text": "promoter", "start": 126, "end": 134}]}, {"trigger": {"text": "activation", "start": 83, "end": 93}, "arguments": [{"role": "Cause", "text": "BSAP", "start": 69, "end": 73}, {"role": "Theme", "text": "BLK", "start": 117, "end": 120}, {"role": "Site", "text": "promoter", "start": 126, "end": 134}]}, {"trigger": {"text": "important", "start": 764, "end": 773}, "arguments": [{"role": "Theme", "text": "blk", "start": 778, "end": 781}, {"role": "Site", "text": "promoter", "start": 782, "end": 790}]}, {"trigger": {"text": "important", "start": 1029, "end": 1038}, "arguments": [{"role": "Cause", "text": "BSAP", "start": 992, "end": 996}, {"role": "Theme", "text": "regulation", "start": 1059, "end": 1069}]}, {"trigger": {"text": "activate", "start": 1227, "end": 1235}, "arguments": [{"role": "Cause", "text": "AML1", "start": 1197, "end": 1201}, {"role": "Theme", "text": "transcription", "start": 1249, "end": 1262}]}, {"trigger": {"text": "activate", "start": 1227, "end": 1235}, "arguments": [{"role": "Cause", "text": "BSAP", "start": 1206, "end": 1210}, {"role": "Theme", "text": "transcription", "start": 1249, "end": 1262}]}, {"trigger": {"text": "important factor", "start": 1398, "end": 1414}, "arguments": [{"role": "Cause", "text": "AML1", "start": 1387, "end": 1391}, {"role": "Theme", "text": "regulating", "start": 1419, "end": 1429}]}], "regulation": [{"trigger": {"text": "regulation", "start": 1059, "end": 1069}, "arguments": [{"role": "Theme", "text": "blk", "start": 1077, "end": 1080}]}, {"trigger": {"text": "regulating", "start": 1419, "end": 1429}, "arguments": [{"role": "Theme", "text": "blk", "start": 1463, "end": 1466}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1249, "end": 1262}, "arguments": [{"role": "Theme", "text": "blk", "start": 1236, "end": 1239}]}]}}, "schema": []}
{"input": "c-Maf induces monocytic differentiation and apoptosis in bipotent myeloid progenitors. \nThe transcriptional mechanisms that drive colony-forming unit granulocyte-macrophage (CFU-GM) myeloid progenitors to differentiate into cells of either the granulocytic or monocytic lineage are not fully understood. We have shown that the c-Maf and c-Myb transcription factors physically interact in myeloid cells to form inhibitory complexes that hinder transactivation of c-Myb target genes through direct binding to Myb consensus sites. These complexes arise in a developmentally regulated pattern, peaking at the promyelocyte stage, or in cell model systems, appearing soon after the induction of monocytic differentiation. We wished to determine if this developmentally related interaction is a consequence of myeloid differentiation or an intrinsic differentiating stimulus. Because the elevated Myb:Maf status seen in differentiating cells can be recapitulated by overexpression of c-Maf in myeloid cell lines, we inducibly expressed the c-Maf cDNA in 2 bipotent human myeloid progenitor cells. Elevated levels of c-Maf protein led to marked increases in Myb:Maf complexes and the accumulation of monocyte/macrophage cells, followed by eventual programmed cell death. Analysis of targets that could mediate these phenotypic changes indicated that c-Maf likely plays a key role in myeloid cell development through dual mechanisms; inhibition of a select set of c-Myb regulated targets, such as Bcl-2 and CD13/APN, coupled with the activation of as yet undefined differentiation-promoting genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "physically interact", "start": 365, "end": 384}, "arguments": [{"role": "Theme", "text": "c-Maf", "start": 327, "end": 332}, {"role": "Theme2", "text": "c-Myb", "start": 337, "end": 342}]}], "gene expression": [{"trigger": {"text": "overexpression", "start": 959, "end": 973}, "arguments": [{"role": "Theme", "text": "c-Maf", "start": 977, "end": 982}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 1425, "end": 1435}, "arguments": [{"role": "Cause", "text": "c-Maf", "start": 1342, "end": 1347}, {"role": "Theme", "text": "Bcl-2", "start": 1488, "end": 1493}]}, {"trigger": {"text": "inhibition", "start": 1425, "end": 1435}, "arguments": [{"role": "Cause", "text": "c-Maf", "start": 1342, "end": 1347}, {"role": "Theme", "text": "CD13", "start": 1498, "end": 1502}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 959, "end": 973}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 959, "end": 973}]}, {"trigger": {"text": "Elevated levels", "start": 1090, "end": 1105}, "arguments": [{"role": "Theme", "text": "c-Maf", "start": 1109, "end": 1114}]}], "regulation": [{"trigger": {"text": "regulated", "start": 1461, "end": 1470}, "arguments": [{"role": "Cause", "text": "c-Myb", "start": 1455, "end": 1460}, {"role": "Theme", "text": "Bcl-2", "start": 1488, "end": 1493}]}, {"trigger": {"text": "regulated", "start": 1461, "end": 1470}, "arguments": [{"role": "Cause", "text": "c-Myb", "start": 1455, "end": 1460}, {"role": "Theme", "text": "CD13", "start": 1498, "end": 1502}]}]}}, "schema": []}
{"input": "Nuclear factor-kappaB-dependent induction of interleukin-8 gene expression by tumor necrosis factor alpha: evidence for an antioxidant sensitive activating pathway distinct from nuclear translocation. \nTumor necrosis factor alpha (TNFalpha) is a pluripotent activator of inflammation by inducing a proinflammatory cytokine cascade. This phenomenon is mediated, in part, through inducible expression of the CXC chemokine, interleukin-8 (IL-8). In this study, we investigate the role of TNFalpha-inducible reactive oxygen species (ROS) in IL-8 expression by \"monocyte-like\" U937 histiocytic lymphoma cells. TNFalpha is a rapid activator of IL-8 gene expression by U937, producing a 50-fold induction of mRNA within 1 hour of treatment. In gene transfection assays, the effect of TNFalpha requires the presence of an inducible nuclear factor-kappaB (NF-kappaB) (Rel A) binding site in the IL-8 promoter. TNFalpha treatment induces a rapid translocation of the 65 kD transcriptional activator NF-kappaB subunit, Rel A, whose binding in the nucleus occurs before changes in intracellular ROS. Pretreatment (or up to 15 minutes posttreatment) relative to TNFalpha with the antioxidant dimethyl sulfoxide (DMSO) (2% [vol/vol]) blocks 80% of NF-kappaB-dependent transcription. Surprisingly, however, DMSO has no effect on inducible Rel A binding. Similar selective effects on NF-kappaB transcription are seen with the unrelated antioxidants, N-acetylcysteine (NAC) and vitamin C. These data indicate that TNFalpha induces a delayed ROS-dependent signalling pathway that is required for NF-kappaB transcriptional activation and is separable from that required for its nuclear translocation. Further definition of this pathway will yield new insights into inflammation initiated by TNFalpha signalling. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1021, "end": 1028}, "arguments": [{"role": "Theme", "text": "Rel A", "start": 1008, "end": 1013}]}, {"trigger": {"text": "binding", "start": 1330, "end": 1337}, "arguments": [{"role": "Theme", "text": "Rel A", "start": 1324, "end": 1329}]}], "gene expression": [{"trigger": {"text": "gene expression", "start": 59, "end": 74}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 45, "end": 58}]}, {"trigger": {"text": "expression", "start": 388, "end": 398}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 436, "end": 440}]}, {"trigger": {"text": "expression", "start": 542, "end": 552}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 537, "end": 541}]}, {"trigger": {"text": "gene expression", "start": 643, "end": 658}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 638, "end": 642}]}], "localization": [{"trigger": {"text": "translocation", "start": 186, "end": 199}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 45, "end": 58}, {"role": "ToLoc", "text": "nuclear", "start": 178, "end": 185}]}, {"trigger": {"text": "translocation", "start": 936, "end": 949}, "arguments": [{"role": "Theme", "text": "Rel A", "start": 1008, "end": 1013}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 32, "end": 41}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 59, "end": 74}, {"role": "Cause", "text": "tumor necrosis factor alpha", "start": 78, "end": 105}]}, {"trigger": {"text": "activating pathway", "start": 145, "end": 163}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 45, "end": 58}]}, {"trigger": {"text": "inducible", "start": 378, "end": 387}, "arguments": [{"role": "Theme", "text": "expression", "start": 388, "end": 398}]}, {"trigger": {"text": "activator", "start": 625, "end": 634}, "arguments": [{"role": "Cause", "text": "TNFalpha", "start": 605, "end": 613}, {"role": "Theme", "text": "gene expression", "start": 643, "end": 658}]}, {"trigger": {"text": "producing", "start": 668, "end": 677}, "arguments": [{"role": "Cause", "text": "TNFalpha", "start": 605, "end": 613}, {"role": "Theme", "text": "induction", "start": 688, "end": 697}]}, {"trigger": {"text": "induces", "start": 920, "end": 927}, "arguments": [{"role": "Cause", "text": "TNFalpha", "start": 901, "end": 909}, {"role": "Theme", "text": "translocation", "start": 936, "end": 949}]}], "regulation": [{"trigger": {"text": "dependent", "start": 22, "end": 31}, "arguments": [{"role": "Theme", "text": "induction", "start": 32, "end": 41}]}, {"trigger": {"text": "sensitive", "start": 135, "end": 144}, "arguments": [{"role": "Theme", "text": "activating pathway", "start": 145, "end": 163}]}, {"trigger": {"text": "role", "start": 477, "end": 481}, "arguments": [{"role": "Theme", "text": "expression", "start": 542, "end": 552}]}, {"trigger": {"text": "effect", "start": 1304, "end": 1310}, "arguments": [{"role": "Theme", "text": "binding", "start": 1330, "end": 1337}]}], "transcription": [{"trigger": {"text": "induction", "start": 688, "end": 697}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 638, "end": 642}]}]}}, "schema": []}
{"input": "Neutrophil maturation and the role of retinoic acid. \nNeutrophil maturation occurs in well defined morphological stages that correlate with the acquisition of molecular markers associated with neutrophil function. A variety of factors are known to play a role in terminal neutrophil maturation, including the vitamin A derivative, retinoic acid. Retinoic acid can directly modulate gene expression via binding to its nuclear receptors, which can, in turn, activate transcription of target genes. A role for retinoic acid during neutrophil maturation has been suggested from a variety of sources. Here we present a review of the mechanism of retinoic acid receptor action and the major evidence showing that normal retinoid signaling is required for neutrophil maturation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Induction of Bcl-x(L) expression by human T-cell leukemia virus type 1 Tax through NF-kappaB in apoptosis-resistant T-cell transfectants with Tax. \nHuman T-cell leukemia virus type 1 (HTLV-1) Tax is thought to play a pivotal role in immortalization of T cells. We have recently shown that the expression of Tax protected the mouse T-cell line CTLL-2 against apoptosis induced by interleukin-2 (IL-2) deprivation and converted its growth from being IL-2 dependent to being IL-2 independent. In this study, we demonstrate that constitutive expression of bcl-xl but not bcl-2, bcl-xs, bak, bad, or bax was associated with apoptosis resistance after IL-2 deprivation in CTLL-2 cells that expressed Tax. Transient-transfection assays showed that bcl-x promoter was transactivated by wild-type Tax. Similar effects were observed in mutant Tax retaining transactivating ability through NF-kappaB. Deletion or substitution of a putative NF-kappaB binding site identified in the bcl-x promoter significantly decreased Tax-induced transactivation. This NF-kappaB-like element was able to form a complex with NF-kappaB family proteins in vitro. Furthermore, Tax-induced transactivation of the bcl-x promoter was also diminished by the mutant IkappaBalpha, which specifically inhibits NF-kappaB activity. Our findings suggest that constitutive expression of Bcl-x(L) induced by Tax through the NF-kappaB pathway contributes to the inhibition of apoptosis in CTLL-2 cells after IL-2 deprivation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 22, "end": 32}, "arguments": [{"role": "Theme", "text": "Bcl-x(L)", "start": 13, "end": 21}]}, {"trigger": {"text": "transfectants", "start": 123, "end": 136}, "arguments": [{"role": "Theme", "text": "Tax", "start": 142, "end": 145}]}, {"trigger": {"text": "expression", "start": 293, "end": 303}, "arguments": [{"role": "Theme", "text": "Tax", "start": 307, "end": 310}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "bcl-xl", "start": 552, "end": 558}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 567, "end": 572}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "bcl-xs", "start": 574, "end": 580}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "bak", "start": 582, "end": 585}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "bad", "start": 587, "end": 590}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "bax", "start": 595, "end": 598}]}, {"trigger": {"text": "expressed", "start": 684, "end": 693}, "arguments": [{"role": "Theme", "text": "Tax", "start": 694, "end": 697}]}, {"trigger": {"text": "expression", "start": 1332, "end": 1342}, "arguments": [{"role": "Theme", "text": "Bcl-x(L)", "start": 1346, "end": 1354}]}], "negative regulation": [{"trigger": {"text": "deprivation", "start": 400, "end": 411}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 394, "end": 398}]}, {"trigger": {"text": "deprivation", "start": 651, "end": 662}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 646, "end": 650}]}, {"trigger": {"text": "diminished", "start": 1206, "end": 1216}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 1159, "end": 1174}, {"role": "Cause", "text": "IkappaBalpha", "start": 1231, "end": 1243}]}, {"trigger": {"text": "deprivation", "start": 1470, "end": 1481}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1465, "end": 1469}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "expression", "start": 22, "end": 32}]}, {"trigger": {"text": "by", "start": 33, "end": 35}, "arguments": [{"role": "Theme", "text": "Induction", "start": 0, "end": 9}, {"role": "Cause", "text": "Tax", "start": 71, "end": 74}]}, {"trigger": {"text": "transactivated", "start": 760, "end": 774}, "arguments": [{"role": "Theme", "text": "bcl-x", "start": 741, "end": 746}, {"role": "Site", "text": "promoter", "start": 747, "end": 755}, {"role": "Cause", "text": "Tax", "start": 788, "end": 791}]}, {"trigger": {"text": "effects", "start": 801, "end": 808}, "arguments": [{"role": "Theme", "text": "bcl-x", "start": 741, "end": 746}, {"role": "Site", "text": "promoter", "start": 747, "end": 755}]}, {"trigger": {"text": "transactivation", "start": 1159, "end": 1174}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1147, "end": 1150}, {"role": "Theme", "text": "bcl-x", "start": 1182, "end": 1187}, {"role": "Site", "text": "promoter", "start": 1188, "end": 1196}]}, {"trigger": {"text": "induced", "start": 1355, "end": 1362}, "arguments": [{"role": "Theme", "text": "expression", "start": 1332, "end": 1342}]}, {"trigger": {"text": "by", "start": 1363, "end": 1365}, "arguments": [{"role": "Theme", "text": "induced", "start": 1355, "end": 1362}, {"role": "Cause", "text": "Tax", "start": 1366, "end": 1369}]}]}}, "schema": []}
{"input": "Interferons inhibit activation of STAT6 by interleukin 4 in human monocytes by inducing SOCS-1 gene expression. \nInterferons (IFNs) inhibit induction by IL-4 of multiple genes in human monocytes. However, the mechanism by which IFNs mediate this inhibition has not been defined. IL-4 activates gene expression by inducing tyrosine phosphorylation, homodimerization, and nuclear translocation of the latent transcription factor, STAT6 (signal transducer and activator of transcription-6). STAT6-responsive elements are characteristically present in the promoters of IL-4-inducible genes. Because STAT6 activation is essential for IL-4-induced gene expression, we examined the ability of type I and type II IFNs to regulate activation of STAT6 by IL-4 in primary human monocytes. Pretreatment of monocytes with IFN-beta or IFN-gamma, but not IL-1, IL-2, macrophage colony-stimulating factor, granulocyte/macrophage colony-stimulating factor, IL-6, or transforming growth factor beta suppressed activation of STAT6 by IL-4. This inhibition was associated with decreased tyrosine phosphorylation and nuclear translocation of STAT6 and was not evident unless the cells were preincubated with IFN for at least 1 hr before IL-4 stimulation. Furthermore, inhibition by IFN could be blocked by cotreatment with actinomycin D and correlated temporally with induction of the JAK/STAT inhibitory gene, SOCS-1. Forced expression of SOCS-1 in a macrophage cell line, RAW264, markedly suppressed trans-activation of an IL-4-inducible reporter as well as IL-6- and IFN-gamma-induced reporter gene activity. These findings demonstrate that IFNs inhibit IL-4-induced activation of STAT6 and STAT6-dependent gene expression, at least in part, by inducing expression of SOCS-1. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "homodimerization", "start": 348, "end": 364}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 428, "end": 433}]}], "gene expression": [{"trigger": {"text": "expression", "start": 100, "end": 110}, "arguments": [{"role": "Theme", "text": "SOCS-1", "start": 88, "end": 94}]}, {"trigger": {"text": "expression", "start": 1405, "end": 1415}, "arguments": [{"role": "Theme", "text": "SOCS-1", "start": 1419, "end": 1425}]}, {"trigger": {"text": "expression", "start": 1736, "end": 1746}, "arguments": [{"role": "Theme", "text": "SOCS-1", "start": 1750, "end": 1756}]}], "localization": [{"trigger": {"text": "translocation", "start": 378, "end": 391}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 370, "end": 377}, {"role": "Theme", "text": "STAT6", "start": 428, "end": 433}]}, {"trigger": {"text": "translocation", "start": 1104, "end": 1117}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1096, "end": 1103}, {"role": "Theme", "text": "STAT6", "start": 1121, "end": 1126}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 12, "end": 19}, "arguments": [{"role": "Theme", "text": "activation", "start": 20, "end": 30}, {"role": "Cause", "text": "inducing", "start": 79, "end": 87}]}, {"trigger": {"text": "suppressed", "start": 981, "end": 991}, "arguments": [{"role": "Cause", "text": "IFN-beta", "start": 809, "end": 817}, {"role": "Theme", "text": "activation", "start": 992, "end": 1002}]}, {"trigger": {"text": "suppressed", "start": 981, "end": 991}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 821, "end": 830}, {"role": "Theme", "text": "activation", "start": 992, "end": 1002}]}, {"trigger": {"text": "suppressed", "start": 981, "end": 991}, "arguments": [{"role": "Cause", "text": "IL-1", "start": 840, "end": 844}, {"role": "Theme", "text": "activation", "start": 992, "end": 1002}]}, {"trigger": {"text": "suppressed", "start": 981, "end": 991}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 846, "end": 850}, {"role": "Theme", "text": "activation", "start": 992, "end": 1002}]}, {"trigger": {"text": "suppressed", "start": 981, "end": 991}, "arguments": [{"role": "Cause", "text": "IL-6", "start": 940, "end": 944}, {"role": "Theme", "text": "activation", "start": 992, "end": 1002}]}, {"trigger": {"text": "suppressed", "start": 981, "end": 991}, "arguments": [{"role": "Cause", "text": "transforming growth factor beta", "start": 949, "end": 980}, {"role": "Theme", "text": "activation", "start": 992, "end": 1002}]}, {"trigger": {"text": "decreased", "start": 1057, "end": 1066}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1076, "end": 1091}]}, {"trigger": {"text": "decreased", "start": 1057, "end": 1066}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1104, "end": 1117}]}, {"trigger": {"text": "inhibit", "start": 1628, "end": 1635}, "arguments": [{"role": "Theme", "text": "activation", "start": 1649, "end": 1659}, {"role": "Cause", "text": "inducing", "start": 1727, "end": 1735}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 331, "end": 346}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 322, "end": 330}, {"role": "Theme", "text": "STAT6", "start": 428, "end": 433}]}, {"trigger": {"text": "phosphorylation", "start": 1076, "end": 1091}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1067, "end": 1075}, {"role": "Theme", "text": "STAT6", "start": 1121, "end": 1126}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 20, "end": 30}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 34, "end": 39}, {"role": "Cause", "text": "interleukin 4", "start": 43, "end": 56}]}, {"trigger": {"text": "inducing", "start": 79, "end": 87}, "arguments": [{"role": "Theme", "text": "expression", "start": 100, "end": 110}]}, {"trigger": {"text": "inducing", "start": 313, "end": 321}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 279, "end": 283}, {"role": "Theme", "text": "phosphorylation", "start": 331, "end": 346}]}, {"trigger": {"text": "inducing", "start": 313, "end": 321}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 279, "end": 283}, {"role": "Theme", "text": "homodimerization", "start": 348, "end": 364}]}, {"trigger": {"text": "inducing", "start": 313, "end": 321}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 279, "end": 283}, {"role": "Theme", "text": "translocation", "start": 378, "end": 391}]}, {"trigger": {"text": "activation", "start": 601, "end": 611}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 595, "end": 600}]}, {"trigger": {"text": "activation", "start": 722, "end": 732}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 736, "end": 741}, {"role": "Cause", "text": "IL-4", "start": 745, "end": 749}]}, {"trigger": {"text": "activation", "start": 992, "end": 1002}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1006, "end": 1011}, {"role": "Cause", "text": "IL-4", "start": 1015, "end": 1019}]}, {"trigger": {"text": "induction", "start": 1347, "end": 1356}, "arguments": [{"role": "Theme", "text": "SOCS-1", "start": 1390, "end": 1396}]}, {"trigger": {"text": "activation", "start": 1649, "end": 1659}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1636, "end": 1640}, {"role": "Theme", "text": "STAT6", "start": 1663, "end": 1668}]}, {"trigger": {"text": "inducing", "start": 1727, "end": 1735}, "arguments": [{"role": "Theme", "text": "expression", "start": 1736, "end": 1746}]}], "regulation": [{"trigger": {"text": "regulate", "start": 713, "end": 721}, "arguments": [{"role": "Theme", "text": "activation", "start": 722, "end": 732}]}]}}, "schema": []}
{"input": "Increased IkappaB expression and diminished nuclear NF-kappaB in human mononuclear cells following hydrocortisone injection. \nWe have recently demonstrated that hydrocortisone and other glucocorticoids inhibit reactive oxygen species (ROS) generation by mononuclear (MNC) and polymorphonuclear leucocytes (PMNL). Since NF-kappaB/IkappaB system regulates the transcription of proinflammatory genes, including those responsible for ROS generation, we tested the hypothesis that hydrocortisone may stimulate IkappaB production thus inhibiting NF-kappaB translocation from the cytosol into the nucleus in MNC, in vivo. One hundred milligram of hydrocortisone was injected intravenously into 4 normal subjects. Blood samples were obtained prior to the injection and at 1, 2, 4, 8 and 24 hr after the injection. Nuclear extracts and total cell lysates were prepared from MNC by standard techniques. IkappaB levels in MNC homogenates increased at 1 hr, peaked at 2-4 hr, started to decrease at 8 hr, and returned to baseline levels at 24 hr. NF-kappaB in MNC nuclear extracts decreased at 1 hr, reached a nadir at 4 hr, gradually increased at 8 hr and returned back to baseline levels at 24 hr. The total protein content of NF-kappaB subunit (P65) in MNC lysates also showed a decrease following hydrocortisone injection. This decrease was observed at 2 hr, reached a nadir at 4 hr, and returned to baseline levels at 24 hr. ROS generation inhibition paralleled NF-kappaB levels in the nucleus. It was inhibited at 1 hr, reached a nadir at 2-4 hr, started to increase at 8 hr, and returned to basal levels at 24 hr. Our data demonstrate that hydrocortisone induces IkappaB and suppresses NF-kappaB expression in MNC in parallel. IkappaB further reduces the translocation of NF-kappaB into the nucleus thus preventing the expression of proinflammatory genes. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "decrease", "start": 1270, "end": 1278}, "arguments": [{"role": "Theme", "text": "P65", "start": 1236, "end": 1239}]}, {"trigger": {"text": "returned to baseline levels", "start": 1380, "end": 1407}, "arguments": [{"role": "Theme", "text": "decrease", "start": 1270, "end": 1278}]}]}}, "schema": []}
{"input": "Renal cell carcinoma-derived gangliosides suppress nuclear factor-kappaB activation in T cells. \nActivation of the transcription factor nuclear factor-kappaB (NFkappaB) is impaired in T cells from patients with renal cell carcinomas (RCCs). In circulating T cells from a subset of patients with RCCs, the suppression of NFkappaB binding activity is downstream from the stimulus-induced degradation of the cytoplasmic factor IkappaBalpha. Tumor-derived soluble products from cultured RCC explants inhibit NFkappaB activity in T cells from healthy volunteers, despite a normal level of stimulus-induced IkappaBalpha degradation in these cells. The inhibitory agent has several features characteristic of a ganglioside, including sensitivity to neuraminidase but not protease treatment; hydrophobicity; and molecular weight less than 3 kDa. Indeed, we detected gangliosides in supernatants from RCC explants and not from adjacent normal kidney tissue. Gangliosides prepared from RCC supernatants, as well as the purified bovine gangliosides G(m1) and G(d1a), suppressed NFkappaB binding activity in T cells and reduced expression of the cytokines IL-2 and IFN-gamma. Taken together, our findings suggest that tumor-derived gangliosides may blunt antitumor immune responses in patients with RCCs. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1116, "end": 1126}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1144, "end": 1148}]}, {"trigger": {"text": "expression", "start": 1116, "end": 1126}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1153, "end": 1162}]}], "negative regulation": [{"trigger": {"text": "normal level", "start": 568, "end": 580}, "arguments": [{"role": "Theme", "text": "degradation", "start": 614, "end": 625}]}, {"trigger": {"text": "reduced", "start": 1108, "end": 1115}, "arguments": [{"role": "Theme", "text": "expression", "start": 1116, "end": 1126}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 378, "end": 385}, "arguments": [{"role": "Theme", "text": "degradation", "start": 386, "end": 397}]}, {"trigger": {"text": "induced", "start": 593, "end": 600}, "arguments": [{"role": "Theme", "text": "degradation", "start": 614, "end": 625}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 386, "end": 397}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 424, "end": 436}]}, {"trigger": {"text": "degradation", "start": 614, "end": 625}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 601, "end": 613}]}]}}, "schema": []}
{"input": "Affinity-driven peptide selection of an NFAT inhibitor more selective than cyclosporin A [see comments] \nThe flow of information from calcium-mobilizing receptors to nuclear factor of activated T cells (NFAT)-dependent genes is critically dependent on interaction between the phosphatase calcineurin and the transcription factor NFAT. A high-affinity calcineurin-binding peptide was selected from combinatorial peptide libraries based on the calcineurin docking motif of NFAT. This peptide potently inhibited NFAT activation and NFAT-dependent expression of endogenous cytokine genes in T cells, without affecting the expression of other cytokines that require calcineurin but not NFAT. Substitution of the optimized peptide sequence into the natural calcineurin docking site increased the calcineurin responsiveness of NFAT. Compounds that interfere selectively with the calcineurin-NFAT interaction without affecting calcineurin phosphatase activity may be useful as therapeutic agents that are less toxic than current drugs. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Leukotriene B4 stimulates c-fos and c-jun gene transcription and AP-1 binding activity in human monocytes. \nWe have examined the effect of leukotriene B4 (LTB4), a potent lipid proinflammatory mediator, on the expression of the proto-oncogenes c-jun and c-fos. In addition, we looked at the modulation of nuclear factors binding specifically to the AP-1 element after LTB4 stimulation. LTB4 increased the expression of the c-fos gene in a time- and concentration-dependent manner. The c-jun mRNA, which is constitutively expressed in human peripheral-blood monocytes at relatively high levels, was also slightly augmented by LTB4, although to a much lower extent than c-fos. The kinetics of expression of the two genes were also slightly different, with c-fos mRNA reaching a peak at 15 min after stimulation and c-jun at 30 min. Both messages rapidly declined thereafter. Stability of the c-fos and c-jun mRNA was not affected by LTB4, as assessed after actinomycin D treatment. Nuclear transcription studies in vitro showed that LTB4 increased the transcription of the c-fos gene 7-fold and the c-jun gene 1.4-fold. Resting monocytes contained nuclear factors binding to the AP-1 element, but stimulation of monocytes with LTB4 induced greater AP-1-binding activity of nuclear proteins. These results indicate that LTB4 may regulate the production of different cytokines by modulating the yield and/or the function of transcription factors such as AP-1-binding proto-oncogene products. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 210, "end": 220}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 244, "end": 249}]}, {"trigger": {"text": "expression", "start": 210, "end": 220}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 254, "end": 259}]}, {"trigger": {"text": "expression", "start": 405, "end": 415}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 423, "end": 428}]}, {"trigger": {"text": "expression", "start": 691, "end": 701}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 754, "end": 759}]}, {"trigger": {"text": "expression", "start": 691, "end": 701}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 813, "end": 818}]}], "negative regulation": [{"trigger": {"text": "declined", "start": 852, "end": 860}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 754, "end": 759}]}, {"trigger": {"text": "declined", "start": 852, "end": 860}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 813, "end": 818}]}], "positive regulation": [{"trigger": {"text": "stimulates", "start": 15, "end": 25}, "arguments": [{"role": "Theme", "text": "transcription", "start": 47, "end": 60}]}, {"trigger": {"text": "increased", "start": 391, "end": 400}, "arguments": [{"role": "Theme", "text": "expression", "start": 405, "end": 415}]}, {"trigger": {"text": "high levels", "start": 581, "end": 592}, "arguments": [{"role": "Theme", "text": "expressed", "start": 521, "end": 530}]}, {"trigger": {"text": "augmented", "start": 612, "end": 621}, "arguments": [{"role": "Theme", "text": "expressed", "start": 521, "end": 530}]}, {"trigger": {"text": "reaching a peak", "start": 765, "end": 780}, "arguments": [{"role": "Theme", "text": "expression", "start": 691, "end": 701}]}, {"trigger": {"text": "increased", "start": 1036, "end": 1045}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1050, "end": 1063}]}], "regulation": [{"trigger": {"text": "effect", "start": 129, "end": 135}, "arguments": [{"role": "Theme", "text": "expression", "start": 210, "end": 220}]}, {"trigger": {"text": "affected", "start": 919, "end": 927}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 890, "end": 895}]}, {"trigger": {"text": "affected", "start": 919, "end": 927}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 900, "end": 905}]}], "transcription": [{"trigger": {"text": "transcription", "start": 47, "end": 60}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 26, "end": 31}]}, {"trigger": {"text": "transcription", "start": 47, "end": 60}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 36, "end": 41}]}, {"trigger": {"text": "expressed", "start": 521, "end": 530}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 485, "end": 490}]}, {"trigger": {"text": "expression", "start": 691, "end": 701}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 754, "end": 759}]}, {"trigger": {"text": "expression", "start": 691, "end": 701}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 813, "end": 818}]}, {"trigger": {"text": "transcription", "start": 1050, "end": 1063}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1071, "end": 1076}]}, {"trigger": {"text": "transcription", "start": 1050, "end": 1063}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1097, "end": 1102}]}]}}, "schema": []}
{"input": "Transcription factor activation and functional stimulation of human monocytes. \nActivation of expression of genes encoding transcription factors: c-fos and c-jun and formation of AP1 transcriptional complex in human monocytes was investigated. It was found that lipopolysaccharide induced strongly both c-fos and c-jun expression as well as AP1 formation. Interferon gamma activated strongly c-fos and weakly c-jun and AP1. Tumor necrosis factor induced slightly c-fos and had almost no effect on c-jun and AP1. The data suggest that differences in functional responses elicited in monocytes by all three factors may be dependent on different routes on nuclear signalling employed by the factors. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 94, "end": 104}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 146, "end": 151}]}, {"trigger": {"text": "expression", "start": 94, "end": 104}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 156, "end": 161}]}, {"trigger": {"text": "expression", "start": 319, "end": 329}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 303, "end": 308}]}, {"trigger": {"text": "expression", "start": 319, "end": 329}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 313, "end": 318}]}], "positive regulation": [{"trigger": {"text": "Activation", "start": 80, "end": 90}, "arguments": [{"role": "Theme", "text": "expression", "start": 94, "end": 104}]}, {"trigger": {"text": "induced", "start": 281, "end": 288}, "arguments": [{"role": "Theme", "text": "expression", "start": 319, "end": 329}]}, {"trigger": {"text": "activated", "start": 373, "end": 382}, "arguments": [{"role": "Cause", "text": "Interferon gamma", "start": 356, "end": 372}, {"role": "Theme", "text": "c-fos", "start": 392, "end": 397}]}, {"trigger": {"text": "activated", "start": 373, "end": 382}, "arguments": [{"role": "Cause", "text": "Interferon gamma", "start": 356, "end": 372}, {"role": "Theme", "text": "c-jun", "start": 409, "end": 414}]}, {"trigger": {"text": "induced", "start": 446, "end": 453}, "arguments": [{"role": "Cause", "text": "Tumor necrosis factor", "start": 424, "end": 445}, {"role": "Theme", "text": "c-fos", "start": 463, "end": 468}]}, {"trigger": {"text": "dependent", "start": 620, "end": 629}, "arguments": [{"role": "Theme", "text": "induced", "start": 281, "end": 288}]}, {"trigger": {"text": "dependent", "start": 620, "end": 629}, "arguments": [{"role": "Theme", "text": "activated", "start": 373, "end": 382}]}, {"trigger": {"text": "dependent", "start": 620, "end": 629}, "arguments": [{"role": "Theme", "text": "induced", "start": 446, "end": 453}]}, {"trigger": {"text": "dependent", "start": 620, "end": 629}, "arguments": [{"role": "Theme", "text": "effect", "start": 487, "end": 493}]}], "regulation": [{"trigger": {"text": "effect", "start": 487, "end": 493}, "arguments": [{"role": "Cause", "text": "Tumor necrosis factor", "start": 424, "end": 445}, {"role": "Theme", "text": "c-jun", "start": 497, "end": 502}]}]}}, "schema": []}
{"input": "Interferon-gamma potentiates the antiviral activity and the expression of interferon-stimulated genes induced by interferon-alpha in U937 cells. \nBinding of type I interferon (IFN-alpha/beta) to specific receptors results in the rapid transcriptional activation, independent of protein synthesis, of IFN-alpha-stimulated genes (ISGs) in human fibroblasts and HeLa and Daudi cell lines. The binding of ISGF3 (IFN-stimulated gene factor 3) to the conserved IFN-stimulated response element (ISRE) results in transcriptional activation. This factor is composed of a DNA-binding protein (ISGF3 gamma), which normally is present in the cytoplasm, and other IFN-alpha-activated proteins which preexist as latent cytoplasmic precursors (ISGF3 alpha). We have found that ISG expression in the monocytic U937 cell line differs from most cell lines previously examined. U937 cells express both type I and type II IFN receptors, but only IFN-alpha is capable of inducing antiviral protection in these cells. Pretreatment with IFN-gamma potentiates the IFN-alpha-induced protection, but IFN-gamma alone does not have any antiviral activity. ISG15 mRNA accumulation in U937 cells is not detectable before 6 h of IFN-alpha treatment, peaks at 24 h, and requires protein synthesis. Although IFN-gamma alone does not induce ISG expression, IFN-gamma pretreatment markedly increases and hastens ISG expression and transcriptional induction. Nuclear extracts assayed for the presence of ISRE binding factors by electrophoretic mobility shift assays show that ISGF3 is induced by IFN-alpha within 6 h from undetectable basal levels in untreated U937 cells. Activation of ISGF3 alpha, the latent component of ISGF3, occurs rapidly. However, the increase in ISGF3 activity ultimately correlates with the accumulation of ISGF3 gamma induced by IFN-alpha or IFN-gamma. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"localization": [{"trigger": {"text": "present", "start": 615, "end": 622}, "arguments": [{"role": "Theme", "text": "ISGF3 gamma", "start": 583, "end": 594}, {"role": "AtLoc", "text": "cytoplasm", "start": 630, "end": 639}]}], "positive regulation": [{"trigger": {"text": "accumulation", "start": 1139, "end": 1151}, "arguments": [{"role": "Theme", "text": "ISG15", "start": 1128, "end": 1133}]}, {"trigger": {"text": "detectable", "start": 1173, "end": 1183}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1139, "end": 1151}]}, {"trigger": {"text": "requires", "start": 1238, "end": 1246}, "arguments": [{"role": "Theme", "text": "detectable", "start": 1173, "end": 1183}]}, {"trigger": {"text": "accumulation", "start": 1782, "end": 1794}, "arguments": [{"role": "Theme", "text": "ISGF3 gamma", "start": 1798, "end": 1809}, {"role": "Cause", "text": "IFN-gamma", "start": 1834, "end": 1843}]}, {"trigger": {"text": "accumulation", "start": 1782, "end": 1794}, "arguments": [{"role": "Theme", "text": "ISGF3 gamma", "start": 1798, "end": 1809}]}]}}, "schema": []}
{"input": "A lymphoid cell-specific nuclear factor containing c-Rel-like proteins preferentially interacts with interleukin-6 kappa B-related motifs whose activities are repressed in lymphoid cells. \nThe proto-oncoprotein c-Rel is a member of the nuclear factor kappa B transcription factor family, which includes the p50 and p65 subunits of nuclear factor kappa B. We show here that c-Rel binds to kappa B sites as homodimers as well as heterodimers with p50. These homodimers and heterodimers show distinct DNA-binding specificities and affinities for various kappa B motifs. In particular, the c-Rel homodimer has a high affinity for interleukin-6 (IL-6) and beta interferon kappa B sites. In spite of its association with p50 in vitro, however, we found a lymphoid cell-specific nuclear factor in vivo that contains c-Rel but not p50 epitopes; this factor, termed IL-6 kappa B binding factor II, appears to contain the c-Rel homodimer and preferentially recognizes several IL-6 kappa B-related kappa B motifs. Although it has been previously shown that the IL-6 kappa B motif functions as a potent IL-1/tumor necrosis factor-responsive element in nonlymphoid cells, its activity was found to be repressed in lymphoid cells such as a Jurkat T-cell line. We also present evidence that IL-6 kappa B binding factor II functions as a repressor specific for IL-6 kappa B-related kappa B motifs in lymphoid cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 379, "end": 384}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 373, "end": 378}]}, {"trigger": {"text": "homodimers", "start": 405, "end": 415}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 373, "end": 378}]}, {"trigger": {"text": "heterodimers", "start": 427, "end": 439}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 373, "end": 378}, {"role": "Theme2", "text": "p50", "start": 445, "end": 448}]}, {"trigger": {"text": "binding specificities", "start": 502, "end": 523}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 373, "end": 378}]}, {"trigger": {"text": "affinities", "start": 528, "end": 538}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 373, "end": 378}]}, {"trigger": {"text": "high affinity", "start": 608, "end": 621}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 586, "end": 591}, {"role": "Theme2", "text": "IL-6", "start": 641, "end": 645}, {"role": "Site2", "text": "kappa B sites", "start": 667, "end": 680}]}, {"trigger": {"text": "high affinity", "start": 608, "end": 621}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 586, "end": 591}, {"role": "Theme2", "text": "beta interferon", "start": 651, "end": 666}, {"role": "Site2", "text": "kappa B sites", "start": 667, "end": 680}]}, {"trigger": {"text": "association", "start": 698, "end": 709}, "arguments": [{"role": "Theme", "text": "p50", "start": 715, "end": 718}, {"role": "Theme2", "text": "IL-6", "start": 857, "end": 861}]}, {"trigger": {"text": "association", "start": 698, "end": 709}, "arguments": [{"role": "Theme", "text": "p50", "start": 715, "end": 718}]}, {"trigger": {"text": "recognizes", "start": 947, "end": 957}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 857, "end": 861}]}]}}, "schema": []}
{"input": "The promoter of the CD19 gene is a target for the B-cell-specific transcription factor BSAP. \nThe CD19 protein is expressed on the surface of all B-lymphoid cells with the exception of terminally differentiated plasma cells and has been implicated as a signal-transducing receptor in the control of proliferation and differentiation. Here we demonstrate complete correlation between the expression pattern of the CD19 gene and the B-cell-specific transcription factor BSAP in a large panel of B-lymphoid cell lines. The human CD19 gene has been cloned, and several BSAP-binding sites have been mapped by in vitro protein-DNA binding studies. In particular, a high-affinity BSAP-binding site instead of a TATA sequence is located in the -30 promoter region upstream of a cluster of heterogeneous transcription start sites. Moreover, this site is occupied by BSAP in vivo in a CD19-expressing B-cell line but not in plasma or HeLa cells. This high-affinity site has been conserved in the promoters of both human and mouse CD19 genes and was furthermore shown to confer B-cell specificity to a beta-globin reporter gene in transient transfection experiments. In addition, BSAP was found to be the only abundant DNA-binding activity of B-cell nuclear extracts that interacts with the CD19 promoter. Together, this evidence strongly implicates BSAP in the regulation of the CD19 gene. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "target", "start": 35, "end": 41}, "arguments": [{"role": "Site", "text": "promoter", "start": 4, "end": 12}, {"role": "Theme", "text": "CD19", "start": 20, "end": 24}, {"role": "Theme2", "text": "BSAP", "start": 87, "end": 91}]}, {"trigger": {"text": "occupied", "start": 845, "end": 853}, "arguments": [{"role": "Theme", "text": "BSAP", "start": 857, "end": 861}]}, {"trigger": {"text": "binding", "start": 1212, "end": 1219}, "arguments": [{"role": "Theme", "text": "BSAP", "start": 1169, "end": 1173}]}, {"trigger": {"text": "interacts", "start": 1261, "end": 1270}, "arguments": [{"role": "Theme", "text": "BSAP", "start": 1169, "end": 1173}, {"role": "Theme2", "text": "CD19", "start": 1280, "end": 1284}, {"role": "Site2", "text": "promoter", "start": 1285, "end": 1293}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 114, "end": 123}, "arguments": [{"role": "Theme", "text": "CD19", "start": 98, "end": 102}]}, {"trigger": {"text": "expression", "start": 387, "end": 397}, "arguments": [{"role": "Theme", "text": "CD19", "start": 413, "end": 417}]}], "regulation": [{"trigger": {"text": "regulation", "start": 1351, "end": 1361}, "arguments": [{"role": "Cause", "text": "BSAP", "start": 1339, "end": 1343}, {"role": "Theme", "text": "CD19", "start": 1369, "end": 1373}]}]}}, "schema": []}
{"input": "SRC-related proto-oncogenes and transcription factors in primary human T cells: modulation by cyclosporin A and FK506. \nActivation of T lymphocytes induces transcription of genes encoding for lymphokines. Interleukin-2 (IL-2) gene expression is controlled transcriptionally by the cooperative activity of specific trans-activating factors that bind to the IL-2 enhancer. Cyclosporin A (CsA) and FK506 inhibit the production of IL-2 in T lymphocytes at the level of gene transcription. A member of the src gene family, the lymphocyte-specific protein tyrosine kinase, p56lck, has been implicated in IL-2 production. CsA was found not to inhibit lck gene expression, nor the activity of the lck gene product. However, CsA and FK506 inhibit the appearance of DNA binding activity of factors that bind to the NF-AT and AP-1 sites in the IL-2 enhancer. Since the induction of NF-AT and AP-1 is induced by the same stimuli that stimulate IL-2 production, these results indicate that the immunosuppressant action of CsA and FK506 is exerted at the level of these trans-activating factors. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 344, "end": 348}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 356, "end": 360}, {"role": "Site", "text": "enhancer", "start": 361, "end": 369}]}], "gene expression": [{"trigger": {"text": "production", "start": 603, "end": 613}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 598, "end": 602}]}, {"trigger": {"text": "expression", "start": 653, "end": 663}, "arguments": [{"role": "Theme", "text": "lck", "start": 644, "end": 647}]}, {"trigger": {"text": "production", "start": 937, "end": 947}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 932, "end": 936}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 401, "end": 408}, "arguments": [{"role": "Theme", "text": "gene transcription", "start": 465, "end": 483}]}, {"trigger": {"text": "inhibit", "start": 636, "end": 643}, "arguments": [{"role": "Theme", "text": "lck", "start": 644, "end": 647}]}, {"trigger": {"text": "inhibit", "start": 636, "end": 643}, "arguments": [{"role": "Theme", "text": "expression", "start": 653, "end": 663}]}], "positive regulation": [{"trigger": {"text": "stimulate", "start": 922, "end": 931}, "arguments": [{"role": "Theme", "text": "production", "start": 937, "end": 947}]}], "regulation": [{"trigger": {"text": "controlled", "start": 245, "end": 255}, "arguments": [{"role": "Theme", "text": "transcriptionally", "start": 256, "end": 273}]}, {"trigger": {"text": "implicated", "start": 584, "end": 594}, "arguments": [{"role": "Cause", "text": "p56lck", "start": 567, "end": 573}, {"role": "Theme", "text": "production", "start": 603, "end": 613}]}], "transcription": [{"trigger": {"text": "transcriptionally", "start": 256, "end": 273}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 220, "end": 224}]}, {"trigger": {"text": "gene transcription", "start": 465, "end": 483}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 427, "end": 431}]}]}}, "schema": []}
{"input": "The development of functionally responsive T cells. \nThe work reviewed in this article separates T cell development into four phases. First is an expansion phase prior to TCR rearrangement, which appears to be correlated with programming of at least some response genes for inducibility. This phase can occur to some extent outside of the thymus. However, the profound T cell deficit of nude mice indicates that the thymus is by far the most potent site for inducing the expansion per se, even if other sites can induce some response acquisition. Second is a controlled phase of TCR gene rearrangement. The details of the regulatory mechanism that selects particular loci for rearrangement are still not known. It seems that the rearrangement of the TCR gamma loci in the gamma delta lineage may not always take place at a developmental stage strictly equivalent to the rearrangement of TCR beta in the alpha beta lineage, and it is not clear just how early the two lineages diverge. In the TCR alpha beta lineage, however, the final gene rearrangement events are accompanied by rapid proliferation and an interruption in cellular response gene inducibility. The loss of conventional responsiveness is probably caused by alterations at the level of signaling, and may be a manifestation of the physiological state that is a precondition for selection. Third is the complex process of selection. Whereas peripheral T cells can undergo forms of positive selection (by antigen-driven clonal expansion) and negative selection (by abortive stimulation leading to anergy or death), neither is exactly the same phenomenon that occurs in the thymic cortex. Negative selection in the cortex appears to be a suicidal inversion of antigen responsiveness: instead of turning on IL-2 expression, the activated cell destroys its own chromatin. The genes that need to be induced for this response are not yet identified, but it is unquestionably a form of activation. It is interesting that in humans and rats, cortical thymocytes undergoing negative selection can still induce IL-2R alpha expression and even be rescued in vitro, if exogenous IL-2 is provided. Perhaps murine thymocytes are denied this form of rescue because they shut off IL-2R beta chain expression at an earlier stage or because they may be uncommonly Bcl-2 deficient (cf. Sentman et al., 1991; Strasser et al., 1991). Even so, medullary thymocytes remain at least partially susceptible to negative selection even as they continue to mature . ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1771, "end": 1781}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1766, "end": 1770}]}, {"trigger": {"text": "expression", "start": 2075, "end": 2085}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 2063, "end": 2074}]}, {"trigger": {"text": "expression", "start": 2243, "end": 2253}, "arguments": [{"role": "Theme", "text": "IL-2R beta chain", "start": 2226, "end": 2242}]}], "negative regulation": [{"trigger": {"text": "inversion", "start": 1707, "end": 1716}, "arguments": [{"role": "Theme", "text": "responsiveness", "start": 1728, "end": 1742}]}, {"trigger": {"text": "deficient", "start": 2314, "end": 2323}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 2308, "end": 2313}]}], "positive regulation": [{"trigger": {"text": "responsiveness", "start": 1728, "end": 1742}, "arguments": [{"role": "Theme", "text": "turning", "start": 1755, "end": 1762}]}, {"trigger": {"text": "turning", "start": 1755, "end": 1762}, "arguments": [{"role": "Theme", "text": "expression", "start": 1771, "end": 1781}]}, {"trigger": {"text": "induce", "start": 2056, "end": 2062}, "arguments": [{"role": "Theme", "text": "expression", "start": 2075, "end": 2085}]}]}}, "schema": []}
{"input": "Regulation of c-jun expression during induction of monocytic differentiation by okadaic acid. \nThe present work has examined the effects of okadaic acid, an inhibitor of type 1 and 2A protein phosphatases, on the regulation of c-jun expression during monocytic differentiation of U-937 leukemia cells. The results demonstrate that okadaic acid treatment is associated with induction of a differentiated monocyte phenotype characterized by: (a) growth arrest; (b) increases in Mac-1 cell surface antigen expression; (c) down-regulation of c-myc transcripts; and (d) induction of tumor necrosis factor gene expression. This induction of monocytic differentiation was associated with transient increases in c-jun mRNA levels, which were maximal at 6 h. Similar effects were obtained for the c-fos gene. Run-on analysis demonstrated detectable levels of c-jun transcription in U-937 cells and that this rate is increased approximately 40-fold following okadaic acid exposure. c-jun mRNA levels were superinduced in cells treated with both okadaic acid and cycloheximide, whereas inhibition of protein synthesis had little, if any, effect on okadaic acid-induced c-jun transcription. The half-life of c-jun mRNA was similar (45-50 min) in both untreated and okadaic acid-induced cells. In contrast, treatment with both okadaic acid and cycloheximide was associated with stabilization (t 1/2 = 90 min) of c-jun transcripts. Taken together, these findings indicate that the induction of c-jun transcription by okadaic acid is controlled primarily by a transcriptional mechanism. Since previous studies have demonstrated that the c-jun gene is autoinduced by Jun/AP-1, we also studied transcription of c-jun promoter (positions -132/+170)-reporter gene constructs with and without a mutated AP-1 element. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 20, "end": 30}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 14, "end": 19}]}, {"trigger": {"text": "expression", "start": 233, "end": 243}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 227, "end": 232}]}, {"trigger": {"text": "expression", "start": 503, "end": 513}, "arguments": [{"role": "Theme", "text": "Mac-1 cell surface antigen", "start": 476, "end": 502}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 157, "end": 166}, "arguments": [{"role": "Theme", "text": "type 1", "start": 170, "end": 176}]}, {"trigger": {"text": "inhibitor", "start": 157, "end": 166}, "arguments": [{"role": "Theme", "text": "2A protein phosphatases", "start": 181, "end": 204}]}, {"trigger": {"text": "down-regulation", "start": 519, "end": 534}, "arguments": [{"role": "Theme", "text": "transcripts", "start": 544, "end": 555}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 373, "end": 382}, "arguments": [{"role": "Theme", "text": "increases", "start": 463, "end": 472}]}, {"trigger": {"text": "induction", "start": 373, "end": 382}, "arguments": [{"role": "Theme", "text": "down-regulation", "start": 519, "end": 534}]}, {"trigger": {"text": "increases", "start": 463, "end": 472}, "arguments": [{"role": "Theme", "text": "expression", "start": 503, "end": 513}]}, {"trigger": {"text": "increases", "start": 691, "end": 700}, "arguments": [{"role": "Theme", "text": "levels", "start": 715, "end": 721}]}, {"trigger": {"text": "Similar effects", "start": 750, "end": 765}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 788, "end": 793}]}, {"trigger": {"text": "increased", "start": 907, "end": 916}, "arguments": [{"role": "Theme", "text": "transcription", "start": 856, "end": 869}]}, {"trigger": {"text": "superinduced", "start": 995, "end": 1007}, "arguments": [{"role": "Theme", "text": "levels", "start": 983, "end": 989}]}, {"trigger": {"text": "superinduced", "start": 995, "end": 1007}, "arguments": [{"role": "Theme", "text": "superinduced", "start": 995, "end": 1007}]}, {"trigger": {"text": "induced", "start": 1150, "end": 1157}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1164, "end": 1177}]}, {"trigger": {"text": "stabilization", "start": 1365, "end": 1378}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1399, "end": 1404}]}, {"trigger": {"text": "induction", "start": 1467, "end": 1476}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1486, "end": 1499}]}, {"trigger": {"text": "autoinduced", "start": 1636, "end": 1647}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1622, "end": 1627}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 20, "end": 30}]}, {"trigger": {"text": "effects", "start": 129, "end": 136}, "arguments": [{"role": "Theme", "text": "regulation", "start": 213, "end": 223}]}, {"trigger": {"text": "regulation", "start": 213, "end": 223}, "arguments": [{"role": "Theme", "text": "expression", "start": 233, "end": 243}]}, {"trigger": {"text": "had little, if any, effect", "start": 1107, "end": 1133}, "arguments": [{"role": "Theme", "text": "induced", "start": 1150, "end": 1157}]}, {"trigger": {"text": "controlled", "start": 1519, "end": 1529}, "arguments": [{"role": "Theme", "text": "induction", "start": 1467, "end": 1476}]}], "transcription": [{"trigger": {"text": "transcripts", "start": 544, "end": 555}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 538, "end": 543}]}, {"trigger": {"text": "levels", "start": 715, "end": 721}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 704, "end": 709}]}, {"trigger": {"text": "transcription", "start": 856, "end": 869}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 850, "end": 855}]}, {"trigger": {"text": "levels", "start": 983, "end": 989}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 972, "end": 977}]}, {"trigger": {"text": "transcription", "start": 1164, "end": 1177}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1158, "end": 1163}]}, {"trigger": {"text": "transcription", "start": 1486, "end": 1499}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1480, "end": 1485}]}]}}, "schema": []}
{"input": "Activation of NF-kappa B by interleukin 2 in human blood monocytes. \nWe report here that interleukin 2 (IL-2) acts on human blood monocytes by enhancing binding activity of the transcription factor NF-kappa B to its consensus sequence in the 5' regulatory enhancer region of the IL-2 receptor alpha chain (p55). Similarly, IL-2 activates NF-kappa B in the human monocytic cell line U 937, but not in resting human T-cells. This effect is detectable within 15 min and peaks 1 h after exposure to IL-2. Enhanced NF-kappa B binding activity is followed by functional activation in that inducibility of the IL-2 receptor alpha chain is mediated by enhanced NF-kappa B binding and that a heterologous promoter containing the NF-kappa B consensus sequence (-291 to -245) of the IL-2 receptor alpha chain gene is activated. In addition, IL-2 is capable of increasing transcript levels of the p50 gene coding for the p50 subunit of the NF-kappa B transcription factor, whereas mRNA levels of the p65 NF-kappa B gene remained unchanged. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 153, "end": 169}, "arguments": [{"role": "Theme", "text": "IL-2 receptor alpha chain", "start": 279, "end": 304}]}], "positive regulation": [{"trigger": {"text": "enhancing", "start": 143, "end": 152}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 104, "end": 108}, {"role": "Theme", "text": "binding activity", "start": 153, "end": 169}]}, {"trigger": {"text": "inducibility", "start": 583, "end": 595}, "arguments": [{"role": "Theme", "text": "IL-2 receptor alpha chain", "start": 603, "end": 628}]}, {"trigger": {"text": "mediated", "start": 632, "end": 640}, "arguments": [{"role": "Theme", "text": "inducibility", "start": 583, "end": 595}]}, {"trigger": {"text": "activated", "start": 806, "end": 815}, "arguments": [{"role": "Theme", "text": "IL-2 receptor alpha chain", "start": 772, "end": 797}]}, {"trigger": {"text": "increasing", "start": 849, "end": 859}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 830, "end": 834}, {"role": "Theme", "text": "transcript levels", "start": 860, "end": 877}]}, {"trigger": {"text": "unchanged", "start": 1017, "end": 1026}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 830, "end": 834}, {"role": "Theme", "text": "mRNA levels", "start": 969, "end": 980}]}], "transcription": [{"trigger": {"text": "transcript levels", "start": 860, "end": 877}, "arguments": [{"role": "Theme", "text": "p50", "start": 885, "end": 888}]}, {"trigger": {"text": "mRNA levels", "start": 969, "end": 980}, "arguments": [{"role": "Theme", "text": "p65", "start": 988, "end": 991}]}]}}, "schema": []}
{"input": "The regulation of the human tumor necrosis factor alpha promoter region in macrophage, T cell, and B cell lines. \nThe 1311-base pair human tumor necrosis factor (TNF) alpha promoter region was fused to the luciferase (Luc) reporter gene and studied in a transient transfection system in three TNF producing cell lines, the U937 macrophage cell line, the MLA 144 T cell line, and the 729-6 B cell line. This full length promoter construct can be induced by phorbol 13-myristate acetate (PMA) in each of these cell types. Analysis of a series of 5'-truncations showed several peaks of basal and PMA induced activity suggesting the presence of several positive and negative regulatory elements. A PMA responsive element was localized to a region between -95 and -36 bp relative to the transcription start site. Within this region, single AP-2- and AP-1- like consensus sequences were noted. These AP-2 and AP-1 sites were each modified with a double point mutation. A modest (20-50%) reduction in TNF promoter activity was observed with the AP-2 site mutation. However, mutation of the AP-1 site markedly diminished both the basal and PMA-activated promoter activity. Also co-transfections of the wild-type promoter construct with an AP-1/c-jun expression vector resulted in augmented basal and PMA-induced promoter activity. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "co-transfections", "start": 1170, "end": 1186}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1236, "end": 1241}]}], "negative regulation": [{"trigger": {"text": "reduction", "start": 981, "end": 990}, "arguments": [{"role": "Theme", "text": "TNF", "start": 994, "end": 997}, {"role": "Site", "text": "promoter", "start": 998, "end": 1006}]}, {"trigger": {"text": "diminished", "start": 1102, "end": 1112}, "arguments": [{"role": "Theme", "text": "TNF", "start": 994, "end": 997}, {"role": "Site", "text": "promoter", "start": 998, "end": 1006}]}, {"trigger": {"text": "diminished", "start": 1102, "end": 1112}, "arguments": [{"role": "Theme", "text": "activated", "start": 1136, "end": 1145}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 445, "end": 452}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor (TNF) alpha", "start": 139, "end": 172}, {"role": "Site", "text": "promoter region", "start": 173, "end": 188}]}, {"trigger": {"text": "activated", "start": 1136, "end": 1145}, "arguments": [{"role": "Theme", "text": "TNF", "start": 994, "end": 997}, {"role": "Site", "text": "promoter", "start": 998, "end": 1006}]}, {"trigger": {"text": "co-transfections", "start": 1170, "end": 1186}, "arguments": [{"role": "Theme", "text": "co-transfections", "start": 1170, "end": 1186}]}, {"trigger": {"text": "augmented", "start": 1272, "end": 1281}, "arguments": [{"role": "Theme", "text": "TNF", "start": 994, "end": 997}, {"role": "Site", "text": "promoter", "start": 998, "end": 1006}, {"role": "Cause", "text": "co-transfections", "start": 1170, "end": 1186}]}, {"trigger": {"text": "induced", "start": 1296, "end": 1303}, "arguments": [{"role": "Theme", "text": "TNF", "start": 994, "end": 997}, {"role": "Site", "text": "promoter", "start": 998, "end": 1006}]}], "regulation": [{"trigger": {"text": "regulation", "start": 4, "end": 14}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 28, "end": 55}, {"role": "Site", "text": "promoter region", "start": 56, "end": 71}]}]}}, "schema": []}
{"input": "Redox status of cells influences constitutive or induced NF-kappa B translocation and HIV long terminal repeat activity in human T and monocytic cell lines. \nWe have tested the hypothesis that cellular activation events occurring in T lymphocytes and monocytes and mediated through translocation of the transcription factor NF-kappa B are dependent upon the constitutive redox status of these cells. We used phenolic, lipid-soluble, chain-breaking antioxidants (butylated hydroxyanisole (BHA), nordihydroquairetic acid, or alpha-tocopherol (vitamin E) to show that peroxyl radical scavenging in unstimulated and PMA- or TNF-stimulated cells blocks the functions depending on NF-kappa B activation. BHA was found to suppress not only PMA- or TNF-induced, but also constitutive, HIV-enhancer activity concomitant to an inhibition of NF-kappa B binding activity in both lymphoblastoid T (J.Jhan) and monocytic (U937) cell lines. This was also true for KBF (p50 homodimer) binding activity in U937 cells. Secretion of TNF, the product of another NF-kappa B-dependent gene, was abolished by BHA in PMA-stimulated U937 cells. The anti-oxidative effect of BHA was accompanied by an increase in thiol, but not glutathione, content in stimulated and unstimulated T cell, whereas TNF stimulation itself barely modified the cellular thiol level. Oxidative stress obtained by the addition of H2O2 to the culture medium of J.Jhan or U937 cells could not by itself induce NF-kappa B activation. These observations suggest that TNF and PMA do not lead to NF-kappa B activation through induction of changes in the cell redox status. Rather, TNF and PMA can exert their effect only if cells are in an appropriate redox status, because prior modification toward reduction with BHA treatment prevents this activation. It appears that a basal redox equilibrium tending toward oxidation is a prerequisite for full activation of transduction pathways regulating the activity of NF-kappa B-dependent genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 969, "end": 985}, "arguments": [{"role": "Theme", "text": "p50", "start": 954, "end": 957}]}]}}, "schema": []}
{"input": "Natural variants of the HIV-1 long terminal repeat: analysis of promoters with duplicated DNA regulatory motifs. \nSequence variation in the long terminal repeat (LTR) region of HIV-1 was analyzed in viral isolates of 17 infected individuals. Two classes of LTR size variants were found. One HIV-1 variant was detected containing an additional binding site for the transcription factor Sp1. Another LTR size variation was observed in four patients in a region just upstream of the NF-kappa B enhancer. This variation was the result of a duplication of a short DNA sequence (CTG-motif). Cell culture experiments demonstrated that the natural variant with four Sp1 sites had a slightly higher promoter activity and viral replication rate than the isogenic control LTR with three Sp1 sites. No positive effect of the duplicated CTG-motif could be detected. In order to measure small differences in virus production more accurately, equal amounts of a size variant and the wild-type plasmid were cotransfected into T-cells. The virus with four Sp1 sites did outgrow the three Sp1 virus in 35 days of culture and CTG-monomer virus outcompeted the CTG-dimer virus in 42 days. Based on these results we estimate a 5-10% difference in virus production of the LTR variants when compared to that of wild-type. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Transcription of the hypersensitive site HS2 enhancer in erythroid cells. \nIn the human genome, the erythroid-specific hypersensitive site HS2 enhancer regulates the transcription of the downstream beta-like globin genes 10-50 kilobases away. The mechanism of HS2 enhancer function is not known. The present study employs RNA protection assays to analyze the transcriptional status of the HS2 enhancer in transfected recombinant chloramphenicol acetyltransferase (CAT) plasmids. In erythroid K562 cells in which the HS2 enhancer is active, the HS2 sequence directs the synthesis of long enhancer transcripts that are initiated apparently from within the enhancer and elongated through the intervening DNA into the cis-linked CAT gene. In nonerythroid HL-60 cells in which the HS2 enhancer is inactive, long enhancer transcripts are not detectable. Splitting the HS2 enhancer between two tandem Ap1 sites abolishes the synthesis of a group of long enhancer transcripts and results in loss of enhancer function and transcriptional silencing of the cis-linked CAT gene. In directing the synthesis of RNA through the intervening DNA and the gene by a tracking and transcription mechanism, the HS2 enhancer may (i) open up the chromatin structure of a gene domain and (ii) deliver enhancer binding proteins to the promoter sequence where they may stimulate the transcription of the gene at the cap site. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "regulates", "start": 152, "end": 161}, "arguments": [{"role": "Theme", "text": "transcription", "start": 166, "end": 179}]}], "transcription": [{"trigger": {"text": "transcription", "start": 166, "end": 179}, "arguments": [{"role": "Theme", "text": "beta-like globin", "start": 198, "end": 214}]}]}}, "schema": []}
{"input": "Phorbol ester reduces constitutive nuclear NF kappa B and inhibits HIV-1 production in mature human monocytic cells. \nNF kappa B is a potent mediator of specific gene expression in human monocytes and has been shown to play a role in transcription of the HIV-1 genome in promonocytic leukemias. There is little information available on the response of NF kappa B to cytokines in normal human monocytes. We have used a 32P-labeled oligonucleotide derived from human immunodeficiency virus (HIV-1) long terminal repeat, which contains a tandem repeat of the NF kappa B binding sequence, as a probe in a gel retardation assay to study this transcription factor. Using this assay, we have detected NF kappa B in extracts of nuclei from normal human monocytes. Treatment of normal monocytes with 12-0-tetradecanoyl phorbol-13-acetate (TPA) for 4-24 h caused the complete disappearance of NF kappa B from nuclear extracts of monocytes. A similar result was obtained with the mature monocytic leukemia cell line THP-1. The constitutive transcription factor SP1 was unaffected by addition of TPA. The disappearance of NF kappa B from the nucleus was concentration dependent between 10 and 50 ng/ml of phorbol ester. In THP-1 cells, TPA also induced a new, faster-migrating NF kappa B species not induced in monocytes. Protein kinase C inhibitor staurosporine, but not cyclic nucleotide-dependent protein kinase inhibitor HA-1004, also dramatically reduced constitutive levels of nuclear NF kappa B. Finally, TPA addition to monocytes infected with HIV-1 inhibited HIV-1 replication, as determined by reverse transcriptase assays, in a concentration-dependent manner. These results are in striking contrast to the increase in nuclear NF kappa B and HIV-1 replication induced by phorbol esters in promonocytic leukemia cells U937 and HL-60, and emphasize the importance of studying cytokine regulation of HIV-1 in normal monocytes. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "unaffected", "start": 1058, "end": 1068}, "arguments": [{"role": "Theme", "text": "SP1", "start": 1050, "end": 1053}]}]}}, "schema": []}
{"input": "Targeted degradation of c-Fos, but not v-Fos, by a phosphorylation-dependent signal on c-Jun. \nThe proto-oncogene products c-Fos and c-Jun heterodimerize through their leucine zippers to form the AP-1 transcription factor. The transcriptional activity of the heterodimer is regulated by signal-dependent phosphorylation and dephosphorylation events. The stability of c-Fos was found to also be controlled by intracellular signal transduction. In transient expression and in vitro degradation experiments, the stability of c-Fos was decreased when the protein was dimerized with phosphorylated c-Jun. c-Jun protein isolated from phorbol ester-induced cells did not target c-Fos for degradation, which suggests that c-Fos is transiently stabilized after stimulation of cell growth. v-Fos protein, the retroviral counterpart of c-Fos, was not susceptible to degradation targeted by c-Jun. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "heterodimerize", "start": 139, "end": 153}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 123, "end": 128}, {"role": "Theme2", "text": "c-Jun", "start": 133, "end": 138}]}, {"trigger": {"text": "dimerized", "start": 563, "end": 572}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 522, "end": 527}, {"role": "Theme2", "text": "c-Jun", "start": 593, "end": 598}]}, {"trigger": {"text": "targeted", "start": 867, "end": 875}, "arguments": [{"role": "Theme", "text": "v-Fos", "start": 780, "end": 785}, {"role": "Theme2", "text": "c-Jun", "start": 879, "end": 884}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 532, "end": 541}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 522, "end": 527}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 578, "end": 592}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 593, "end": 598}]}], "positive regulation": [{"trigger": {"text": "Targeted", "start": 0, "end": 8}, "arguments": [{"role": "Theme", "text": "degradation", "start": 9, "end": 20}]}, {"trigger": {"text": "through", "start": 154, "end": 161}, "arguments": [{"role": "Theme", "text": "heterodimerize", "start": 139, "end": 153}]}, {"trigger": {"text": "when", "start": 542, "end": 546}, "arguments": [{"role": "Theme", "text": "decreased", "start": 532, "end": 541}, {"role": "Cause", "text": "dimerized", "start": 563, "end": 572}]}, {"trigger": {"text": "target", "start": 664, "end": 670}, "arguments": [{"role": "Cause", "text": "c-Jun", "start": 600, "end": 605}, {"role": "Theme", "text": "degradation", "start": 681, "end": 692}]}, {"trigger": {"text": "after", "start": 746, "end": 751}, "arguments": [{"role": "Theme", "text": "stabilized", "start": 735, "end": 745}]}, {"trigger": {"text": "susceptible", "start": 840, "end": 851}, "arguments": [{"role": "Theme", "text": "v-Fos", "start": 780, "end": 785}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 9, "end": 20}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 24, "end": 29}]}, {"trigger": {"text": "degradation", "start": 9, "end": 20}, "arguments": [{"role": "Theme", "text": "v-Fos", "start": 39, "end": 44}]}, {"trigger": {"text": "stability", "start": 354, "end": 363}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 367, "end": 372}]}, {"trigger": {"text": "degradation", "start": 681, "end": 692}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 671, "end": 676}]}, {"trigger": {"text": "stabilized", "start": 735, "end": 745}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 714, "end": 719}]}, {"trigger": {"text": "degradation", "start": 855, "end": 866}, "arguments": [{"role": "Theme", "text": "v-Fos", "start": 780, "end": 785}]}], "regulation": [{"trigger": {"text": "controlled", "start": 394, "end": 404}, "arguments": [{"role": "Theme", "text": "stability", "start": 354, "end": 363}]}]}}, "schema": []}
{"input": "Alpha-lipoic acid is a potent inhibitor of NF-kappa B activation in human T cells. \nAcquired immunodeficiency syndrome (AIDS) results from infection with a human immunodeficiency virus (HIV). The long terminal repeat (LTR) region of HIV proviral DNA contains binding sites for nuclear factor kappa B (NF-kappa B), and this transcriptional activator appears to regulate HIV activation. Recent findings suggest an involvement of reactive oxygen species (ROS) in signal transduction pathways leading to NF-kappa B activation. The present study was based on reports that antioxidants which eliminate ROS should block the activation of NF-kappa B and subsequently HIV transcription, and thus antioxidants can be used as therapeutic agents for AIDS. Incubation of Jurkat T cells (1 x 10(6) cells/ml) with a natural thiol antioxidant, alpha-lipoic acid, prior to the stimulation of cells was found to inhibit NF-kappa B activation induced by tumor necrosis factor-alpha (25 ng/ml) or by phorbol 12-myristate 13-acetate (50 ng/ml). The inhibitory action of alpha-lipoic acid was found to be very potent as only 4 mM was needed for a complete inhibition, whereas 20 mM was required for N-acetylcysteine. These results indicate that alpha-lipoic acid may be effective in AIDS therapeutics. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Activation of lymphokine genes in T cells: role of cis-acting DNA elements that respond to T cell activation signals. \nActivation of T cells is initiated by the recognition of antigen on antigen presenting cells to exert the effector functions in immune and inflammatory responses. Two types of helper T cell (Th) clones (Th1 and Th2) are defined on the basis of different patterns of cytokine (lymphokine) secretion. They determine the outcome of an antigenic response toward humoral or cell-mediated immunity. Although lymphokine genes are coordinately regulated upon antigen stimulation, they are regulated by the mechanisms common to all as well as those which are unique to each gene. For most lymphokine genes, a combination of phorbol esters (phorbol 12-myristate 13 acetate, PMA) and calcium ionophores (A23187) is required for their maximal induction. Yet phorbol ester alone or calcium ionophore alone produce several lymphokines. The production of the granulocyte-macrophage colony stimulating factor (GM-CSF) is completely dependent on the two signals. We have previously found a cis-acting region spanning the GM-CSF promoter region (positions -95 to +27) that confers inducibility to reporter genes in transient transfection assays. Further analysis identified three elements required for efficient induction, referred to as GM2, GC-box and conserved lymphokine element (CLE0). GM2 defines a binding site for protein(s) whose binding is inducible by PMA. One protein, NF-GM2 is similar to the transcription factor NF-kB. GC-box is a binding site for constitutively bound proteins. CLEO defines a binding site for protein(s) whose optimum binding is stimulated by PMA and A23187. Viral trans-activators such as Tax (human T cell leukemia virus-1, HTLV-1) and E2 (bovine papilloma virus, BPV) proteins are other agents which activate lymphokine gene expression by bypassing T cell receptor (TCR) mediated signaling. The trans-activation domain of E2 and Tax is interchangeable although they have no obvious sequence homology between them. The viral trans-activators appear to target specific DNA binding protein such as NF-kB and Sp1 to cis-acting DNA site and promote lymphokine gene expression without TCR-mediated stimulation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "target", "start": 2088, "end": 2094}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 2142, "end": 2145}]}], "gene expression": [{"trigger": {"text": "production", "start": 945, "end": 955}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1013, "end": 1019}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 1035, "end": 1044}, "arguments": [{"role": "Theme", "text": "production", "start": 945, "end": 955}]}, {"trigger": {"text": "target", "start": 2088, "end": 2094}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1724, "end": 1727}, {"role": "Theme", "text": "target", "start": 2088, "end": 2094}]}, {"trigger": {"text": "target", "start": 2088, "end": 2094}, "arguments": [{"role": "Cause", "text": "E2", "start": 1772, "end": 1774}, {"role": "Theme", "text": "target", "start": 2088, "end": 2094}]}]}}, "schema": []}
{"input": "I kappa B/MAD-3 masks the nuclear localization signal of NF-kappa B p65 and requires the transactivation domain to inhibit NF-kappa B p65 DNA binding. \nThe active nuclear form of the NF-kappa B transcription factor complex is composed of two DNA binding subunits, NF-kappa B p65 and NF-kappa B p50, both of which share extensive N-terminal sequence homology with the v-rel oncogene product. The NF-kappa B p65 subunit provides the transactivation activity in this complex and serves as an intracellular receptor for a cytoplasmic inhibitor of NF-kappa B, termed I kappa B. In contrast, NF-kappa B p50 alone fails to stimulate kappa B-directed transcription, and based on prior in vitro studies, is not directly regulated by I kappa B. To investigate the molecular basis for the critical regulatory interaction between NF-kappa B and I kappa B/MAD-3, a series of human NF-kappa B p65 mutants was identified that functionally segregated DNA binding, I kappa B-mediated inhibition, and I kappa B-induced nuclear exclusion of this transcription factor. Results from in vivo expression studies performed with these NF-kappa B p65 mutants revealed the following: 1) I kappa B/MAD-3 completely inhibits NF-kappa B p65-dependent transcriptional activation mediated through the human immunodeficiency virus type 1 kappa B enhancer in human T lymphocytes, 2) the binding of I kappa B/MAD-3 to NF-kappa B p65 is sufficient to retarget NF-kappa B p65 from the nucleus to the cytoplasm, 3) selective deletion of the functional nuclear localization signal present in the Rel homology domain of NF-kappa B p65 disrupts its ability to engage I kappa B/MAD-3, and 4) the unique C-terminus of NF-kappa B p65 attenuates its own nuclear localization and contains sequences that are required for I kappa B-mediated inhibition of NF-kappa B p65 DNA binding activity. Together, these findings suggest that the nuclear localization signal and transactivation domain of NF-kappa B p65 constitute a bipartite system that is critically involved in the inhibitory function of I kappa B/MAD-3. Unexpectedly, our in vivo studies also demonstrate that I kappa B/MAD-3 binds directly to NF-kappa B p50. This interaction is functional as it leads to retargeting of NF-kappa B p50 from the nucleus to the cytoplasm. However, no loss of DNA binding activity is observed, presumably reflecting the unique C-terminal domain that is distinct from that present in NF-kappa B p65. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 142, "end": 149}, "arguments": [{"role": "Theme", "text": "p65", "start": 134, "end": 137}]}, {"trigger": {"text": "complex", "start": 215, "end": 222}, "arguments": [{"role": "Theme", "text": "p65", "start": 275, "end": 278}, {"role": "Theme2", "text": "p50", "start": 294, "end": 297}]}, {"trigger": {"text": "binding", "start": 246, "end": 253}, "arguments": [{"role": "Theme", "text": "p65", "start": 275, "end": 278}]}, {"trigger": {"text": "binding", "start": 246, "end": 253}, "arguments": [{"role": "Theme", "text": "p50", "start": 294, "end": 297}]}, {"trigger": {"text": "receptor", "start": 503, "end": 511}, "arguments": [{"role": "Theme", "text": "p65", "start": 406, "end": 409}]}, {"trigger": {"text": "binding", "start": 1353, "end": 1360}, "arguments": [{"role": "Theme", "text": "MAD-3", "start": 1374, "end": 1379}, {"role": "Theme2", "text": "p65", "start": 1394, "end": 1397}]}, {"trigger": {"text": "engage", "start": 1619, "end": 1625}, "arguments": [{"role": "Theme", "text": "p65", "start": 1591, "end": 1594}, {"role": "Theme2", "text": "MAD-3", "start": 1636, "end": 1641}]}, {"trigger": {"text": "binding", "start": 1827, "end": 1834}, "arguments": [{"role": "Theme", "text": "p65", "start": 1819, "end": 1822}]}, {"trigger": {"text": "binds", "start": 2137, "end": 2142}, "arguments": [{"role": "Theme", "text": "MAD-3", "start": 2131, "end": 2136}, {"role": "Theme2", "text": "p50", "start": 2166, "end": 2169}]}], "localization": [{"trigger": {"text": "retarget", "start": 1415, "end": 1423}, "arguments": [{"role": "Theme", "text": "p65", "start": 1435, "end": 1438}, {"role": "ToLoc", "text": "cytoplasm", "start": 1463, "end": 1472}]}, {"trigger": {"text": "localization", "start": 1717, "end": 1729}, "arguments": [{"role": "Theme", "text": "p65", "start": 1686, "end": 1689}, {"role": "ToLoc", "text": "nuclear", "start": 1709, "end": 1716}]}, {"trigger": {"text": "retargeting", "start": 2217, "end": 2228}, "arguments": [{"role": "Theme", "text": "p50", "start": 2243, "end": 2246}, {"role": "ToLoc", "text": "cytoplasm", "start": 2271, "end": 2280}]}], "negative regulation": [{"trigger": {"text": "masks", "start": 16, "end": 21}, "arguments": [{"role": "Cause", "text": "MAD-3", "start": 10, "end": 15}, {"role": "Site", "text": "nuclear localization signal", "start": 26, "end": 53}, {"role": "Theme", "text": "p65", "start": 68, "end": 71}]}, {"trigger": {"text": "inhibit", "start": 115, "end": 122}, "arguments": [{"role": "Cause", "text": "MAD-3", "start": 10, "end": 15}, {"role": "Theme", "text": "binding", "start": 142, "end": 149}]}, {"trigger": {"text": "deletion", "start": 1487, "end": 1495}, "arguments": [{"role": "Site", "text": "nuclear localization signal", "start": 1514, "end": 1541}, {"role": "Theme", "text": "p65", "start": 1591, "end": 1594}]}, {"trigger": {"text": "disrupts", "start": 1595, "end": 1603}, "arguments": [{"role": "Cause", "text": "deletion", "start": 1487, "end": 1495}, {"role": "Theme", "text": "engage", "start": 1619, "end": 1625}]}, {"trigger": {"text": "attenuates", "start": 1690, "end": 1700}, "arguments": [{"role": "CSite", "text": "C-terminus", "start": 1661, "end": 1671}, {"role": "Cause", "text": "p65", "start": 1686, "end": 1689}, {"role": "Theme", "text": "localization", "start": 1717, "end": 1729}]}, {"trigger": {"text": "inhibition", "start": 1794, "end": 1804}, "arguments": [{"role": "Theme", "text": "binding", "start": 1827, "end": 1834}]}], "positive regulation": [{"trigger": {"text": "sufficient", "start": 1401, "end": 1411}, "arguments": [{"role": "Cause", "text": "binding", "start": 1353, "end": 1360}, {"role": "Theme", "text": "retarget", "start": 1415, "end": 1423}]}, {"trigger": {"text": "required", "start": 1762, "end": 1770}, "arguments": [{"role": "CSite", "text": "C-terminus", "start": 1661, "end": 1671}, {"role": "Cause", "text": "p65", "start": 1686, "end": 1689}, {"role": "Theme", "text": "inhibition", "start": 1794, "end": 1804}]}, {"trigger": {"text": "leads", "start": 2208, "end": 2213}, "arguments": [{"role": "Cause", "text": "binds", "start": 2137, "end": 2142}, {"role": "Theme", "text": "retargeting", "start": 2217, "end": 2228}]}], "regulation": [{"trigger": {"text": "regulated", "start": 711, "end": 720}, "arguments": [{"role": "Theme", "text": "p50", "start": 597, "end": 600}]}]}}, "schema": []}
{"input": "Simple derivation of TFIID-dependent RNA polymerase II transcription systems from Schizosaccharomyces pombe and other organisms, and factors required for transcriptional activation. \nResolution of whole cell extract through two chromatographic steps yields a single protein fraction requiring only the addition of TFIID for the initiation of transcription at RNA polymerase II promoters. This approach allows the convenient generation of RNA polymerase II transcription systems from Saccharomyces cerevisiae, human lymphocytes, and Schizosaccharomyces pombe. TFIIDs from all three organisms are interchangeable among all three systems. The S. cerevisiae and Sch. pombe systems support effects of acidic activator proteins, provided a further protein fraction from S. cerevisiae is supplied. This further fraction is distinct from the mediator of transcriptional activation described previously and represents a second component in addition to general initiation factors that may facilitate a response to acidic activators. ", "output": {"json_structures": {}}, "schema": []}
{"input": "NF-kappa B-dependent induction of the NF-kappa B p50 subunit gene promoter underlies self-perpetuation of human immunodeficiency virus transcription in monocytic cells. \nThe molecular mechanisms underlying the sustained nuclear translocation of NF-kappa B observed in U937 monocytic cells chronically infected with human immunodeficiency virus (HIV) were studied. The activity of the promoter regulating the synthesis of the p105 precursor of the NF-kappa B p50 subunit was enhanced in these cells. Deletions in this promoter indicated that this upregulation was mediated through the NF-kappa B- but not the AP-1-binding motif, by bona fide p50/p65 heterodimers. Analysis of cytosolic extracts indicated that NF-kappa B levels were increased in HIV-infected cells. In contrast to the transient NF-kappa B activation induced by phorbol ester, the permanent NF-kappa B translocation induced by HIV infection was not dependent on PKC isoenzymes alpha and beta as shown by the use of a specific inhibitor (GF 109203X). These observations indicate that during chronic HIV infection of U937 cells, continuous NF-kappa B (p50/p65) translocation results in p105 promoter upregulation with subsequent cytosolic NF-kappa B accumulation, ready for further translocation. This HIV-mediated mechanism results in a self-perpetuating loop of NF-kappa B production. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "synthesis", "start": 408, "end": 417}, "arguments": [{"role": "Theme", "text": "p105", "start": 425, "end": 429}]}], "localization": [{"trigger": {"text": "translocation", "start": 1124, "end": 1137}, "arguments": [{"role": "Theme", "text": "p50", "start": 1115, "end": 1118}]}, {"trigger": {"text": "translocation", "start": 1124, "end": 1137}, "arguments": [{"role": "Theme", "text": "p65", "start": 1119, "end": 1122}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 991, "end": 1000}, "arguments": [{"role": "Theme", "text": "PKC isoenzymes alpha", "start": 927, "end": 947}]}, {"trigger": {"text": "inhibitor", "start": 991, "end": 1000}, "arguments": [{"role": "Theme", "text": "beta", "start": 952, "end": 956}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 21, "end": 30}, "arguments": [{"role": "Theme", "text": "p50", "start": 49, "end": 52}, {"role": "Site", "text": "promoter", "start": 66, "end": 74}]}, {"trigger": {"text": "perpetuation", "start": 90, "end": 102}, "arguments": [{"role": "Theme", "text": "transcription", "start": 135, "end": 148}]}, {"trigger": {"text": "enhanced", "start": 474, "end": 482}, "arguments": [{"role": "Theme", "text": "regulating", "start": 393, "end": 403}]}, {"trigger": {"text": "results", "start": 1138, "end": 1145}, "arguments": [{"role": "Cause", "text": "translocation", "start": 1124, "end": 1137}, {"role": "Theme", "text": "upregulation", "start": 1163, "end": 1175}]}, {"trigger": {"text": "upregulation", "start": 1163, "end": 1175}, "arguments": [{"role": "Theme", "text": "p105", "start": 1149, "end": 1153}, {"role": "Site", "text": "promoter", "start": 1154, "end": 1162}]}], "regulation": [{"trigger": {"text": "underlies", "start": 75, "end": 84}, "arguments": [{"role": "Cause", "text": "induction", "start": 21, "end": 30}, {"role": "Theme", "text": "perpetuation", "start": 90, "end": 102}]}, {"trigger": {"text": "regulating", "start": 393, "end": 403}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 408, "end": 417}]}, {"trigger": {"text": "mediated", "start": 563, "end": 571}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 474, "end": 482}, {"role": "Cause", "text": "p50", "start": 641, "end": 644}]}, {"trigger": {"text": "mediated", "start": 563, "end": 571}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 474, "end": 482}, {"role": "Cause", "text": "p65", "start": 645, "end": 648}]}, {"trigger": {"text": "mediated", "start": 563, "end": 571}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 474, "end": 482}]}], "transcription": [{"trigger": {"text": "transcription", "start": 135, "end": 148}, "arguments": [{"role": "Theme", "text": "p50", "start": 49, "end": 52}]}]}}, "schema": []}
{"input": "TAR-independent transactivation by Tat in cells derived from the CNS: a novel mechanism of HIV-1 gene regulation. \nThe Tat protein of human immunodeficiency virus type 1 (HIV-1) is essential for productive infection and is a potential target for antiviral therapy. Tat, a potent activator of HIV-1 gene expression, serves to greatly increase the rate of transcription directed by the viral promoter. This induction, which seems to be an important component in the progression of acquired immune deficiency syndrome (AIDS), may be due to increased transcriptional initiation, increased transcriptional elongation, or a combination of these processes. Much attention has been focused on the interaction of Tat with a specific RNA target termed TAR (transactivation responsive) which is present in the leader sequence of all HIV-1 mRNAs. This interaction is believed to be an important component of the mechanism of transactivation. In this report we demonstrate that in certain CNS-derived cells Tat is capable of activating HIV-1 through a TAR-independent pathway. A Tat-responsive element is found upstream within the viral promoter that in glial-derived cell lines allows transactivation in the absence of TAR. Deletion mapping and hybrid promoter constructs demonstrate that the newly identified Tat-responsive element corresponds to a sequence within the viral long terminal repeat (LTR) previously identified as the HIV-1 enhancer, or NF-kappa B domain. DNA band-shift analysis reveals NF-kappa B binding activity in glial cells that differs from that present in T lymphoid cells. Further, we observe that TAR-deleted mutants of HIV-1 demonstrate normal late gene expression in glial cells as evidenced by syncytia formation and production of viral p24 antigen. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 689, "end": 700}, "arguments": [{"role": "Theme", "text": "Tat", "start": 704, "end": 707}]}], "gene expression": [{"trigger": {"text": "production", "start": 1733, "end": 1743}, "arguments": [{"role": "Theme", "text": "p24", "start": 1753, "end": 1756}]}]}}, "schema": []}
{"input": "Mitogen stimulation of T-cells increases c-Fos and c-Jun protein levels, AP-1 binding and AP-1 transcriptional activity. \nWe have analysed the effect of mitogenic lectins on c-Fos and c-Jun protein levels as well as on activator protein-1 (AP-1) binding and enhancer activity in Jurkat T-cells. Both c-Fos and c-Jun protein levels were increased after Con A and PHA stimulation. Since T-cell stimulation increases both intracellular Ca2+ and cAMP levels and activates protein kinase C (PKC), the possible involvement of these intracellular messengers in c-Fos and c-Jun induction was tested. PMA, which directly activates PKC, mimicked the effect of the lectins on c-Fos and c-Jun, but elevation of either intracellular Ca2+ or cAMP levels had little or no effect. The mitogen-induced increase of c-Fos and c-Jun immunoreactivity was inhibited by H-7, a kinase inhibitor with relatively high specificity for PKC, and less efficiently by H-8, a structurally related kinase inhibitor less active on PKC, but more active on cyclic nucleotide-dependent kinases. Con A stimulation was found to increase both binding of AP-1 to the AP-1 consensus sequence, TRE, and AP-1 enhancer activity, in Jurkat cells. PMA was also found to increase the AP-1 enhancer activity, whereas elevation of Ca2+ or cAMP had only minor effects. We conclude that stimulation with mitogenic lectins is sufficient to increase both c-Fos and c-Jun protein levels, AP-1 binding and AP-1 enhancer activity in Jurkat cells and that they act via mechanisms that could involve the activation of PKC. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibited", "start": 834, "end": 843}, "arguments": [{"role": "Theme", "text": "increase", "start": 785, "end": 793}]}, {"trigger": {"text": "inhibitor", "start": 861, "end": 870}, "arguments": [{"role": "Theme", "text": "PKC", "start": 908, "end": 911}]}, {"trigger": {"text": "inhibitor", "start": 972, "end": 981}, "arguments": [{"role": "Theme", "text": "PKC", "start": 908, "end": 911}]}, {"trigger": {"text": "inhibitor", "start": 972, "end": 981}, "arguments": [{"role": "Theme", "text": "PKC", "start": 997, "end": 1000}]}], "positive regulation": [{"trigger": {"text": "increases", "start": 31, "end": 40}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 41, "end": 46}]}, {"trigger": {"text": "increases", "start": 31, "end": 40}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 51, "end": 56}]}, {"trigger": {"text": "increased", "start": 336, "end": 345}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 300, "end": 305}]}, {"trigger": {"text": "increased", "start": 336, "end": 345}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 310, "end": 315}]}, {"trigger": {"text": "induction", "start": 570, "end": 579}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 554, "end": 559}]}, {"trigger": {"text": "induction", "start": 570, "end": 579}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 564, "end": 569}]}, {"trigger": {"text": "activates", "start": 612, "end": 621}, "arguments": [{"role": "Theme", "text": "PKC", "start": 622, "end": 625}]}, {"trigger": {"text": "mimicked the effect of the lectins", "start": 627, "end": 661}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 665, "end": 670}]}, {"trigger": {"text": "mimicked the effect of the lectins", "start": 627, "end": 661}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 675, "end": 680}]}, {"trigger": {"text": "increase", "start": 785, "end": 793}, "arguments": [{"role": "Theme", "text": "immunoreactivity", "start": 813, "end": 829}]}, {"trigger": {"text": "increase", "start": 1387, "end": 1395}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 1401, "end": 1406}]}, {"trigger": {"text": "increase", "start": 1387, "end": 1395}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 1411, "end": 1416}]}, {"trigger": {"text": "activation", "start": 1545, "end": 1555}, "arguments": [{"role": "Theme", "text": "PKC", "start": 1559, "end": 1562}]}], "regulation": [{"trigger": {"text": "effect", "start": 143, "end": 149}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 174, "end": 179}]}, {"trigger": {"text": "effect", "start": 143, "end": 149}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 184, "end": 189}]}, {"trigger": {"text": "involvement", "start": 505, "end": 516}, "arguments": [{"role": "Theme", "text": "induction", "start": 570, "end": 579}]}, {"trigger": {"text": "effect", "start": 757, "end": 763}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 665, "end": 670}]}, {"trigger": {"text": "effect", "start": 757, "end": 763}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 675, "end": 680}]}, {"trigger": {"text": "immunoreactivity", "start": 813, "end": 829}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 797, "end": 802}]}, {"trigger": {"text": "immunoreactivity", "start": 813, "end": 829}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 807, "end": 812}]}, {"trigger": {"text": "involve", "start": 1533, "end": 1540}, "arguments": [{"role": "Theme", "text": "activation", "start": 1545, "end": 1555}]}]}}, "schema": []}
{"input": "Okadaic acid is a potent inducer of AP-1, NF-kappa B, and tumor necrosis factor-alpha in human B lymphocytes. \nTreatment of human B lymphocytes with an optimal concentration of okadaic acid, an inhibitor of phosphatases 1 and 2A, resulted in the induction of the transcription factor, AP-1 and a marked increase in NF-kappa B levels. In contrast, no effect on the levels of the octamer binding proteins, Oct-1 or Oct-2, were found. Since both AP-1 and NF-kappa B have been reported to be important in the induction of the tumor necrosis factor-alpha (TNF-alpha) gene we examined the effects of okadaic acid on TNF-alpha mRNA levels. Treatment with okadaic acid resulted in a striking increase in TNF-alpha mRNA transcripts within 1 h of stimulation and large amounts of TNF-alpha were released into the culture media. Although okadaic acid provides a potent inductive signal for AP-1 and NF-kappa B it did not induce either B cell proliferation or immunoglobulin secretion. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "induction", "start": 505, "end": 514}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 551, "end": 560}]}], "localization": [{"trigger": {"text": "released", "start": 785, "end": 793}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 770, "end": 779}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 194, "end": 203}, "arguments": [{"role": "Theme", "text": "phosphatases 1", "start": 207, "end": 221}]}, {"trigger": {"text": "inhibitor", "start": 194, "end": 203}, "arguments": [{"role": "Theme", "text": "2A", "start": 226, "end": 228}]}], "positive regulation": [{"trigger": {"text": "inducer", "start": 25, "end": 32}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 58, "end": 85}]}, {"trigger": {"text": "effect", "start": 350, "end": 356}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 404, "end": 409}]}, {"trigger": {"text": "effect", "start": 350, "end": 356}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 413, "end": 418}]}, {"trigger": {"text": "important", "start": 488, "end": 497}, "arguments": [{"role": "Theme", "text": "induction", "start": 505, "end": 514}]}, {"trigger": {"text": "increase", "start": 684, "end": 692}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 696, "end": 705}]}, {"trigger": {"text": "large amounts", "start": 753, "end": 766}, "arguments": [{"role": "Cause", "text": "increase", "start": 684, "end": 692}, {"role": "Theme", "text": "released", "start": 785, "end": 793}]}], "regulation": [{"trigger": {"text": "important", "start": 488, "end": 497}, "arguments": [{"role": "Theme", "text": "induction", "start": 505, "end": 514}]}, {"trigger": {"text": "effects", "start": 583, "end": 590}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 610, "end": 619}]}]}}, "schema": []}
{"input": "A novel Ets-related transcription factor, Elf-1, binds to human immunodeficiency virus type 2 regulatory elements that are required for inducible trans activation in T cells. \nHuman immunodeficiency virus type 1 (HIV-1) and HIV-2 are structurally related retroviruses which both cause AIDS in humans. Although both viruses establish latency in quiescent human-peripheral-blood T cells, the asymptomatic phase of HIV-2 infection may be more prolonged than that of HIV-1. The latent phases of both HIV-1 and HIV-2 infection have been shown to be disrupted by T-cell activation, a process that requires host cell transcription factors. In the case of HIV-1, the transcription factor NF-kappa B is sufficient for inducible transcriptional activation. In contrast, factors in addition to NF-kappa B are required to activate HIV-2 transcription in infected T cells. In this report, we demonstrate that a novel Ets-related transcription factor, Elf-1, binds specifically to two purine-rich motifs in the HIV-2 enhancer. Mutagenesis experiments demonstrated that these Elf-1 binding sites are required for induction of HIV-2 transcription following T-cell-receptor-mediated T-cell activation. Moreover, Elf-1 is the only factor present in activated T-cell nuclear extracts that binds to these sites in electrophoretic mobility shift assays. Thus, Elf-1 is a novel transcription factor that appears to be required for the T-cell-receptor-mediated trans activation of HIV-2 gene expression. These results may explain differences in the clinical spectra of diseases caused by HIV-1 and HIV-2 and may also have implications for the design of therapeutic approaches to HIV-2 infection. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 49, "end": 54}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 42, "end": 47}]}, {"trigger": {"text": "binds", "start": 945, "end": 950}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 938, "end": 943}]}, {"trigger": {"text": "binds", "start": 1270, "end": 1275}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 1195, "end": 1200}]}]}}, "schema": []}
{"input": "Human immunodeficiency virus type 1 Nef protein inhibits NF-kappa B induction in human T cells. \nHuman immunodeficiency virus type 1 (HIV-1) can establish a persistent and latent infection in CD4+ T lymphocytes (W.C.Greene, N.Engl.J. Med.324:308-317, 1991; S.M.Schnittman, M.C.Psallidopoulos, H.C. Lane, L.Thompson, M.Baseler, F.Massari, C.H.Fox, N.P.Salzman, and A.S.Fauci, Science 245:305-308, 1989). Production of HIV-1 from latently infected cells requires host cell activation by T-cell mitogens (T.Folks, D.M.Powell, M.M.Lightfoote, S.Benn, M.A. Martin, and A.S.Fauci, Science 231:600-602, 1986; D.Zagury, J. Bernard, R.Leonard, R.Cheynier, M.Feldman, P.S.Sarin, and R.C. Gallo, Science 231:850-853, 1986). This activation is mediated by the host transcription factor NF-kappa B [G.Nabel and D.Baltimore, Nature (London) 326:711-717, 1987]. We report here that the HIV-1-encoded Nef protein inhibits the induction of NF-kappa B DNA-binding activity by T- cell mitogens. However, Nef does not affect the DNA-binding activity of other transcription factors implicated in HIV-1 regulation, including SP-1, USF, URS, and NF-AT. Additionally, Nef inhibits the induction of HIV-1- and interleukin 2-directed gene expression, and the effect on HIV-1 transcription depends on an intact NF-kappa B-binding site. These results indicate that defective recruitment of NF-kappa B may underlie Nef's negative transcriptional effects on the HIV-1 and interleukin 2 promoters. Further evidence suggests that Nef inhibits NF-kappa B induction by interfering with a signal derived from the T-cell receptor complex. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1013, "end": 1020}, "arguments": [{"role": "Theme", "text": "SP-1", "start": 1103, "end": 1107}]}], "negative regulation": [{"trigger": {"text": "negative transcriptional effects", "start": 1392, "end": 1424}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 1442, "end": 1455}, {"role": "Site", "text": "promoters", "start": 1456, "end": 1465}]}], "positive regulation": [{"trigger": {"text": "underlie", "start": 1377, "end": 1385}, "arguments": [{"role": "Theme", "text": "negative transcriptional effects", "start": 1392, "end": 1424}]}], "regulation": [{"trigger": {"text": "affect", "start": 998, "end": 1004}, "arguments": [{"role": "Cause", "text": "Nef", "start": 985, "end": 988}, {"role": "Theme", "text": "binding", "start": 1013, "end": 1020}]}]}}, "schema": []}
{"input": "A novel mitogen-inducible gene product related to p50/p105-NF-kappa B participates in transactivation through a kappa B site. \nA Rel-related, mitogen-inducible, kappa B-binding protein has been cloned as an immediate-early activation gene of human peripheral blood T cells. The cDNA has an open reading frame of 900 amino acids capable of encoding a 97-kDa protein. This protein is most similar to the 105-kDa precursor polypeptide of p50-NF-kappa B. Like the 105-kDa precursor, it contains an amino-terminal Rel-related domain of about 300 amino acids and a carboxy-terminal domain containing six full cell cycle or ankyrin repeats. In vitro-translated proteins, truncated downstream of the Rel domain and excluding the repeats, bind kappa B sites. We refer to the kappa B-binding, truncated protein as p50B by analogy with p50-NF-kappa B and to the full-length protein as p97. p50B is able to form heteromeric kappa B-binding complexes with RelB, as well as with p65 and p50, the two subunits of NF-kappa B. Transient-transfection experiments in embryonal carcinoma cells demonstrate a functional cooperation between p50B and RelB or p65 in transactivation of a reporter plasmid dependent on a kappa B site. The data imply the existence of a complex family of NF-kappa B-like transcription factors. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 774, "end": 781}, "arguments": [{"role": "Theme", "text": "p50B", "start": 804, "end": 808}]}, {"trigger": {"text": "binding", "start": 920, "end": 927}, "arguments": [{"role": "Theme", "text": "p50B", "start": 879, "end": 883}]}, {"trigger": {"text": "binding", "start": 920, "end": 927}, "arguments": [{"role": "Theme", "text": "RelB", "start": 943, "end": 947}]}, {"trigger": {"text": "binding", "start": 920, "end": 927}, "arguments": [{"role": "Theme", "text": "p65", "start": 965, "end": 968}]}, {"trigger": {"text": "binding", "start": 920, "end": 927}, "arguments": [{"role": "Theme", "text": "p50", "start": 973, "end": 976}]}, {"trigger": {"text": "complexes", "start": 928, "end": 937}, "arguments": [{"role": "Theme", "text": "p50B", "start": 879, "end": 883}, {"role": "Theme2", "text": "RelB", "start": 943, "end": 947}]}, {"trigger": {"text": "complexes", "start": 928, "end": 937}, "arguments": [{"role": "Theme", "text": "p50B", "start": 879, "end": 883}, {"role": "Theme2", "text": "p65", "start": 965, "end": 968}]}, {"trigger": {"text": "complexes", "start": 928, "end": 937}, "arguments": [{"role": "Theme", "text": "p50B", "start": 879, "end": 883}, {"role": "Theme2", "text": "p50", "start": 973, "end": 976}]}]}}, "schema": []}
{"input": "Transcriptional regulation during T-cell development: the alpha TCR gene as a molecular model. \nThe regulation of gene expression during lymphocyte differentiation is a complex process involving interactions between multiple positive and negative transcriptional regulatory elements. In this article, transcriptional regulation of the archetypal T-cell-specific gene, alpha TCR, is discussed. Major recent developments, including the identification of novel families of transcription factors that regulate multiple T-cell genes during thymocyte ontogeny and T-cell activation, are described. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "regulation", "start": 16, "end": 26}, "arguments": [{"role": "Theme", "text": "Transcriptional", "start": 0, "end": 15}]}, {"trigger": {"text": "transcriptional regulation", "start": 301, "end": 327}, "arguments": [{"role": "Theme", "text": "alpha TCR", "start": 368, "end": 377}]}], "transcription": [{"trigger": {"text": "Transcriptional", "start": 0, "end": 15}, "arguments": [{"role": "Theme", "text": "alpha TCR", "start": 58, "end": 67}]}]}}, "schema": []}
{"input": "An 11-base-pair DNA sequence motif apparently unique to the human interleukin 4 gene confers responsiveness to T-cell activation signals. \nWe have identified a DNA segment that confers responsiveness to antigen stimulation signals on the human interleukin (IL) 4 gene in Jurkat cells. The human IL-4 gene, of 10 kilobases, is composed of four exons and three introns. A cis-acting element (P sequence) resides in the 5' upstream region; no additional DNA segments with enhancer activity were identified in the human IL-4 gene. For further mapping purposes, a fusion promoter was constructed with the granulocyte/macrophage colony-stimulating factor basic promoter containing 60 base pairs of sequence upstream from the cap site of the mouse granulocyte/macrophage colony-stimulating factor gene and various lengths of the 5' upstream sequence of the IL-4 gene. The P sequence was located between positions -79 and -69 relative to the transcription start site of the human IL-4 gene, and this location was confirmed by base-substitution mutations. The plasmids carrying multiple copies of the P sequence showed higher responsiveness to the stimulation. The binding protein(s) that recognize the P sequence of the IL-4 gene were identified by DNA-mobility-shift assays. The binding of NF(P) (a DNA binding protein that specifically recognizes the P sequence) to the P sequence was abolished when oligonucleotides carrying base substitutions were used, indicating that the NF(P) interaction is sequence-specific and that binding specificity of the protein paralleled the sequence requirements for IL-4 expression in vivo. The P sequence does not share homology with the 5' upstream sequence of the IL-2 gene, even though surrounding sequences of the IL-4 gene share high homology with the IL-2 gene. We conclude that a different set of proteins recognize IL-2 and IL-4 genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recognize", "start": 1180, "end": 1189}, "arguments": [{"role": "Site", "text": "P sequence", "start": 1194, "end": 1204}, {"role": "Theme", "text": "IL-4", "start": 1212, "end": 1216}]}, {"trigger": {"text": "recognize", "start": 1842, "end": 1851}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1852, "end": 1856}]}, {"trigger": {"text": "recognize", "start": 1842, "end": 1851}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1861, "end": 1865}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1599, "end": 1609}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1594, "end": 1598}]}], "positive regulation": [{"trigger": {"text": "confers", "start": 177, "end": 184}, "arguments": [{"role": "Theme", "text": "responsiveness", "start": 185, "end": 199}]}, {"trigger": {"text": "requirements", "start": 1577, "end": 1589}, "arguments": [{"role": "Theme", "text": "expression", "start": 1599, "end": 1609}]}], "regulation": [{"trigger": {"text": "responsiveness", "start": 185, "end": 199}, "arguments": [{"role": "Theme", "text": "interleukin (IL) 4", "start": 244, "end": 262}]}]}}, "schema": []}
{"input": "Activation of the human immunodeficiency virus type 1 enhancer is not dependent on NFAT-1. \nThe function of a putative NFAT-1 site in the human immunodeficiency virus type 1 enhancer has been analyzed. Activation by the T-cell antigen receptor is minimal in Jurkat cells and is mediated by the kappa B sites. The putative NFAT-1 region is not required for the response to anti-CD3 or to mitogens in T-cell, B-cell, or monocyte/macrophage leukemia lines, nor is it a cis-acting negative regulatory element. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Interleukin 6-induced differentiation of a human B cell line into IgM-secreting plasma cells is mediated by c-fos. \nThe role of the protooncogene c-fos in interleukin (IL) 6-induced B cell differentiation was assessed. Treatment of SKW 6.4 cells with IL 6 induced a transient and early stimulation of c-fos sense mRNA expression. The effect appeared within 30 min and returned to basal levels after 2 h. The addition of antisense oligonucleotides to c-fos significantly inhibited IL 6-induced IgM production by SKW 6.4 cells (p less than 0.001), whereas control oligonucleotides had no inhibitory effect. These results indicate that activation of c-fos is involved in IL 6-induced differentiation of SKW 6.4 cells into IgM-secreting cells. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "returned", "start": 368, "end": 376}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 286, "end": 297}]}], "positive regulation": [{"trigger": {"text": "stimulation", "start": 286, "end": 297}, "arguments": [{"role": "Theme", "text": "expression", "start": 318, "end": 328}]}, {"trigger": {"text": "appeared", "start": 341, "end": 349}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 286, "end": 297}]}, {"trigger": {"text": "activation", "start": 633, "end": 643}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 647, "end": 652}]}], "transcription": [{"trigger": {"text": "expression", "start": 318, "end": 328}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 301, "end": 306}]}]}}, "schema": []}
{"input": "Binding of erythroid and non-erythroid nuclear proteins to the silencer of the human epsilon-globin-encoding gene. \nTo clarify the molecular mechanisms involved in the developmental control of hemoglobin-encoding genes we have been studying the expression of these genes in human cells in continuous culture. We have previously reported the presence of a transcriptional control element with the properties of a silencer extending from -392 to -177 bp relative to the cap site of the human epsilon-globin-encoding gene [Cao et al., Proc.Natl.Acad.Sci.USA 86 (1989) 5306-5309]. We also showed that this silencer has stronger inhibitory activity in HeLa cells, as compared to K562 human erythroleukemia cells. Using deletion mutants and cis-cloned synthetic oligodeoxyribonucleotides in transient expression assays, nucleotide sequences responsible for this effect have now been further delimited to 44 bp located from -294 to -251 bp. Gel electrophoresis mobility shift assays and DNaseI footprinting assays demonstrate that these negative regulatory sequences are recognized differently by proteins present in nuclear extracts obtained from HeLa and K562 cells. Two binding proteins are detected in K562 nuclear extracts, while only one is found in extracts from HeLa cells. Possible mechanisms by which these proteins may regulate transcription of the epsilon-globin-encoding gene in erythroid and non-erythroid cells are discussed. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "regulate", "start": 1323, "end": 1331}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1332, "end": 1345}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1332, "end": 1345}, "arguments": [{"role": "Theme", "text": "epsilon-globin", "start": 1353, "end": 1367}]}]}}, "schema": []}
{"input": "T cell-specific negative regulation of transcription of the human cytokine IL-4. \nIL-4 secreted by activated T cells is a pleiotropic cytokine affecting growth and differentiation of diverse cell types such as T cells, B cells, and mast cells. We investigated the upstream regulatory elements of the human IL-4 promoter. A novel T cell-specific negative regulatory element (NRE) composed of two protein-binding sites were mapped in the 5' flanking region of the IL-4 gene: -311CTCCCTTCT-303 (NRE-I) and -288CTTTTTGCTT-TGC-300 (NRE-II). A T cell-specific protein Neg-1 and a ubiquitous protein Neg-2 binding to NRE-I and NRE-II, respectively, were identified. Furthermore, a positive regulatory element was found 45 bp downstream of the NRE. The enhancer activity of the PRE was completely suppressed when the NRE was present. These data suggest that IL-4 promoter activity is normally down-regulated by an NRE via repression of the enhancer positive regulatory element. These data may have implications for the stringent control of IL-4 expression in T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 599, "end": 606}, "arguments": [{"role": "Theme", "text": "Neg-1", "start": 562, "end": 567}]}, {"trigger": {"text": "binding", "start": 599, "end": 606}, "arguments": [{"role": "Theme", "text": "Neg-2", "start": 593, "end": 598}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1037, "end": 1047}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1032, "end": 1036}]}], "localization": [{"trigger": {"text": "secreted", "start": 87, "end": 95}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 82, "end": 86}]}], "negative regulation": [{"trigger": {"text": "negative regulation", "start": 16, "end": 35}, "arguments": [{"role": "Theme", "text": "transcription", "start": 39, "end": 52}]}, {"trigger": {"text": "down-regulated", "start": 885, "end": 899}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 850, "end": 854}, {"role": "Site", "text": "promoter", "start": 855, "end": 863}]}], "regulation": [{"trigger": {"text": "control", "start": 1021, "end": 1028}, "arguments": [{"role": "Theme", "text": "expression", "start": 1037, "end": 1047}]}], "transcription": [{"trigger": {"text": "transcription", "start": 39, "end": 52}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 75, "end": 79}]}]}}, "schema": []}
{"input": "Human T cell activation through the activation-inducer molecule/CD69 enhances the activity of transcription factor AP-1. \nThe induction of the AP-1 transcription factor has been ascribed to the early events leading to T cell differentiation and activation. We have studied the regulation of AP-1 activity in human peripheral blood T lymphocytes stimulated through the activation inducer molecule (AIM)/CD69 activation pathway. Phorbol esters are required to induce AIM/CD69 cell-surface expression as well as for triggering the proliferation of T cells in conjunction with anti-AIM mAb. Mobility shift assays showed that addition of anti-AIM mAb to PMA-treated T lymphocytes markedly enhanced the binding activity of AP-1 to its cognate sequence, the phorbol ester response element. In contrast, anti-AIM mAb did not induce any change in the binding activity of NF-kappa B, a transcription factor whose activity is also regulated by protein kinase C. The increase in AP-1-binding activity was accompanied by the marked stimulation of the transcription of c-fos but not that of c-jun. Blockade of the DNA-binding complexes with an anti-Fos mAb demonstrated a direct participation of c-Fos in the AP-1 complexes induced by anti-AIM mAb. Most of the AP-1 activity could be eliminated when the anti-AIM mAb was added to the culture medium in the presence of cycloheximide, suggesting that de novo protein synthesis is crucial for the induction of AP-1-binding activity. These data provide the evidence that activation of human peripheral blood T cells through the AIM activation pathway regulate the activity of AP-1. Therefore, this pathway appears as a crucial step in the initiation of early T cell activation events. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "participation", "start": 1165, "end": 1178}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 1182, "end": 1187}]}], "localization": [{"trigger": {"text": "expression", "start": 487, "end": 497}, "arguments": [{"role": "Theme", "text": "CD69", "start": 469, "end": 473}, {"role": "AtLoc", "text": "cell-surface", "start": 474, "end": 486}]}], "positive regulation": [{"trigger": {"text": "required to induce", "start": 446, "end": 464}, "arguments": [{"role": "Theme", "text": "expression", "start": 487, "end": 497}]}, {"trigger": {"text": "stimulation", "start": 1019, "end": 1030}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1038, "end": 1051}]}, {"trigger": {"text": "induced", "start": 1210, "end": 1217}, "arguments": [{"role": "Theme", "text": "participation", "start": 1165, "end": 1178}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1038, "end": 1051}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1055, "end": 1060}]}, {"trigger": {"text": "transcription", "start": 1038, "end": 1051}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1077, "end": 1082}]}]}}, "schema": []}
{"input": "The B cell-specific nuclear factor OTF-2 positively regulates transcription of the human class II transplantation gene, DRA. \nThe promoter of the major histocompatibility class II gene DRA contains an octamer element (ATTTGCAT) that is required for efficient DRA expression in B cells. Several DNA-binding proteins are known to bind this sequence. The best characterized are the B cell-specific OTF-2 and the ubiquitous OTF-1. This report directly demonstrates that OTF-2 but not OTF-1 regulates the DRA gene. In vitro transcription analysis using protein fractions enriched for the octamer-binding protein OTF-2 demonstrate a positive functional role for OTF-2 in DRA gene transcription. In contrast, OTF-1-enriched protein fractions did not affect DRA gene transcription although it functionally enhanced the transcription of another gene. Recombinant OTF-2 protein produced by in vitro transcription/translation could also enhance DRA gene transcription in vitro. In vivo transient transfection studies utilizing an OTF-2 expression vector resulted in similar findings: that OTF-2 protein enhanced DRA gene transcription, and that this effect requires an intact octamer element. Together these results constitute the first direct evidence of a positive role for the lymphoid-specific octamer-binding factor in DRA gene transcription. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 328, "end": 332}, "arguments": [{"role": "Theme", "text": "DRA", "start": 185, "end": 188}, {"role": "Site", "text": "ATTTGCAT", "start": 218, "end": 226}]}], "gene expression": [{"trigger": {"text": "expression", "start": 263, "end": 273}, "arguments": [{"role": "Theme", "text": "DRA", "start": 259, "end": 262}]}], "positive regulation": [{"trigger": {"text": "positively regulates", "start": 41, "end": 61}, "arguments": [{"role": "Cause", "text": "OTF-2", "start": 35, "end": 40}, {"role": "Theme", "text": "transcription", "start": 62, "end": 75}]}, {"trigger": {"text": "required", "start": 236, "end": 244}, "arguments": [{"role": "Cause", "text": "DRA", "start": 185, "end": 188}, {"role": "CSite", "text": "ATTTGCAT", "start": 218, "end": 226}, {"role": "Theme", "text": "expression", "start": 263, "end": 273}]}, {"trigger": {"text": "role", "start": 647, "end": 651}, "arguments": [{"role": "Cause", "text": "OTF-2", "start": 656, "end": 661}, {"role": "Theme", "text": "transcription", "start": 674, "end": 687}]}, {"trigger": {"text": "enhance", "start": 926, "end": 933}, "arguments": [{"role": "Cause", "text": "OTF-2", "start": 854, "end": 859}, {"role": "Theme", "text": "transcription", "start": 943, "end": 956}]}, {"trigger": {"text": "enhanced", "start": 1092, "end": 1100}, "arguments": [{"role": "Cause", "text": "OTF-2", "start": 1078, "end": 1083}, {"role": "Theme", "text": "transcription", "start": 1110, "end": 1123}]}, {"trigger": {"text": "requires", "start": 1146, "end": 1154}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 1092, "end": 1100}]}, {"trigger": {"text": "positive role", "start": 1247, "end": 1260}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1322, "end": 1335}]}], "regulation": [{"trigger": {"text": "regulates", "start": 486, "end": 495}, "arguments": [{"role": "Cause", "text": "OTF-2", "start": 466, "end": 471}, {"role": "Theme", "text": "DRA", "start": 500, "end": 503}]}, {"trigger": {"text": "regulates", "start": 486, "end": 495}, "arguments": [{"role": "Cause", "text": "OTF-1", "start": 480, "end": 485}, {"role": "Theme", "text": "DRA", "start": 500, "end": 503}]}, {"trigger": {"text": "affect", "start": 743, "end": 749}, "arguments": [{"role": "Cause", "text": "OTF-1", "start": 702, "end": 707}, {"role": "Theme", "text": "transcription", "start": 759, "end": 772}]}], "transcription": [{"trigger": {"text": "transcription", "start": 62, "end": 75}, "arguments": [{"role": "Theme", "text": "DRA", "start": 120, "end": 123}]}, {"trigger": {"text": "transcription", "start": 674, "end": 687}, "arguments": [{"role": "Theme", "text": "DRA", "start": 665, "end": 668}]}, {"trigger": {"text": "transcription", "start": 759, "end": 772}, "arguments": [{"role": "Theme", "text": "DRA", "start": 750, "end": 753}]}, {"trigger": {"text": "transcription", "start": 889, "end": 902}, "arguments": [{"role": "Theme", "text": "OTF-2", "start": 854, "end": 859}]}, {"trigger": {"text": "transcription", "start": 943, "end": 956}, "arguments": [{"role": "Theme", "text": "DRA", "start": 934, "end": 937}]}, {"trigger": {"text": "transcription", "start": 1110, "end": 1123}, "arguments": [{"role": "Theme", "text": "DRA", "start": 1101, "end": 1104}]}, {"trigger": {"text": "transcription", "start": 1322, "end": 1335}, "arguments": [{"role": "Theme", "text": "DRA", "start": 1313, "end": 1316}]}]}}, "schema": []}
{"input": "Specific NF-kappa B subunits act in concert with Tat to stimulate human immunodeficiency virus type 1 transcription. \nNF-kappa B is a protein complex which functions in concert with the tat-I gene product to stimulate human immunodeficiency virus (HIV) transcription. To determine whether specific members of the NF-kappa B family contribute to this effect, we have examined the abilities of different NF-kappa B subunits to act with Tat-I to stimulate transcription of HIV in Jurkat T-leukemia cells. We have found that the p49(100) DNA binding subunit, together with p65, can act in concert with Tat-I to stimulate the expression of HIV-CAT plasmid. Little effect was observed with 50-kDa forms of p105 NF-kappa B or rel, in combination with p65 or full-length c-rel, which do not stimulate the HIV enhancer in these cells. These findings suggest that the combination of p49(100) and p65 NF-kappa B can act in concert with the tat-I gene product to stimulate the synthesis of HIV RNA. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding subunit", "start": 538, "end": 553}, "arguments": [{"role": "Theme", "text": "p49(100)", "start": 525, "end": 533}]}], "gene expression": [{"trigger": {"text": "expression", "start": 621, "end": 631}, "arguments": [{"role": "Theme", "text": "CAT", "start": 639, "end": 642}]}], "positive regulation": [{"trigger": {"text": "stimulate", "start": 607, "end": 616}, "arguments": [{"role": "Theme", "text": "expression", "start": 621, "end": 631}]}, {"trigger": {"text": "effect", "start": 659, "end": 665}, "arguments": [{"role": "Theme", "text": "expression", "start": 621, "end": 631}, {"role": "Cause", "text": "p105", "start": 700, "end": 704}]}, {"trigger": {"text": "effect", "start": 659, "end": 665}, "arguments": [{"role": "Theme", "text": "expression", "start": 621, "end": 631}, {"role": "Cause", "text": "rel", "start": 719, "end": 722}]}, {"trigger": {"text": "effect", "start": 659, "end": 665}, "arguments": [{"role": "Theme", "text": "expression", "start": 621, "end": 631}, {"role": "Cause", "text": "p65", "start": 744, "end": 747}]}, {"trigger": {"text": "effect", "start": 659, "end": 665}, "arguments": [{"role": "Theme", "text": "expression", "start": 621, "end": 631}, {"role": "Cause", "text": "c-rel", "start": 763, "end": 768}]}]}}, "schema": []}
{"input": "Heterodimerization and transcriptional activation in vitro by NF-kappa B proteins. \nThe NF-kappa B family of transcription proteins represents multiple DNA binding, rel related polypeptides that contribute to regulation of genes involved in immune responsiveness and inflammation, as well as activation of the HIV long terminal repeat. In this study multiple NF-kappa B related polypeptides ranging from 85 to 45 kDa were examined for their capacity to interact with the PRDII regulatory element of interferon beta and were shown to possess distinct intrinsic DNA binding affinities for this NF-kappa B site and form multiple DNA binding homo- and heterodimer complexes in co-renaturation experiments. Furthermore, using DNA templates containing two copies of the PRDII domain linked to the rabbit beta globin gene, the purified polypeptides specifically stimulated NF-kappa B dependent transcription in an in vitro reconstitution assay as heterodimers but not as p50 homodimers. These experiments emphasize the role of NF-kappa B dimerization as a distinct level of transcriptional control that may permit functional diversification of a limited number of regulatory proteins. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Oct2 transactivation from a remote enhancer position requires a B-cell-restricted activity. \nPrevious cotransfection experiments had demonstrated that ectopic expression of the lymphocyte-specific transcription factor Oct2 could efficiently activate a promoter containing an octamer motif. Oct2 expression was unable to stimulate a multimerized octamer enhancer element in HeLa cells, however. We have tested a variety of Oct2 isoforms generated by alternative splicing for the capability to activate an octamer enhancer in nonlymphoid cells and a B-cell line. Our analyses show that several Oct2 isoforms can stimulate from a remote position but that this stimulation is restricted to B cells. This result indicates the involvement of either a B-cell-specific cofactor or a specific modification of a cofactor or the Oct2 protein in Oct2-mediated enhancer activation. Mutational analyses indicate that the carboxy-terminal domain of Oct2 is critical for enhancer activation. Moreover, this domain conferred enhancing activity when fused to the Oct1 protein, which by itself was unable to stimulate from a remote position. The glutamine-rich activation domain present in the amino-terminal portion of Oct2 and the POU domain contribute only marginally to the transactivation function from a distal position. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 159, "end": 169}, "arguments": [{"role": "Theme", "text": "Oct2", "start": 218, "end": 222}]}, {"trigger": {"text": "expression", "start": 295, "end": 305}, "arguments": [{"role": "Theme", "text": "Oct2", "start": 290, "end": 294}]}], "positive regulation": [{"trigger": {"text": "generated", "start": 436, "end": 445}, "arguments": [{"role": "Theme", "text": "Oct2", "start": 422, "end": 426}]}]}}, "schema": []}
{"input": "Transcription factor AP-2 activates gene expression of HTLV-I. \nThe HTLV-I LTR contains three conserved regulatory elements known as 21 base pair repeats which are required for stimulation of gene expression by the transactivator protein tax. Mutagenesis indicates that the 21 bp repeats can be subdivided into three motifs, A, B and C, each of which influences the level of tax activation. The A site in the 21 bp repeat has strong homology with previously described binding sites for the transcription factor AP-2. We demonstrated that AP-2 mRNA was present in T-lymphocytes and that cellular factors from both non-transformed and transformed T-lymphocytes specifically bound to the consensus motif for AP-2 in each 21 bp. To determine the role of AP-2 in the regulation of the HTLV-I LTR gene expression, we used an AP-2 cDNA in DNA binding and transient expression assays. Gel retardation and methylation interference studies revealed that bacterially produced AP-2 bound specifically and with high affinity to all three 21 bp repeats, and that it required the core sequence AGGC for specific binding. Binding of AP-2 prevented the subsequent binding of members of the CREB/ATF family to an adjacent regulatory motif in the 21 bp repeat. Transfection of an AP-2 expression construct into T-lymphocytes activated gene expression from the HTLV-I LTR. At least two 21 bp repeats were required for high levels of AP-2 activation and mutagenesis of the AP-2 consensus binding sequences in the 21 bp repeats eliminate this activation. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "activation", "start": 379, "end": 389}, "arguments": [{"role": "Theme", "text": "tax", "start": 375, "end": 378}]}], "regulation": [{"trigger": {"text": "influences the level", "start": 351, "end": 371}, "arguments": [{"role": "Theme", "text": "activation", "start": 379, "end": 389}]}]}}, "schema": []}
{"input": "The human myelomonocytic cell line U-937 as a model for studying alterations in steroid-induced monokine gene expression: marked enhancement of lipopolysaccharide-stimulated interleukin-1 beta messenger RNA levels by 1,25-dihydroxyvitamin D3. \nThe active metabolite of vitamin D, 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3], is a potent regulator of human monocyte/macrophage function in vitro. To establish a model for 1,25-(OH)2D3 regulation of human monocyte monokine synthesis, three human cell lines (U-937, THP-1, and HL-60) were examined for: 1) the presence of functional 1,25-(OH)2D3 receptors; 2) the accumulation of interleukin-1 beta (IL-1 beta) mRNA and IL-1 beta protein in response to lipopolysaccharide (LPS); and 3) the regulation of this response by 1,25-(OH)2D3. All three cell lines expressed vitamin D receptor and had increased levels of IL-1 beta mRNA in response to LPS. Preincubation of cells with 1,25-(OH)2D3 augmented IL-1 beta mRNA levels only in U-937 and HL-60 cells. From these data, and taking into consideration their state of differentiation and relative ease of culture, U-937 was chosen over HL-60 and THP-1 as the cell line we further characterized. In U-937 cells, optimum time and dose of pretreatment with 1,25-(OH)2D3 were determined to be 12-24 h at a receptor saturating concentration of 1,25-(OH)2D3 (10 nM). Preincubation of cells with 1,25-(OH)2D3 had no effect on the time course of IL-1 beta mRNA appearance in response to LPS. However, exposure of U-937 cells to 1,25-(OH)2D3 increased by 200% the level of IL-1 beta mRNA detected and decreased by three orders of magnitude the concentration of LPS required to achieve steady state mRNA levels equivalent to those observed in U-937 cells not preincubated with the hormone.2+o ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 799, "end": 808}, "arguments": [{"role": "Theme", "text": "vitamin D receptor", "start": 809, "end": 827}]}], "positive regulation": [{"trigger": {"text": "enhancement", "start": 129, "end": 140}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 163, "end": 173}]}, {"trigger": {"text": "stimulated", "start": 163, "end": 173}, "arguments": [{"role": "Theme", "text": "levels", "start": 207, "end": 213}]}, {"trigger": {"text": "accumulation", "start": 607, "end": 619}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 643, "end": 652}]}, {"trigger": {"text": "accumulation", "start": 607, "end": 619}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 663, "end": 672}]}, {"trigger": {"text": "increased", "start": 836, "end": 845}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 856, "end": 865}]}, {"trigger": {"text": "augmented", "start": 932, "end": 941}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 942, "end": 951}]}, {"trigger": {"text": "in response to", "start": 1453, "end": 1467}, "arguments": [{"role": "Theme", "text": "appearance", "start": 1442, "end": 1452}]}, {"trigger": {"text": "increased", "start": 1522, "end": 1531}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1553, "end": 1562}]}], "regulation": [{"trigger": {"text": "regulation", "start": 733, "end": 743}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 607, "end": 619}]}, {"trigger": {"text": "effect", "start": 1398, "end": 1404}, "arguments": [{"role": "Theme", "text": "in response to", "start": 1453, "end": 1467}]}], "transcription": [{"trigger": {"text": "levels", "start": 207, "end": 213}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 174, "end": 192}]}, {"trigger": {"text": "appearance", "start": 1442, "end": 1452}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1427, "end": 1436}]}]}}, "schema": []}
{"input": "NF-kappa B activation by tumor necrosis factor alpha in the Jurkat T cell line is independent of protein kinase A, protein kinase C, and Ca(2+)-regulated kinases. \nNF-kappa B is a DNA-binding regulatory factor able to control transcription of a number of genes, including human immunodeficiency virus (HIV) genes. In T cells, NF-kappa B is activated upon cellular treatment by phorbol esters and the cytokine tumor necrosis factor alpha (TNF alpha). In the present work, we investigated the molecular events leading to NF-kappa B activation by TNF alpha in a human T cell line (Jurkat) and its subclone JCT6, which presents a deficiency in the PKA transduction pathway. We found that in both cell lines, both phorbol ester and TNF alpha were able to activate NF-kappa B. Phorbol activation was positively modulated by Ca2+ influx while TNF alpha activation was not. Furthermore, while PMA activation was inhibited by the PKC inhibitor staurosporin, the TNF alpha effect was unchanged. TNF alpha did not activate cAMP production and its signal was not modulated by cAMP activators. Moreover, cAMP activators did not activate NF-kappa B in Jurkat cells. Thus, TNF alpha-induced NF-kappa B activation was found to be mediated by none of the major signal-mediating kinases such as protein kinase C (PKC), protein kinase A, or Ca(2+)-regulated kinases. Furthermore, we found that cytoplasmic acidification facilitated NF-kappa B activation by both TNF alpha and PKC, by a mechanism that increases NF-kappa B/I kappa B dissociation without affecting the NF-kappa B translocation step. ", "output": {"json_structures": {}}, "schema": []}
{"input": "USF-related transcription factor, HIV-TF1, stimulates transcription of human immunodeficiency virus-1. \nThe transcription factor HIV-TF1, which binds to a region about 60 bp upstream from the enhancer of the human immunodeficiency virus-1 (HIV-1), was purified from human B cells. HIV-TF1 had a molecular weight of 39,000. Binding of HIV-TF1 to the HIV long terminal repeat (LTR) activated transcription from the HIV promoter in vitro. The HIV-TF1-binding site in HIV LTR was similar to the site recognized by upstream stimulatory factor (USF) in the adenovirus major late promoter. DNA-binding properties of HIV-TF1 suggested that HIV-TF1 might be identical or related to USF. Interestingly, treatment of purified HIV-TF1 by phosphatase greatly reduced its DNA-binding activity, suggesting that phosphorylation of HIV-TF1 was essential for DNA binding. The disruption of HIV-TF1-binding site induced a 60% decrease in the level of transcription from the HIV promoter in vivo. These results suggest that HIV-TF1 is involved in transcriptional regulation of HIV-1. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 144, "end": 149}, "arguments": [{"role": "Theme", "text": "HIV-TF1", "start": 129, "end": 136}]}, {"trigger": {"text": "Binding", "start": 323, "end": 330}, "arguments": [{"role": "Theme", "text": "HIV-TF1", "start": 334, "end": 341}]}, {"trigger": {"text": "recognized", "start": 496, "end": 506}, "arguments": [{"role": "Theme", "text": "USF", "start": 539, "end": 542}]}, {"trigger": {"text": "binding", "start": 587, "end": 594}, "arguments": [{"role": "Theme", "text": "HIV-TF1", "start": 609, "end": 616}]}, {"trigger": {"text": "binding", "start": 762, "end": 769}, "arguments": [{"role": "Theme", "text": "HIV-TF1", "start": 715, "end": 722}]}, {"trigger": {"text": "binding", "start": 845, "end": 852}, "arguments": [{"role": "Theme", "text": "HIV-TF1", "start": 815, "end": 822}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 746, "end": 753}, "arguments": [{"role": "Theme", "text": "binding", "start": 762, "end": 769}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 796, "end": 811}, "arguments": [{"role": "Theme", "text": "HIV-TF1", "start": 815, "end": 822}]}], "positive regulation": [{"trigger": {"text": "essential", "start": 827, "end": 836}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 796, "end": 811}, {"role": "Theme", "text": "binding", "start": 845, "end": 852}]}]}}, "schema": []}
{"input": "Nuclear transcription factors that bind to elements of the IL-2 promoter. Induction requirements in primary human T cells. \nPrior studies have identified several elements that contribute to the activity of the IL-2 promoter in the stimulated T cell line, Jurkat. The sites and their corresponding nuclear binding factors include: NF-kappa B, AP-1, AP-3, OCT-1, and NF-AT. The latter \"nuclear factor for activated T cells\" likely contributes to the tissue specificity of IL-2 gene expression. Using electrophoretic mobility shift assays, we have studied these transcription factors in primary T cells from human blood to verify their presence in a physiologic setting and to identify the signals that stimulate factor activity. All factors are induced in the nuclei of T cells upon activation with mitogens but not with exogenous IL-2 growth factor. However, the signaling requirements and sensitivity to protein synthesis inhibitors differ considerably. Only the activities for NF-AT and AP-1 sites require two signals for optimal induction, i.e., PMA plus either lectin or antibody to the CD3 or CD28 surface molecules. Other factors are induced by lectin, antibody, and/or PMA alone. After appropriate stimulation, both NF-AT and AP-1 are peculiarly sensitive to the protein synthesis inhibitor anisomycin. Our data correlate the activity of NF-AT and AP-1 in gel shift assays with the two signals requirements for IL-2 gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 35, "end": 39}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 59, "end": 63}, {"role": "Site", "text": "promoter", "start": 64, "end": 72}]}], "gene expression": [{"trigger": {"text": "expression", "start": 480, "end": 490}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 470, "end": 474}]}, {"trigger": {"text": "expression", "start": 1427, "end": 1437}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1417, "end": 1421}]}], "positive regulation": [{"trigger": {"text": "stimulate", "start": 700, "end": 709}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 354, "end": 359}]}, {"trigger": {"text": "induced", "start": 743, "end": 750}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 354, "end": 359}, {"role": "Cause", "text": "IL-2", "start": 829, "end": 833}]}, {"trigger": {"text": "induced", "start": 743, "end": 750}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 354, "end": 359}]}, {"trigger": {"text": "requirements", "start": 872, "end": 884}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 354, "end": 359}]}, {"trigger": {"text": "induced", "start": 1139, "end": 1146}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 354, "end": 359}]}, {"trigger": {"text": "requirements", "start": 1400, "end": 1412}, "arguments": [{"role": "Theme", "text": "expression", "start": 1427, "end": 1437}]}], "regulation": [{"trigger": {"text": "contribute", "start": 176, "end": 186}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 210, "end": 214}, {"role": "Site", "text": "promoter", "start": 215, "end": 223}]}, {"trigger": {"text": "contributes", "start": 429, "end": 440}, "arguments": [{"role": "Theme", "text": "specificity", "start": 455, "end": 466}]}, {"trigger": {"text": "specificity", "start": 455, "end": 466}, "arguments": [{"role": "Theme", "text": "expression", "start": 480, "end": 490}]}]}}, "schema": []}
{"input": "An erythroid specific enhancer upstream to the gene encoding the cell-type specific transcription factor GATA-1. \nThe transcription factor GATA-1 is expressed in a subset of hemopoietic cells, where it mediates the cell-type specific expression of several genes. We have cloned the mouse and human GATA-1 genes. A region upstream to the first exon, and highly conserved between mouse and man, acts as an erythroid specific enhancer in transient assays, if linked to the GATA-1 or to the SV40 promoter. The activity of the enhancer is almost completely dependent on the integrity of a dimeric GATA-1 binding site. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 149, "end": 158}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 139, "end": 145}]}]}}, "schema": []}
{"input": "Clone pAT 133 identifies a gene that encodes another human member of a class of growth factor-induced genes with almost identical zinc-finger domains. \nWe report the structure and regulation of a gene represented by clone pAT 133, which is induced upon transition from a resting state (G0) through the early phase of the cell cycle (G1). The pAT 133 gene is immediately induced, with FOS-like kinetics, in human T cells and in fibroblasts. Primary structure analysis showed that the encoded protein contains three tandem zinc-finger sequences of the type Cys2-Xaa12-His2. This zinc-finger region, which is thought to bind DNA in a sequence-specific manner, is similar (greater than 80% on the amino acid level) to two previously described transcription factors pAT 225/EGR1 and pAT 591/EGR2. Except for the conserved zinc-finger domains, the amino acid sequences of the three proteins are distinct. This structural similarity suggests that the pAT 133 gene encodes a transcription factor with a specific biological function. Comparing the regulation of these related zinc-finger-encoding genes showed coordinate induction upon mitogenic stimulation of resting T lymphocytes and of resting fibroblasts. However, upon transition from a proliferating (G1) to a resting state of the cell cycle the three genes were differently regulated. In human histiocytic U937 cells mRNA of clone pAT 133 was constitutively expressed, whereas mRNA of pAT 225/EGR1 was induced upon induction of terminal differentiation. In contrast mRNA representing pAT 591/EGR2 was not expressed in these cells. This difference in gene regulation suggests distinct biological roles in the control of cell proliferation for the respective proteins. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "induced", "start": 1451, "end": 1458}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 1442, "end": 1446}]}], "regulation": [{"trigger": {"text": "regulation", "start": 1039, "end": 1049}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 769, "end": 773}]}, {"trigger": {"text": "regulation", "start": 1039, "end": 1049}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 786, "end": 790}]}, {"trigger": {"text": "regulated", "start": 1323, "end": 1332}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 769, "end": 773}]}, {"trigger": {"text": "regulated", "start": 1323, "end": 1332}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 786, "end": 790}]}], "transcription": [{"trigger": {"text": "expressed", "start": 1554, "end": 1563}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 1541, "end": 1545}]}]}}, "schema": []}
{"input": "Every enhancer works with every promoter for all the combinations tested: could new regulatory pathways evolve by enhancer shuffling? \nThe promoters and enhancers of cell type-specific genes are often conserved in evolution, and hence one might expect that a given enhancer has evolved to work best with its own promoter. While this expectation may be realized in some cases, we have not found evidence for it. A total of 27 combinations of different promoters and enhancers were tested by transfection into cultured cells. We found that the relative efficiency of the enhancers is approximately the same, irrespective of the type of promoter used, i.e., there was no strong preference for any given enhancer/promoter combination. Notably, we do not see particularly strong transcription when the immunoglobulin kappa enhancer (or the immunoglobulin heavy chain enhancer) is used to activate a kappa gene promoter. We propose that a generally permissive enhancer/promoter interaction is of evolutionary benefit for higher eukaryotes: by enhancer shuffling, genes could be easily brought under a new type of inducibility/cell type specificity. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Towards a molecular understanding of T-cell differentiation. \nLymphoid differentiation is one of the best studied examples of mammalian development. Here Hans Clevers and Michael Owen describe how the cloning of the genes that encode T-cell-specific membrane proteins allows the identification of transcription factors that control the expression of these T-cell genes. Such transcription factors play a key role in the development of the mature T-cell phenotype by functioning as 'master regulators of T-cell differentiation'. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Transcription factor requirements for U2 snRNA-encoding gene activation in B lymphoid cells. \nTranscription of a human U2 small nuclear RNA(snRNA)-encoding gene in HeLa cells requires a distal enhancer element, which is composed of one octamer motif (Oct) and three Sp 1-binding sites. To study the transcription factor requirement in B-cells, different U2 enhancer constructions were transfected into the lymphoid cell line, BJA-B. The results showed that the activation of U2 snRNA transcription in B-cells also requires an enhancer comprising both the Oct and at least one Sp 1-binding site. Deletion of all the Sp 1-binding sites from the enhancer reduces transcription by 80-90% in HeLa, as well as in BJA-B cells, whereas the removal of the octamer-binding site reduces transcription to levels below detection in both cell types. Enhancers containing a single Oct have, nevertheless, the capacity to partially activate U2 snRNA transcription in both HeLa cells, in which only OTF-1 is expressed, and in BJA-B cells in which OTF-2 is the predominantly expressed octamer-binding factor. The most likely interpretation of our results is that both the ubiquitous transcription factor, OTF-1, and the B-cell-specific transcription factor, OTF-2, can activate U2 snRNA transcription. The results also revealed a similar functional cooperation between the transcription factors which bind to the Oct and the adjacent Sp 1-binding site in BJA-B cells, as has been observed in HeLa cells, since a template which contains a weak binding site for OTFs expresses wild-type levels of U2 snRNA in both cell types when the weak octamer-binding site is combined with a Sp 1-binding site. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 991, "end": 1000}, "arguments": [{"role": "Theme", "text": "OTF-1", "start": 982, "end": 987}]}, {"trigger": {"text": "expressed", "start": 1057, "end": 1066}, "arguments": [{"role": "Theme", "text": "OTF-2", "start": 1030, "end": 1035}]}]}}, "schema": []}
{"input": "Kappa B-specific DNA binding proteins are differentially inhibited by enhancer mutations and biological oxidation. \nKappa B (kappa B) enhancer binding proteins isolated from the nuclei of activated human T cells produce two distinct nucleoprotein complexes when incubated with the kappa B element from the interleukin-2 receptor-alpha (IL-2R alpha) gene. These two DNA-protein complexes are composed of at least four host proteins (p50, p55, p75, p85), each of which shares structural similarity with the v-rel oncogene product. Nuclear expression of these proteins is induced with distinctly biphasic kinetics following phorbol ester activation of T cells (p55/p75 early and p50/p85 late). DNA-protein crosslinking studies have revealed that the more rapidly migrating B2 complex contains both p50 and p55 while the more slowly migrating B1 complex is composed of p50, p55, p75, and p85. Site-directed mutagenesis of the wild-type IL-2R alpha kappa B enhancer (GGGGAATCTCCC) has revealed that the binding of p50 and p55 (B2 complex) is particularly sensitive to alteration of the 5' triplet of deoxyguanosine residues. In contrast, formation of the B1 complex, reflecting the binding of p75 and p85, critically depends upon the more 3' sequences of this enhancer element. DNA binding by all four of these Rel-related factors is blocked by selective chemical modification of lysine and arginine residues, suggesting that both of these basic amino acids are required for binding to the kappa B element. Similarly, covalent modification of free sulfhydryl groups with diamide (reversible) or N-ethylmaleimide (irreversible) results in a complete loss of DNA binding activity. In contrast, mild oxidation with glucose oxidase selectively inhibits p75 and p85 binding while not blocking p50 and p55 interactions. These findings suggest that reduced cysteine thiols play an important role in the DNA binding activity of this family of Rel-related transcription factors. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 998, "end": 1005}, "arguments": [{"role": "Theme", "text": "p50", "start": 1009, "end": 1012}]}, {"trigger": {"text": "binding", "start": 998, "end": 1005}, "arguments": [{"role": "Theme", "text": "p55", "start": 1017, "end": 1020}]}, {"trigger": {"text": "binding", "start": 1177, "end": 1184}, "arguments": [{"role": "Theme", "text": "p75", "start": 1188, "end": 1191}]}, {"trigger": {"text": "binding", "start": 1177, "end": 1184}, "arguments": [{"role": "Theme", "text": "p85", "start": 1196, "end": 1199}]}, {"trigger": {"text": "binding", "start": 1277, "end": 1284}, "arguments": [{"role": "Theme", "text": "p50", "start": 865, "end": 868}]}, {"trigger": {"text": "binding", "start": 1277, "end": 1284}, "arguments": [{"role": "Theme", "text": "p55", "start": 870, "end": 873}]}, {"trigger": {"text": "binding", "start": 1277, "end": 1284}, "arguments": [{"role": "Theme", "text": "p75", "start": 875, "end": 878}]}, {"trigger": {"text": "binding", "start": 1277, "end": 1284}, "arguments": [{"role": "Theme", "text": "p85", "start": 884, "end": 887}]}, {"trigger": {"text": "binding", "start": 1756, "end": 1763}, "arguments": [{"role": "Theme", "text": "p75", "start": 1744, "end": 1747}]}, {"trigger": {"text": "binding", "start": 1756, "end": 1763}, "arguments": [{"role": "Theme", "text": "p85", "start": 1752, "end": 1755}]}, {"trigger": {"text": "interactions", "start": 1795, "end": 1807}, "arguments": [{"role": "Theme", "text": "p50", "start": 1783, "end": 1786}]}, {"trigger": {"text": "interactions", "start": 1795, "end": 1807}, "arguments": [{"role": "Theme", "text": "p55", "start": 1791, "end": 1794}]}], "gene expression": [{"trigger": {"text": "expression", "start": 537, "end": 547}, "arguments": [{"role": "Theme", "text": "p55", "start": 658, "end": 661}]}, {"trigger": {"text": "expression", "start": 537, "end": 547}, "arguments": [{"role": "Theme", "text": "p75", "start": 662, "end": 665}]}, {"trigger": {"text": "expression", "start": 537, "end": 547}, "arguments": [{"role": "Theme", "text": "p50", "start": 676, "end": 679}]}, {"trigger": {"text": "expression", "start": 537, "end": 547}, "arguments": [{"role": "Theme", "text": "p85", "start": 680, "end": 683}]}], "localization": [{"trigger": {"text": "migrating", "start": 760, "end": 769}, "arguments": [{"role": "Theme", "text": "p50", "start": 795, "end": 798}]}, {"trigger": {"text": "migrating", "start": 760, "end": 769}, "arguments": [{"role": "Theme", "text": "p55", "start": 803, "end": 806}]}, {"trigger": {"text": "migrating", "start": 829, "end": 838}, "arguments": [{"role": "Theme", "text": "p50", "start": 865, "end": 868}]}, {"trigger": {"text": "migrating", "start": 829, "end": 838}, "arguments": [{"role": "Theme", "text": "p55", "start": 870, "end": 873}]}, {"trigger": {"text": "migrating", "start": 829, "end": 838}, "arguments": [{"role": "Theme", "text": "p75", "start": 875, "end": 878}]}, {"trigger": {"text": "migrating", "start": 829, "end": 838}, "arguments": [{"role": "Theme", "text": "p85", "start": 884, "end": 887}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 1329, "end": 1336}, "arguments": [{"role": "Theme", "text": "binding", "start": 1277, "end": 1284}]}, {"trigger": {"text": "loss", "start": 1644, "end": 1648}, "arguments": [{"role": "Theme", "text": "binding", "start": 1277, "end": 1284}]}, {"trigger": {"text": "inhibits", "start": 1735, "end": 1743}, "arguments": [{"role": "Theme", "text": "binding", "start": 1756, "end": 1763}]}, {"trigger": {"text": "blocking", "start": 1774, "end": 1782}, "arguments": [{"role": "Theme", "text": "interactions", "start": 1795, "end": 1807}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 569, "end": 576}, "arguments": [{"role": "Theme", "text": "expression", "start": 537, "end": 547}]}, {"trigger": {"text": "depends", "start": 1212, "end": 1219}, "arguments": [{"role": "Theme", "text": "binding", "start": 1177, "end": 1184}]}], "regulation": [{"trigger": {"text": "sensitive", "start": 1050, "end": 1059}, "arguments": [{"role": "Theme", "text": "binding", "start": 998, "end": 1005}]}]}}, "schema": []}
{"input": "Activity of the kappa B enhancer of the interleukin-2 receptor alpha chain in somatic cell hybrids is accompanied by the nuclear localization of NF-kappa B. \nThe two nuclear proteins NF-kappa B (consisting of subunits p50 and p65) and the DNA-binding subunit of NF-kappa B (p50) by itself, also called KBF1, are constitutively expressed and localized in the nucleus of the human T-cell line IARC 301.5. In order to define the roles of these two factors, which bind to the same kappa B enhancers, in transcription activation we have prepared somatic cell hybrids between IARC 301.5 and a murine myeloma. Most hybrids express both KBF1 and NF-kappa B in their nuclei, but one hybrid expresses only KBF1. The kappa B enhancer of the gene encoding the interleukin-2 (IL-2) receptor alpha chain (IL-2R alpha) is functional only in the hybrids expressing nuclear NF-kappa B. These findings show that nuclear NF-kappa B is necessary to activate the kappa B enhancer, while KBF1 by itself is not sufficient. We propose that KBF1 is a competitive inhibitor of NF-kappa B and discuss how these factors may be involved in the transient expression of IL-2 and IL-2R alpha genes during the immune response. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 460, "end": 464}, "arguments": [{"role": "Theme", "text": "p50", "start": 274, "end": 277}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 327, "end": 336}, "arguments": [{"role": "Theme", "text": "p50", "start": 274, "end": 277}]}, {"trigger": {"text": "express", "start": 616, "end": 623}, "arguments": [{"role": "Theme", "text": "KBF1", "start": 629, "end": 633}]}, {"trigger": {"text": "expresses", "start": 681, "end": 690}, "arguments": [{"role": "Theme", "text": "KBF1", "start": 696, "end": 700}]}, {"trigger": {"text": "expression", "start": 1125, "end": 1135}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1139, "end": 1143}]}, {"trigger": {"text": "expression", "start": 1125, "end": 1135}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 1148, "end": 1159}]}], "localization": [{"trigger": {"text": "localized", "start": 341, "end": 350}, "arguments": [{"role": "Theme", "text": "p50", "start": 274, "end": 277}, {"role": "AtLoc", "text": "nucleus", "start": 358, "end": 365}]}]}}, "schema": []}
{"input": "Stimulation of interferon beta gene transcription in vitro by purified NF-kappa B and a novel TH protein. \nThe human interferon beta (IFN-beta) regulatory element consists of multiple enhanson domains which are targets for transcription factors involved in inducible expression of the promoter. To further characterize the protein-DNA interactions mediating IFN-beta induction, positive regulatory domain (PRD) II binding proteins were purified from phorbol ester induced Jurkat T-cells and from IFN primed, cycloheximide/polyinosinic-polycytidylic acid treated HeLa S3 cells. From HeLa cells, two major proteins of 52 and 45 kilodaltons (kD) copurified with DNA binding activity, whereas from T-cells, four proteins--a major protein of 52 kD and three minor proteins of 82, 67, and 43-47 kD--were purified. Also, an induction specific DNA binding protein was purified from HeLa cells that interacted with the (AAGTGA)4 tetrahexamer sequence and the PRDI domain. This protein is immunologically distinct from IRF-1/ISGF2. Uninduced or Sendai virus induced HeLa extracts were used to examine transcription in vitro using a series of IFN beta promoter deletions. Deletions upstream of the PRDII element increased transcription in the uninduced extract, indicating predominantly negative regulation of the promoter. A 2-4-fold increase in IFN-beta promoter transcription was observed in Sendai virus induced extracts, and deletion of PRDI and PRDII elements decreased this induced level of transcription. When purified PRDII and tetrahexamer binding proteins were added to the induced extract, a 4-fold increase in transcription was observed. These experiments demonstrate that it is possible to modulate IFN-beta transcription in vitro but indicate that additional proteins may be required to fully activate IFN-beta transcription. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 267, "end": 277}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 134, "end": 142}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 1455, "end": 1464}, "arguments": [{"role": "Theme", "text": "increase", "start": 1324, "end": 1332}]}], "positive regulation": [{"trigger": {"text": "Stimulation", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "transcription", "start": 36, "end": 49}]}, {"trigger": {"text": "inducible", "start": 257, "end": 266}, "arguments": [{"role": "Theme", "text": "expression", "start": 267, "end": 277}]}, {"trigger": {"text": "mediating", "start": 348, "end": 357}, "arguments": [{"role": "Theme", "text": "induction", "start": 367, "end": 376}]}, {"trigger": {"text": "induction", "start": 367, "end": 376}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 358, "end": 366}]}, {"trigger": {"text": "increased", "start": 1201, "end": 1210}, "arguments": [{"role": "Theme", "text": "transcription", "start": 36, "end": 49}]}, {"trigger": {"text": "increase", "start": 1324, "end": 1332}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1354, "end": 1367}]}, {"trigger": {"text": "increase", "start": 1600, "end": 1608}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1354, "end": 1367}]}, {"trigger": {"text": "activate", "start": 1797, "end": 1805}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1815, "end": 1828}]}], "regulation": [{"trigger": {"text": "targets", "start": 211, "end": 218}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 134, "end": 142}, {"role": "Site", "text": "enhanson domains", "start": 184, "end": 200}]}], "transcription": [{"trigger": {"text": "transcription", "start": 36, "end": 49}, "arguments": [{"role": "Theme", "text": "interferon beta", "start": 15, "end": 30}]}, {"trigger": {"text": "transcription", "start": 1354, "end": 1367}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 1336, "end": 1344}]}, {"trigger": {"text": "transcription", "start": 1815, "end": 1828}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 1806, "end": 1814}]}]}}, "schema": []}
{"input": "Characterization of an immediate-early gene induced in adherent monocytes that encodes I kappa B-like activity. \nWe have cloned a group of cDNAs representing mRNAs that are rapidly induced following adherence of human monocytes. One of the induced transcripts (MAD-3) encodes a protein of 317 amino acids with one domain containing five tandem repeats of the cdc10/ankyrin motif, which is 60% similar (46% identical) to the ankyrin repeat region of the precursor of NF-kappa B/KBF1 p50. The C-terminus has a putative protein kinase C phosphorylation site. In vitro translated MAD-3 protein was found to specifically inhibit the DNA-binding activity of the p50/p65 NF-kappa B complex but not that of the p50/p50 KBF1 factor or of other DNA-binding proteins. The MAD-3 cDNA encodes an I kappa B-like protein that is likely to be involved in regulation of transcriptional responses to NF-kappa B, including adhesion-dependent pathways of monocyte activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 632, "end": 648}, "arguments": [{"role": "Theme", "text": "p50", "start": 656, "end": 659}]}, {"trigger": {"text": "binding activity", "start": 632, "end": 648}, "arguments": [{"role": "Theme", "text": "p65", "start": 660, "end": 663}]}, {"trigger": {"text": "binding activity", "start": 632, "end": 648}, "arguments": [{"role": "Theme", "text": "p50", "start": 703, "end": 706}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 616, "end": 623}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 632, "end": 648}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 240, "end": 247}, "arguments": [{"role": "Theme", "text": "MAD-3", "start": 261, "end": 266}]}]}}, "schema": []}
{"input": "Platelet-activating factor induces phospholipid turnover, calcium flux, arachidonic acid liberation, eicosanoid generation, and oncogene expression in a human B cell line. \nPlatelet-activating factor is a potent mediator of the inflammatory response. Studies of the actions of platelet-activating factor have centered mainly around neutrophils, monocytes, and platelets. In this report we begin to uncover the influence of platelet-activating factor on B lymphocytes. Employing the EBV-transformed human B cell line SKW6.4, we demonstrate that platelet-activating factor significantly alters membrane phospholipid metabolism indicated by the incorporation of 32P into phosphatidylcholine, phosphatidylinositol, and phosphatidic acid but not significantly into phosphatidylethanolamine at concentrations ranging from 10(-9) to 10(-6) M. The inactive precursor, lyso-platelet-activating factor, at a concentration as high as 10(-7) M had no effect on any of the membrane phospholipids. We also show that platelet-activating factor from 10(-12) to 10(-6) M induced rapid and significant elevation in intracellular calcium levels, whereas lyso-platelet-activating factor was again ineffective. We further demonstrate the impact of platelet-activating factor binding to B cells by measuring platelet-activating factor induced arachidonic acid release and 5-hydroxyeicosatetraenoic acid production. Moreover, platelet-activating factor was capable of inducing transcription of the nuclear proto-oncogenes c-fos and c-jun. Finally we explored the possible role of 5-hydroxyeicosatetraenoic acid as a regulator of arachidonic acid liberation demonstrating that endogenous 5-lipoxygenase activity modulates platelet-activating factor induced arachidonic acid release perhaps acting at the level of phospholipase A2. In summary, platelet-activating factor is shown here to have a direct and profound effect on a pure B cell line. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "inducing", "start": 1445, "end": 1453}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1454, "end": 1467}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1454, "end": 1467}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1499, "end": 1504}]}, {"trigger": {"text": "transcription", "start": 1454, "end": 1467}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1509, "end": 1514}]}]}}, "schema": []}
{"input": "Inhibition of protein phosphatases by okadaic acid induces AP1 in human T cells. \nTo examine the role of protein phosphatases in T cell activation, Jurkat cells were treated with okadaic acid, an inhibitor of type 1 and 2A phosphatases, and nuclear extracts were examined for the presence of AP1 as a measure of early T cell activation. Okadaic acid was found to be a potent inducer of AP1. In contrast to phorbol esters such as phorbol myristate acetate (PMA), the induction of AP1 by okadaic acid occurs predominantly by transcriptional activation of the jun and fos family of proto-oncogenes. Surprisingly, while the addition of phytohemagglutinin further enhanced the induction of AP1, the addition of PMA inhibited it. Okadaic acid treatment was found to dramatically increase mRNA transcripts of the jun family of proto-oncogenes including c-jun, junD, and junB and to a lesser extent the fos family including c-fos and fra-1. By comparison, PMA is a very inefficient inducer of the jun gene family in Jurkat cells. Similar to its effect on the induction of AP1 by okadaic acid, PMA inhibits the induction of c-jun mRNA by okadaic acid. Transfection of c-jun promoter constructs confirmed the marked difference between PMA and okadaic acid in inducing c-jun transcription. The induction of AP1 by okadaic acid suggests that protein phosphatases 1 and 2A (PP1 and PP2A) may be involved in T cell activation as important negative regulators of the transcription factor AP1. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibits", "start": 1089, "end": 1097}, "arguments": [{"role": "Theme", "text": "induction", "start": 1102, "end": 1111}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 773, "end": 781}, "arguments": [{"role": "Theme", "text": "mRNA transcripts", "start": 782, "end": 798}]}, {"trigger": {"text": "induction", "start": 1102, "end": 1111}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1115, "end": 1120}]}, {"trigger": {"text": "inducing", "start": 1249, "end": 1257}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1264, "end": 1277}]}], "transcription": [{"trigger": {"text": "mRNA transcripts", "start": 782, "end": 798}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 846, "end": 851}]}, {"trigger": {"text": "mRNA transcripts", "start": 782, "end": 798}, "arguments": [{"role": "Theme", "text": "junD", "start": 853, "end": 857}]}, {"trigger": {"text": "mRNA transcripts", "start": 782, "end": 798}, "arguments": [{"role": "Theme", "text": "junB", "start": 863, "end": 867}]}, {"trigger": {"text": "mRNA transcripts", "start": 782, "end": 798}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 916, "end": 921}]}, {"trigger": {"text": "mRNA transcripts", "start": 782, "end": 798}, "arguments": [{"role": "Theme", "text": "fra-1", "start": 926, "end": 931}]}, {"trigger": {"text": "transcription", "start": 1264, "end": 1277}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1258, "end": 1263}]}]}}, "schema": []}
{"input": "Transactivation of the human immunodeficiency virus promoter by human herpesvirus 6 (HHV-6) strains GS and Z-29 in primary human T lymphocytes and identification of transactivating HHV-6(GS) gene fragments. \nHuman herpesvirus 6 (HHV-6) can activate the human immunodeficiency virus (HIV) promoter and accelerate cytopathic effects in HIV-infected human T cells. This study examines the regions of the HIV promoter required for HHV-6 transactivation in a heterogeneous population of primary human T lymphocytes with or without antigenic stimulation. Two different strains of HHV-6, GS and Z29, transactivated the HIV promoter. The GS strain transactivated the promoter in both stimulated and resting T cells, while the Z29 strain increased HIV promoter activity only in stimulated T cells. Three DNA clones containing HHV-6(GS) genomic fragments transactivated the HIV promoter in cotransfected T cells. A 21.4-kb DNA clone, pZVB70, showed the highest transactivating ability, while two other DNA fragments, pZVB10 (6.2 kb) and pZVH14 (8.7 kb), showed lower activity. One of these clones, pZVH14, activated the HIV promoter construct containing a mutation in the NF kappa B site. However, this mutated NF kappa B promoter was not transactivated during HHV-6(GS) infection or after cotransfection with pZVB70 or pZVB10. These data indicate that the NF kappa B sites of the HIV promoter are essential for its transactivation during HHV-6(GS) infection. By increasing HIV promoter activity in primary T lymphocytes, HHV-6 may consequently increase HIV replication, leading to an increase in the cytopathic effect on coinfected human T cells. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Regulation of M-CSF expression by M-CSF: role of protein kinase C and transcription factor NF kappa B. \nMacrophage-colony-stimulating factor (M-CSF), also referred to as CSF-1, regulates the survival, growth, differentiation and functional activity of monocytes by binding to a single class of high-affinity cell surface receptors, known to be the product of the c-fms protooncogene. The detection of both M-CSF and c-fms expression by cells of the monocyte lineage has suggested that M-CSF may act by an autocrine mechanism. Interestingly, it has been shown that M-CSF can induce the expression of its own gene. Although sensitivity to M-CSF can be modulated by regulation of receptor expression and function, M-CSF responsiveness is largely determined at a postreceptor level. To date, little is known about the intracellular pathway of M-CSF signal transduction. We have therefore investigated the changes in protein kinase C (PKC) activity upon exposure of monocytes to M-CSF. We show that M-CSF activates and translocates PKC. Inhibition of PKC by the isoquinoline derivative H7 abolishes induction of M-CSF by M-CSF. Furthermore, activation of PKC was pertussis-toxin-sensitive and was associated with the detection of an NF kappa B protein in nuclear extracts of M-CSF-induced blood monocytes but not in monocytes exposed to medium treatment only. The results suggest that M-CSF induction of M-CSF involves G proteins, PKC and NF kappa B. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 265, "end": 272}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 142, "end": 147}]}], "gene expression": [{"trigger": {"text": "expression", "start": 20, "end": 30}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 14, "end": 19}]}, {"trigger": {"text": "expression", "start": 422, "end": 432}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 406, "end": 411}]}, {"trigger": {"text": "expression", "start": 422, "end": 432}, "arguments": [{"role": "Theme", "text": "c-fms", "start": 416, "end": 421}]}, {"trigger": {"text": "expression", "start": 585, "end": 595}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 564, "end": 569}]}], "negative regulation": [{"trigger": {"text": "abolishes", "start": 1084, "end": 1093}, "arguments": [{"role": "Theme", "text": "induction", "start": 1094, "end": 1103}]}], "positive regulation": [{"trigger": {"text": "act", "start": 495, "end": 498}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 485, "end": 490}]}, {"trigger": {"text": "induce", "start": 574, "end": 580}, "arguments": [{"role": "Cause", "text": "M-CSF", "start": 564, "end": 569}, {"role": "Theme", "text": "expression", "start": 585, "end": 595}]}, {"trigger": {"text": "induction", "start": 1094, "end": 1103}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 1107, "end": 1112}, {"role": "Cause", "text": "M-CSF", "start": 1116, "end": 1121}]}, {"trigger": {"text": "induction", "start": 1386, "end": 1395}, "arguments": [{"role": "Cause", "text": "M-CSF", "start": 1380, "end": 1385}, {"role": "Theme", "text": "M-CSF", "start": 1399, "end": 1404}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 20, "end": 30}, {"role": "Cause", "text": "M-CSF", "start": 34, "end": 39}]}]}}, "schema": []}
{"input": "HIV1 infection of human monocytes and macrophages promotes induction or translocation of NF-KB-related factors. \nIn 1991, we demonstrated, using electrophoretic mobility shift assays, that 3 different factors (termed B1, B2 and B3) with affinity for the KB-enhancer target sequence were specifically detected in nuclear extracts from HIV1-infected monocytes and macrophages. The B2 factor was induced in the nuclei of these cells only upon HIV1 infection. The B3 factor was only slightly evident in nuclei of uninfected cells but was readily detectable in nuclei of infected monocytes. Its expression remained very low in nuclei of HIV1-infected macrophages. In this paper, we demonstrate that the B2 factor is expressed in the cytosol of monocytes and macrophages as a DNA-binding protein, indicating that it is not associated with an inhibitor (IKB). This factor remained clustered in the cytosol and was translocated to the nuclei only after HIV1 infection. The B3 factor is detected in the cytosol only when cells are HIV1-infected. The role of HIV1 infection in the expression and the translocation of these factors is discussed. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Induction of NF-kappa B during monocyte differentiation is associated with activation of HIV-gene expression. \nCells of the monocyte-macrophage lineage are important targets of HIV infection. We report here that the phenotypic differentiation of monocyte cell lines induced by phorbol esters or tumour necrosis factor alpha (TNF alpha) is associated with expression of nuclear factor kappa B (NF-kappa B). In parallel with such differentiation, HIV transcription, monitored using an HIV long terminal repeat reporter gene construct, is activated in such cells under the influence of enhanced NF-kappa B expression. Also, in a promonocyte cell line chronically infected with HIV, NF-kappa B expression and HIV transcription were enhanced on stimulation with phorbol ester or TNF alpha. Thus, stimulation of monocyte cell lines by phorbol esters or TNF alpha induces cell differentiation and activates HIV transcription. Such a process may have fundamental implications in AIDS pathogenesis in vivo and may be important in disease progression induced by opportunistic infections directly or indirectly involving macrophages. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Expression of c-jun, jun B and jun D proto-oncogenes in human peripheral-blood granulocytes. \nWe have found that purified human peripheral-blood granulocytes express constitutively significant levels of proto-oncogenes c-jun, jun B and jun D mRNA. Upon functional activation of granulocytes by 4 beta-phorbol 12-myristate 13-acetate (PMA), the levels of c-jun, jun B and jun D transcripts were increased. The three jun genes showed a similar time course in their induction by PMA, maximal mRNA levels being reached after 60 min of induction. These results suggest that expression of c-jun, jun B and jun D genes might be involved in terminal granulocyte differentiation or in regulating granulocyte functionality. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 14, "end": 19}]}, {"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "jun B", "start": 21, "end": 26}]}, {"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "jun D", "start": 31, "end": 36}]}, {"trigger": {"text": "expression", "start": 569, "end": 579}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 583, "end": 588}]}, {"trigger": {"text": "expression", "start": 569, "end": 579}, "arguments": [{"role": "Theme", "text": "jun B", "start": 590, "end": 595}]}, {"trigger": {"text": "expression", "start": 569, "end": 579}, "arguments": [{"role": "Theme", "text": "jun D", "start": 600, "end": 605}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 394, "end": 403}, "arguments": [{"role": "Theme", "text": "levels", "start": 344, "end": 350}]}, {"trigger": {"text": "induction", "start": 463, "end": 472}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 354, "end": 359}]}, {"trigger": {"text": "induction", "start": 463, "end": 472}, "arguments": [{"role": "Theme", "text": "jun B", "start": 361, "end": 366}]}, {"trigger": {"text": "induction", "start": 463, "end": 472}, "arguments": [{"role": "Theme", "text": "jun D", "start": 371, "end": 376}]}], "transcription": [{"trigger": {"text": "express", "start": 158, "end": 165}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 219, "end": 224}]}, {"trigger": {"text": "express", "start": 158, "end": 165}, "arguments": [{"role": "Theme", "text": "jun B", "start": 226, "end": 231}]}, {"trigger": {"text": "express", "start": 158, "end": 165}, "arguments": [{"role": "Theme", "text": "jun D", "start": 236, "end": 241}]}, {"trigger": {"text": "levels", "start": 344, "end": 350}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 354, "end": 359}]}, {"trigger": {"text": "levels", "start": 344, "end": 350}, "arguments": [{"role": "Theme", "text": "jun B", "start": 361, "end": 366}]}, {"trigger": {"text": "levels", "start": 344, "end": 350}, "arguments": [{"role": "Theme", "text": "jun D", "start": 371, "end": 376}]}, {"trigger": {"text": "mRNA levels", "start": 489, "end": 500}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 354, "end": 359}]}, {"trigger": {"text": "mRNA levels", "start": 489, "end": 500}, "arguments": [{"role": "Theme", "text": "jun B", "start": 361, "end": 366}]}, {"trigger": {"text": "mRNA levels", "start": 489, "end": 500}, "arguments": [{"role": "Theme", "text": "jun D", "start": 371, "end": 376}]}]}}, "schema": []}
{"input": "Transforming growth factor-beta suppresses human B lymphocyte Ig production by inhibiting synthesis and the switch from the membrane form to the secreted form of Ig mRNA. \nTransforming growth factor-beta (TGF-beta) inhibits B cell Ig secretion and reduces B cell membrane Ig expression. The addition of TGF-beta to human B lymphocyte cultures stimulated with Staphylococcus aureus Cowan strain I and IL-2 completely inhibited B cell Ig secretion (greater than 90%) and decreased B cell surface IgM, IgD, kappa L chain, and lambda L chain expression. In contrast, TGF-beta had only minimal effects on two other B cell membrane proteins, HLA-DR and CD20. Internal labeling with [35S]methionine and immunoprecipitation with anti-IgM, anti-kappa, and anti-lambda antibodies revealed a striking reduction in kappa L chain in the presence of TGF-beta. A less pronounced reduction in lambda L chain and microH chain was also noted. Northern blot analysis of RNA purified from B cells treated with TGF-beta for varying time intervals revealed a significant decrease in steady state kappa and lambda L chain mRNA levels. Furthermore, a significant decrease in the switch from the membrane forms of mu and gamma to their respective secreted forms was noted in the presence of TGF-beta. Nuclear run-on experiments demonstrated decreased transcription of kappa L chain. The effects of TGF-beta on two transcriptional regulatory factors, Oct-2 and nuclear factor (NF) kappa B, known to be important in Ig gene transcription were examined. Oct-2 mRNA levels and both Oct-2 and NF-kappa B proteins in nuclear extracts were not altered by treatment with TGF-beta. In contrast, levels of the transcriptional factor AP-1, which is not known to be important in B cell Ig production, were reduced by TGF-beta. These findings demonstrate that TGF-beta decreases B lymphocyte Ig secretion by inhibiting the synthesis of Ig mRNA and inhibiting the switch from the membrane form to the secreted forms of mu and gamma mRNA. The mechanism by which TGF-beta inhibits Ig chain synthesis is unclear although it does not involve inhibition of the binding of NF-kappa B or Oct-2 to their respective target sequences. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 2117, "end": 2124}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 2142, "end": 2147}]}], "gene expression": [{"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "kappa L chain", "start": 504, "end": 517}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "lambda L chain", "start": 523, "end": 537}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 469, "end": 478}, "arguments": [{"role": "Theme", "text": "expression", "start": 538, "end": 548}]}, {"trigger": {"text": "reduction", "start": 790, "end": 799}, "arguments": [{"role": "Theme", "text": "kappa L chain", "start": 803, "end": 816}]}, {"trigger": {"text": "reduction", "start": 864, "end": 873}, "arguments": [{"role": "Theme", "text": "lambda L chain", "start": 877, "end": 891}]}, {"trigger": {"text": "levels", "start": 1104, "end": 1110}, "arguments": [{"role": "Theme", "text": "kappa", "start": 1074, "end": 1079}]}, {"trigger": {"text": "levels", "start": 1104, "end": 1110}, "arguments": [{"role": "Theme", "text": "lambda L chain", "start": 1084, "end": 1098}]}, {"trigger": {"text": "decreased", "start": 1316, "end": 1325}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1326, "end": 1339}]}, {"trigger": {"text": "inhibition", "start": 2099, "end": 2109}, "arguments": [{"role": "Theme", "text": "binding", "start": 2117, "end": 2124}]}], "regulation": [{"trigger": {"text": "effects", "start": 589, "end": 596}, "arguments": [{"role": "Theme", "text": "CD20", "start": 647, "end": 651}]}, {"trigger": {"text": "effects", "start": 1362, "end": 1369}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 1425, "end": 1430}]}, {"trigger": {"text": "altered", "start": 1612, "end": 1619}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 1553, "end": 1558}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1326, "end": 1339}, "arguments": [{"role": "Theme", "text": "kappa L chain", "start": 1343, "end": 1356}]}]}}, "schema": []}
{"input": "Inhibition of HIV-1 replication and NF-kappa B activity by cysteine and cysteine derivatives. \nHIV-1 proviral DNA contains two binding sites for the transcription factor NF-kappa B. HIV-1-infected individuals have, on average, abnormally high levels of tumour necrosis factor alpha (TNF alpha) and abnormally low plasma cysteine levels. We therefore investigated the effects of cysteine and related thiols on HIV-1 replication and NF-kappa B expression. The experiments in this report show that cysteine or N-acetylcysteine (NAC) raise the intracellular glutathione (GSH) level and inhibit HIV-1 replication in persistently infected Molt-4 and U937 cells. However, inhibition of HIV-1 replication appears not to be directly correlated with GSH levels. Cysteine and NAC also inhibit NF-kappa B activity as determined by electrophoretic mobility shift assays and chloramphenicol acetyl-transferase (CAT) gene expression under control of NF-kappa B binding sites in uninfected cells. This suggests that the cysteine deficiency in HIV-1-infected individuals may cause an over-expression of NF-kappa B-dependent genes and enhance HIV-1 replication. NAC may be considered for the treatment of HIV-1-infected individuals. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 907, "end": 917}, "arguments": [{"role": "Theme", "text": "CAT", "start": 897, "end": 900}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 774, "end": 781}, "arguments": [{"role": "Theme", "text": "control", "start": 924, "end": 931}]}], "positive regulation": [{"trigger": {"text": "high levels", "start": 238, "end": 249}, "arguments": [{"role": "Theme", "text": "TNF alpha", "start": 283, "end": 292}]}], "regulation": [{"trigger": {"text": "control", "start": 924, "end": 931}, "arguments": [{"role": "Theme", "text": "expression", "start": 907, "end": 917}]}]}}, "schema": []}
{"input": "A nuclear factor NF-GM2 that interacts with a regulatory region of the GM-CSF gene essential for its induction in responses to T-cell activation: purification from human T-cell leukemia line Jurkat cells and similarity to NF-kappa B. \nActivation of T cells by antigen, lectin, or a combination of phorbol-12-myristate acetate (PMA) and calcium ionophore (A23187) leads to the induction of genes for a set of lymphokines, including granulocyte-macrophage colony-stimulating factor (GM-CSF). We demonstrated in earlier studies that the upstream region of the mouse GM-CSF promoter at positions between -95 and -73 is essential for transcriptional activation in response to PMA/A23187. This region contains two DNA-binding motifs, GM2 and GC-box. The GM2 sequence (GGTAGTTCCC) is recognized by an inducible factor NF-GM2; the other (CCGCCC) by constitutive factors A1, A2, and B. To elucidate the mechanism of GM-CSF gene activation, we have purified the inducible factor NF-GM2 from the nuclear extract of stimulated Jurkat cells on the basis of specific DNA-binding activity. The purified NF-GM2 consists of 50 (p50) and 65 kDa (p65) polypeptides and has a binding activity specific for both the GM-CSF and immunoglobulin kappa (GGAAAGTCCC) enhancers. Electrophoretically purified p50 alone can form a protein-DNA complex, but in the mixture, p50 associates preferentially with p65 to form the NF-GM2 complex. In addition, p65 gave per se, with low affinity, a protein-DNA complex that migrated more slowly than native NF-GM2 complex. Furthermore, an antiserum against KBF1 (identical to 50 kDa NF-kappa B protein) reacted with the p50 of NF-GM2, indicating that the NF-GM2 polypeptide cannot be immunologically differentiated from the 50 kDa subunit of NF-kappa B. The purified NF-GM2 activated in vitro transcription from the kappa B enhancer, while it failed to stimulate transcription from the GM-CSF promoter harboring the GM2 sequence. This suggests that the activation mechanism of the GM-CSF gene through the GM2/GC-box sequence is different from that of genes carrying the kappa B enhancer alone. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 1156, "end": 1172}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1195, "end": 1201}, {"role": "Site", "text": "enhancers", "start": 1240, "end": 1249}]}, {"trigger": {"text": "complex", "start": 1313, "end": 1320}, "arguments": [{"role": "Theme", "text": "p50", "start": 1280, "end": 1283}]}, {"trigger": {"text": "associates", "start": 1346, "end": 1356}, "arguments": [{"role": "Theme", "text": "p50", "start": 1342, "end": 1345}, {"role": "Theme2", "text": "p65", "start": 1377, "end": 1380}]}, {"trigger": {"text": "complex", "start": 1472, "end": 1479}, "arguments": [{"role": "Theme", "text": "p65", "start": 1422, "end": 1425}]}, {"trigger": {"text": "reacted", "start": 1614, "end": 1621}, "arguments": [{"role": "Theme", "text": "p50", "start": 1631, "end": 1634}]}], "gene expression": [{"trigger": {"text": "induction", "start": 101, "end": 110}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 71, "end": 77}]}, {"trigger": {"text": "induction", "start": 376, "end": 385}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 481, "end": 487}]}, {"trigger": {"text": "activation", "start": 1964, "end": 1974}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1992, "end": 1998}]}], "positive regulation": [{"trigger": {"text": "essential", "start": 83, "end": 92}, "arguments": [{"role": "Theme", "text": "responses", "start": 114, "end": 123}]}, {"trigger": {"text": "leads", "start": 363, "end": 368}, "arguments": [{"role": "Theme", "text": "induction", "start": 376, "end": 385}]}, {"trigger": {"text": "essential", "start": 615, "end": 624}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 629, "end": 655}]}, {"trigger": {"text": "transcriptional activation", "start": 629, "end": 655}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 563, "end": 569}]}, {"trigger": {"text": "activation", "start": 919, "end": 929}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 907, "end": 913}]}, {"trigger": {"text": "stimulate", "start": 1864, "end": 1873}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1874, "end": 1887}]}, {"trigger": {"text": "through", "start": 2004, "end": 2011}, "arguments": [{"role": "Theme", "text": "activation", "start": 1964, "end": 1974}]}], "regulation": [{"trigger": {"text": "responses", "start": 114, "end": 123}, "arguments": [{"role": "Theme", "text": "induction", "start": 101, "end": 110}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1874, "end": 1887}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1897, "end": 1903}]}]}}, "schema": []}
{"input": "Synergism between two distinct elements of the HTLV-I enhancer during activation by the trans-activator of HTLV-I. \nWe have conducted functional studies of the enhancer elements of human T-cell leukemia virus type I (HTLV-I) using the human T-cell lines Jurkat and MOLT 4, which are negative for HTLV-I, and MT-2 and TL-Mor, which carry the proviral genome of HTLV-I. Two distinct elements have been implicated in function of the HTLV-I enhancer. One is the 21-base-pair (bp) core element that is responsible for trans-activation by the HTLV-I trans-activator p40tax and that has the ability to bind to cyclic-AMP responsive element binding factor (CREB)-like factor(s). The other is a region interposed between the 21-bp elements. In this study we demonstrate that a subfragment (C26) in the region between the 21-bp elements is involved in trans-activation by p40tax, possibly through binding to an NF-kappa B-like nuclear factor or factors. Formation of the protein-DNA complex with the C26 subfragment was positively affected by p40tax. The C26 element conferred partial responsiveness to p40tax when linked to one copy of the 21-bp element that, by itself, showed little activation in response to p40tax. However, the C26 element alone, even when repeated, could not be activated by p40tax, unlike other NF-kappa B-binding elements. In contrast, the C26 element itself was profoundly activated upon stimulation with 12-O-tetradecanoylphorbol-13-acetate. These findings therefore suggest that the HTLV-I enhancer contains multiple functional elements, including binding sites for at least CREB- and NF-kappa B-like factors, which synergistically cooperate in activation of the HTLV-I enhancer in response to p40tax. Our results also demonstrate that TPA-dependent activation of the HTLV-I enhancer may be mediated through the C26 element. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 595, "end": 599}, "arguments": [{"role": "Theme", "text": "CREB", "start": 649, "end": 653}]}]}}, "schema": []}
{"input": "Inhibition of phorbol ester-induced monocytic differentiation by dexamethasone is associated with down-regulation of c-fos and c-jun (AP-1). \nPrevious studies have shown that treatment of human myeloid leukemia cells with 12-O-tetradecanoylphorbol-13-acetate (TPA) is associated with induction of monocytic differentiation and expression of the c-jun and c-fos early response genes. The present work demonstrates that the glucocorticoid dexamethasone inhibits TPA-induced increases in c-jun and c-fos mRNA levels in U-937 leukemia cells. These findings were associated with a block in appearance of the monocytic phenotype, including inhibition of TPA-induced increases in lamin A, lamin C, and vimentin transcripts. Other studies have demonstrated that TPA-induced monocytic differentiation and expression of the c-jun and c-fos genes in myeloid leukemia cells are regulated by protein kinase C (PKC). The finding that dexamethasone has no effect on TPA-induced activation of PKC suggests that this glucocorticoid inhibits signals downstream or parallel to this enzyme. Nuclear run-on assays demonstrate that: (1) induction of c-jun and c-fos expression by TPA is regulated by transcriptional mechanisms, (2) TPA-induced expression of c-jun and c-fos does not require protein synthesis, and (3) TPA-induced expression of both genes is inhibited at the transcriptional level by dexamethasone. To further define the effects of dexamethasone at the molecular level, we prepared a series of deleted c-jun promoter fragments linked to the chloramphenicol acetyltransferase (CAT) gene. Increases in CAT activity during transient expression of these constructs in TPA-treated U-937 cells could be assigned to the region (-97 to -20) of the promoter that contains the AP-1 binding site. This induction of CAT activity was sensitive to dexamethasone. These findings suggest that dexamethasone down-regulates TPA-induced transcription of the c-jun gene during monocytic differentiation by inhibiting activation of the AP-1 site. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 796, "end": 806}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 814, "end": 819}]}, {"trigger": {"text": "expression", "start": 796, "end": 806}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 824, "end": 829}]}, {"trigger": {"text": "expression", "start": 1144, "end": 1154}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1128, "end": 1133}]}, {"trigger": {"text": "expression", "start": 1144, "end": 1154}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1138, "end": 1143}]}, {"trigger": {"text": "expression", "start": 1222, "end": 1232}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1236, "end": 1241}]}, {"trigger": {"text": "expression", "start": 1222, "end": 1232}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1246, "end": 1251}]}], "negative regulation": [{"trigger": {"text": "down-regulation", "start": 98, "end": 113}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 117, "end": 122}]}, {"trigger": {"text": "down-regulation", "start": 98, "end": 113}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 127, "end": 132}]}, {"trigger": {"text": "inhibits", "start": 451, "end": 459}, "arguments": [{"role": "Theme", "text": "increases", "start": 472, "end": 481}]}, {"trigger": {"text": "inhibition", "start": 634, "end": 644}, "arguments": [{"role": "Theme", "text": "increases", "start": 660, "end": 669}]}, {"trigger": {"text": "inhibited", "start": 1336, "end": 1345}, "arguments": [{"role": "Theme", "text": "induced", "start": 1300, "end": 1307}]}, {"trigger": {"text": "down-regulates", "start": 1885, "end": 1899}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1912, "end": 1925}]}], "positive regulation": [{"trigger": {"text": "increases", "start": 472, "end": 481}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 485, "end": 490}]}, {"trigger": {"text": "increases", "start": 472, "end": 481}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 495, "end": 500}]}, {"trigger": {"text": "increases", "start": 660, "end": 669}, "arguments": [{"role": "Theme", "text": "lamin A", "start": 673, "end": 680}]}, {"trigger": {"text": "increases", "start": 660, "end": 669}, "arguments": [{"role": "Theme", "text": "lamin C", "start": 682, "end": 689}]}, {"trigger": {"text": "increases", "start": 660, "end": 669}, "arguments": [{"role": "Theme", "text": "vimentin", "start": 695, "end": 703}]}, {"trigger": {"text": "activation", "start": 963, "end": 973}, "arguments": [{"role": "Theme", "text": "PKC", "start": 977, "end": 980}]}, {"trigger": {"text": "induction", "start": 1115, "end": 1124}, "arguments": [{"role": "Theme", "text": "expression", "start": 1144, "end": 1154}]}, {"trigger": {"text": "induced", "start": 1214, "end": 1221}, "arguments": [{"role": "Theme", "text": "expression", "start": 1222, "end": 1232}]}, {"trigger": {"text": "require", "start": 1261, "end": 1268}, "arguments": [{"role": "Theme", "text": "induced", "start": 1214, "end": 1221}]}, {"trigger": {"text": "induced", "start": 1300, "end": 1307}, "arguments": [{"role": "Theme", "text": "at the transcriptional level", "start": 1346, "end": 1374}]}, {"trigger": {"text": "Increases", "start": 1581, "end": 1590}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1594, "end": 1597}]}, {"trigger": {"text": "induction", "start": 1785, "end": 1794}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1798, "end": 1801}]}, {"trigger": {"text": "induced", "start": 1904, "end": 1911}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1912, "end": 1925}]}], "regulation": [{"trigger": {"text": "regulated", "start": 866, "end": 875}, "arguments": [{"role": "Theme", "text": "expression", "start": 796, "end": 806}]}, {"trigger": {"text": "effect", "start": 941, "end": 947}, "arguments": [{"role": "Theme", "text": "activation", "start": 963, "end": 973}]}, {"trigger": {"text": "regulated", "start": 1165, "end": 1174}, "arguments": [{"role": "Theme", "text": "induction", "start": 1115, "end": 1124}]}, {"trigger": {"text": "sensitive", "start": 1815, "end": 1824}, "arguments": [{"role": "Theme", "text": "induction", "start": 1785, "end": 1794}]}], "transcription": [{"trigger": {"text": "at the transcriptional level", "start": 1346, "end": 1374}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1128, "end": 1133}]}, {"trigger": {"text": "at the transcriptional level", "start": 1346, "end": 1374}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1138, "end": 1143}]}, {"trigger": {"text": "transcription", "start": 1912, "end": 1925}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1933, "end": 1938}]}]}}, "schema": []}
{"input": "Evaluation of the role of ligand and thermal activation of specific DNA binding by in vitro synthesized human glucocorticoid receptor. \nWe have used a DNA-binding/immunoprecipitation assay to analyze the capacity of human glucocorticoid receptor (hGR), generated in rabbit reticulocyte lysates, to bind DNA. In vitro translated hGR was indistinguishable from native hGR, as determined by migration on sodium dodecyl sulfate-polyacrylamide gels, sedimentation on sucrose density gradients, and reactivity with antipeptide antibodies generated against hGR. In addition, cell-free synthesized hGR was capable of specific binding to glucocorticoid response element (GRE)-containing DNA fragments. Using this assay system, we have evaluated the contributions of ligand binding and heat activation to DNA binding by these glucocorticoid receptors. In vitro translated hGR was capable of selective DNA binding even in the absence of glucocorticoid. Treatment with dexamethasone or the antiglucocorticoid RU486 had no additional effect on the DNA-binding capacity when receptor preparations were maintained at 0 C (no activation). In contrast, addition of either ligand or antagonist in combination with a heat activation step promoted DNA binding by approximately 3-fold over that of heat-activated unliganded receptors. Agonist (dexamethasone) was slightly more effective in supporting specific DNA binding than antagonist (RU486). DNA binding by in vitro synthesized GR was blocked by the addition of sodium molybdate to the receptor preparations before steroid addition and thermal activation. Addition of KCl resulted in less DNA binding either due to blockage of DNA-receptor complex formation or disruption of the complexes. The specificity of DNA binding by cell-free synthesized hGR was analyzed further by examining the abilities of various DNAs to compete for binding to a naturally occurring GRE found in the mouse mammary tumor virus-long terminal repeat. Oligonucleotides containing the consensus GRE were the most efficient competitors, and fragments containing regulatory sequences from glucocorticoid-repressible genes were somewhat competitive, whereas single stranded oligonucleotides were unable to compete for mouse mammary tumor virus-long terminal repeat DNA binding, except when competitor was present at extremely high concentrations. Together these studies indicate that hGR synthesized in rabbit reticulocyte lysates displays many of the same properties, including GRE-specific DNA binding, observed for glucocorticoid receptor present in cytosolic extracts of mammalian cells and tissues. Similarities between the effects of dexamethasone and RU486 suggest that the antiglucocorticoid properties of RU486 do not occur at the level of specific DNA binding. ", "output": {"json_structures": {}}, "schema": []}
{"input": "One base pair change abolishes the T cell-restricted activity of a kB-like proto-enhancer element from the interleukin 2 promoter. \nThe inducible, T cell-specific enhancers of murine and human Interleukin 2 (Il-2) genes contain the kB-like sequence GGGATTTCACC as an essential cis-acting enhancer motif. When cloned in multiple copies this so-called TCEd (distal T cell element) acts as an inducible proto-enhancer element in E14 T lymphoma cells, but not in HeLa cells. In extracts of induced, Il-2 secreting El4 cells three individual protein factors bind to TCEd DNA. The binding of the most prominent factor, named TCF-1 (T cell factor 1), is correlated with the proto-enhancer activity of TCEd. TCF-1 consists of two polypeptides of about 50 kD and 105 kD; the former seems to be related to the 50 kD polypeptide of NF-kB. Purified NF-kB is also able to bind to the TCEd, but TCF-1 binds stronger than NF-kB to TCEd DNA. The conversion of the TCEd to a 'perfect' NF-kB binding site leads to a tighter binding of NF-kB to TCEd DNA and, as a functional consequence, to the activity of the 'converted' TCEd motifs in HeLa cells. Thus, the substitution of the underlined A residue to a C within the GGGATTTCACC motif abolishes its T cell-restricted activity and leads to its functioning in both El4 cells and HeLa cells. These results indicate that lymphocyte-specific factors binding to the TCEd are involved in the control of T cell specific-transcription of the Il-2 gene. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 575, "end": 582}, "arguments": [{"role": "Theme", "text": "TCF-1", "start": 619, "end": 624}]}, {"trigger": {"text": "binds", "start": 887, "end": 892}, "arguments": [{"role": "Theme", "text": "TCF-1", "start": 881, "end": 886}]}], "localization": [{"trigger": {"text": "secreting", "start": 500, "end": 509}, "arguments": [{"role": "Theme", "text": "Il-2", "start": 495, "end": 499}]}], "regulation": [{"trigger": {"text": "control", "start": 1418, "end": 1425}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1445, "end": 1458}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1445, "end": 1458}, "arguments": [{"role": "Theme", "text": "Il-2", "start": 1466, "end": 1470}]}]}}, "schema": []}
{"input": "Negative regulation of human immunodeficiency virus type 1 expression in monocytes: role of the 65-kDa plus 50-kDa NF-kappa B dimer. \nAlthough monocytic cells can provide a reservoir for viral production in vivo, their regulation of human immunodeficiency virus type 1 (HIV-1) transcription can be either latent, restricted, or productive. These differences in gene expression have not been molecularly defined. In THP-1 cells with restricted HIV expression, there is an absence of DNA-protein binding complex formation with the HIV-1 promoter-enhancer associated with markedly less viral RNA production. This absence of binding was localized to the NF-kappa B region of the HIV-1 enhancer; the 65-kDa plus 50-kDa NF-kappa B heterodimer was preferentially lost. Adding purified NF-kappa B protein to nuclear extracts from cells with restricted expression overcomes this lack of binding. In addition, treatment of these nuclear extracts with sodium deoxycholate restored their ability to form the heterodimer, suggesting the presence of an inhibitor of NF-kappa B activity. Furthermore, treatment of nuclear extracts from these cells that had restricted expression with lipopolysaccharide increased viral production and NF-kappa B activity. Antiserum specific for NF-kappa B binding proteins, but not c-rel-specific antiserum, disrupted heterodimer complex formation. Thus, both NF-kappa B-binding complexes are needed for optimal viral transcription. Binding of the 65-kDa plus 50-kDa heterodimer to the HIV-1 enhancer can be negatively regulated in monocytes, providing one mechanism restricting HIV-1 gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "heterodimer", "start": 725, "end": 736}, "arguments": [{"role": "Theme", "text": "65-kDa", "start": 695, "end": 701}, {"role": "Theme2", "text": "50-kDa", "start": 707, "end": 713}]}, {"trigger": {"text": "Binding", "start": 1451, "end": 1458}, "arguments": [{"role": "Theme", "text": "65-kDa", "start": 1466, "end": 1472}]}, {"trigger": {"text": "Binding", "start": 1451, "end": 1458}, "arguments": [{"role": "Theme", "text": "50-kDa", "start": 1478, "end": 1484}]}, {"trigger": {"text": "heterodimer", "start": 1485, "end": 1496}, "arguments": [{"role": "Theme", "text": "65-kDa", "start": 1466, "end": 1472}, {"role": "Theme2", "text": "50-kDa", "start": 1478, "end": 1484}]}], "negative regulation": [{"trigger": {"text": "lost", "start": 756, "end": 760}, "arguments": [{"role": "Theme", "text": "heterodimer", "start": 725, "end": 736}]}, {"trigger": {"text": "overcomes", "start": 855, "end": 864}, "arguments": [{"role": "Theme", "text": "lost", "start": 756, "end": 760}]}, {"trigger": {"text": "disrupted", "start": 1326, "end": 1335}, "arguments": [{"role": "Theme", "text": "heterodimer", "start": 725, "end": 736}]}, {"trigger": {"text": "negatively regulated", "start": 1526, "end": 1546}, "arguments": [{"role": "Theme", "text": "Binding", "start": 1451, "end": 1458}]}], "positive regulation": [{"trigger": {"text": "restored", "start": 961, "end": 969}, "arguments": [{"role": "Theme", "text": "heterodimer", "start": 725, "end": 736}]}]}}, "schema": []}
{"input": "Isolation of a candidate repressor/activator, NF-E1 (YY-1, delta), that binds to the immunoglobulin kappa 3' enhancer and the immunoglobulin heavy-chain mu E1 site. \nWe have determined that the developmental control of immunoglobulin kappa 3' enhancer (kappa E3') activity is the result of the combined influence of positive- and negative-acting elements. We show that a central core in the kappa E3' enhancer is active at the pre-B-cell stage but is repressed by flanking negative-acting elements. The negative-acting sequences repress enhancer activity in a position- and orientation-independent manner at the pre-B-cell stage. We have isolated a human cDNA clone encoding a zinc finger protein (NF-E1) that binds to the negative-acting segment of the kappa E3' enhancer. This protein also binds to the immunoglobulin heavy-chain enhancer mu E1 site. NF-E1 is encoded by the same gene as the YY-1 protein, which binds to the adeno-associated virus P5 promoter. NF-E1 is also the human homologue of the mouse delta protein, which binds to ribosomal protein gene promoters. The predicted amino acid sequence of this protein contains features characteristic of transcriptional activators as well as transcriptional repressors. Cotransfection studies with this cDNA indicate that it can repress basal promoter activity. The apparent dual function of this protein is discussed. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 72, "end": 77}, "arguments": [{"role": "Theme", "text": "NF-E1", "start": 46, "end": 51}]}, {"trigger": {"text": "binds", "start": 710, "end": 715}, "arguments": [{"role": "Theme", "text": "NF-E1", "start": 698, "end": 703}]}, {"trigger": {"text": "binds", "start": 792, "end": 797}, "arguments": [{"role": "Theme", "text": "NF-E1", "start": 698, "end": 703}]}, {"trigger": {"text": "binds", "start": 914, "end": 919}, "arguments": [{"role": "Theme", "text": "YY-1", "start": 894, "end": 898}]}, {"trigger": {"text": "binds", "start": 1031, "end": 1036}, "arguments": [{"role": "Theme", "text": "delta", "start": 1010, "end": 1015}]}]}}, "schema": []}
{"input": "Regulation of interleukin-1 beta production by glucocorticoids in human monocytes: the mechanism of action depends on the activation signal. \nGlucocorticoids are known to downregulate interleukin-1 beta production in monocytic cells by two different mechanims: direct inhibition of the gene transcription and destabilization of the preformed interleukin-1 beta mRNA. Now we have examined the effect of the nature of the monocyte activating signal on these two inhibitory mechanims. When human monocytes were preincubated with dexamethasone for 1 hour and then stimulated either with bacterial lipopolysaccharide or phorbol myristate, it was found that dexamethasone inhibited the lipopolysaccharide-induced interleukin-1 beta protein production, but the phorbol myristate-induced production was increased 3-10 fold. This difference was also seen at the mRNA level. When dexamethasone was added to the cultures 3 hours after the stimulators, it clearly decreased the interleukin-1 beta mRNA levels regardless of the stimulator used (although the effect was clearly weaker on the PMA-induced mRNA). Thus these data suggest that the phorbol myristate-induced signal (prolonged protein kinase C activation?) cannot be inhibited by prior incubation with dexamethasone and it also protects the induced mRNA for the degradative action of dexamethasone. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 33, "end": 43}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 14, "end": 32}]}, {"trigger": {"text": "production", "start": 203, "end": 213}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 184, "end": 202}]}, {"trigger": {"text": "production", "start": 734, "end": 744}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 707, "end": 725}]}], "negative regulation": [{"trigger": {"text": "downregulate", "start": 171, "end": 183}, "arguments": [{"role": "Theme", "text": "production", "start": 203, "end": 213}, {"role": "Cause", "text": "destabilization", "start": 309, "end": 324}]}, {"trigger": {"text": "downregulate", "start": 171, "end": 183}, "arguments": [{"role": "Theme", "text": "production", "start": 203, "end": 213}]}, {"trigger": {"text": "destabilization", "start": 309, "end": 324}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 342, "end": 360}]}, {"trigger": {"text": "inhibited", "start": 666, "end": 675}, "arguments": [{"role": "Theme", "text": "induced", "start": 699, "end": 706}]}, {"trigger": {"text": "decreased", "start": 952, "end": 961}, "arguments": [{"role": "Theme", "text": "levels", "start": 990, "end": 996}]}, {"trigger": {"text": "inhibited", "start": 1214, "end": 1223}, "arguments": [{"role": "Theme", "text": "induced", "start": 1148, "end": 1155}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 699, "end": 706}, "arguments": [{"role": "Theme", "text": "production", "start": 734, "end": 744}]}, {"trigger": {"text": "induced", "start": 772, "end": 779}, "arguments": [{"role": "Theme", "text": "production", "start": 734, "end": 744}]}, {"trigger": {"text": "increased", "start": 795, "end": 804}, "arguments": [{"role": "Theme", "text": "induced", "start": 772, "end": 779}]}, {"trigger": {"text": "induced", "start": 1082, "end": 1089}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 966, "end": 984}]}, {"trigger": {"text": "induced", "start": 1148, "end": 1155}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 966, "end": 984}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "production", "start": 33, "end": 43}]}, {"trigger": {"text": "depends", "start": 107, "end": 114}, "arguments": [{"role": "Theme", "text": "Regulation", "start": 0, "end": 10}]}, {"trigger": {"text": "effect", "start": 392, "end": 398}, "arguments": [{"role": "Theme", "text": "destabilization", "start": 309, "end": 324}]}, {"trigger": {"text": "regardless of", "start": 997, "end": 1010}, "arguments": [{"role": "Theme", "text": "decreased", "start": 952, "end": 961}]}], "transcription": [{"trigger": {"text": "preformed", "start": 332, "end": 341}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 342, "end": 360}]}, {"trigger": {"text": "levels", "start": 990, "end": 996}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 966, "end": 984}]}]}}, "schema": []}
{"input": "Identification of transcriptional suppressor proteins that bind to the negative regulatory element of the human immunodeficiency virus type 1. \nTwo different proteins which independently bound to neighboring sequences within the negative regulatory element (NRE) of human immunodeficiency virus type 1 (HIV-1) were detected in the nuclear extract of a virus-infected human T cell line. One of the factors bound to a novel dyad symmetrical sequence. This sequence is well conserved in various HIV-1 isolates and partial homology was found with the promoter region of the human retinoblastoma gene. Similar DNA binding activity was detected in a variety of virus-uninfected human T cell lines and HeLa cells by means of a gel mobility shift assay. The other factor bound to a putative AP-1 recognition sequence predicted for the HIV-1 NRE. However, this factor did not bind to a typical AP-1 site. The insertion of multiple copies of the binding site for the former or latter factor into a heterologous promoter reduced the promoter activity to one-tenth or one-third, respectively. Thus, each factor may function as a novel negative regulator of transcription. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Constitutive activation of NF-kB in human thymocytes. \nNF-kB is a eukaryotic transcription regulatory factor. In T cells and T cell lines, NF-kB is bound to a cytoplasmic proteic inhibitor, the IkB. Treatment of T cells with mitogens (phorbol esters) or cytokines (TNF alpha) induces NF-kB nuclear translocation and the subsequent expression of NF-kB dependent T cell genes. Here we examined the activation of NF-kB in human T cell thymic progenitors. We report differences in (Ca2+)i requirement for NF-kB activation in thymocytes as compared to mature T cells. Furthermore, our results indicated that thymocytes have a constitutively active form of NF-kB, suggesting that they are activated in vivo. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Suppression of signals required for activation of transcription factor NF-kappa B in cells constitutively expressing the HTLV-I Tax protein. \nTransient short-term expression of the Tax protein of human T-cell leukemia virus type-I (HTLV-I) leads to activation of the pleiotropic transcription factor NF-kappa B. Consistent with findings obtained with transient expression assays, we observed marked accumulation of the transcription factor NF-kappa B in the nucleus of Namalwa B lymphoid cells, which constitutively express Tax. In contrast, NF-kappa B activity was not detected in the nucleus following long-term expression of Tax in Jurkat T lymphocytes. The ability of both mitogens and cytokines to activate NF-kappa B was also blocked in Jurkat cells constitutively expressing Tax. However, the activation of other mitogen-inducible transcription factors, such as Fos and Jun, was unaffected. Thus, depending on the cellular environment, the short- and long-term effects of Tax expression can be quite different. Consequently, one function of Tax in cells infected with HTLV-I might involve cell-type-specific suppression, as opposed to activation, of distinct signal pathways. The cells lines described here should be useful for the delineation of signaling pathways utilized in the selective regulation of gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 106, "end": 116}, "arguments": [{"role": "Theme", "text": "Tax", "start": 128, "end": 131}]}, {"trigger": {"text": "expression", "start": 163, "end": 173}, "arguments": [{"role": "Theme", "text": "Tax", "start": 181, "end": 184}]}, {"trigger": {"text": "express", "start": 516, "end": 523}, "arguments": [{"role": "Theme", "text": "Tax", "start": 524, "end": 527}]}, {"trigger": {"text": "expression", "start": 614, "end": 624}, "arguments": [{"role": "Theme", "text": "Tax", "start": 628, "end": 631}]}, {"trigger": {"text": "expressing", "start": 771, "end": 781}, "arguments": [{"role": "Theme", "text": "Tax", "start": 782, "end": 785}]}, {"trigger": {"text": "expression", "start": 983, "end": 993}, "arguments": [{"role": "Theme", "text": "Tax", "start": 979, "end": 982}]}], "negative regulation": [{"trigger": {"text": "unaffected", "start": 886, "end": 896}, "arguments": [{"role": "Cause", "text": "expressing", "start": 771, "end": 781}, {"role": "Theme", "text": "activation", "start": 800, "end": 810}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 800, "end": 810}, "arguments": [{"role": "Theme", "text": "Fos", "start": 869, "end": 872}]}, {"trigger": {"text": "activation", "start": 800, "end": 810}, "arguments": [{"role": "Theme", "text": "Jun", "start": 877, "end": 880}]}], "regulation": [{"trigger": {"text": "depending", "start": 904, "end": 913}, "arguments": [{"role": "Theme", "text": "expression", "start": 983, "end": 993}]}]}}, "schema": []}
{"input": "Stimulation of the human immunodeficiency virus type 2 (HIV-2) gene expression by the cytomegalovirus and HIV-2 transactivator gene. \nHuman immunodeficiency virus (HIV) often causes latent infection. Transactivation by some DNA viruses has been implicated in inducing HIV-1 replication and pathogenesis. The transactivator (IE-2) gene of the human cytomegalovirus (CMV) can enhance HIV-2 as well as HIV-1 gene expression in vitro. This inducer can act in concert with the HIV-2 tat gene and T-cell activation in enhancing gene expression in human CD4+ lymphocytes. While the HIV-2 and HIV-1 tat genes and T-cell activators apparently employ independent modes of action, the CMV transactivator in combination with the HIV-2 tat or T-cell activators may employ a gene activation pathway with some common and some distinct components. Both HIV-2 and CMV transactivators enhance HIV-2 gene expression by transcriptional activation involving transcript initiation as well as elongation, with CMV transactivator affecting elongation more than the initiation. A significant proportion of transcripts appear to terminate prematurely in the absence of transactivators. Deletion mutation analysis of the HIV-2 long terminal repeat (LTR) suggests that the element that responds to CMV transactivation in human CD4+ lymphocytes is either a diffuse one or located downstream of the HIV-2 enhancer element. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Human immunodeficiency virus type-2 gene expression: two enhancers and their activation by T-cell activators. \nThe human immunodeficiency viruses (HIVs) may include a spectrum of retroviruses with varying potential to infect their host, undergo long periods of latent infection, and induce pathology. Since expression of the viruses is in large part regulated by the sequence elements in their long terminal repeats (LTRs), this study was directed to an analysis of the regulatory elements in the HIV-2 LTR. The HIV-2 LTR was found to contain two enhancers. One of these enhancers is, in part, identical to the HIV-1 enhancer. This enhancer in HIV-1 is the T-cell activation response element; in HIV-2, however, it is the second enhancer that is mainly responsible for activation in response to T-cell activators. The second enhancer interacts with two nuclear binding proteins (85 kD and 27 kD mobility) that appear to be required for optimal enhancer function and activation. Observations such as these encourage the speculation that there may be subtle differences in the regulation of HIV-1 and HIV-2 expression that may be relevant to the possible longer latency and reduced pathogenicity of HIV-2. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Induction of NF-KB during monocyte differentiation by HIV type 1 infection. \nThe production of human immunodeficiency virus type 1 (HIV-1) progeny was followed in the U937 promonocytic cell line after stimulation either with retinoic acid or PMA, and in purified human monocytes and macrophages. Electrophoretic mobility shift assays and Southwestern blotting experiments were used to detect the binding of cellular transactivation factor NF-KB to the double repeat-KB enhancer sequence located in the long terminal repeat. PMA treatment, and not retinoic acid treatment of the U937 cells acts in inducing NF-KB expression in the nuclei. In nuclear extracts from monocytes or macrophages, induction of NF-KB occurred only if the cells were previously infected with HIV-1. When U937 cells were infected with HIV-1, no induction of NF-KB factor was detected, whereas high level of progeny virions was produced, suggesting that this factor was not required for viral replication. These results indicate that in monocytic cell lineage, HIV-1 could mimic some differentiation/activation stimuli allowing nuclear NF-KB expression. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Positive and negative regulation of immunoglobulin gene expression by a novel B-cell-specific enhancer element. \nA new B-cell-specific enhancer element has been identified 3' of E4 and the octamerlike motifs in the human immunoglobulin heavy-chain gene enhancer. Tandem copies of this 67-bp MnlI-AluI fragment, when fused to the chloramphenicol acetyltransferase gene driven by the conalbumin promoter, stimulated transcription in B cells but not in Jurkat T cells or HeLa cells. Footprinting analysis revealed that the identical sequence CCGAAACTGAAAAGG, designated E6, was protected by nuclear extracts from B cells, T cells, or HeLa cells. Gel mobility shift assays using a synthetic E6 motif detected a B-cell-specific complex in addition to a ubiquitous band found also in T cells and HeLa cells. In agreement with the results of gel retardation assays, tandem copies of the E6 motif stimulated transcription in ARH77 and Raji cells but not in Jurkat or HeLa cells. Furthermore, a mutant E6 motif lost both in vitro binding activity and in vivo enhancer activity. In striking contrast to the mouse Ig heavy-chain enhancer, in which the octamer motif acts as a B-cell-specific enhancer element, the human enhancer contains an octamerlike sequence with one base substitution which bound octamer-binding proteins with only very low affinity and showed no enhancer activity of its own. Interestingly, the MnlI-AluI fragment could suppress the basal-level activity of the conalbumin promoter in both Jurkat and HeLa cells. Moreover, simian virus 40 enhancer activity was blocked by the MnlI-AluI fragment in HeLa cells but not in B cells. Thus, the novel enhancer element identified in this study is probably a target site for both positive and negative factors. ", "output": {"json_structures": {}}, "schema": []}
{"input": "The NF kappa B independent cis-acting sequences in HIV-1 LTR responsive to T-cell activation. \nThe rate of transcription initiation directed by the long terminal repeat (LTR) of HIV-1 increases in response to mitogenic stimuli of T cells. Here we show that the response of the HIV-1 LTR may be governed by two independent sequences located 5' to the site of transcription initiation sequences that bind either NFAT-1 or NF kappa B. The rate of LTR-directed gene expression increased in response to treatment with either a phorbol ester or tumor necrosis factor alpha if either the NFAT-1 or NF kappa B binding sites were deleted, but failed to respond to these mitogenic stimuli if both sequences were absent. The HIV-1 mutant virus containing both NF kappa B and NFAT-1 deletion was able to replicate although at a much decreased growth rate, while the deletion of NFAT-1 alone increased the viral growth rate in Jurkat cells. Neither deletion of NF kappa B nor deletion of NFAT-1 decreased activation of viral replication by phorbol ester. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 398, "end": 402}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 410, "end": 416}]}]}}, "schema": []}
{"input": "Comparison of constitutive and inducible transcriptional enhancement mediated by kappa B-related sequences: modulation of activity in B cells by human T-cell leukemia virus type I tax gene. \nThe kappa B sequence (GGGACTTTCC) binds a factor, NF-kappa B, that is constitutively found in its functional, DNA binding form only in B lymphocytes. A factor with apparently indistinguishable sequence specificity can be induced in many other cell types, where it is used to regulate inducible gene expression. For example, kappa B-related sequences have been shown to be important for the transcription of a few inducible genes, such as the interleukin 2 receptor alpha-chain gene and the beta-interferon gene. However, these genes are not constitutively active in B lymphocytes, suggesting that other regulatory mechanisms must play a role in determining the patterns of expression. We have investigated the constitutive and inducible transcriptional activity mediated by five kappa B-related sequence elements in two different cell types. We show that in S194 plasma cells the activity of each element correlates well with the relative affinity of B-cell-derived NF-kappa B for that element. This leads to significantly lower transcription enhancement by sites derived from the interleukin 2 receptor or T-cell receptor genes in S194 cells. However, in either EL-4 (T) cells or S194 cells, both lower-affinity sites can be significantly induced by the tax gene product of human T-cell leukemia virus type I, showing that NF-kappa B activity can be modulated even in a B-cell line that constitutively expresses this factor. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "active", "start": 747, "end": 753}, "arguments": [{"role": "Theme", "text": "interleukin 2 receptor alpha-chain", "start": 633, "end": 667}]}, {"trigger": {"text": "active", "start": 747, "end": 753}, "arguments": [{"role": "Theme", "text": "beta-interferon", "start": 681, "end": 696}]}], "transcription": [{"trigger": {"text": "transcription", "start": 581, "end": 594}, "arguments": [{"role": "Theme", "text": "interleukin 2 receptor alpha-chain", "start": 633, "end": 667}]}, {"trigger": {"text": "transcription", "start": 581, "end": 594}, "arguments": [{"role": "Theme", "text": "beta-interferon", "start": 681, "end": 696}]}]}}, "schema": []}
{"input": "Isolation of a rel-related human cDNA that potentially encodes the 65-kD subunit of NF-kappa B [published erratum appears in Science 1991 Oct 4;254(5028):11] \nA DNA probe that spanned a domain conserved among the proto-oncogene c-rel, the Drosophila morphogen dorsal, and the p50 DNA binding subunit of NF-kappa B was generated from Jurkat T cell complementary DNA with the polymerase chain reaction (PCR) and degenerate oligonucleotides. This probe was used to identify a rel-related complementary DNA that hybridized to a 2.6-kilobase messenger RNA present in human T and B lymphocytes. In vitro transcription and translation of the complementary DNA resulted in the synthesis of a protein with an apparent molecular size of 65 kilodaltons (kD). The translated protein showed weak DNA binding with a specificity for the kappa B binding motif. This protein-DNA complex comigrated with the complex obtained with the purified human p65 NF-kappa B subunit and binding was inhibited by I kappa B-alpha and -beta proteins. In addition, the 65-kD protein associated with the p50 subunit of NF-kappa B and the kappa B probe to form a complex with the same electrophoretic mobility as the NF-kappa B-DNA complex. Therefore the rel-related 65-kD protein may represent the p65 subunit of the active NF-kappa B transcription factor complex. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associated", "start": 1050, "end": 1060}, "arguments": [{"role": "Theme", "text": "p50", "start": 1070, "end": 1073}]}]}}, "schema": []}
{"input": "Murine and human T-lymphocyte GATA-3 factors mediate transcription through a cis-regulatory element within the human T-cell receptor delta gene enhancer. \nA family of transcriptional activators has recently been identified in chickens; these transcriptional activators recognize a common consensus motif (WGATAR) through a conserved C4 zinc finger DNA-binding domain. One of the members of this multigene family, cGATA-3, is most abundantly expressed in the T-lymphocyte cell lineage. Analysis of human and murine GATA-3 factors shows a striking degree of amino acid sequence identity and similar patterns of tissue specificity of expression in these three organisms. The murine and human factors are abundantly expressed in a variety of human and murine T-cell lines and can activate transcription through a tissue-specific GATA-binding site identified within the human T-cell receptor delta gene enhancer. We infer that the murine and human GATA-3 proteins play a central and highly conserved role in vertebrate T-cell-specific transcriptional regulation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "through", "start": 67, "end": 74}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 30, "end": 36}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 441, "end": 450}, "arguments": [{"role": "Theme", "text": "cGATA-3", "start": 413, "end": 420}]}, {"trigger": {"text": "expression", "start": 631, "end": 641}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 514, "end": 520}]}, {"trigger": {"text": "expressed", "start": 712, "end": 721}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 514, "end": 520}]}]}}, "schema": []}
{"input": "Processing of the precursor of NF-kappa B by the HIV-1 protease during acute infection. \nTranscription of the human immunodeficiency virus type-1 (HIV-1) genome is regulated in part by cellular factors and is stimulated by activation of latently infected T cells. T-cell activation also correlates with the induction of the factor NF-kappa B which binds to two adjacent sites in the HIV-1 long terminal repeat. This factor consists of two DNA-binding subunits of relative molecular mass 50,000 (50K) associated with two 65K subunits. It is located in the nucleus in mature B cells, but is present in other cell types as an inactive cytoplasmic complex. External stimuli, including those that activate T cells, result in nuclear translocation of active NF-kappa B. The cloning of the complementary DNA for the 50K subunit helped to identify an exclusively cytoplasmic 105K precursor (p105) (V.B., P.K. and A.I., manuscript submitted). The expression of active NF-kappa B might therefore also be regulated by the extent of processing of p105. Because HIV-1 requires active NF-kappa B for efficient transcription, we tested the effect of HIV-1 infection on the processing of the human 105K precursor. We show here that the HIV-1 protease can process p105 and increases levels of active nuclear NF-kappa B complex. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "process", "start": 1239, "end": 1246}, "arguments": [{"role": "Cause", "text": "protease", "start": 1226, "end": 1234}, {"role": "Theme", "text": "process", "start": 1239, "end": 1246}]}], "protein catabolism": [{"trigger": {"text": "process", "start": 1239, "end": 1246}, "arguments": [{"role": "Theme", "text": "p105", "start": 1247, "end": 1251}]}]}}, "schema": []}
{"input": "HIV enhancer activity perpetuated by NF-kappa B induction on infection of monocytes [see comments] \nPermissiveness to replication of human immunodeficiency virus (HIV) differs in T lymphocytes and macrophages. In T cells, HIV transcription is poorly detected in vivo. Cloned, normal T lymphocytes show very little, if any, basal activity of the HIV enhancer and low nuclear expression of NF-kappa B, a potent transcriptional activator of the HIV enhancer. In contrast, fixed tissue macrophages express detectable HIV proteins, indicating permanent virus transcription. One explanation for the perpetuation of virus infection in macrophages could be sustained nuclear NF-kappa B expression. However, the U937 monocytic cell line, which is fully permissive to HIV replication, is known to express only low levels of nuclear NF-kappa B. We show here that chronic HIV infection results in both induction of a nuclear factor with antigenic properties indistinguishable from those of NF-kappa B and permanently increased HIV enhancer activity. This phenomenon, which is independent of tumour necrosis factor, is associated with HIV replication, and is thus likely to explain at least in part the perpetuation of HIV infection in monocytes. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Tissue-specific expression of the platelet GPIIb gene. \nOne of the major objectives in the study of thrombogenesis is to determine the mechanisms by which a hematopoietic progenitor is activated and committed to the megakaryocytic lineage. Recent development of primary cultures of human megakaryocytes and the molecular cloning of genes that are specific to this lineage offer the possibility of getting some insights into the genetic mechanisms that control megakaryocytopoiesis. One gene of interest is the glycoprotein IIb (GPIIb) gene; GPIIb, the alpha subunit of the platelet cytoadhesin GPIIb-IIIa, is produced in megakaryocytes at an early stage of the differentiation, whereas the other subunit of this complex, GPIIIa, is expressed in other cells. For these reasons, the 5'-flanking region of the GPIIb gene was used to identify the regions that interact with DNA-binding nuclear factors. A fragment extending from -643 to +33 is capable of controlling the tissue-specific expression of the CAT gene in transfection experiments. Within this region, we have identified several sequences that are implicated in DNA protein interactions as shown in DNAse I footprints and gel mobility shift assays. One region, centered at -54, is similar to a nuclear factor E1-binding site, and a region located at position -233 contains a CCAAT motif. Two domains centered at positions -345 and -540, respectively, bind proteins that are present in megakaryocytic cells and nonrelated cells as well. Finally, two other domains, located at positions -460 and -510, interact with proteins that are only present in megakaryocytic cells. In addition, deletion of the region containing these two domains results in a significant decrease of the promoter activity. It is very likely that these domains bind megakaryocyte-specific nuclear proteins acting as positive transcription factors. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 856, "end": 864}, "arguments": [{"role": "Site", "text": "5'-flanking region", "start": 781, "end": 799}, {"role": "Theme", "text": "GPIIb", "start": 807, "end": 812}]}], "gene expression": [{"trigger": {"text": "expression", "start": 16, "end": 26}, "arguments": [{"role": "Theme", "text": "GPIIb", "start": 43, "end": 48}]}, {"trigger": {"text": "produced", "start": 609, "end": 617}, "arguments": [{"role": "Theme", "text": "GPIIb", "start": 541, "end": 546}]}, {"trigger": {"text": "expressed", "start": 732, "end": 741}, "arguments": [{"role": "Theme", "text": "GPIIIa", "start": 721, "end": 727}]}, {"trigger": {"text": "expression", "start": 983, "end": 993}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1001, "end": 1004}]}], "regulation": [{"trigger": {"text": "capable of controlling", "start": 940, "end": 962}, "arguments": [{"role": "Theme", "text": "expression", "start": 983, "end": 993}]}]}}, "schema": []}
{"input": "Cortivazol mediated induction of glucocorticoid receptor messenger ribonucleic acid in wild-type and dexamethasone-resistant human leukemic (CEM) cells. \nCortivazol is a phenylpyrazolo glucocorticoid of high potency and unusual structure. In both wild-type and highly dexamethasone(dex)-resistant clones of the human leukemic cell line CEM, exposure to cortivazol leads to cell death. It has been shown recently that in wild-type CEM cells but not in a dex-resistant, glucocorticoid receptor(GR)-defective clone ICR-27 TK-3, dex induces GR mRNA. To test the hypothesis that cortivazol acts in dex-resistant cells by making use of the residual GR found there, wild-type and dex-resistant clones were treated with various concentrations of cortivazol and induction of GR mRNA was studied. Cortivazol significantly induced GR mRNA in the normal CEM-C7 as well as in two classes of dex-resistant clones, although the dex-resistant clones needed at least 10 times more cortivazol than the normal cells for significant GR mRNA induction. Increased levels of GR mRNA were noticed as early as 3 h after treatment. A general correlation between induction of GR mRNA and lysis of the normal and dex-resistant cells was found. Positive induction of GR mRNA might be one of the earliest crucial steps in the lysis of normal and dex-resistant CEM cells, or might serve as a marker for the process. However, the lysis pathway in the dex-resistant cells is defective in that dex-resistant clones needed significantly more cortivazol than the normal cells for lysis of the cells. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "induction", "start": 20, "end": 29}, "arguments": [{"role": "Theme", "text": "glucocorticoid receptor", "start": 33, "end": 56}]}, {"trigger": {"text": "induces", "start": 529, "end": 536}, "arguments": [{"role": "Theme", "text": "GR", "start": 537, "end": 539}]}, {"trigger": {"text": "induction", "start": 753, "end": 762}, "arguments": [{"role": "Theme", "text": "GR", "start": 766, "end": 768}]}, {"trigger": {"text": "induced", "start": 812, "end": 819}, "arguments": [{"role": "Theme", "text": "GR", "start": 820, "end": 822}]}, {"trigger": {"text": "induction", "start": 1021, "end": 1030}, "arguments": [{"role": "Theme", "text": "GR", "start": 1013, "end": 1015}]}, {"trigger": {"text": "Increased", "start": 1032, "end": 1041}, "arguments": [{"role": "Theme", "text": "levels", "start": 1042, "end": 1048}]}, {"trigger": {"text": "induction", "start": 1136, "end": 1145}, "arguments": [{"role": "Theme", "text": "GR", "start": 1149, "end": 1151}]}, {"trigger": {"text": "Positive induction", "start": 1216, "end": 1234}, "arguments": [{"role": "Theme", "text": "GR", "start": 1238, "end": 1240}]}], "transcription": [{"trigger": {"text": "levels", "start": 1042, "end": 1048}, "arguments": [{"role": "Theme", "text": "GR", "start": 1052, "end": 1054}]}]}}, "schema": []}
{"input": "Human tumor necrosis factor alpha gene regulation in phorbol ester stimulated T and B cell lines. \nThe minimal region of the human tumor necrosis factor alpha (TNF-alpha) gene promoter necessary for its transcriptional induction by phorbol esters (PMA) in human T and B lymphocyte cell lines has been localized between -52 and +89 nucleotides (nt) relative to the gene's transcriptional start site. Comparison of these sequences to those required to mediate virus or lipopolysaccharide (LPS) induction of the gene reveal significant differences, and thus, the sequence requirements for PMA induction are distinct from those that mediate induction by virus or LPS. Although three sites in the TNF-alpha promoter (kappa 1, kappa 2, and kappa 3) specifically bind the transcription factor NF-kappa B in lymphoid nuclear extracts, TNF-alpha mRNA induction by PMA does not correlate with NF-kappa B binding activities displayed by different T and B cell lines. Moreover, kappa 1-kappa 3 can each be deleted from the TNF-alpha promoter with little effect on the gene's inducibility by PMA. Therefore, TNF-alpha mRNA induction by PMA, like its induction by virus and LPS, is not primarily mediated by NF-kappa B, but rather is mediated through other sequences and protein factors. Surprisingly, multimers of kappa 1-kappa 3 can confer PMA inducibility on a heterologous promoter in a B (Raji), but not a T (HUT78) cell line. However they are not functional on a truncated TNF-alpha promoter, indicating that promoter context and cell type specificity influence the PMA inducible function of these NF-kappa B binding sites. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 756, "end": 760}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 692, "end": 701}, {"role": "Site", "text": "kappa 1", "start": 712, "end": 719}]}, {"trigger": {"text": "bind", "start": 756, "end": 760}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 692, "end": 701}, {"role": "Site", "text": "kappa 2", "start": 721, "end": 728}]}, {"trigger": {"text": "bind", "start": 756, "end": 760}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 692, "end": 701}, {"role": "Site", "text": "kappa 3", "start": 734, "end": 741}]}], "positive regulation": [{"trigger": {"text": "necessary", "start": 185, "end": 194}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 160, "end": 169}, {"role": "CSite", "text": "promoter", "start": 176, "end": 184}, {"role": "Theme", "text": "transcriptional induction", "start": 203, "end": 228}]}, {"trigger": {"text": "transcriptional induction", "start": 203, "end": 228}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 160, "end": 169}]}, {"trigger": {"text": "mediate", "start": 450, "end": 457}, "arguments": [{"role": "Theme", "text": "induction", "start": 492, "end": 501}]}, {"trigger": {"text": "induction", "start": 492, "end": 501}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 160, "end": 169}]}, {"trigger": {"text": "requirements", "start": 569, "end": 581}, "arguments": [{"role": "Theme", "text": "transcriptional induction", "start": 203, "end": 228}]}, {"trigger": {"text": "mediate", "start": 629, "end": 636}, "arguments": [{"role": "Theme", "text": "induction", "start": 637, "end": 646}]}, {"trigger": {"text": "induction", "start": 637, "end": 646}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 160, "end": 169}]}, {"trigger": {"text": "induction", "start": 842, "end": 851}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 827, "end": 836}]}, {"trigger": {"text": "inducibility", "start": 1063, "end": 1075}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1011, "end": 1020}]}, {"trigger": {"text": "induction", "start": 1110, "end": 1119}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1095, "end": 1104}]}, {"trigger": {"text": "induction", "start": 1137, "end": 1146}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1095, "end": 1104}]}, {"trigger": {"text": "mediated", "start": 1182, "end": 1190}, "arguments": [{"role": "Theme", "text": "induction", "start": 1110, "end": 1119}]}, {"trigger": {"text": "mediated", "start": 1182, "end": 1190}, "arguments": [{"role": "Theme", "text": "induction", "start": 1137, "end": 1146}]}], "regulation": [{"trigger": {"text": "regulation", "start": 39, "end": 49}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 6, "end": 33}]}]}}, "schema": []}
{"input": "Reactive oxygen intermediates as apparently widely used messengers in the activation of the NF-kappa B transcription factor and HIV-1. \nHydrogen peroxide and oxygen radicals are agents commonly produced during inflammatory processes. In this study, we show that micromolar concentrations of H2O2 can induce the expression and replication of HIV-1 in a human T cell line. The effect is mediated by the NF-kappa B transcription factor which is potently and rapidly activated by an H2O2 treatment of cells from its inactive cytoplasmic form. N-acetyl-L-cysteine (NAC), a well characterized antioxidant which counteracts the effects of reactive oxygen intermediates (ROI) in living cells, prevented the activation of NF-kappa B by H2O2. NAC and other thiol compounds also blocked the activation of NF-kappa B by cycloheximide, double-stranded RNA, calcium ionophore, TNF-alpha, active phorbol ester, interleukin-1, lipopolysaccharide and lectin. This suggests that diverse agents thought to activate NF-kappa B by distinct intracellular pathways might all act through a common mechanism involving the synthesis of ROI. ROI appear to serve as messengers mediating directly or indirectly the release of the inhibitory subunit I kappa B from NF-kappa B. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Contribution of NF-kappa B and Sp1 binding motifs to the replicative capacity of human immunodeficiency virus type 1: distinct patterns of viral growth are determined by T-cell types. \nStarting with a replication-incompetent molecular clone of human immunodeficiency virus type 1, lacking all the NF-kappa B and Sp1 binding sites present in the native long terminal repeat (LTR), proviruses containing reconstructed LTRs with individual or combinations of NF-kappa B and Sp1 elements were generated and evaluated for their capacity to produce virus progeny following transfection-cocultivation. Virus stocks obtained from these experiments exhibited a continuum of replicative capacities in different human T-cell types depending on which element(s) was present in the LTR. For example, in experiments involving proviral clones with LTRs containing one or two NF-kappa B elements (and no Sp1 binding sites), a hierarchy of cellular permissivity to virus replication (peripheral blood lymphocytes = MT4 greater than H9 greater than CEM greater than Jurkat) was observed. Of note was the associated emergence of second-site LTR revertants which involved an alteration of the TATA box. These results suggest that the human immunodeficiency virus type 1 LTR possesses functional redundancy which ensures virus replication in different T-cell types and is capable of changing depending on the particular combination of transcriptional factors present. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Purification of TCF-1 alpha, a T-cell-specific transcription factor that activates the T-cell receptor C alpha gene enhancer in a context-dependent manner. \nThe differentiation of T cells into functionally diverse subpopulations is controlled in part, by transcriptional activation and silencing; however, little is known in detail about the proteins that influence this developmental process. We have purified a new T-cell-specific factor, TCF-1 alpha, that is implicated in the activation of genes encoding a major component of the human T-cell receptor (TCR). TCF-1 alpha, originally identified and purified through its binding sites on the HIV-1 promoter, was found to bind to the TCR alpha enhancer and to promoters for several genes expressed at significantly earlier stages of T-cell development than the TCR alpha gene (e.g., p56lck and CD3 delta). Sequences related to the TCF-1 alpha binding motif (5'-GGCACCCTTTGA-3') are also found in the human TCR delta (and possibly TCR beta) enhancers. Southwestern and gel renaturation experiments with the use of purified protein fractions revealed that TCF-1 alpha activity is derived from a family of 57- to 53-kD proteins that are abundantly expressed in mature and immature T-cell lines (Jurkat, CCRF-CEM) and not in mature B cells (JY, Namalwa) or nonlymphoid (HeLa) cell lines. A small 95-bp fragment of the TCR alpha control region that contains the TCF-1 alpha binding site juxtaposed between a cAMP-response element (the CRE or T alpha 1 motif) and the binding site for a distinct lymphoid-specific protein (TCF-2 alpha) behaved as a potent T-cell-specific enhancer in vivo. Tandem copies of this enhancer functioned synergistically in mature (Jurkat) T-cell lines as well as resting and activated immature (CCRF-CEM) T-cell lines. Mutation of the TCF-1 alpha binding site diminished enhancer activity and disrupted the synergism observed in vivo between tandem enhancer repeats. The TCF-1 alpha binding site was also required for TCR alpha enhancer activity in transcriptionally active extracts from Jurkat but not HeLa cells, confirming that TCF-1 alpha is a T-cell-specific transcription factor. Curiously, the TCF-1 alpha binding element was inactive in vivo when removed from its neighboring elements on the TCR alpha enhancer and positioned in one or more copies upstream of a heterologous promoter. Thus, the transcriptional activity of TCF-1 alpha appears to depend on the TCF-2 alpha and T alpha 1 (CREB) transcription factors and the context of its binding site within the TCR alpha enhancer. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 673, "end": 677}, "arguments": [{"role": "Theme", "text": "TCF-1 alpha", "start": 563, "end": 574}, {"role": "Theme2", "text": "TCR alpha", "start": 685, "end": 694}, {"role": "Site2", "text": "enhancer", "start": 695, "end": 703}]}, {"trigger": {"text": "bind", "start": 673, "end": 677}, "arguments": [{"role": "Theme", "text": "TCF-1 alpha", "start": 563, "end": 574}, {"role": "Theme2", "text": "TCR alpha", "start": 685, "end": 694}, {"role": "Site2", "text": "promoters", "start": 711, "end": 720}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 739, "end": 748}, "arguments": [{"role": "Theme", "text": "TCR alpha", "start": 812, "end": 821}]}, {"trigger": {"text": "expressed", "start": 739, "end": 748}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 834, "end": 840}]}, {"trigger": {"text": "expressed", "start": 739, "end": 748}, "arguments": [{"role": "Theme", "text": "CD3 delta", "start": 845, "end": 854}]}], "positive regulation": [{"trigger": {"text": "activates", "start": 73, "end": 82}, "arguments": [{"role": "Cause", "text": "TCF-1 alpha", "start": 16, "end": 27}, {"role": "Theme", "text": "T-cell receptor C alpha", "start": 87, "end": 110}, {"role": "Site", "text": "enhancer", "start": 116, "end": 124}]}, {"trigger": {"text": "promoters", "start": 711, "end": 720}, "arguments": [{"role": "Theme", "text": "expressed", "start": 739, "end": 748}]}, {"trigger": {"text": "derived", "start": 1129, "end": 1136}, "arguments": [{"role": "Theme", "text": "TCF-1 alpha", "start": 1105, "end": 1116}]}, {"trigger": {"text": "required", "start": 1978, "end": 1986}, "arguments": [{"role": "Theme", "text": "TCR alpha", "start": 1991, "end": 2000}, {"role": "Site", "text": "enhancer", "start": 2001, "end": 2009}]}, {"trigger": {"text": "depend", "start": 2427, "end": 2433}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 2376, "end": 2400}, {"role": "Cause", "text": "TCR alpha", "start": 2543, "end": 2552}, {"role": "CSite", "text": "enhancer", "start": 2553, "end": 2561}]}, {"trigger": {"text": "depend", "start": 2427, "end": 2433}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 2376, "end": 2400}, {"role": "Cause", "text": "TCF-2 alpha", "start": 2441, "end": 2452}]}, {"trigger": {"text": "depend", "start": 2427, "end": 2433}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 2376, "end": 2400}, {"role": "Cause", "text": "CREB", "start": 2468, "end": 2472}]}], "transcription": [{"trigger": {"text": "transcriptional activity", "start": 2376, "end": 2400}, "arguments": [{"role": "Theme", "text": "TCF-1 alpha", "start": 2404, "end": 2415}]}]}}, "schema": []}
{"input": "A novel T-cell trans-activator that recognizes a phorbol ester-inducible element of the interleukin-2 promoter. \nThe interleukin 2 (IL-2) gene promoter is recognized by several cell-type-specific and ubiquitous transcriptional regulators that integrate information transmitted by various signaling systems leading to IL-2 production and T-cell activation. Using a combination of transfection, protein-DNA binding, and in vitro transcription methods, we have discovered the novel T-cell-specific transcriptional activator TCF-1 (for T-Cell Factor-1), which recognizes a T-cell-specific response element (TCE) located within the IL-2 promoter. Although the TCE is similar in sequence to a consensus NF kappa B site, several criteria indicate that TCF-1 is distinct from NF kappa B. However, like NF kappa B, TCF-1 activity is induced by phorbol esters and other T-cell activators. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recognizes", "start": 36, "end": 46}, "arguments": [{"role": "Site", "text": "phorbol ester-inducible element", "start": 49, "end": 80}, {"role": "Theme", "text": "interleukin-2", "start": 88, "end": 101}]}, {"trigger": {"text": "recognized", "start": 155, "end": 165}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 117, "end": 130}, {"role": "Site", "text": "promoter", "start": 143, "end": 151}]}, {"trigger": {"text": "recognizes", "start": 556, "end": 566}, "arguments": [{"role": "Theme", "text": "TCF-1", "start": 521, "end": 526}]}], "gene expression": [{"trigger": {"text": "production", "start": 322, "end": 332}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 317, "end": 321}]}], "positive regulation": [{"trigger": {"text": "leading", "start": 306, "end": 313}, "arguments": [{"role": "Theme", "text": "production", "start": 322, "end": 332}]}, {"trigger": {"text": "induced", "start": 824, "end": 831}, "arguments": [{"role": "Theme", "text": "TCF-1", "start": 806, "end": 811}]}]}}, "schema": []}
{"input": "Two distinct transcription factors that bind the immunoglobulin enhancer microE5/kappa 2 motif. \nActivity of the immunoglobulin heavy and kappa light chain gene enhancers depends on a complex interplay of ubiquitous and developmentally regulated proteins. Two complementary DNAs were isolated that encode proteins, denoted ITF-1 and ITF-2, that are expressed in a variety of cell types and bind the microE5/kappa 2 motif found in both heavy and kappa light chain enhancers. The complementary DNAs are the products of distinct genes, yet both ITF-1 and ITF-2 are structurally and functionally similar. The two proteins interact with one another through their putative helix-loop-helix motifs and each possesses a distinct domain that dictates transcription activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 390, "end": 394}, "arguments": [{"role": "Theme", "text": "ITF-1", "start": 323, "end": 328}]}, {"trigger": {"text": "bind", "start": 390, "end": 394}, "arguments": [{"role": "Theme", "text": "ITF-2", "start": 333, "end": 338}]}, {"trigger": {"text": "interact", "start": 618, "end": 626}, "arguments": [{"role": "Theme", "text": "ITF-1", "start": 542, "end": 547}, {"role": "Theme2", "text": "ITF-2", "start": 552, "end": 557}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 349, "end": 358}, "arguments": [{"role": "Theme", "text": "ITF-1", "start": 323, "end": 328}]}, {"trigger": {"text": "expressed", "start": 349, "end": 358}, "arguments": [{"role": "Theme", "text": "ITF-2", "start": 333, "end": 338}]}]}}, "schema": []}
{"input": "A factor known to bind to endogenous Ig heavy chain enhancer only in lymphocytes is a ubiquitously active transcription factor. \nThe transcriptional enhancer located in the first intron of the immunoglobulin heavy chain constant region is a major determinant of B-cell-specific expression of immunoglobulin genes. Like other enhancers, the Ig heavy chain enhancer contains several short sequence motifs that bind specific transcription factors. Each binding site contributes to the overall activity of the enhancer, however no single element seems absolutely required for activity. For a better understanding of the Ig heavy chain enhancer components, we have cloned and analyzed individual sequence elements. We find that the factor that binds to the E3 enhancer motif, CATGTGGC, is a ubiquitous transcription factor. It is present in an active form in both B cells and non-B cells, where it can mediate transcriptional activation in vitro and in vivo. However, despite its ability to activate transcription of a transfected reporter gene, the factor is apparently unable to bind to the endogenous Ig heavy chain enhancer in non-lymphoid cells: In previous experiments by others, the characteristic in vivo footprint of this factor, designated NF-muE3, was detected in B cells but not in non-B cells. From this and other findings the picture emerges that there are at least three categories of factors which mediate cell-type-specific transcription in B lymphocytes: (a) cell-specific factors such as Oct-2A and Oct-2B that are not expressed in most other cell types: (b) ubiquitous factors such as NF-kappa B that are constitutively active in B cells but are sequestered in an inactive form in other cells; (c) ubiquitously active factors, exemplified by the one binding to the E3 sequence motif. This factor is present in an active form in a variety of cell types but is apparently unable to bind to the endogenous Ig heavy chain enhancer in non-B cells, perhaps due to a non-permissive chromatin structure of the Ig heavy chain locus. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 1895, "end": 1899}, "arguments": [{"role": "Theme", "text": "NF-muE3", "start": 1245, "end": 1252}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 1533, "end": 1542}, "arguments": [{"role": "Theme", "text": "Oct-2A", "start": 1502, "end": 1508}]}, {"trigger": {"text": "expressed", "start": 1533, "end": 1542}, "arguments": [{"role": "Theme", "text": "Oct-2B", "start": 1513, "end": 1519}]}], "positive regulation": [{"trigger": {"text": "active", "start": 1828, "end": 1834}, "arguments": [{"role": "Theme", "text": "NF-muE3", "start": 1245, "end": 1252}]}]}}, "schema": []}
{"input": "Transcriptional and post-transcriptional regulation of c-jun expression during monocytic differentiation of human myeloid leukemic cells. \nAP-1, the polypeptide product of c-jun, recognizes and binds to specific DNA sequences and stimulates transcription of genes responsive to certain growth factors and phorbol esters such as 12-O-tetradecanoylphorbol-13-acetate (TPA). We studied the effects of TPA on the regulation of c-jun gene expression in HL-60 cells during monocytic differentiation. Low levels of c-jun transcripts were detectable in untreated HL-60 leukemic cells, increased significantly by 6 h, and reached near maximal levels by 24 h of exposure to 32 nM TPA. Similar kinetics of c-jun induction by TPA were observed in human U-937 and THP-1 monocytic leukemia cells. Similar findings were obtained with bryostatin 1 (10 nM), another activator of protein kinase C and inducer of monocytic differentiation. Furthermore, 1,25-dihydroxyvitamin D3 (0.5 microM), a structurally distinct agent which also induces HL-60 monocytic differentiation, increased c-jun expression. TPA treatment of HL-60 cells in the presence of cycloheximide was associated with superinduction of c-jun transcripts. Run-on analysis demonstrated detectable levels of c-jun gene transcription in untreated HL-60 cells, and that exposure to TPA increases this rate 3.3-fold. Treatment of HL-60 cells with both TPA and cycloheximide had no effect on the rates of c-jun transcription. The half-life of c-jun RNA as determined by treating HL-60 cells with TPA and actinomycin D was 30 min. In contrast, the half-life of c-jun RNA in TPA-treated HL-60 cells exposed to cycloheximide and actinomycin D was greater than 2 h. These findings suggested that the increase in c-jun RNA observed during TPA-induced monocytic differentiation is mediated by both transcriptional and post-transcriptional mechanisms. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recognizes", "start": 179, "end": 189}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 172, "end": 177}]}, {"trigger": {"text": "binds", "start": 194, "end": 199}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 172, "end": 177}]}], "gene expression": [{"trigger": {"text": "expression", "start": 61, "end": 71}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 55, "end": 60}]}, {"trigger": {"text": "expression", "start": 434, "end": 444}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 423, "end": 428}]}, {"trigger": {"text": "expression", "start": 1071, "end": 1081}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1065, "end": 1070}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 577, "end": 586}, "arguments": [{"role": "Theme", "text": "transcripts", "start": 514, "end": 525}]}, {"trigger": {"text": "induction", "start": 701, "end": 710}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 695, "end": 700}]}, {"trigger": {"text": "increased", "start": 1055, "end": 1064}, "arguments": [{"role": "Theme", "text": "expression", "start": 1071, "end": 1081}]}, {"trigger": {"text": "associated with superinduction", "start": 1149, "end": 1179}, "arguments": [{"role": "Theme", "text": "transcripts", "start": 1189, "end": 1200}]}, {"trigger": {"text": "increases", "start": 1328, "end": 1337}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1263, "end": 1276}]}, {"trigger": {"text": "effect", "start": 1422, "end": 1428}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1451, "end": 1464}]}, {"trigger": {"text": "increase", "start": 1736, "end": 1744}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1748, "end": 1753}]}, {"trigger": {"text": "mediated", "start": 1815, "end": 1823}, "arguments": [{"role": "Theme", "text": "increase", "start": 1736, "end": 1744}]}], "regulation": [{"trigger": {"text": "effects", "start": 387, "end": 394}, "arguments": [{"role": "Theme", "text": "regulation", "start": 409, "end": 419}]}, {"trigger": {"text": "regulation", "start": 409, "end": 419}, "arguments": [{"role": "Theme", "text": "expression", "start": 434, "end": 444}]}], "transcription": [{"trigger": {"text": "transcripts", "start": 514, "end": 525}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 508, "end": 513}]}, {"trigger": {"text": "transcripts", "start": 1189, "end": 1200}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1183, "end": 1188}]}, {"trigger": {"text": "transcription", "start": 1263, "end": 1276}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1252, "end": 1257}]}, {"trigger": {"text": "transcription", "start": 1451, "end": 1464}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1445, "end": 1450}]}]}}, "schema": []}
{"input": "Identification of a novel factor that interacts with an immunoglobulin heavy-chain promoter and stimulates transcription in conjunction with the lymphoid cell-specific factor OTF2. \nThe tissue-specific expression of the MOPC 141 immunoglobulin heavy-chain gene was studied by using in vitro transcription. B-cell-specific transcription of this gene was dependent on the octamer element 5'-ATGCAAAG-3', located in the upstream region of this promoter and in the promoters of all other immunoglobulin heavy- and light-chain genes. The interaction of purified octamer transcription factors 1 and 2 (OTF1 and OTF2) with the MOPC 141 promoter was studied by using electrophoretic mobility shift assays and DNase I footprinting. Purified OTF1 from HeLa cells and OTF1 and OTF2 from B cells bound to identical sequences within the heavy-chain promoter. The OTF interactions we observed extended over the heptamer element 5'-CTCAGGA-3', and it seems likely that the binding of the purified factors involves cooperation between octamer and heptamer sites in this promoter. In addition to these elements, we identified a second regulatory element, the N element with the sequence 5'-GGAACCTCCCCC-3'. The N element could independently mediate low levels of transcription in both B-cell and HeLa-cell extracts, and, in conjunction with the octamer element, it can promote high levels of transcription in B-cell extracts. The N element bound a transcription factor, NTF, that is ubiquitous in cell-type distribution, and NTF was distinct from any of the previously described proteins that bind to similar sequences. Based on these results, we propose that NTF and OTF2 interactions (both with their cognate DNA elements and possibly at the protein-protein level) may be critical to B-cell-specific expression and that these interactions provide additional pathways for regulating gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 784, "end": 789}, "arguments": [{"role": "Theme", "text": "OTF1", "start": 732, "end": 736}]}, {"trigger": {"text": "bound", "start": 784, "end": 789}, "arguments": [{"role": "Theme", "text": "OTF1", "start": 757, "end": 761}]}, {"trigger": {"text": "bound", "start": 784, "end": 789}, "arguments": [{"role": "Theme", "text": "OTF2", "start": 766, "end": 770}]}, {"trigger": {"text": "binding", "start": 958, "end": 965}, "arguments": [{"role": "Theme", "text": "OTF1", "start": 596, "end": 600}]}, {"trigger": {"text": "binding", "start": 958, "end": 965}, "arguments": [{"role": "Theme", "text": "OTF2", "start": 605, "end": 609}]}], "regulation": [{"trigger": {"text": "involves", "start": 990, "end": 998}, "arguments": [{"role": "Theme", "text": "binding", "start": 958, "end": 965}]}]}}, "schema": []}
{"input": "Involvement of a second lymphoid-specific enhancer element in the regulation of immunoglobulin heavy-chain gene expression. \nTo determine whether enhancer elements in addition to the highly conserved octamer (OCTA)-nucleotide motif are important for lymphoid-specific expression of the immunoglobulin heavy-chain (IgH) gene, we have investigated the effect of mutating the binding site for a putative additional lymphoid-specific transcription factor, designated NF-microB, in the murine IgH enhancer. We demonstrate that the NF-microB-binding site plays a critical role in the IgH enhancer, because mutation of the microB DNA motif decreased transcriptional activity of the IgH enhancer in cells of the B-cell lineage but not in nonlymphoid cells. This effect was comparable to or even stronger than the effect of a mutation in the OCTA site. Moreover, combined mutation of both microB and OCTA sites further reduced enhancer activity in lymphoid cells. Interestingly, alteration of either the microB or E3 site in a 70-base-pair fragment of the IgH enhancer that lacks the binding site for OCTA abolished enhancer activity in lymphoid cells completely. Nevertheless, a multimer of the microB motif alone showed no enhancer activity. DNase footprinting analysis corroborated the functional data showing that a lymphoid-specific protein binds to the microB DNA motif. Our results suggest that the microB element is a new crucial element important for lymphoid-specific expression of the IgH gene but that interaction with another enhancer element is essential for its activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 373, "end": 380}, "arguments": [{"role": "Theme", "text": "NF-microB", "start": 463, "end": 472}]}]}}, "schema": []}
{"input": "The expression of c-fos, c-jun, and c-myc genes is regulated by heat shock in human lymphoid cells. \nThe effect of heat shock on the expression of the nuclear protooncogenes c-fos, c-jun, and c-myc was studied in human lymphoid cells. Heat shock caused an increase in c-fos and c-jun mRNA levels and a decrease in c-myc mRNA levels in pre-B (Hyon) and T (DND-41) cell lines as well as in freshly isolated normal human thymocytes. The changes in the mRNA levels of these protooncogenes in Hyon cells were most pronounced at 42 and 43 degrees C; kinetic analysis demonstrated that the changes could be detected within 30 min of heat shock. Altered transcription of c-fos and c-myc genes was the primary effect of heat shock. Secondarily, heat shock of Hyon cells stabilized the c-myc mRNA level by increasing its half-life from 24 to 45 min. The overall effect of heat shock on c-myc mRNA level, however, was a marked inhibition of its transcription. These results demonstrate that the transcription of nuclear protooncogenes is regulated by heat shock indicating a role for nuclear protooncogenes in the stress response of lymphoid cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 4, "end": 14}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 18, "end": 23}]}, {"trigger": {"text": "expression", "start": 4, "end": 14}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 25, "end": 30}]}, {"trigger": {"text": "expression", "start": 4, "end": 14}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 36, "end": 41}]}, {"trigger": {"text": "expression", "start": 133, "end": 143}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 174, "end": 179}]}, {"trigger": {"text": "expression", "start": 133, "end": 143}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 181, "end": 186}]}, {"trigger": {"text": "expression", "start": 133, "end": 143}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 192, "end": 197}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 302, "end": 310}, "arguments": [{"role": "Theme", "text": "levels", "start": 325, "end": 331}]}, {"trigger": {"text": "inhibition", "start": 916, "end": 926}, "arguments": [{"role": "Theme", "text": "transcription", "start": 934, "end": 947}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 256, "end": 264}, "arguments": [{"role": "Theme", "text": "levels", "start": 289, "end": 295}]}, {"trigger": {"text": "detected", "start": 600, "end": 608}, "arguments": [{"role": "Theme", "text": "changes", "start": 434, "end": 441}]}, {"trigger": {"text": "increasing", "start": 796, "end": 806}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 776, "end": 781}]}], "regulation": [{"trigger": {"text": "regulated", "start": 51, "end": 60}, "arguments": [{"role": "Theme", "text": "expression", "start": 4, "end": 14}]}, {"trigger": {"text": "effect", "start": 105, "end": 111}, "arguments": [{"role": "Theme", "text": "expression", "start": 133, "end": 143}]}, {"trigger": {"text": "changes", "start": 434, "end": 441}, "arguments": [{"role": "Theme", "text": "levels", "start": 289, "end": 295}]}, {"trigger": {"text": "changes", "start": 434, "end": 441}, "arguments": [{"role": "Theme", "text": "levels", "start": 325, "end": 331}]}, {"trigger": {"text": "Altered", "start": 638, "end": 645}, "arguments": [{"role": "Theme", "text": "transcription", "start": 646, "end": 659}]}, {"trigger": {"text": "effect", "start": 852, "end": 858}, "arguments": [{"role": "Theme", "text": "level", "start": 887, "end": 892}]}], "transcription": [{"trigger": {"text": "levels", "start": 289, "end": 295}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 268, "end": 273}]}, {"trigger": {"text": "levels", "start": 289, "end": 295}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 278, "end": 283}]}, {"trigger": {"text": "levels", "start": 325, "end": 331}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 314, "end": 319}]}, {"trigger": {"text": "transcription", "start": 646, "end": 659}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 663, "end": 668}]}, {"trigger": {"text": "transcription", "start": 646, "end": 659}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 673, "end": 678}]}, {"trigger": {"text": "level", "start": 887, "end": 892}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 876, "end": 881}]}, {"trigger": {"text": "transcription", "start": 934, "end": 947}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 876, "end": 881}]}]}}, "schema": []}
{"input": "Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells. \nA powerful enhancer has been mapped to an 18-bp DNA segment located 11 kb 5' to the human epsilon-globin gene within the dominant control or locus-activating region. This enhancer is inducible in K562 human erythroleukemia cells, increasing linked gamma-globin promoter/luciferase gene expression to 170-fold over an enhancerless construct. The enhancer consists of tandem AP-1-binding sites, phased 10 bp apart, which are both required for full activity. DNA-protein binding assays with nuclear extracts from induced cells demonstrate a high molecular weight complex on the enhancer. The formation of this complex also requires both AP-1 sites and correlates with maximal enhancer activity. Induction of the enhancer may have a role in the increase in globin gene transcription that characterizes erythroid maturation. Enhancer activity appears to be mediated by the binding of a complex of proteins from the jun and fos families to tandem AP-1 consensus sequences. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 420, "end": 430}, "arguments": [{"role": "Theme", "text": "luciferase", "start": 404, "end": 414}]}], "positive regulation": [{"trigger": {"text": "increasing", "start": 364, "end": 374}, "arguments": [{"role": "Theme", "text": "expression", "start": 420, "end": 430}]}, {"trigger": {"text": "required", "start": 562, "end": 570}, "arguments": [{"role": "Theme", "text": "increasing", "start": 364, "end": 374}]}]}}, "schema": []}
{"input": "Adherence-dependent increase in human monocyte PDGF(B) mRNA is associated with increases in c-fos, c-jun, and EGR2 mRNA. \nAdherence is an important initial step in the transition of a circulating monocyte to a tissue macrophage. This differentiation is accompanied by an augmented capacity to generate growth factors. We hypothesized that adherence itself might be an important trigger for a sequence of gene activation culminating in cells with increased mRNA encoding profibrotic growth factors such as platelet-derived growth factor B subunit (PDGF[B]) and transforming growth factor-beta (TGF-beta). After in vitro adherence, human monocytes had a biphasic increase in PDGF(B) mRNA with peaks at 6 h and 13 d. No increase in TGF-beta mRNA was observed. The 6-h increase in PDGF(B) mRNA was adherence dependent, and in addition, was abrogated when the cytoskeletal integrity was compromised by cytochalasin D. The 6-h increase in PDGF(B) mRNA was unaltered by adherence in the presence of the monocyte stimulus lipopolysaccharide. Adherence to either fibronectin or collagen-coated plastic had little consistent effect on PDGF(B) mRNA accumulation. The increased PDGF(B) mRNA observed in adherent monocytes was accompanied by increases in mRNAs of the early growth response genes c-fos (maximal at 20 min), c-jun, and EGR2 (maximal at 6-24 h). The increase in c-jun and EGR2, but not c-fos, mRNA was also abrogated by cytochalasin D. These observations suggest that adherence results in increases of c-fos, c-jun, EGR2, and PDGF(B) mRNA. In addition, the increases in c-jun, EGR2, and PDGF(B) may depend on cytoskeletal rearrangement. Modulation of these events at the time of adherence offers a mechanism by which differential priming of the cells may be accomplished. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "abrogated", "start": 836, "end": 845}, "arguments": [{"role": "Theme", "text": "increase", "start": 765, "end": 773}]}, {"trigger": {"text": "abrogated", "start": 1408, "end": 1417}, "arguments": [{"role": "Theme", "text": "increase", "start": 1351, "end": 1359}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 20, "end": 28}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 47, "end": 54}]}, {"trigger": {"text": "increases", "start": 79, "end": 88}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 110, "end": 114}]}, {"trigger": {"text": "increases", "start": 79, "end": 88}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 92, "end": 97}]}, {"trigger": {"text": "increases", "start": 79, "end": 88}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 99, "end": 104}]}, {"trigger": {"text": "culminating", "start": 420, "end": 431}, "arguments": [{"role": "Theme", "text": "increased", "start": 446, "end": 455}]}, {"trigger": {"text": "increased", "start": 446, "end": 455}, "arguments": [{"role": "Theme", "text": "PDGF[B]", "start": 547, "end": 554}]}, {"trigger": {"text": "increased", "start": 446, "end": 455}, "arguments": [{"role": "Theme", "text": "TGF-beta", "start": 593, "end": 601}]}, {"trigger": {"text": "increase", "start": 661, "end": 669}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 673, "end": 680}]}, {"trigger": {"text": "increase", "start": 717, "end": 725}, "arguments": [{"role": "Theme", "text": "TGF-beta", "start": 729, "end": 737}]}, {"trigger": {"text": "increase", "start": 765, "end": 773}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 777, "end": 784}]}, {"trigger": {"text": "increase", "start": 921, "end": 929}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 933, "end": 940}]}, {"trigger": {"text": "in the presence of", "start": 973, "end": 991}, "arguments": [{"role": "Theme", "text": "unaltered", "start": 950, "end": 959}]}, {"trigger": {"text": "accumulation", "start": 1138, "end": 1150}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 1125, "end": 1132}]}, {"trigger": {"text": "increased", "start": 1156, "end": 1165}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 1166, "end": 1173}]}, {"trigger": {"text": "increases", "start": 1229, "end": 1238}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1283, "end": 1288}]}, {"trigger": {"text": "increases", "start": 1229, "end": 1238}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1310, "end": 1315}]}, {"trigger": {"text": "increases", "start": 1229, "end": 1238}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 1321, "end": 1325}]}, {"trigger": {"text": "increase", "start": 1351, "end": 1359}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1363, "end": 1368}]}, {"trigger": {"text": "increase", "start": 1351, "end": 1359}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 1373, "end": 1377}]}, {"trigger": {"text": "increase", "start": 1351, "end": 1359}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1387, "end": 1392}]}, {"trigger": {"text": "results in increases", "start": 1479, "end": 1499}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1503, "end": 1508}]}, {"trigger": {"text": "results in increases", "start": 1479, "end": 1499}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1510, "end": 1515}]}, {"trigger": {"text": "results in increases", "start": 1479, "end": 1499}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 1517, "end": 1521}]}, {"trigger": {"text": "results in increases", "start": 1479, "end": 1499}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 1527, "end": 1534}]}, {"trigger": {"text": "increases", "start": 1558, "end": 1567}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1571, "end": 1576}]}, {"trigger": {"text": "increases", "start": 1558, "end": 1567}, "arguments": [{"role": "Theme", "text": "EGR2", "start": 1578, "end": 1582}]}, {"trigger": {"text": "increases", "start": 1558, "end": 1567}, "arguments": [{"role": "Theme", "text": "PDGF(B)", "start": 1588, "end": 1595}]}], "regulation": [{"trigger": {"text": "dependent", "start": 804, "end": 813}, "arguments": [{"role": "Theme", "text": "increase", "start": 765, "end": 773}]}, {"trigger": {"text": "unaltered", "start": 950, "end": 959}, "arguments": [{"role": "Theme", "text": "increase", "start": 921, "end": 929}]}, {"trigger": {"text": "effect", "start": 1115, "end": 1121}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1138, "end": 1150}]}, {"trigger": {"text": "depend", "start": 1600, "end": 1606}, "arguments": [{"role": "Theme", "text": "increases", "start": 1558, "end": 1567}]}, {"trigger": {"text": "Modulation", "start": 1638, "end": 1648}, "arguments": [{"role": "Theme", "text": "increases", "start": 1558, "end": 1567}]}]}}, "schema": []}
{"input": "Interferon-gamma and the sexual dimorphism of autoimmunity. \nThe sexual difference in the incidence of autoimmune diseases has remained an enigma for many years. In the examination of the induction of autoimmunity in transgenic mice, evidence has been obtained further implicating the lymphokine interferon-gamma in the etiology of autoimmunity. Sex steroid regulation of the production of this molecule, as well as other cytokines, may help explain the gender-specific differences in the immune system, including autoimmunity. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 376, "end": 386}, "arguments": [{"role": "Theme", "text": "interferon-gamma", "start": 296, "end": 312}]}], "regulation": [{"trigger": {"text": "regulation", "start": 358, "end": 368}, "arguments": [{"role": "Theme", "text": "production", "start": 376, "end": 386}]}]}}, "schema": []}
{"input": "Single cell assay of a transcription factor reveals a threshold in transcription activated by signals emanating from the T-cell antigen receptor. \nStimulation of T lymphocytes through their antigen receptor leads to the appearance of several transcription factors, including NF-AT and NF-kappa B, which are involved in regulating genes required for immunologic activation. To investigate the activity of a single transcription factor in individual viable cells, we have applied an assay that uses the fluorescence-activated cell sorter to quantitate beta-galactosidase (beta-gal). We have analyzed the distribution of NF-AT transcriptional activity among T cells undergoing activation by using a construct in which three tandem copies of the NF-AT-binding site directs transcription of the lacZ gene. Unexpectedly, stimulation of cloned stably transfected Jurkat T cells leads to a bimodal pattern of beta-gal expression in which some cells express no beta-gal and others express high levels. This expression pattern cannot be accounted for by cell-cycle position or heritable variation. Further results, in which beta-gal activity is correlated with NF-AT-binding activity, indicate that the concentration of NF-AT must exceed a critical threshold before transcription initiates. This threshold likely reflects the NF-AT concentration-dependent assembly of transcription complexes at the promoter. Similar constructs controlled by NF-kappa B or the entire interleukin-2 enhancer show bimodal expression patterns during induction, suggesting that thresholds set by the concentration of transcription factors may be a common property of inducible genes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 910, "end": 920}, "arguments": [{"role": "Theme", "text": "beta-gal", "start": 901, "end": 909}]}, {"trigger": {"text": "express", "start": 941, "end": 948}, "arguments": [{"role": "Theme", "text": "beta-gal", "start": 952, "end": 960}]}, {"trigger": {"text": "express", "start": 972, "end": 979}, "arguments": [{"role": "Theme", "text": "beta-gal", "start": 952, "end": 960}]}, {"trigger": {"text": "expression", "start": 1493, "end": 1503}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 1457, "end": 1470}]}], "positive regulation": [{"trigger": {"text": "leads", "start": 871, "end": 876}, "arguments": [{"role": "Theme", "text": "express", "start": 941, "end": 948}]}, {"trigger": {"text": "leads", "start": 871, "end": 876}, "arguments": [{"role": "Theme", "text": "express", "start": 972, "end": 979}]}, {"trigger": {"text": "high levels", "start": 980, "end": 991}, "arguments": [{"role": "Theme", "text": "express", "start": 972, "end": 979}]}, {"trigger": {"text": "induction", "start": 1520, "end": 1529}, "arguments": [{"role": "Theme", "text": "expression", "start": 1493, "end": 1503}]}], "regulation": [{"trigger": {"text": "directs", "start": 761, "end": 768}, "arguments": [{"role": "Theme", "text": "transcription", "start": 769, "end": 782}]}, {"trigger": {"text": "accounted", "start": 1027, "end": 1036}, "arguments": [{"role": "Theme", "text": "expression", "start": 910, "end": 920}]}, {"trigger": {"text": "show", "start": 1480, "end": 1484}, "arguments": [{"role": "Theme", "text": "expression", "start": 1493, "end": 1503}]}], "transcription": [{"trigger": {"text": "transcription", "start": 769, "end": 782}, "arguments": [{"role": "Theme", "text": "lacZ", "start": 790, "end": 794}]}]}}, "schema": []}
{"input": "Two distinct signal transmission pathways in T lymphocytes are inhibited by complexes formed between an immunophilin and either FK506 or rapamycin. \nProliferation and immunologic function of T lymphocytes are initiated by signals from the antigen receptor that are inhibited by the immunosuppressant FK506 but not by its structural analog, rapamycin. On the other hand, interleukin 2 (IL-2)-induced signals are blocked by rapamycin but not by FK506. Remarkably, these two drugs inhibit each other's actions, raising the possibility that both act by means of a common immunophilin (immunosuppressant binding protein). We find that the dissociation constant of rapamycin to the FK506 binding protein FKBP (Kd = 0.2 nM) is close to the dissociation constant of FK506 to FKBP (Kd = 0.4 nM) and to their effective biologic inhibitory concentrations. However, an excess of rapamycin is needed to revert FK506-mediated inhibition of IL-2 production, apoptosis, and transcriptional activation of NF-AT, a T-cell-specific transcription factor necessary for IL-2 gene activation. Similarly, an excess of FK506 is needed to revert rapamycin-mediated inhibition of IL-2-induced proliferation. The drug concentrations required for antagonism may be explained by the relative affinity of the drugs to, and by the abundance of, the immunophilin FKBP. FKBP has been shown to catalyze the interconversion of the cis- and trans-rotamers of the peptidyl-prolyl amide bond of peptide substrates; here we show that rapamycin, like FK506, is a potent inhibitor of the rotamase activity of FKBP (Ki = 0.2 nM). Neither FKBP binding nor inhibition of rotamase activity of FKBP alone is sufficient to explain the biologic actions of these drugs. Rather, these findings suggest that immunophilin bound to FK506 interferes with antigen receptor-induced signals, while rapamycin bound to the immunophilin interferes with IL-2-induced signals. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 931, "end": 941}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 926, "end": 930}]}], "negative regulation": [{"trigger": {"text": "needed to revert", "start": 880, "end": 896}, "arguments": [{"role": "Theme", "text": "inhibition", "start": 912, "end": 922}]}, {"trigger": {"text": "inhibition", "start": 912, "end": 922}, "arguments": [{"role": "Theme", "text": "production", "start": 931, "end": 941}]}], "positive regulation": [{"trigger": {"text": "necessary", "start": 1034, "end": 1043}, "arguments": [{"role": "Theme", "text": "activation", "start": 1058, "end": 1068}]}, {"trigger": {"text": "activation", "start": 1058, "end": 1068}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1048, "end": 1052}]}]}}, "schema": []}
{"input": "Transcriptional down-regulation of c-myc expression by protein synthesis-dependent and -independent pathways in a human T lymphoblastic tumor cell line. \nWe show that in the human T lymphoblastic tumor cell line Molt4 c-myc mRNA and protein expression is down-regulated after exposure to dimethyl sulfoxide, to phorbol myristate acetate, or to the calcium ionophore A23187, which raises the intracellular calcium concentration. A block to RNA elongation is largely responsible for decreased c-myc transcription. Although negative regulation by dimethyl sulfoxide takes place even when protein synthesis is inhibited by cycloheximide, the phorbol myristate acetate effect is blocked to some extent only by cycloheximide. The calcium ionophore-induced c-myc suppression, however, strictly requires de novo protein synthesis. Therefore, two different negative regulatory pathways are involved in c-myc regulation: one which is independent and one which depends on de novo protein synthesis. The latter one appears to be mediated by a rapidly calcium-dependent induced gene product. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 41, "end": 51}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 35, "end": 40}]}, {"trigger": {"text": "expression", "start": 241, "end": 251}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 218, "end": 223}]}], "negative regulation": [{"trigger": {"text": "down-regulation", "start": 16, "end": 31}, "arguments": [{"role": "Theme", "text": "expression", "start": 41, "end": 51}]}, {"trigger": {"text": "down-regulated", "start": 255, "end": 269}, "arguments": [{"role": "Theme", "text": "expression", "start": 241, "end": 251}]}, {"trigger": {"text": "decreased", "start": 481, "end": 490}, "arguments": [{"role": "Theme", "text": "transcription", "start": 497, "end": 510}]}, {"trigger": {"text": "negative regulation", "start": 521, "end": 540}, "arguments": [{"role": "Theme", "text": "expression", "start": 241, "end": 251}]}, {"trigger": {"text": "effect", "start": 664, "end": 670}, "arguments": [{"role": "Theme", "text": "expression", "start": 241, "end": 251}]}, {"trigger": {"text": "blocked", "start": 674, "end": 681}, "arguments": [{"role": "Theme", "text": "effect", "start": 664, "end": 670}]}, {"trigger": {"text": "suppression", "start": 756, "end": 767}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 750, "end": 755}]}], "positive regulation": [{"trigger": {"text": "when", "start": 580, "end": 584}, "arguments": [{"role": "Theme", "text": "negative regulation", "start": 521, "end": 540}]}, {"trigger": {"text": "requires", "start": 787, "end": 795}, "arguments": [{"role": "Theme", "text": "suppression", "start": 756, "end": 767}]}], "regulation": [{"trigger": {"text": "responsible", "start": 465, "end": 476}, "arguments": [{"role": "Theme", "text": "decreased", "start": 481, "end": 490}]}, {"trigger": {"text": "regulation", "start": 899, "end": 909}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 893, "end": 898}]}], "transcription": [{"trigger": {"text": "expression", "start": 241, "end": 251}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 218, "end": 223}]}, {"trigger": {"text": "transcription", "start": 497, "end": 510}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 491, "end": 496}]}]}}, "schema": []}
{"input": "Induction of immediate early response genes by macrophage colony-stimulating factor in normal human monocytes. \nA group of coordinately induced protooncogenes, cytoskeletal, and extracellular matrix genes have been termed immediate early response genes, and their induction has been associated with growth factor-stimulated cell proliferation. We have investigated the induction of these genes by macrophage-CSF (M-CSF) in human monocytes that do not proliferate in response to M-CSF but require the factor for optimal cell differentiation. Normal human monocytes were isolated, carefully washed, and incubated for 36 to 48 h in fetal bovine serum-containing medium. At the end of this incubation the resting cells were stimulated with M-CSF, and RNA was isolated for analysis by Northern blotting. RNA from control resting cells contained low to undetectable levels of c-jun, fibronectin receptor, and actin mRNA. Within 15 to 30 min of addition of M-CSF, however, there was a dramatic coordinate induction of these genes. The c-jun gene expression was very transient and was not detectable by 60 min after M-CSF addition. In contrast, the expression of actin and fibronectin receptor mRNA was more sustained, and the expression of these genes remained elevated at 24 to 48 h after M-CSF addition. We also observed the induction of the myelomonocytic specific tyrosine kinase hck gene simultaneously with the other immediate early response genes. The protein synthesis inhibitor cycloheximide did not block the induction of any of these genes, and in fact, super-induced the expression of c-jun and hck. Nuclear run on transcription of the c-jun, hck, and actin genes. Therefore, in normal human monocytes M-CSF induces immediate early response genes without inducing cell proliferation. These genes may then play a role in altering the physiologic status of the cells in response to CSF. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1039, "end": 1049}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1028, "end": 1033}]}, {"trigger": {"text": "expression", "start": 1576, "end": 1586}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1590, "end": 1595}]}, {"trigger": {"text": "expression", "start": 1576, "end": 1586}, "arguments": [{"role": "Theme", "text": "hck", "start": 1600, "end": 1603}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 998, "end": 1007}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 870, "end": 875}]}, {"trigger": {"text": "after", "start": 1102, "end": 1107}, "arguments": [{"role": "Theme", "text": "expression", "start": 1039, "end": 1049}, {"role": "Cause", "text": "M-CSF", "start": 1108, "end": 1113}]}, {"trigger": {"text": "induction", "start": 1320, "end": 1329}, "arguments": [{"role": "Theme", "text": "hck", "start": 1377, "end": 1380}]}, {"trigger": {"text": "super-induced", "start": 1558, "end": 1571}, "arguments": [{"role": "Theme", "text": "expression", "start": 1576, "end": 1586}]}], "transcription": [{"trigger": {"text": "levels", "start": 860, "end": 866}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 870, "end": 875}]}, {"trigger": {"text": "transcription", "start": 1620, "end": 1633}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1641, "end": 1646}]}, {"trigger": {"text": "transcription", "start": 1620, "end": 1633}, "arguments": [{"role": "Theme", "text": "hck", "start": 1648, "end": 1651}]}]}}, "schema": []}
{"input": "Stimulation of a human T-cell clone with anti-CD3 or tumor necrosis factor induces NF-kappa B translocation but not human immunodeficiency virus 1 enhancer-dependent transcription. \nThe expression of transiently transfected expression vectors under the control of the long terminal repeat (LTR) of the human immunodeficiency virus (HIV) or its enhancer sequence and the translocation of the HIV enhancer-binding protein NF-kappa B were analyzed in two human T-cell clones stimulated through their T-cell receptor complex or by tumor necrosis factor or phorbol 12-myristate 13-acetate. We found a dissociation of NF-kappa B translocation from transactivation of either the HIV LTR or the HIV enhancer. Interleukin 2 induced proliferation but not NF-kappa B translocation or LTR transactivation. Phorbol ester or specific antigen recognition induced HIV LTR transactivation, whereas stimulation with tumor necrosis factor or antibody to CD3 did not. The two latter signals were nevertheless able to induce NF-kappa B translocation with a pattern in the band-shift assay indistinguishable from that observed using phorbol ester. Our finding that induction of NF-kappa B by tumor necrosis factor or antibody to CD3 is not sufficient to induce HIV enhancer-dependent transcription in cloned T cells contrasts with results obtained in most lymphoblastoid T-cell lines and indicates that normal T lymphocytes differ from tumoral T cells in terms of requirements for HIV LTR activation. Furthermore, our results suggest that events linked to T-cell activation, in addition to NF-kappa B translocation per se, induce functional interactions of the NF-kappa B complex with the HIV enhancer. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Lymphoid specific gene expression of the adenovirus early region 3 promoter is mediated by NF-kappa B binding motifs. \nA primary site of infection by human adenoviruses is lymphoid cells. However, analysis of the viral control elements and the cellular factors that regulate adenoviral gene expression in lymphocytes has not been reported. The adenovirus early region 3 (ES) gene products are involved in the maintenance of viral persistence by complexing with the class I MHC antigens, thus preventing their cell surface expression with a resultant decrease in host immunologic destruction. To determine whether different cellular factors were involved in E3 regulation in lymphocytes as compared with HeLa cells, both DNA binding and transfection analysis with the E3 promoter in both cell types were performed. These studies detected two novel domains referred to as L1 and L2 with a variety of lymphoid but not HeLa extracts. Each of these domains possessed strong homology to motifs previously found to bind the cellular factor NF-kappa B. Transfections of E3 constructs linked to the chloramphenicol acetyltransferase gene revealed that mutagenesis of the distal NF-kappa B motif (L2) had minimal effects on promoter expression in HeLa cells, but resulted in dramatic decreases in expression by lymphoid cells. In contrast, mutagenesis of proximal NF-kappa B motif (L1) had minimal effects on gene expression in both HeLa cells and lymphoid cells but resulted in a small, but reproducible, increase in gene expression in lymphoid cells when coupled to the L2 mutation. Reversing the position and subsequent mutagenesis of the L1 and L2 domains indicated that the primary sequence of these motifs rather than their position in the E3 promoter was critical for regulating gene expression. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {}}, "schema": []}
{"input": "Characterization of defensin resistance phenotypes associated with mutations in the phoP virulence regulon of Salmonella typhimurium. \nThe defensin sensitivities of Salmonella typhimurium strains with mutations in the phoP/phoQ two-component virulence regulon were tested by using purified defensins NP-1 and NP-2. Strains with mutations in either gene of the regulatory pair (phoP [transcriptional activator] or phoQ [membrane sensor kinase]) had increased sensitivities to defensin. The predicted periplasmic domain of the PhoQ protein contained a markedly anionic domain that could interact with cationic proteins and that could be responsible for resistance to defensin. Because insertion mutations in phoP are polar on phoQ, we constructed strains that expressed the PhoQ protein in the absence of PhoP to test whether resistance to defensin requires only the phoQ gene product. We found that resistance to defensin requires the function of both components of this regulatory system, because strains expressing PhoQ without PhoP were still markedly sensitive to defensins. This implied that a pag (phoP-activated gene) product is responsible for defensin resistance. We also tested for the ability of defensins NP-1, NP-5, and HNP-1 to activate pag expression and found that these peptides have no effect. Defensin resistance is not the only virulence characteristic controlled by the PhoP-PhoQ regulon because mutations in pagC, as well as ones in the phoP locus that resulted in constitutive pag activation (phenotype PhoPc), had no effect on defensin resistance, even though they rendered the organism avirulent and deficient in survival within macrophages. The virulence defect conferred by mutations in the phoP-phoQ two-component regulatory system is not completely explained by alterations in resistance to cationic proteins and involves the control of other proteins necessary for S. typhimurium survival within macrophages. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 758, "end": 767}, "arguments": [{"role": "Theme", "text": "PhoQ", "start": 772, "end": 776}]}, {"trigger": {"text": "expressing", "start": 1005, "end": 1015}, "arguments": [{"role": "Theme", "text": "PhoQ", "start": 1016, "end": 1020}]}, {"trigger": {"text": "expressing", "start": 1005, "end": 1015}, "arguments": [{"role": "Theme", "text": "PhoP", "start": 1029, "end": 1033}]}]}}, "schema": []}
{"input": "Involvement of cyclic AMP-dependent protein kinases in the signal transduction pathway for interleukin-1. \nExpression of a highly specific protein inhibitor for cyclic AMP-dependent protein kinases in interleukin-1 (IL-1)-responsive cells blocked IL-1-induced gene transcription that was driven by the kappa immunoglobulin enhancer or the human immunodeficiency virus long terminal repeat. This inhibitor did not affect protein kinase C-mediated gene transcription, suggesting that cyclic AMP-dependent protein kinases are involved in the signal transduction pathway for IL-1 in a number of responsive cell types. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Lipopolysaccharide is a potent monocyte/macrophage-specific stimulator of human immunodeficiency virus type 1 expression. \nLipopolysaccharide (LPS) potently stimulates human immunodeficiency virus type 1-long terminal repeat (HIV-1-LTR) CAT constructs transfected into monocyte/macrophage-like cell lines but not a T cell line. This effect appears to be mediated through the induction of nuclear factor kappa B (NF-kappa B). Electrophoretic mobility shift assays demonstrate that LPS induces a DNA binding activity indistinguishable from NF-kappa B in U937 and THP-1 cells. LPS is also shown to dramatically increase HIV-1 production from a chronically infected monocyte/macrophage-like cloned cell line, U1, which produces very low levels of HIV-1 at baseline. The stimulation of viral production from this cell line occurs only if these cells are treated with granulocyte/macrophage colony-stimulating factor (GM-CSF) before treatment with LPS. This stimulation of HIV-1 production is correlated with an increase in the level of HIV-1 RNA and and activation of NF-kappa B. LPS is not able to induce HIV-1 production in a cloned T cell line. The effect of LPS on HIV-1 replication occurs at picogram per milliliter concentrations and may be clinically significant in understanding the variability of the natural history of HIV-1 infection. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Inducible nuclear factor binding to the kappa B elements of the human immunodeficiency virus enhancer in T cells can be blocked by cyclosporin A in a signal-dependent manner. \nCyclosporin A (CsA) is thought to exert its immunosuppressive effects by inhibiting the expression of a distinct set of lymphokine genes which are induced upon T-cell activation, among them the gene coding for interleukin-2. In addition, the activation of the human immunodeficiency virus (HIV) is partially suppressed. To better understand the molecular mechanisms underlying suppression by CsA, we have investigated the effects of this drug on transcription factors in T cells. Here we report that the formation of two distinct mitogen-inducible DNA-binding complexes, the kappa B complex within the HIV enhancer and the NFAT-1 complex within the interleukin-2 enhancer, is inhibited in the presence of CsA. The kappa B-binding activity with the HIV enhancer is inhibited only if it is activated via the mitogen phytohemagglutinin whereas phorbol myristate acetate-mediated activation is completely insensitive to the drug. This suggests a model in which functionally indistinguishable kappa B complexes can be activated via two separate pathways of signal transduction distinguishable by CsA. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "formation", "start": 680, "end": 689}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 799, "end": 805}, {"role": "Theme2", "text": "interleukin-2", "start": 825, "end": 838}, {"role": "Site2", "text": "enhancer", "start": 839, "end": 847}]}], "gene expression": [{"trigger": {"text": "expression", "start": 264, "end": 274}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 386, "end": 399}]}], "negative regulation": [{"trigger": {"text": "inhibiting", "start": 249, "end": 259}, "arguments": [{"role": "Theme", "text": "expression", "start": 264, "end": 274}]}, {"trigger": {"text": "inhibited", "start": 852, "end": 861}, "arguments": [{"role": "Theme", "text": "formation", "start": 680, "end": 689}]}]}}, "schema": []}
{"input": "Cell-specific differences in activation of NF-kappa B regulatory elements of human immunodeficiency virus and beta interferon promoters by tumor necrosis factor. \nThree aspects of the involvement of tumor necrosis factor in human immunodeficiency virus (HIV) pathogenesis were examined. Tumor necrosis factor alpha (TNF-alpha) mRNA production was analyzed by polymerase chain reaction amplification in monocytic U937 cells and in a chronically HIV infected U937 cell line (U9-IIIB). TNF-alpha RNA was undetectable in U937 cells, whereas a low constitutive level was detected in U9-IIIB cells. Paramyxovirus infection induced a 5- to 10-fold increase in the steady-state level of TNF-alpha RNA in U9-IIIB cells compared with U937 cells, suggesting that HIV-infected monocytic cells produced higher levels of TNF-alpha than did normal cells after a secondary virus infection. The effects of TNF-alpha on gene expression were examined by transient expression assays using reporter chloramphenicol acetyltransferase plasmids linked to regulatory elements from the HIV long terminal repeat (LTR) and the beta interferon promoter. In U937 and Jurkat T lymphoid cells, the inducibility of the different hybrid promoters by TNF-alpha or phorbol ester varied in a cell type- and promoter context-specific manner; the levels of gene activity of NF-kappa B-containing plasmids correlated directly with induction of NF-kappa B DNA-binding activity. Although the intact beta interferon promoter was only weakly stimulated by phorbol ester or TNF-alpha, multimers of the PRDII NF-kappa B-binding domain were inducible by both agents. TNF-alpha was able to increase expression of the HIV LTR in T cells, but in monocytic cells, TNF-alpha did not induce the HIV LTR above a constitutive level of activity. This level of NF-kappa B-independent activity appears to be sufficient for virus multiplication, since TNF-alpha treatment had no effect on the kinetics of de novo HIV type 1 (HIV-1) infection and viral RNA production in U937 cells. However, in Jurkat cells, TNF-alpha dramatically enhanced the spread of HIV-1 through the cell population and increased viral RNA synthesis, indicating that in T cells HIV-1 multiplication was stimulated by TNF-alpha treatment. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "produced", "start": 781, "end": 789}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 807, "end": 816}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 617, "end": 624}, "arguments": [{"role": "Theme", "text": "increase", "start": 641, "end": 649}]}, {"trigger": {"text": "increase", "start": 641, "end": 649}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 679, "end": 688}]}, {"trigger": {"text": "higher levels", "start": 790, "end": 803}, "arguments": [{"role": "Theme", "text": "produced", "start": 781, "end": 789}]}, {"trigger": {"text": "stimulated", "start": 1498, "end": 1508}, "arguments": [{"role": "Theme", "text": "beta interferon", "start": 1457, "end": 1472}, {"role": "Site", "text": "promoter", "start": 1473, "end": 1481}, {"role": "Cause", "text": "TNF-alpha", "start": 1529, "end": 1538}]}, {"trigger": {"text": "stimulated", "start": 1498, "end": 1508}, "arguments": [{"role": "Theme", "text": "beta interferon", "start": 1457, "end": 1472}, {"role": "Site", "text": "promoter", "start": 1473, "end": 1481}]}], "transcription": [{"trigger": {"text": "production", "start": 332, "end": 342}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 316, "end": 325}]}, {"trigger": {"text": "undetectable", "start": 501, "end": 513}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 483, "end": 492}]}, {"trigger": {"text": "detected", "start": 566, "end": 574}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 483, "end": 492}]}]}}, "schema": []}
{"input": "Astrocytes and glioblastoma cells express novel octamer-DNA binding proteins distinct from the ubiquitous Oct-1 and B cell type Oct-2 proteins. \nThe 'octamer' sequence, ATGCAAAT or its complement ATTTGCAT, is a key element for the transcriptional regulation of immunoglobulin genes in B-lymphocytes as well as a number of housekeeping genes in all cell types. In lymphocytes, the octamer-binding protein Oct-2A and variants thereof are thought to contribute to the B-cell specific gene expression, while the ubiquitous protein Oct-1 seems to control general octamer site-dependent transcription. Various other genes, for example interleukin-1 and MHC class II genes, contain an octamer sequence in the promoter and are expressed in cells of both the immune and nervous systems. This prompted us to analyze the octamer-binding proteins in the latter cells. Using the electrophoretic mobility shift assay, at least six novel octamer binding proteins were detected in nuclear extracts of cultured mouse astrocytes. These proteins are differentially expressed in human glioblastoma and neuroblastoma cell lines. The nervous system-derived (N-Oct) proteins bound to the octamer DNA sequence in a manner which is indistinguishable from the Oct-1 and Oct-2A proteins. The relationship of the N-Oct proteins to Oct-1 and Oct-2A was analyzed by proteolytic clipping bandshift assays and by their reactivity towards antisera raised against recombinant Oct-1 and Oct-2A proteins. On the basis of these assays, all N-Oct-factors were found to be distinct from the ubiquitous Oct-1 and the lymphoid-specific Oct-2A proteins. In melanoma cells that contain the N-Oct-3 factor, a transfected lymphocyte-specific promoter was neither activated nor was it repressed upon contransfection with an Oct-2A expression vector. We therefore speculate that N-Oct-3 and other N-Oct factors have a specific role in gene expression in cells of the nervous system. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Cloning of a mitogen-inducible gene encoding a kappa B DNA-binding protein with homology to the rel oncogene and to cell-cycle motifs. \nWe have cloned and characterized a mitogen-inducible gene isolated from human T cells that predicts a protein of 968 amino acids. The amino-terminal domain has regions homologous to the oncogene rel and to the developmentally important gene dorsal of Drosophila. The carboxy-terminal domain contains repeat structures found in a variety of proteins that are involved in cell-cycle control of yeast and in tissue differentiation in Drosophila and Ceanorhabditis elegans, as well as in the putative human oncogene bcl-3 and in the ankyrin protein. A truncated form of the product of this gene translated in vitro is a DNA-binding protein which interacts specifically with the kappa B binding site found in many inducible genes, including the enhancer in human immunodeficiency virus. This gene is yet another in a growing list of important regulatory molecules whose expression is transcriptionally induced upon cellular activation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Regulation of gene expression with double-stranded phosphorothioate oligonucleotides. \nAlteration of gene transcription by inhibition of specific transcriptional regulatory proteins is necessary for determining how these factors participate in cellular differentiation. The functions of these proteins can be antagonized by several methods, each with specific limitations. Inhibition of sequence-specific DNA-binding proteins was achieved with double-stranded (ds) phosphorothioate oligonucleotides that contained octamer or kappa B consensus sequences. The phosphorothioate oligonucleotides specifically bound either octamer transcription factor or nuclear factor (NF)-kappa B. The modified oligonucleotides accumulated in cells more effectively than standard ds oligonucleotides and modulated gene expression in a specific manner. Octamer-dependent activation of a reporter plasmid or NF-kappa B-dependent activation of the human immunodeficiency virus (HIV) enhancer was inhibited when the appropriate phosphorothioate oligonucleotide was added to a transiently transfected B cell line. Addition of phosphorothioate oligonucleotides that contained the octamer consensus to Jurkat T leukemia cells inhibited interleukin-2 (IL-2) secretion to a degree similar to that observed with a mutated octamer site in the IL-2 enhancer. The ds phosphorothioate oligonucleotides probably compete for binding of specific transcription factors and may provide anti-viral, immunosuppressive, or other therapeutic effects. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "secretion", "start": 1231, "end": 1240}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1225, "end": 1229}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1200, "end": 1209}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1231, "end": 1240}, {"role": "CSite", "text": "mutated octamer site", "start": 1285, "end": 1305}, {"role": "Cause", "text": "IL-2", "start": 1313, "end": 1317}]}, {"trigger": {"text": "inhibited", "start": 1200, "end": 1209}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1231, "end": 1240}]}]}}, "schema": []}
{"input": "Differences in transcriptional enhancers of HIV-1 and HIV-2. Response to T cell activation signals. \nT cell activation results in high levels of HIV replication and is thought to be one mechanism leading to the conversion from latent to active viral infection. In HIV-1, the sequences that respond to these signaling events are found in the long terminal repeat (LTR) and comprise the transcriptional enhancer, which contains two conserved binding sites for the nuclear factor kappa B (NF kappa B). The corresponding region in the second AIDS retrovirus, HIV-2, contains a conserved and a divergent NF kappa B binding site. We demonstrate that the HIV-1 LTR responds better than the HIV-2 LTR to T cell activation signals. These qualitative differences in the response to T cell activation are reproduced not only when HIV-1 or HIV-2 enhancers are placed upstream of a heterologous promoter but also when these enhancers are switched between their respective LTR. In electrophoretic mobility shift assays, NF kappa B binds to both conserved sites in the HIV-1 transcriptional enhancer and only to the single conserved site in the HIV-2 transcriptional enhancer. Instead of NF kappa B, the activator protein 3 binds to the divergent site in HIV-2. In conclusion, HIV-1 and HIV-2 are differentially regulated by T cell activation signals, and this difference may account for the longer period of viral latency observed with HIV-2 than with HIV-1 infection. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 1209, "end": 1214}, "arguments": [{"role": "Theme", "text": "activator protein 3", "start": 1189, "end": 1208}]}]}}, "schema": []}
{"input": "An in vitro globin gene switching model based on differentiated embryonic stem cells. \nWe used mouse embryonic stem (ES) cells to study globin gene expression and switching in vitro. We show that ES-derived embryoid bodies express the full complement of mouse embryonic globin genes in the correct temporal order and that on further differentiation, a switch occurs to the fetal/adult genes. In addition, the erythroid-specific transcription factor NF-E1 was shown to be expressed coordinately with that of globin in embryoid bodies. We conclude from these experiments that the ES cell system provides a good model to study hematopoietic development. When the human epsilon- or beta-globin genes driven by the dominant control region (DCR) are introduced into this system, the human epsilon-globin gene, in contrast to the beta-globin gene, is not deregulated by the presence of the DCR and is expressed strictly as an embryonic gene. We conclude from this that the epsilon-globin gene is not regulated by competition with other genes in the human beta-globin locus. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 471, "end": 480}, "arguments": [{"role": "Theme", "text": "NF-E1", "start": 449, "end": 454}]}, {"trigger": {"text": "expressed", "start": 894, "end": 903}, "arguments": [{"role": "Theme", "text": "epsilon-globin", "start": 783, "end": 797}]}], "negative regulation": [{"trigger": {"text": "deregulated", "start": 848, "end": 859}, "arguments": [{"role": "Theme", "text": "epsilon-globin", "start": 783, "end": 797}]}], "regulation": [{"trigger": {"text": "deregulated", "start": 848, "end": 859}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 823, "end": 834}]}, {"trigger": {"text": "regulated", "start": 993, "end": 1002}, "arguments": [{"role": "Theme", "text": "epsilon-globin", "start": 966, "end": 980}]}]}}, "schema": []}
{"input": "Functional analysis of cis-linked regulatory sequences in the HLA DRA promoter by transcription in vitro. \nTwo consensus sequences, called X and Y boxes, capable of binding nuclear proteins and regulating expression in B cells have been defined within the immediate upstream region of major histocompatibility complex (MHC) class II promoters. Unlike other class II promoters, the HLA-DR alpha (DRA) promoter also contains one element identical to the \"octamer\" motif of immunoglobulin variable region promoters that is responsible for B cell-specific transcription. This \"octamer\" in the context of DRA appears capable of binding both the ubiquitous (OTF-1) and lymphoid-specific (OTF-2) \"octamer\" binding proteins, but at least one other distinct \"octamer\" complex was found. In order to characterize the function of cis-acting elements, we have developed an in vitro system in which a DRA promoter construct is transcribed more efficiently in extracts from B cells than in extracts from class II-negative HeLa cells. 5' deletion constructs which lacked the Y box, but retained the \"octamer\" motif and TATA box were completely inactive, and internal deletion of the Y box reduced transcription by 95%. Using supercoiled, but not linear templates, we observed differences in transcription efficiencies from templates lacking or disrupting the X consensus element that reflect effects of random replacement of X box sequences in transient expression assays. Demonstration of the complete dependence on the Y box in this system suggests that, despite its demonstrated importance in the DRA promoter, the DRA \"octamer\" does not utilize OTF-2 in a manner analogous to immunoglobulin promoters in B cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 623, "end": 630}, "arguments": [{"role": "Theme", "text": "OTF-1", "start": 652, "end": 657}]}, {"trigger": {"text": "binding", "start": 623, "end": 630}, "arguments": [{"role": "Theme", "text": "OTF-2", "start": 682, "end": 687}]}], "regulation": [{"trigger": {"text": "utilize", "start": 1626, "end": 1633}, "arguments": [{"role": "Theme", "text": "OTF-2", "start": 1634, "end": 1639}]}]}}, "schema": []}
{"input": "Characterization of the human immunodeficiency virus type 1 enhancer-binding proteins from the human T-cell line Jurkat. \nThe transcription of the human immunodeficiency virus type 1 (HIV-1) is under the control of cellular proteins that bind to the viral long terminal repeat (LTR). Among the protein-binding regions of the HIV-1 LTR is the transcription-enhancer region. We show that at least one inducible, C1, and one constitutive, C2, protein can bind to the HIV enhancer in Jurkat cells. The two proteins differ in their surface charge, since they are separable by anion-exchange chromatography. Bivalent cations such as Mg2+ and Zn2+ differentially affect their binding to oligonucleotides which contain the HIV-enhancer domain. Both C1 and C2 proteins also bind to a similar sequence found in the interleukin-2-receptor alpha-subunit enhancer. The inducible C1 protein was partially purified by three chromatographic steps and characterized by u.v. cross-linking as a 47 kDa protein. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 452, "end": 456}, "arguments": [{"role": "Theme", "text": "C1", "start": 410, "end": 412}]}, {"trigger": {"text": "bind", "start": 452, "end": 456}, "arguments": [{"role": "Theme", "text": "C2", "start": 436, "end": 438}]}, {"trigger": {"text": "binding", "start": 669, "end": 676}, "arguments": [{"role": "Theme", "text": "C1", "start": 410, "end": 412}]}, {"trigger": {"text": "binding", "start": 669, "end": 676}, "arguments": [{"role": "Theme", "text": "C2", "start": 436, "end": 438}]}, {"trigger": {"text": "bind", "start": 765, "end": 769}, "arguments": [{"role": "Theme", "text": "C1", "start": 741, "end": 743}, {"role": "Theme2", "text": "interleukin-2-receptor alpha-subunit", "start": 805, "end": 841}, {"role": "Site2", "text": "enhancer", "start": 842, "end": 850}]}, {"trigger": {"text": "bind", "start": 765, "end": 769}, "arguments": [{"role": "Theme", "text": "C2", "start": 748, "end": 750}, {"role": "Theme2", "text": "interleukin-2-receptor alpha-subunit", "start": 805, "end": 841}, {"role": "Site2", "text": "enhancer", "start": 842, "end": 850}]}], "regulation": [{"trigger": {"text": "affect", "start": 656, "end": 662}, "arguments": [{"role": "Theme", "text": "binding", "start": 669, "end": 676}]}]}}, "schema": []}
{"input": "The ubiquitous octamer-binding protein(s) is sufficient for transcription of immunoglobulin genes. \nAll immunoglobulin genes contain a conserved octanucleotide promoter element, ATGCAAAT, which has been shown to be required for their normal B-cell-specific transcription. Proteins that bind this octamer have been purified, and cDNAs encoding octamer-binding proteins have been cloned. Some of these proteins (referred to as OTF-2) are lymphoid specific, whereas at least one other, and possibly more (referred to as OTF-1), is found ubiquitously in all cell types. The exact role of these different proteins in directing the tissue-specific expression of immunoglobulin genes is unclear. We have identified two human pre-B-cell lines that contain extremely low levels of OTF-2 yet still express high levels of steady-state immunoglobulin heavy-chain mRNA in vivo and efficiently transcribe an immunoglobulin gene in vitro. Addition of a highly enriched preparation of OTF-1 made from one of these pre-B cells or from HeLa cells specifically stimulated in vitro transcription of an immunoglobulin gene. Furthermore, OFT-1 appeared to have approximately the same transactivation ability as OTF-2 when normalized for binding activity. These results suggest that OTF-1, without OTF-2, is sufficient for transcription of immunoglobulin genes and that OTF-2 alone is not responsible for the B-cell-specific regulation of immunoglobulin gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "made", "start": 975, "end": 979}, "arguments": [{"role": "Theme", "text": "OTF-1", "start": 969, "end": 974}]}], "positive regulation": [{"trigger": {"text": "transactivation", "start": 1162, "end": 1177}, "arguments": [{"role": "Theme", "text": "OFT-1", "start": 1116, "end": 1121}]}, {"trigger": {"text": "transactivation", "start": 1162, "end": 1177}, "arguments": [{"role": "Theme", "text": "OTF-2", "start": 1189, "end": 1194}]}]}}, "schema": []}
{"input": "Tax-independent binding of multiple cellular factors to Tax-response element DNA of HTLV-I. \nThe human T-cell leukemia virus type I (HTLV-I) promoter contains three copies of imperfect repeats of a 21-base pair sequence designated here as TRE (Tax-response element) that is responsive to the virally encoded transactivator protein Tax. We have identified and separated four nuclear proteins from C81-66-45 cells, an HTLV-I immortalized Tax-expressing human T-lymphocyte line (Salahuddin et al., 1983), that interact with the TRE-DNA, none of which are identical with the Tax-protein. The proteins identified have molecular weights of about 32, 36 to 42, 50 and 110 kD. Four different methods were used to identify the proteins. First, from different cell lines three or all four of the nuclear proteins were specifically cross-linked by UV irradiation to the radioactively labeled TRE-DNA fragment. Second, TRE-DNA binding proteins sedimented through a glycerol density gradient at rates corresponding to proteins of native molecular weights of 35 to 50 kD and 110 kD. Third, only the 50 kD protein was retained on a biotinylated DNA-streptavidin matrix when the DNA fragment contained the TRE-DNA. Fourth, extensive purification by several cycles of TRE-DNA affinity chromatography resulted in the 32, 36 to 42 and 110 kD proteins and to less extent the 50 kD factor. Two abundant proteins of 75 and 80 kD were competed out by poly[d(I-C)] in all reactions. The cAMP-response element CRE, TGACGTCA, present in the 21 base-pair sequence, appears to be essential for specific protein-TRE-DNA interactions because mutation of the two G's destroys this complex. This result suggests that the cAMP response element binding protein, CREB, is involved in the protein-TRE-DNA complex and in mediating the Tax response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 440, "end": 450}, "arguments": [{"role": "Theme", "text": "Tax", "start": 436, "end": 439}]}], "regulation": [{"trigger": {"text": "involved", "start": 1737, "end": 1745}, "arguments": [{"role": "Cause", "text": "CREB", "start": 1728, "end": 1732}, {"role": "Theme", "text": "mediating", "start": 1784, "end": 1793}]}, {"trigger": {"text": "mediating", "start": 1784, "end": 1793}, "arguments": [{"role": "Cause", "text": "CREB", "start": 1728, "end": 1732}, {"role": "Theme", "text": "response", "start": 1802, "end": 1810}]}, {"trigger": {"text": "response", "start": 1802, "end": 1810}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1798, "end": 1801}]}]}}, "schema": []}
{"input": "Cell type specificity and activation requirements for NFAT-1 (nuclear factor of activated T-cells) transcriptional activity determined by a new method using transgenic mice to assay transcriptional activity of an individual nuclear factor. \nNuclear factor of activated T-cells (NFAT-1) is a transcription factor which is considered to be an important regulator in early T-cell activation. We have developed a system to monitor the transcriptional activity of NFAT-1 at the single cell level in whole animals. The system is based on the use of an oligomerized NFAT-1 binding motif that directs transcription of SV40 T-antigen in transgenic mice. This report represents the first demonstration that a multimerized short binding motif can function appropriately in transgenic mice. NFAT-1 activity had previously been thought to be confined to activated T-lymphocytes upon release of intracellular calcium. By targeting NFAT-1-dependent gene expression in transgenic mice we discovered new sites of NFAT-1 activity. Besides in T-lymphocytes NFAT-1 activity could also be induced in T-lymphocyte-depleted spleen cells and purified B-lymphocytes and requires agents that both release intracellular calcium and activate protein kinase C. A difference in the time course of appearance of NFAT-1 activity between T-lymphocytes and non-T-lymphocytes was revealed. Constitutive expression was observed in a small population of cells in the dermis and some mice have developed skin lesions. Interestingly, the tissue pattern of expression of the NFAT-1 activity resembles the expression pattern described for HIV-LTR/tat transgenic mice (Vogel, J., Hinrichs, S. H., Reynolds, R. K., Luciw, P. A., and Jay, G. (1988) Nature 335, 606-611). This similarity in expression and the fact that NFAT-1 has been shown to bind functional sequences in HIV-LTR suggest a role for NFAT-1 in dermal activation of the HIV-LTR. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 1800, "end": 1804}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1775, "end": 1781}]}], "localization": [{"trigger": {"text": "expression", "start": 1517, "end": 1527}, "arguments": [{"role": "AtLoc", "text": "tissue", "start": 1499, "end": 1505}, {"role": "Theme", "text": "NFAT-1", "start": 1535, "end": 1541}]}, {"trigger": {"text": "expression", "start": 1565, "end": 1575}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1535, "end": 1541}, {"role": "AtLoc", "text": "HIV-LTR/tat transgenic mice", "start": 1598, "end": 1625}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1068, "end": 1075}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1038, "end": 1044}]}, {"trigger": {"text": "requires", "start": 1145, "end": 1153}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1038, "end": 1044}]}, {"trigger": {"text": "appearance", "start": 1267, "end": 1277}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1281, "end": 1287}]}]}}, "schema": []}
{"input": "Octamer transcription factors and the cell type-specificity of immunoglobulin gene expression. \nAntibodies are produced exclusively in B lymphocytes. The expression of the antibody-encoding genes, the immunoglobulin (Ig) genes, is also restricted to B cells. The octamer sequence ATGCAAAT is present in the promoter and the enhancer of Ig genes, and plays an important role in its tissue-specific expression. This sequence motif is a binding site for nuclear proteins, the so-called octamer transcription factors (Oct or OTF factors). The Oct-1 protein is present in all cell types analyzed so far, whereas Oct-2A and Oct-2B are found mainly in B lymphocytes. All three proteins show the same sequence specificity and binding affinity. It appears that the B cell-specific expression of Ig genes is mediated at least in part by cell type-specific Oct factors, and that there are both quantitative and qualitative differences between Oct-1 and Oct-2 factors. Recently, a number of other octamer factor variants were identified. Many of these may be created by alternative splicing of a primary transcript of one Oct factor gene and may serve a specific function in the fine tuning of gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "present", "start": 556, "end": 563}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 539, "end": 544}]}, {"trigger": {"text": "found", "start": 629, "end": 634}, "arguments": [{"role": "Theme", "text": "Oct-2A", "start": 607, "end": 613}]}, {"trigger": {"text": "found", "start": 629, "end": 634}, "arguments": [{"role": "Theme", "text": "Oct-2B", "start": 618, "end": 624}]}]}}, "schema": []}
{"input": "Thrombin and thrombin receptor agonist peptide induce early events of T cell activation and synergize with TCR cross-linking for CD69 expression and interleukin 2 production. \nThrombin stimulation of the T leukemic cell line Jurkat induced a transient increase in [Ca2+]i. Proteolytic activity of the enzyme was required for this effect since diisopropyl fluorophosphate-thrombin failed to increase [Ca2+]i. Furthermore, hirudin and anti-thrombin III inhibited the thrombin-induced [Ca2+]i rise in Jurkat T cells. A synthetic thrombin receptor agonist peptide (TRP) of 7 residues (SFLLRNP) was found to be as effective as thrombin for [Ca2+]i mobilization, and both agonists induced Ca2+ release exclusively from internal stores. Thrombin stimulated tyrosine phosphorylation of several proteins of molecular mass 40, 42, 70, 120, and 130 kDa. There was a good correlation between thrombin-induced tyrosine phosphorylation of the latter three proteins and Ca2+ mobilization. Thrombin and TRP also caused translocation of protein kinase C from the cytosol to the plasma membrane. As a likely consequence of these events, thrombin activated the nuclear factor NF-kB. Several cell lines of hematopoietic origin including the leukemic T cell line HPB.ALL and the erythroleukemic cell line K562 were responsive to thrombin, whereas others such as THP1, a myelomonocytic cell line, and BL2, a Burkitt lymphoma were refractory to thrombin or TRP stimulation. The magnitude of the thrombin response in the different cell types paralleled the expression of the thrombin receptor mRNA. We found that activation of Jurkat T cells by a combination of phytohemagglutinin and phorbol 12-myristate 13-acetate led to a dramatic inhibition of thrombin receptor mRNA expression and to a concomitant loss of the thrombin response. Finally, we demonstrate that thrombin and TRP enhanced CD69 expression and interleukin 2 production induced by T cell receptor cross-linking in both Jurkat T cells and peripheral blood lymphocytes. These findings highlight the role of thrombin as a potential regulator of T lymphocyte activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 134, "end": 144}, "arguments": [{"role": "Theme", "text": "CD69", "start": 129, "end": 133}]}, {"trigger": {"text": "production", "start": 163, "end": 173}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 149, "end": 162}]}, {"trigger": {"text": "expression", "start": 1871, "end": 1881}, "arguments": [{"role": "Theme", "text": "CD69", "start": 1866, "end": 1870}]}, {"trigger": {"text": "production", "start": 1900, "end": 1910}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 1886, "end": 1899}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 1711, "end": 1721}, "arguments": [{"role": "Theme", "text": "expression", "start": 1748, "end": 1758}]}], "positive regulation": [{"trigger": {"text": "synergize", "start": 92, "end": 101}, "arguments": [{"role": "Cause", "text": "Thrombin", "start": 0, "end": 8}, {"role": "Theme", "text": "expression", "start": 134, "end": 144}]}, {"trigger": {"text": "synergize", "start": 92, "end": 101}, "arguments": [{"role": "Cause", "text": "Thrombin", "start": 0, "end": 8}, {"role": "Theme", "text": "production", "start": 163, "end": 173}]}, {"trigger": {"text": "synergize", "start": 92, "end": 101}, "arguments": [{"role": "Theme", "text": "expression", "start": 134, "end": 144}]}, {"trigger": {"text": "synergize", "start": 92, "end": 101}, "arguments": [{"role": "Theme", "text": "production", "start": 163, "end": 173}]}, {"trigger": {"text": "enhanced", "start": 1857, "end": 1865}, "arguments": [{"role": "Cause", "text": "thrombin", "start": 1840, "end": 1848}, {"role": "Theme", "text": "induced", "start": 1911, "end": 1918}]}, {"trigger": {"text": "enhanced", "start": 1857, "end": 1865}, "arguments": [{"role": "Theme", "text": "induced", "start": 1911, "end": 1918}]}, {"trigger": {"text": "induced", "start": 1911, "end": 1918}, "arguments": [{"role": "Theme", "text": "expression", "start": 1871, "end": 1881}]}, {"trigger": {"text": "induced", "start": 1911, "end": 1918}, "arguments": [{"role": "Theme", "text": "production", "start": 1900, "end": 1910}]}], "transcription": [{"trigger": {"text": "expression", "start": 1533, "end": 1543}, "arguments": [{"role": "Theme", "text": "thrombin receptor", "start": 1551, "end": 1568}]}, {"trigger": {"text": "expression", "start": 1748, "end": 1758}, "arguments": [{"role": "Theme", "text": "thrombin receptor", "start": 1725, "end": 1742}]}]}}, "schema": []}
{"input": "Sp1 is a critical factor for the monocytic specific expression of human CD14. \nCD14 is a membrane glycoprotein expressed specifically on monocytes and macrophages, and its expression is markedly increased during the process of monocyte differentiation. In order to study CD14 gene regulation, the human CD14 gene was cloned from a partial EcoRI digested chromosome 5 library. A 5.5-kilobase genomic clone contained the full-length CD14 coding sequence and 4.2 kilobases of 5'-upstream sequence. One major and one minor transcription start site were identified 101 and 130 base pairs (bp) upstream, respectively, from the protein translation start ATG. A DNA fragment containing 128 bp of upstream sequence had strong, monocyte-specific promoter activity in the CD14 positive monocytic cell line Mono Mac 6 as compared to the nonmonocytic cell lines HeLa and REX. Four regions in this DNA fragment interact with nuclear proteins isolated from monocytic cells. The Sp1 transcription factor bound to three different regions in the CD14 promoter. Mutation of the major Sp1 binding site (-110 bp) decreased tissue-specific promoter activity, and these results, together with transactivation experiments, demonstrate that Sp1 plays a critical role in the tissue-specific expression of CD14 in monocytic cells. CD14 Sp1 site oligonucleotides bound preferentially to a 105-kDa Sp1 species, which is present in higher relative levels in monocytic than non-monocytic cells, suggesting that modification of Sp1, such as phosphorylation, may explain how the Sp1 site mediates monocytic specific promoter activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 988, "end": 993}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 963, "end": 966}, {"role": "Theme2", "text": "CD14", "start": 1028, "end": 1032}, {"role": "Site2", "text": "promoter", "start": 1033, "end": 1041}]}, {"trigger": {"text": "bound", "start": 1335, "end": 1340}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1369, "end": 1372}]}], "gene expression": [{"trigger": {"text": "expression", "start": 52, "end": 62}, "arguments": [{"role": "Theme", "text": "CD14", "start": 72, "end": 76}]}, {"trigger": {"text": "expressed", "start": 111, "end": 120}, "arguments": [{"role": "Theme", "text": "CD14", "start": 79, "end": 83}]}, {"trigger": {"text": "expression", "start": 1265, "end": 1275}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1279, "end": 1283}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1509, "end": 1524}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1496, "end": 1499}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 195, "end": 204}, "arguments": [{"role": "Theme", "text": "expressed", "start": 111, "end": 120}]}], "regulation": [{"trigger": {"text": "critical", "start": 9, "end": 17}, "arguments": [{"role": "Cause", "text": "Sp1", "start": 0, "end": 3}, {"role": "Theme", "text": "expression", "start": 52, "end": 62}]}, {"trigger": {"text": "regulation", "start": 281, "end": 291}, "arguments": [{"role": "Theme", "text": "CD14", "start": 271, "end": 275}]}, {"trigger": {"text": "role", "start": 1237, "end": 1241}, "arguments": [{"role": "Cause", "text": "Sp1", "start": 1216, "end": 1219}, {"role": "Theme", "text": "expression", "start": 1265, "end": 1275}]}]}}, "schema": []}
{"input": "Tolerance to lipopolysaccharide involves mobilization of nuclear factor kappa B with predominance of p50 homodimers. \nStimulation of the human monocytic cell line Mono Mac 6 with lipopolysaccharide (LPS) leads to rapid and transient expression of cytokines like tumor necrosis factor (TNF). When such cells are precultured for 2 days with a low dose of LPS (20 ng/ml) followed by stimulation with a high dose of LPS (1 microgram/ml), expression of the TNF gene is minimal, i.e. the cells are tolerant. In nuclear run-on analysis, such tolerant cells show only a low degree of transcription, indicating that tolerance operates at or upstream of the transcription level. The CD14 LPS receptor is, however, up-regulated (not down-regulated) in tolerant cells, and LPS can, in fact, still lead to activation of tolerant cells as evidenced by mobilization of the transcription factor nuclear factor kappa B (NF-kappa B). Resolution of the NF-kappa B complex in gel shift analysis shows that the binding protein, mobilized in naive Mono Mac 6 cells, consists mainly of p50-p65 heterodimers, while in tolerant cells, the p50 homodimer is predominant. This increase in p50 homodimers coincides with an increase in p105 mRNA, suggestive of a transcriptional up-regulation of p50. Reporter gene analysis reveals that the NF-kappa B complex mobilized in tolerant cells is functionally inactive in that NF-kappa B-dependent luciferase constructs containing the human immunodeficiency virus long terminal repeat or the TNF 5'-region show only minimal transactivation after LPS stimulation. Similar to Mono Mac 6 cells, primary blood monocytes, when precultured with a low dose of LPS, also become tolerant and produce little TNF after LPS stimulation. The tolerant blood monocytes also up-regulate CD14, and they mobilize NF-kappa B with a predominance of p50 homodimers. Taken together, these results demonstrate that tolerance to LPS is determined by post-receptor mechanisms that involve an altered composition of the NF-kappa B complex. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "mobilization", "start": 41, "end": 53}, "arguments": [{"role": "Theme", "text": "p50", "start": 101, "end": 104}]}, {"trigger": {"text": "mobilized", "start": 1007, "end": 1016}, "arguments": [{"role": "AtLoc", "text": "naive Mono Mac 6 cells", "start": 1020, "end": 1042}, {"role": "Theme", "text": "p50", "start": 1063, "end": 1066}]}, {"trigger": {"text": "mobilized", "start": 1007, "end": 1016}, "arguments": [{"role": "AtLoc", "text": "naive Mono Mac 6 cells", "start": 1020, "end": 1042}, {"role": "Theme", "text": "p65", "start": 1067, "end": 1070}]}, {"trigger": {"text": "mobilized", "start": 1007, "end": 1016}, "arguments": [{"role": "Theme", "text": "p50", "start": 1114, "end": 1117}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 1149, "end": 1157}, "arguments": [{"role": "Theme", "text": "p50", "start": 1161, "end": 1164}]}, {"trigger": {"text": "increase", "start": 1194, "end": 1202}, "arguments": [{"role": "Theme", "text": "p105", "start": 1206, "end": 1210}]}, {"trigger": {"text": "transcriptional up-regulation", "start": 1233, "end": 1262}, "arguments": [{"role": "Theme", "text": "p50", "start": 1266, "end": 1269}]}, {"trigger": {"text": "up-regulate", "start": 1773, "end": 1784}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1785, "end": 1789}]}]}}, "schema": []}
{"input": "Evidence for a trans-acting activator function regulating the expression of the human CD5 antigen. \nInterspecies somatic cell hybrids were generated by fusing the mouse T-lymphoma cell line, BW5147, with normal human T lymphocytes at different stages of differentiation. Thymocytes, activated peripheral T lymphocytes, or an activated T-cell clone were used as human partners, respectively, in three independent fusions. Irrespective of the human cell partner used for fusion, a certain number of hybrids lost CD5 surface expression over a period of time in culture. Analysis at the phenotype and genetic level showed that lack of CD5 expression was due neither to segregation of human autosome 11, on which the CD5 gene has been mapped, nor to deletion of the CD5 structural gene. Furthermore, loss of CD5 surface expression correlated with the absence of specific mRNA. Since these hybrids preferentially segregate human chromosomes, these results indicate the existence of a non-syntenic trans-active locus, or loci, positively controlling the expression of the human CD5 gene. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 62, "end": 72}, "arguments": [{"role": "Theme", "text": "CD5", "start": 86, "end": 89}]}, {"trigger": {"text": "expression", "start": 522, "end": 532}, "arguments": [{"role": "Theme", "text": "CD5", "start": 510, "end": 513}]}, {"trigger": {"text": "expression", "start": 635, "end": 645}, "arguments": [{"role": "Theme", "text": "CD5", "start": 631, "end": 634}]}, {"trigger": {"text": "expression", "start": 815, "end": 825}, "arguments": [{"role": "Theme", "text": "CD5", "start": 803, "end": 806}]}, {"trigger": {"text": "expression", "start": 1047, "end": 1057}, "arguments": [{"role": "Theme", "text": "CD5", "start": 1071, "end": 1074}]}], "negative regulation": [{"trigger": {"text": "lost", "start": 505, "end": 509}, "arguments": [{"role": "Theme", "text": "expression", "start": 522, "end": 532}]}, {"trigger": {"text": "loss", "start": 795, "end": 799}, "arguments": [{"role": "Theme", "text": "expression", "start": 815, "end": 825}]}], "positive regulation": [{"trigger": {"text": "due", "start": 650, "end": 653}, "arguments": [{"role": "Theme", "text": "expression", "start": 635, "end": 645}]}, {"trigger": {"text": "positively controlling", "start": 1020, "end": 1042}, "arguments": [{"role": "Theme", "text": "expression", "start": 1047, "end": 1057}]}], "regulation": [{"trigger": {"text": "regulating", "start": 47, "end": 57}, "arguments": [{"role": "Theme", "text": "expression", "start": 62, "end": 72}]}], "transcription": [{"trigger": {"text": "absence", "start": 846, "end": 853}, "arguments": [{"role": "Theme", "text": "CD5", "start": 803, "end": 806}]}]}}, "schema": []}
{"input": "Alpha-tocopherol inhibits agonist-induced monocytic cell adhesion to cultured human endothelial cells. \nAntioxidants have been proposed to be anti-atherosclerotic agents; however, the mechanisms underlying their beneficial effects are poorly understood. We have examined the effect of alpha-tocopherol (alpha-tcp) on one cellular event in atherosclerotic plaque development, monocyte adhesion to stimulated endothelial cells (ECs). Human umbilical vein ECs were pretreated with alpha-tcp before stimulation with known agonists of monocyte adhesion: IL-1 (10 ng/ml), LPS (10 ng/ml), thrombin (30 U/ml), or PMA (10 nM). Agonist-induced monocytic cell adhesion, but not basal adhesion, was inhibited in a time- and concentration-dependent manner by alpha-tcp. The IC50 of alpha-tcp on an IL-1-induced response was 45 microM. The inhibition correlated with a decrease in steady state levels of E-selectin mRNA and cell surface expression of E-selectin which is consistent with the ability of a monoclonal antibody to E-selectin to inhibit monocytic cell adhesion in this system. Probucol (50 microM) and N-acetylcysteine (20 mM) also inhibited agonist-induced monocytic cell adhesion; whereas, several other antioxidants had no significant effect. Protein kinase C (PKC) does not appear to play a role in the alpha-tcp effect since no suppression of phosphorylation of PKC substrates was observed. Activation of the transcription factor NF-kappa B is reported to be necessary but not sufficient for E-selectin expression in EC. Electrophoretic mobility shift assays failed to show an alpha-tcp-induced decrease in activation of this transcription factor after cytokine stimulation. It has been hypothesized that alpha-tcp acts as an anti-atherosclerotic molecule by inhibiting generation of oxidized LDL--a putative triggering molecule in the atherosclerotic process. Our results point to a novel alternative mechanism of action of alpha-tcp. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 923, "end": 933}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 937, "end": 947}]}, {"trigger": {"text": "expression", "start": 1506, "end": 1516}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1495, "end": 1505}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 855, "end": 863}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 890, "end": 900}]}, {"trigger": {"text": "decrease", "start": 855, "end": 863}, "arguments": [{"role": "Theme", "text": "expression", "start": 923, "end": 933}]}], "positive regulation": [{"trigger": {"text": "necessary", "start": 1462, "end": 1471}, "arguments": [{"role": "Theme", "text": "expression", "start": 1506, "end": 1516}]}]}}, "schema": []}
{"input": "Upregulation of bcl-2 by the Epstein-Barr virus latent membrane protein LMP1: a B-cell-specific response that is delayed relative to NF-kappa B activation and to induction of cell surface markers. \nAn ability of the Epstein-Barr virus latent membrane protein LMP1 to enhance the survival of infected B cells through upregulation of the bcl-2 oncogene was first suggested by experiments involving gene transfection and the selection of stable LMP1+ clones (S.Henderson, M. Rowe, C.Gregory, F.Wang, E.Kieff, and A.Rickinson, Cell 65:1107-1115, 1991). However, it was not possible to ascertain whether Bcl-2 upregulation was a specific consequence of LMP1 expression or an artifact of the selection procedure whereby rare Bcl-2+ cells already present in the starting population might best be able to tolerate the potentially toxic effects of LMP1. We therefore reexamined this issue by using two different experimental approaches that allowed LMP1- induced effects to be monitored immediately following expression of the viral protein and in the absence of selective pressures; activation of the NF-kappa B transcription factor and upregulation of the cell adhesion molecule ICAM-1 were used as early indices of LMP1 function. In the first approach, stable clones of two B-cell lines carrying an LMP1 gene under the control of an inducible metallothionein promoter were induced to express LMP1 in all cells. Activation of NK-kappa B and upregulation of ICAM-1 occurred within 24 h and were followed at 48 to 72 h by upregulation of Bcl-2. In the second approach, we tested the generality of this phenomenon by transiently expressing LMP1 from a strong constitutively active promoter in a range of different cell types. All six B-cell lines tested showed NF-kappa B activation in response to LMP1 expression, and this was followed in five of six lines by expression of ICAM-1 and Bcl-2. In the same experiments, all three non-B-cell lines showed NF-kappa B activation and ICAM-1 upregulation but never any effect upon Bcl-2. We therefore conclude that Bcl-2 upregulation is part of the panoply of cellular changes induced by LMP1 but that the effect is cell type specific. Our data also suggest that whilst NF-kappa B may be an essential component of LMP1 signal transduction, other cell-specific factors may be required to effect some functions of the viral protein. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 653, "end": 663}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 648, "end": 652}]}, {"trigger": {"text": "expression", "start": 1000, "end": 1010}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 940, "end": 944}]}, {"trigger": {"text": "express", "start": 1378, "end": 1385}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1386, "end": 1390}]}, {"trigger": {"text": "expressing", "start": 1619, "end": 1629}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1630, "end": 1634}]}, {"trigger": {"text": "expression", "start": 1793, "end": 1803}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1788, "end": 1792}]}, {"trigger": {"text": "expression", "start": 1851, "end": 1861}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1865, "end": 1871}]}, {"trigger": {"text": "expression", "start": 1851, "end": 1861}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1876, "end": 1881}]}], "positive regulation": [{"trigger": {"text": "Upregulation", "start": 0, "end": 12}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 16, "end": 21}, {"role": "Cause", "text": "LMP1", "start": 72, "end": 76}]}, {"trigger": {"text": "upregulation", "start": 316, "end": 328}, "arguments": [{"role": "Cause", "text": "LMP1", "start": 259, "end": 263}, {"role": "Theme", "text": "bcl-2", "start": 336, "end": 341}]}, {"trigger": {"text": "upregulation", "start": 605, "end": 617}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 599, "end": 604}, {"role": "Cause", "text": "expression", "start": 653, "end": 663}]}, {"trigger": {"text": "induced", "start": 946, "end": 953}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 839, "end": 843}, {"role": "Cause", "text": "LMP1", "start": 940, "end": 944}]}, {"trigger": {"text": "upregulation", "start": 1129, "end": 1141}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1172, "end": 1178}]}, {"trigger": {"text": "induced", "start": 1367, "end": 1374}, "arguments": [{"role": "Theme", "text": "express", "start": 1378, "end": 1385}]}, {"trigger": {"text": "upregulation", "start": 1434, "end": 1446}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1450, "end": 1456}]}, {"trigger": {"text": "upregulation", "start": 1513, "end": 1525}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1529, "end": 1534}]}, {"trigger": {"text": "upregulation", "start": 1975, "end": 1987}, "arguments": [{"role": "Cause", "text": "expression", "start": 1793, "end": 1803}, {"role": "Theme", "text": "ICAM-1", "start": 1968, "end": 1974}]}, {"trigger": {"text": "effect", "start": 2002, "end": 2008}, "arguments": [{"role": "Cause", "text": "expression", "start": 1793, "end": 1803}, {"role": "Theme", "text": "Bcl-2", "start": 2014, "end": 2019}]}, {"trigger": {"text": "upregulation", "start": 2054, "end": 2066}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 2048, "end": 2053}]}]}}, "schema": []}
{"input": "CD14-mediated translocation of nuclear factor-kappa B induced by lipopolysaccharide does not require tyrosine kinase activity. \nDuring the course of serious bacterial infections, lipopolysaccharide (LPS) is believed to interact with macrophage receptors, resulting in the generation of inflammatory mediators and systemic symptoms including hemodynamic instability and shock. CD14, a glycosylphosphatidylinositol-linked antigen, functions as an LPS signaling receptor. A critical issue concerns the mechanism by which CD14, which has no transmembrane domain, transduces its signal following LPS binding. Recently, investigators have hypothesized that CD14-mediated signaling is effected through a receptor-associated tyrosine kinase (TK), suggesting a multicomponent receptor model of LPS signaling. Wild-type Chinese hamster ovary (CHO)-K1 cells can be activated by endotoxin to release arachidonate following transfection with human CD14 (CHO/CD14). Nuclear translocation of cytosolic NF-kappa B is correlated with a number of LPS-inducible responses. We sought to determine if this pathway were present in CHO/CD14 cells and to elucidate the relationship of NF-kappa B activation to the CD14 receptor system. LPS-stimulated translocation of NF-kappa B in CHO/CD14 cells resembled the same response in the murine macrophage-like cell line RAW 264.7. Protein synthesis inhibitors and corticosteroids, which suppress arachidonate release and the synthesis of proinflammatory cytokines, had no effect on translocation of NF-kappa B in CHO/CD14 or RAW 264.7 cells, demonstrating that NF-kappa B translocation is an early event. Although TK activity was consistently observed by immunoblotting extracts from activated RAW 264.7 cells, LPS-induced phosphotyrosine residues were not observed from similarly treated CHO/CD14 cells. Furthermore, the TK inhibitors herbimycin A and genistein failed to inhibit translocation of NF-kappa B in CHO/CD14 or RAW 264.7 cells, although both of these agents inhibited LPS-induced TK activity in RAW 264.7 cells. These results imply that TK activity is not obligatory for CD14-mediated signal transduction to occur in response to LPS. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 595, "end": 602}, "arguments": [{"role": "Theme", "text": "CD14", "start": 518, "end": 522}]}], "gene expression": [{"trigger": {"text": "transfection", "start": 911, "end": 923}, "arguments": [{"role": "Theme", "text": "CD14", "start": 935, "end": 939}]}], "positive regulation": [{"trigger": {"text": "transfection", "start": 911, "end": 923}, "arguments": [{"role": "Theme", "text": "transfection", "start": 911, "end": 923}]}], "regulation": [{"trigger": {"text": "receptor", "start": 459, "end": 467}, "arguments": [{"role": "Theme", "text": "CD14", "start": 376, "end": 380}]}]}}, "schema": []}
{"input": "Regulation of CD14 expression during monocytic differentiation induced with 1 alpha,25-dihydroxyvitamin D3. \nCD14, a monocyte/macrophage receptor for the complex of LPS and LPS binding protein, is a differentiation marker for the monocyte/macrophage lineage. We have analyzed the regulation of CD14 expression during 1 alpha,25-dihydroxyvitamin D3 (VitD3)-induced monocytic differentiation. Using FACS, Northern blotting, and nuclear run-on analyses, we demonstrate that the up-regulation of CD14 expression during monocytic cell maturation is regulated mainly at the level of gene transcription, and that new protein synthesis is required for CD14 induction. We have recently cloned the CD14 5' upstream sequence and demonstrated its tissue-specific promoter activity. Using stable transfection of the monocytoid U937 cell line with a series of deletion mutants of the CD14 5' upstream sequence coupled to a reporter gene construct, we show that bp -128 to -70 is the critical region for the induction of CD14 expression. This region contains two binding sites for the Sp1 transcription factor. A 3-bp mutation at the distal Sp1-binding site not only eliminates Sp1 interaction, but also abolishes most of the VitD3 induction of CD14 expression. Electrophoretic mobility shift analysis does not detect a direct interaction of the CD14 distal Sp1-binding site with the vitamin D3 receptor and its partner, the retinoid X receptor. These data demonstrate that VitD3 induces CD14 indirectly through some intermediary factor, and suggest a critical role for Sp1 in this process. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1048, "end": 1055}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1070, "end": 1073}]}, {"trigger": {"text": "interaction", "start": 1167, "end": 1178}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1163, "end": 1166}]}, {"trigger": {"text": "interaction", "start": 1312, "end": 1323}, "arguments": [{"role": "Theme", "text": "vitamin D3 receptor", "start": 1369, "end": 1388}]}], "gene expression": [{"trigger": {"text": "expression", "start": 19, "end": 29}, "arguments": [{"role": "Theme", "text": "CD14", "start": 14, "end": 18}]}, {"trigger": {"text": "expression", "start": 299, "end": 309}, "arguments": [{"role": "Theme", "text": "CD14", "start": 294, "end": 298}]}, {"trigger": {"text": "expression", "start": 497, "end": 507}, "arguments": [{"role": "Theme", "text": "CD14", "start": 492, "end": 496}]}, {"trigger": {"text": "expression", "start": 1011, "end": 1021}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1006, "end": 1010}]}, {"trigger": {"text": "expression", "start": 1235, "end": 1245}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1230, "end": 1234}]}], "negative regulation": [{"trigger": {"text": "eliminates", "start": 1152, "end": 1162}, "arguments": [{"role": "Theme", "text": "interaction", "start": 1167, "end": 1178}]}, {"trigger": {"text": "abolishes", "start": 1189, "end": 1198}, "arguments": [{"role": "Theme", "text": "induction", "start": 1217, "end": 1226}]}], "positive regulation": [{"trigger": {"text": "up-regulation", "start": 475, "end": 488}, "arguments": [{"role": "Theme", "text": "expression", "start": 497, "end": 507}]}, {"trigger": {"text": "level", "start": 568, "end": 573}, "arguments": [{"role": "Theme", "text": "transcription", "start": 582, "end": 595}]}, {"trigger": {"text": "required", "start": 631, "end": 639}, "arguments": [{"role": "Theme", "text": "induction", "start": 649, "end": 658}]}, {"trigger": {"text": "induction", "start": 649, "end": 658}, "arguments": [{"role": "Theme", "text": "CD14", "start": 644, "end": 648}]}, {"trigger": {"text": "induction", "start": 993, "end": 1002}, "arguments": [{"role": "Theme", "text": "expression", "start": 1011, "end": 1021}]}, {"trigger": {"text": "induction", "start": 1217, "end": 1226}, "arguments": [{"role": "Theme", "text": "expression", "start": 1235, "end": 1245}]}, {"trigger": {"text": "through", "start": 1489, "end": 1496}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1473, "end": 1477}]}, {"trigger": {"text": "critical role", "start": 1537, "end": 1550}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1555, "end": 1558}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 19, "end": 29}]}, {"trigger": {"text": "regulation", "start": 280, "end": 290}, "arguments": [{"role": "Theme", "text": "expression", "start": 299, "end": 309}]}, {"trigger": {"text": "regulated", "start": 544, "end": 553}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 475, "end": 488}, {"role": "Cause", "text": "level", "start": 568, "end": 573}]}], "transcription": [{"trigger": {"text": "transcription", "start": 582, "end": 595}, "arguments": [{"role": "Theme", "text": "CD14", "start": 492, "end": 496}]}]}}, "schema": []}
{"input": "Calcium signalling in T cells stimulated by a cyclophilin B-binding protein. \nThe immunosuppressant drug cyclosporin A blocks a calcium-dependent signal from the T-cell receptor (TCR) that normally leads to T-cell activation. When bound to cyclophilin, cyclosporin A binds and inactivates the key signalling intermediate calcineurin. To identify potential cellular homologues of cyclosporin A that might regulate calcium signalling, we have cloned human genes encoding cyclophilin B-binding-proteins using the yeast two-hybrid system. One gene product, when overexpressed in Jurkat T cells, specifically induced transcription from the interleukin-2 enhancer, by activating the T-cell-specific transcription factors NF-AT and NF-IL2A. This protein, termed calcium-signal modulating cyclophilin ligand (CAML), acts downstream of the TCR and upstream of calcineurin by causing an influx of calcium. CAML appears to be a new participant in the calcium-signal transduction pathway, implicating cyclophilin B in calcium signalling, even in the absence of cyclosporin. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "induced", "start": 604, "end": 611}, "arguments": [{"role": "Theme", "text": "transcription", "start": 612, "end": 625}]}], "transcription": [{"trigger": {"text": "transcription", "start": 612, "end": 625}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 635, "end": 648}]}]}}, "schema": []}
{"input": "Antioxidants inhibit monocyte adhesion by suppressing nuclear factor-kappa B mobilization and induction of vascular cell adhesion molecule-1 in endothelial cells stimulated to generate radicals. \nCell adhesion to endothelial cells stimulated by tumor necrosis factor-alpha (TNF) is due to induction of surface receptors, such as vascular cell adhesion molecule-1 (VCAM-1). The antioxidant pyrrolidine dithiocarbamate (PDTC) specifically inhibits activation of nuclear factor-kappa B (NF-kappa B). Since kappa B motifs are present in VCAM-1 and intercellular adhesion molecule-1 (ICAM-1) promoters, we used PDTC to study the regulatory mechanisms of VCAM-1 and ICAM-1 induction and subsequent monocyte adhesion in TNF-treated human umbilical vein endothelial cells (HUVECs). PDTC or N-acetylcysteine dose dependently reduced TNF-induced VCAM-1 but not ICAM-1 surface protein (also in human umbilical arterial endothelial cells) and mRNA expression (by 70% at 100 mumol/L PDTC) in HUVECs as assessed by flow cytometry and polymerase chain reaction. Gel-shift analysis in HUVECs demonstrated that PDTC prevented NF-kappa B mobilization by TNF, suggesting that only VCAM-1 induction was controlled by NF-kappa B. Since HUVECs released superoxide anions in response to TNF, and H2O2 induces VCAM-1, PDTC may act as a radical scavenger. Although ICAM-1 induction was unaffected, inhibitors of NADPH oxidase (apocynin) or cytochrome P-450 (SKF525a) suppressed VCAM-1 induction by TNF, revealing that several radical-generating systems are involved in its regulation. PDTC, apocynin, or SKF525a decreased adhesion of monocytic U937 cells to TNF-treated HUVECs (by 75% at 100 mumol/L PDTC). Inhibition by anti-VCAM-1 monoclonal antibody 1G11 indicated that U937 adhesion was VCAM-1 dependent and suppression by antioxidants was due to reduced VCAM-1 induction. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 936, "end": 946}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 836, "end": 842}]}, {"trigger": {"text": "expression", "start": 936, "end": 946}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 851, "end": 857}]}], "negative regulation": [{"trigger": {"text": "suppressing", "start": 42, "end": 53}, "arguments": [{"role": "Theme", "text": "induction", "start": 94, "end": 103}]}, {"trigger": {"text": "reduced", "start": 816, "end": 823}, "arguments": [{"role": "Theme", "text": "induced", "start": 828, "end": 835}]}, {"trigger": {"text": "unaffected", "start": 1361, "end": 1371}, "arguments": [{"role": "Theme", "text": "induction", "start": 1347, "end": 1356}]}, {"trigger": {"text": "suppressed", "start": 1442, "end": 1452}, "arguments": [{"role": "Theme", "text": "induction", "start": 1460, "end": 1469}]}, {"trigger": {"text": "reduced", "start": 1826, "end": 1833}, "arguments": [{"role": "Theme", "text": "induction", "start": 1841, "end": 1850}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 94, "end": 103}, "arguments": [{"role": "Theme", "text": "vascular cell adhesion molecule-1", "start": 107, "end": 140}]}, {"trigger": {"text": "induction", "start": 289, "end": 298}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 364, "end": 370}]}, {"trigger": {"text": "induction", "start": 667, "end": 676}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 649, "end": 655}, {"role": "Cause", "text": "TNF", "start": 713, "end": 716}]}, {"trigger": {"text": "induction", "start": 667, "end": 676}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 660, "end": 666}, {"role": "Cause", "text": "TNF", "start": 713, "end": 716}]}, {"trigger": {"text": "induced", "start": 828, "end": 835}, "arguments": [{"role": "Cause", "text": "TNF", "start": 824, "end": 827}, {"role": "Theme", "text": "expression", "start": 936, "end": 946}]}, {"trigger": {"text": "induction", "start": 1169, "end": 1178}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1162, "end": 1168}]}, {"trigger": {"text": "induces", "start": 1278, "end": 1285}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1286, "end": 1292}]}, {"trigger": {"text": "induction", "start": 1347, "end": 1356}, "arguments": [{"role": "Cause", "text": "TNF", "start": 824, "end": 827}, {"role": "Theme", "text": "ICAM-1", "start": 1340, "end": 1346}]}, {"trigger": {"text": "induction", "start": 1460, "end": 1469}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1453, "end": 1459}, {"role": "Cause", "text": "TNF", "start": 1473, "end": 1476}]}, {"trigger": {"text": "induction", "start": 1841, "end": 1850}, "arguments": [{"role": "Cause", "text": "TNF", "start": 824, "end": 827}, {"role": "Theme", "text": "VCAM-1", "start": 1834, "end": 1840}]}], "regulation": [{"trigger": {"text": "regulatory", "start": 624, "end": 634}, "arguments": [{"role": "Theme", "text": "induction", "start": 667, "end": 676}]}, {"trigger": {"text": "controlled", "start": 1183, "end": 1193}, "arguments": [{"role": "Theme", "text": "induction", "start": 1169, "end": 1178}]}, {"trigger": {"text": "regulation", "start": 1548, "end": 1558}, "arguments": [{"role": "Theme", "text": "induction", "start": 1460, "end": 1469}]}], "transcription": [{"trigger": {"text": "expression", "start": 936, "end": 946}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 836, "end": 842}]}, {"trigger": {"text": "expression", "start": 936, "end": 946}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 851, "end": 857}]}]}}, "schema": []}
{"input": "Inducible binding to the c-fos serum response element during T cell activation is regulated by a phosphotyrosine-containing protein. \nThe proto-oncogene c-fos is an immediate-early gene, and one of the first genes transcribed after stimulation of most cells with a variety of ligands. Fos expression may be a pivotal event in converting ligand-receptor interactions at the membrane into functional modulation of cell phenotype. The serum response element (SRE) in the c-fos regulatory region participates in induction of transcription by various growth factors and by phorbol esters and subsequent squelching of transcription. We show that an inducible protein complex (Band A) binds to SRE DNA within 10 min after mitogenic stimulation of human PBL-T, and becomes nondetectable by 60 min. Band A contains the serum response factor plus additional factor(s). A protein that is phosphorylated on a tyrosine residue in resting PBL-T suppresses binding of a component of Band A to the SRE motif. Upon stimulation of the cells, this protein no longer prevents binding of DNA by Band A, and suppression of binding is restored within 30 min. The phosphorylated tyrosine residue itself is important for the protein-protein interaction. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 289, "end": 299}, "arguments": [{"role": "Theme", "text": "Fos", "start": 285, "end": 288}]}], "positive regulation": [{"trigger": {"text": "after", "start": 226, "end": 231}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 214, "end": 225}]}], "transcription": [{"trigger": {"text": "transcribed", "start": 214, "end": 225}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 153, "end": 158}]}]}}, "schema": []}
{"input": "Steel factor affects SCL expression during normal erythroid differentiation. \nSteel factor is one of the growth factors that controls the proliferation and differentiation of hematopoietic cells and SCL, also known as Tcl-5 or Tal-1, is a transcription factor involved in erythropoiesis. In this report, we studied the role of SCL in the proliferation of human peripheral blood burst-forming unit-erythroid (BFU-E) and the effects of Steel factor on SCL expression in proliferating erythroid cells. BFU-E-derived colonies increase progressively in size, as determined by cell number, from day 7 to day 14 of culture, with the greatest increase in colony size (10-fold expansion) occurring between day 7 and day 10. SCL protein levels in BFU-E-derived cells were highest in day 7 cells and decreased progressively from day 7 to day 14 of culture, suggesting an association of SCL with erythroid proliferation. In contrast, SCL mRNA levels did not decrease significantly between day 7 and day 14 cells, suggesting that posttranscriptional mechanisms are largely responsible for the decrease in SCL protein observed. The role of SCL in Steel factor-induced erythroid proliferation was then examined. In BFU-E-derived colonies cultured with Steel factor, colony size was significantly increased compared to control. In day 7 and day 10 erythroid precursors cultured with Steel factor, SCL protein was increased significantly compared to control. The increase in SCL protein levels in early erythroid precursors stimulated with Steel factor suggests one mechanism through which Steel factor may enhance normal erythroid proliferation. SCL mRNA levels assessed by Northern blot in day 7 cells did not increase significantly in response to Steel factor stimulation, suggesting that posttranscriptional mechanisms may also be important in the increase in SCL protein observed in response to Steel. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 25, "end": 35}, "arguments": [{"role": "Theme", "text": "SCL", "start": 21, "end": 24}]}, {"trigger": {"text": "expression", "start": 454, "end": 464}, "arguments": [{"role": "Theme", "text": "SCL", "start": 450, "end": 453}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 789, "end": 798}, "arguments": [{"role": "Theme", "text": "SCL", "start": 715, "end": 718}]}, {"trigger": {"text": "decrease", "start": 946, "end": 954}, "arguments": [{"role": "Theme", "text": "SCL", "start": 922, "end": 925}]}, {"trigger": {"text": "decrease", "start": 1080, "end": 1088}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1092, "end": 1095}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 1397, "end": 1406}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1381, "end": 1384}]}, {"trigger": {"text": "increase", "start": 1446, "end": 1454}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1458, "end": 1461}]}, {"trigger": {"text": "increase", "start": 1695, "end": 1703}, "arguments": [{"role": "Theme", "text": "levels", "start": 1639, "end": 1645}, {"role": "Cause", "text": "Steel factor", "start": 1733, "end": 1745}]}, {"trigger": {"text": "increase", "start": 1835, "end": 1843}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1847, "end": 1850}, {"role": "Cause", "text": "Steel", "start": 1883, "end": 1888}]}], "regulation": [{"trigger": {"text": "affects", "start": 13, "end": 20}, "arguments": [{"role": "Cause", "text": "Steel factor", "start": 0, "end": 12}, {"role": "Theme", "text": "expression", "start": 25, "end": 35}]}, {"trigger": {"text": "effects", "start": 423, "end": 430}, "arguments": [{"role": "Cause", "text": "Steel factor", "start": 434, "end": 446}, {"role": "Theme", "text": "expression", "start": 454, "end": 464}]}, {"trigger": {"text": "responsible", "start": 1060, "end": 1071}, "arguments": [{"role": "Theme", "text": "decrease", "start": 1080, "end": 1088}]}, {"trigger": {"text": "important", "start": 1818, "end": 1827}, "arguments": [{"role": "Theme", "text": "increase", "start": 1835, "end": 1843}]}], "transcription": [{"trigger": {"text": "levels", "start": 1639, "end": 1645}, "arguments": [{"role": "Theme", "text": "SCL", "start": 1630, "end": 1633}]}]}}, "schema": []}
{"input": "Cross-linking CD40 on B cells rapidly activates nuclear factor-kappa B. \nThe B cell-associated surface molecule CD40 functions to regulate B cell responses. Cross-linking CD40 on B cells can lead to homotypic cell adhesion, IL-6 production, and, in combination with cytokines, to Ig isotype switching. Tyrosine kinase activity is increased shortly after engagement of this receptor. Little is known about how the very early events induced by CD40 cross-linking link to cellular responses. In this study, we demonstrate that nuclear factor (NF)-kappa B and NF-kappa B-like transcription factors are activated after cross-linking CD40 on resting human tonsillar B cells and on B cell lines. The activation is rapid and is mediated through a tyrosine kinase-dependent pathway. The complexes detected in electrophoretic mobility shift assays contain p50, p65 (RelA), c-Rel, and most likely other components. By using transient transfection assays, we found that cross-linking CD40 supports NF-kappa B-dependent gene expression. Our results define the NF-kappa B system as an intermediate event in CD40 signaling and suggest that the CD40 pathway can influence the expression of B cell-associated genes with NF-kappa B consensus sites. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Cross-linking", "start": 0, "end": 13}, "arguments": [{"role": "Theme", "text": "CD40", "start": 14, "end": 18}]}, {"trigger": {"text": "Cross-linking", "start": 157, "end": 170}, "arguments": [{"role": "Theme", "text": "CD40", "start": 171, "end": 175}]}, {"trigger": {"text": "engagement", "start": 354, "end": 364}, "arguments": [{"role": "Theme", "text": "CD40", "start": 171, "end": 175}]}, {"trigger": {"text": "cross-linking", "start": 447, "end": 460}, "arguments": [{"role": "Theme", "text": "CD40", "start": 442, "end": 446}]}, {"trigger": {"text": "cross-linking", "start": 614, "end": 627}, "arguments": [{"role": "Theme", "text": "CD40", "start": 628, "end": 632}]}, {"trigger": {"text": "cross-linking", "start": 958, "end": 971}, "arguments": [{"role": "Theme", "text": "CD40", "start": 972, "end": 976}]}], "gene expression": [{"trigger": {"text": "production", "start": 229, "end": 239}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 224, "end": 228}]}], "positive regulation": [{"trigger": {"text": "lead", "start": 191, "end": 195}, "arguments": [{"role": "Cause", "text": "Cross-linking", "start": 157, "end": 170}, {"role": "Theme", "text": "production", "start": 229, "end": 239}]}]}}, "schema": []}
{"input": "Separation of oxidant-initiated and redox-regulated steps in the NF-kappa B signal transduction pathway. \nStudies presented here show that overall NF-kappa B signal transduction begins with a parallel series of stimuli-specific pathways through which cytokines (tumor necrosis factor alpha), oxidants (hydrogen peroxide and mitomycin C), and phorbol ester (phorbol 12-myristate 13-acetate) individually initiate signaling. These initial pathways culminate in a common pathway through which all of the stimulating agents ultimately signal NF-kappa B activation. We distinguish the stimuli-specific pathways by showing that the oxidative stimuli trigger NF-kappa B activation in only one of two human T-cell lines (Wurzburg but not Jurkat), whereas tumor necrosis factor alpha and phorbol 12-myristate 13-acetate readily stimulate in both lines. We propose the common pathway as the simplest way of accounting for the common requirements and properties of the signaling pathway. We include a redox-regulatory mechanism(s) in this common pathway to account for the previously demonstrated redox regulation of NF-kappa B activation in Jurkat cells (in which oxidants don't activate NF-kappa B); we put tyrosine phosphorylation in the common pathway by showing that kinase activity (inhibitable by herbimycin A and tyrphostin 47) is required for NF-kappa B activation by all stimuli tested in both cell lines. Since internal sites of oxidant production have been shown to play a key role in the cytokine-stimulated activation of NF-kappa B, and since tyrosine kinase and phosphatase activities are known to be altered by oxidants, these findings suggest that intracellular redox status controls NF-kappa B activation by regulating tyrosine phosphorylation event(s) within the common step of the NF-kappa B signal transduction pathway. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Transcription-independent turnover of I kappa B alpha during monocyte adherence: implications for a translational component regulating I kappa B alpha/MAD-3 mRNA levels. \nWe identified I kappa B alpha/MAD-3 as an immediate-early gene in human monocytes that is expressed in response to a variety of signals, including adhesion, lipopolysaccharide, and phorbol myristate acetate. Within 5 min of monocyte adhesion, the level of the I kappa B alpha protein is markedly diminished but is rapidly replaced in a cycloheximide-sensitive manner within 20 min. Accompanying the rapid turnover of the I kappa B alpha protein is simultaneous translocation of NF-kappa B-related transcription factors to nuclei of adhered monocytes. The demonstration that NF-kappa B can regulate I kappa B alpha/MAD-3 gene transcription in other cell types suggested that the rapid increase in steady-state I kappa B alpha/MAD-3 mRNA levels we observed within 30 min of monocyte adherence would result from NF-kappa B-dependent transcriptional stimulation of the I kappa B alpha/MAD-3 gene. Nuclear run-on analyses indicated that, instead, while several immediate-early cytokine genes, such as the interleukin 1 beta (IL-1 beta) gene, were transcriptionally activated during monocyte adhesion, the rate of I kappa B alpha/MAD-3 gene transcription remained constant. The adherence-dependent increase in I kappa B alpha/MAD-3 mRNA levels was also not a consequence of mRNA stabilization events. Interestingly, while increases in both IL-1 beta and I kappa B alpha/MAD-3 mRNA levels were detected in nuclei of adherent monocytes, cytoplasmic levels of IL-1 beta mRNA increased during adherence whereas those of I kappa B alpha/MAD-3 mRNA did not. Taken together, our data suggest that two interactive mechanisms regulate monocytic I kappa B alpha/MAD-3 mRNA levels. We propose that adherent monocytes regulate nuclear processing (or decay) of I kappa B alpha/MAD-3 mRNA, thereby increasing mRNA levels without stimulating I kappa B alpha/MAD-3 gene transcription. Moreover, since inhibition of protein synthesis leads to accumulation of I kappa B alpha/MAD-3 mRNA without stimulating I kappa B alpha/MAD-3 gene transcription, we suggest that low cytoplasmic levels of I kappa B alpha/MAD-3 mRNA are maintained by a translation-dependent degradation mechanism. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 261, "end": 270}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 185, "end": 200}]}], "negative regulation": [{"trigger": {"text": "diminished", "start": 467, "end": 477}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 431, "end": 446}]}, {"trigger": {"text": "replaced", "start": 493, "end": 501}, "arguments": [{"role": "Theme", "text": "diminished", "start": 467, "end": 477}]}, {"trigger": {"text": "maintained", "start": 2269, "end": 2279}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 2238, "end": 2253}]}], "positive regulation": [{"trigger": {"text": "in response to", "start": 271, "end": 285}, "arguments": [{"role": "Theme", "text": "expressed", "start": 261, "end": 270}]}, {"trigger": {"text": "increase", "start": 855, "end": 863}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 880, "end": 895}]}, {"trigger": {"text": "transcriptional stimulation", "start": 1001, "end": 1028}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1036, "end": 1051}]}, {"trigger": {"text": "transcriptionally activated", "start": 1213, "end": 1240}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1191, "end": 1200}]}, {"trigger": {"text": "remained constant", "start": 1320, "end": 1337}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1306, "end": 1319}]}, {"trigger": {"text": "increase", "start": 1363, "end": 1371}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1375, "end": 1390}]}, {"trigger": {"text": "consequence", "start": 1424, "end": 1435}, "arguments": [{"role": "Theme", "text": "increase", "start": 1363, "end": 1371}, {"role": "Cause", "text": "stabilization", "start": 1444, "end": 1457}]}, {"trigger": {"text": "stabilization", "start": 1444, "end": 1457}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1375, "end": 1390}]}, {"trigger": {"text": "increases", "start": 1487, "end": 1496}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1505, "end": 1514}]}, {"trigger": {"text": "increases", "start": 1487, "end": 1496}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1519, "end": 1534}]}, {"trigger": {"text": "increased", "start": 1637, "end": 1646}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1622, "end": 1631}]}, {"trigger": {"text": "increased", "start": 1637, "end": 1646}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1681, "end": 1696}]}, {"trigger": {"text": "increasing", "start": 1949, "end": 1959}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1913, "end": 1928}]}, {"trigger": {"text": "without stimulating", "start": 1972, "end": 1991}, "arguments": [{"role": "Theme", "text": "transcription", "start": 2019, "end": 2032}]}, {"trigger": {"text": "leads", "start": 2082, "end": 2087}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 2091, "end": 2103}]}, {"trigger": {"text": "accumulation", "start": 2091, "end": 2103}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 2107, "end": 2122}]}, {"trigger": {"text": "stimulating", "start": 2142, "end": 2153}, "arguments": [{"role": "Theme", "text": "transcription", "start": 2181, "end": 2194}]}], "regulation": [{"trigger": {"text": "regulating", "start": 124, "end": 134}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 135, "end": 150}]}, {"trigger": {"text": "sensitive", "start": 521, "end": 530}, "arguments": [{"role": "Theme", "text": "replaced", "start": 493, "end": 501}]}, {"trigger": {"text": "regulate", "start": 760, "end": 768}, "arguments": [{"role": "Theme", "text": "transcription", "start": 796, "end": 809}]}, {"trigger": {"text": "regulate", "start": 1782, "end": 1790}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1801, "end": 1816}]}], "transcription": [{"trigger": {"text": "transcription", "start": 796, "end": 809}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 769, "end": 784}]}, {"trigger": {"text": "transcription", "start": 1306, "end": 1319}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1279, "end": 1294}]}, {"trigger": {"text": "transcription", "start": 2019, "end": 2032}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1992, "end": 2007}]}, {"trigger": {"text": "transcription", "start": 2181, "end": 2194}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 2154, "end": 2169}]}]}}, "schema": []}
{"input": "E2F-1 and a cyclin-like DNA repair enzyme, uracil-DNA glycosylase, provide evidence for an autoregulatory mechanism for transcription. \nThe cell cycle-dependent transcription factor, E2F-1, regulates the cyclin-like species of the DNA repair enzyme uracil-DNA glycosylase (UDG) gene in human osteosarcoma (Saos-2) cells. We demonstrate, through the deletion of the human UDG promoter sequences, that expression of E2F-1 activates the UDG promoter through several E2F sites. The major putative downstream site for E2F, located in the first exon, serves as a target for E2F-1/DP1 complex binding in vitro. We also provide evidence for the functional relationship between the cyclin-like UDG gene product and E2F. High levels of UDG expression in a transient transfection assay result in the down-regulation of transcriptional activity through elements specific for E2F-mediated transcription. Overexpression of UDG in Saos 2 cells was observed to delay growth late in G1 phase and transiently arrest these cells from progressing into the S phase. This hypothetical model integrates one mechanism of DNA repair with the cell cycle control of gene transcription, likely through E2F. This implicates E2F as a multifunctional target for proteins and enzymes, possibly, responsive to DNA damage through the negative effect of UDG on E2F-mediated transcriptional activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "target", "start": 557, "end": 563}, "arguments": [{"role": "Theme", "text": "E2F-1", "start": 568, "end": 573}]}, {"trigger": {"text": "target", "start": 557, "end": 563}, "arguments": [{"role": "Theme", "text": "DP1", "start": 574, "end": 577}]}, {"trigger": {"text": "complex binding", "start": 578, "end": 593}, "arguments": [{"role": "Theme", "text": "E2F-1", "start": 568, "end": 573}, {"role": "Theme2", "text": "DP1", "start": 574, "end": 577}]}], "gene expression": [{"trigger": {"text": "expression", "start": 400, "end": 410}, "arguments": [{"role": "Theme", "text": "E2F-1", "start": 414, "end": 419}]}, {"trigger": {"text": "product", "start": 694, "end": 701}, "arguments": [{"role": "Theme", "text": "UDG", "start": 685, "end": 688}]}, {"trigger": {"text": "expression", "start": 730, "end": 740}, "arguments": [{"role": "Theme", "text": "UDG", "start": 726, "end": 729}]}, {"trigger": {"text": "Overexpression", "start": 891, "end": 905}, "arguments": [{"role": "Theme", "text": "UDG", "start": 909, "end": 912}]}], "positive regulation": [{"trigger": {"text": "activates", "start": 420, "end": 429}, "arguments": [{"role": "Cause", "text": "expression", "start": 400, "end": 410}, {"role": "Theme", "text": "UDG", "start": 434, "end": 437}, {"role": "Site", "text": "promoter", "start": 438, "end": 446}]}, {"trigger": {"text": "through", "start": 447, "end": 454}, "arguments": [{"role": "Theme", "text": "activates", "start": 420, "end": 429}]}, {"trigger": {"text": "High levels", "start": 711, "end": 722}, "arguments": [{"role": "Theme", "text": "expression", "start": 730, "end": 740}]}, {"trigger": {"text": "Overexpression", "start": 891, "end": 905}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 891, "end": 905}]}], "regulation": [{"trigger": {"text": "regulates", "start": 190, "end": 199}, "arguments": [{"role": "Cause", "text": "E2F-1", "start": 183, "end": 188}, {"role": "Theme", "text": "UDG", "start": 273, "end": 276}]}]}}, "schema": []}
{"input": "Aspirin inhibits nuclear factor-kappa B mobilization and monocyte adhesion in stimulated human endothelial cells. \nBACKGROUND: The induction of vascular cell adhesion molecule-1 (VCAM-1) and E-selectin by tumor necrosis factor-alpha (TNF) is mediated by mobilization of the transcription factor nuclear factor-kappa B (NF-kappa B). Since salicylates have been reported to inhibit NF-kappa B activation by preventing the degradation of its inhibitor I kappa B, we studied a potential inhibition of this pathway by acetylsalicylate (aspirin) in human umbilical vein endothelial cells (HUVECs). METHODS AND RESULTS: Gel-shift analyses demonstrated dose-dependent inhibition of TNF-induced NF-kappa B mobilization by aspirin at concentrations ranging from 1 to 10 mmol/L. Induction of VCAM-1 and E-selectin surface expression by TNF was dose-dependently reduced by aspirin over the same range, while induction of intercellular adhesion molecule-1 (ICAM-1) was hardly affected. Aspirin appeared to prevent VCAM-1 transcription, since it dose-dependently inhibited induction of VCAM-1 mRNA by TNF. As a functional consequence, adhesion of U937 monocytes to TNF-stimulated HUVECs was markedly reduced by aspirin due to suppression of VCAM-1 and E-selectin upregulation. These effects of aspirin were not related to the inhibition of cyclooxygenase activity, since indomethacin was ineffective. CONCLUSIONS: Our data suggest that aspirin inhibits NF-kappa B mobilization, induction of VCAM-1 and E-selectin, and subsequent monocyte adhesion in endothelial cells stimulated by TNF, thereby providing an additional mechanism for therapeutic effects of aspirin. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "expression", "start": 811, "end": 821}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 781, "end": 787}, {"role": "AtLoc", "text": "surface", "start": 803, "end": 810}]}, {"trigger": {"text": "expression", "start": 811, "end": 821}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 792, "end": 802}, {"role": "AtLoc", "text": "surface", "start": 803, "end": 810}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 850, "end": 857}, "arguments": [{"role": "Theme", "text": "Induction", "start": 768, "end": 777}]}, {"trigger": {"text": "prevent", "start": 993, "end": 1000}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1008, "end": 1021}]}, {"trigger": {"text": "inhibited", "start": 1049, "end": 1058}, "arguments": [{"role": "Theme", "text": "induction", "start": 1059, "end": 1068}]}, {"trigger": {"text": "suppression", "start": 1212, "end": 1223}, "arguments": [{"role": "Theme", "text": "upregulation", "start": 1249, "end": 1261}]}, {"trigger": {"text": "inhibits", "start": 1430, "end": 1438}, "arguments": [{"role": "Theme", "text": "induction", "start": 1464, "end": 1473}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 131, "end": 140}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 179, "end": 185}, {"role": "Cause", "text": "TNF", "start": 234, "end": 237}]}, {"trigger": {"text": "induction", "start": 131, "end": 140}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 191, "end": 201}, {"role": "Cause", "text": "TNF", "start": 234, "end": 237}]}, {"trigger": {"text": "mediated", "start": 242, "end": 250}, "arguments": [{"role": "Theme", "text": "induction", "start": 131, "end": 140}]}, {"trigger": {"text": "Induction", "start": 768, "end": 777}, "arguments": [{"role": "Theme", "text": "expression", "start": 811, "end": 821}, {"role": "Cause", "text": "TNF", "start": 825, "end": 828}]}, {"trigger": {"text": "induction", "start": 896, "end": 905}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 944, "end": 950}]}, {"trigger": {"text": "induction", "start": 1059, "end": 1068}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1072, "end": 1078}, {"role": "Cause", "text": "TNF", "start": 1087, "end": 1090}]}, {"trigger": {"text": "upregulation", "start": 1249, "end": 1261}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1227, "end": 1233}]}, {"trigger": {"text": "upregulation", "start": 1249, "end": 1261}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1238, "end": 1248}]}, {"trigger": {"text": "induction", "start": 1464, "end": 1473}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1477, "end": 1483}]}, {"trigger": {"text": "induction", "start": 1464, "end": 1473}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1488, "end": 1498}]}], "regulation": [{"trigger": {"text": "affected", "start": 963, "end": 971}, "arguments": [{"role": "Theme", "text": "induction", "start": 896, "end": 905}]}, {"trigger": {"text": "ineffective", "start": 1374, "end": 1385}, "arguments": [{"role": "Theme", "text": "suppression", "start": 1212, "end": 1223}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1008, "end": 1021}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1001, "end": 1007}]}]}}, "schema": []}
{"input": "Danazol decreases transcription of estrogen receptor gene in human monocytes. \n1. Administration of danazol for over one month reduced the levels of estrogen receptor (ER) and its mRNA to approximately 50 and 20%, respectively in monocytes. 2. Danazol did not alter the degradation rate of ER mRNA in monocytes. 3. Danazol decreased the transcription rate of ER gene to approximately 50% in monocytes in a run-on assay. 4. Danazol may release estrogen predominance via the reduction of transcription for ER gene, which leads to the reduction of ER mRNA and ER expressions in monocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressions", "start": 560, "end": 571}, "arguments": [{"role": "Theme", "text": "ER", "start": 557, "end": 559}]}], "negative regulation": [{"trigger": {"text": "decreases", "start": 8, "end": 17}, "arguments": [{"role": "Theme", "text": "transcription", "start": 18, "end": 31}]}, {"trigger": {"text": "reduced the levels", "start": 127, "end": 145}, "arguments": [{"role": "Theme", "text": "ER", "start": 168, "end": 170}]}, {"trigger": {"text": "decreased", "start": 323, "end": 332}, "arguments": [{"role": "Theme", "text": "transcription", "start": 337, "end": 350}]}, {"trigger": {"text": "reduction", "start": 473, "end": 482}, "arguments": [{"role": "Theme", "text": "transcription", "start": 486, "end": 499}]}, {"trigger": {"text": "reduction", "start": 532, "end": 541}, "arguments": [{"role": "Theme", "text": "expressions", "start": 560, "end": 571}]}], "positive regulation": [{"trigger": {"text": "leads", "start": 519, "end": 524}, "arguments": [{"role": "Cause", "text": "reduction", "start": 473, "end": 482}, {"role": "Theme", "text": "reduction", "start": 532, "end": 541}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 270, "end": 281}, "arguments": [{"role": "Theme", "text": "ER", "start": 290, "end": 292}]}], "regulation": [{"trigger": {"text": "alter", "start": 260, "end": 265}, "arguments": [{"role": "Theme", "text": "degradation", "start": 270, "end": 281}]}], "transcription": [{"trigger": {"text": "transcription", "start": 18, "end": 31}, "arguments": [{"role": "Theme", "text": "estrogen receptor", "start": 35, "end": 52}]}, {"trigger": {"text": "transcription", "start": 337, "end": 350}, "arguments": [{"role": "Theme", "text": "ER", "start": 359, "end": 361}]}, {"trigger": {"text": "transcription", "start": 486, "end": 499}, "arguments": [{"role": "Theme", "text": "ER", "start": 504, "end": 506}]}, {"trigger": {"text": "expressions", "start": 560, "end": 571}, "arguments": [{"role": "Theme", "text": "ER", "start": 545, "end": 547}]}]}}, "schema": []}
{"input": "Cross-linking of CD30 induces HIV expression in chronically infected T cells. \nCD30, a member of the tumor necrosis factor (TNF) receptor family, is expressed constitutively on the surface of the human T cell line ACH-2, which is chronically infected with human immunodeficiency virus type-1 (HIV)-1. We demonstrate that cross-linking CD30 with an anti-CD30-specific monoclonal antibody, which mimics the described biological activities of the CD30 ligand (CD30L), results in HIV expression. CD30 cross-linking does not alter proliferation of ACH-2 cells and the induction of HIV expression is not mediated by endogenous TNF alpha/beta. Furthermore, cross-linking of CD30 leads to NF-kappa B activation and enhanced HIV transcription. Thus, CD30-CD30L interactions mediate the induction of HIV expression by a kappa B-dependent pathway that is independent of TNF. This mechanism may be important in the activation of HIV expression from latently infected CD4+ T cells, especially in lymphoid organs where cell to cell contact is conducive to receptor-ligand interactions. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Cross-linking", "start": 0, "end": 13}, "arguments": [{"role": "Theme", "text": "CD30", "start": 17, "end": 21}]}, {"trigger": {"text": "cross-linking", "start": 321, "end": 334}, "arguments": [{"role": "Theme", "text": "CD30", "start": 335, "end": 339}, {"role": "Theme2", "text": "CD30L", "start": 457, "end": 462}]}, {"trigger": {"text": "cross-linking", "start": 321, "end": 334}, "arguments": [{"role": "Theme", "text": "CD30", "start": 335, "end": 339}]}, {"trigger": {"text": "cross-linking", "start": 497, "end": 510}, "arguments": [{"role": "Theme", "text": "CD30", "start": 492, "end": 496}]}, {"trigger": {"text": "cross-linking", "start": 650, "end": 663}, "arguments": [{"role": "Theme", "text": "CD30", "start": 667, "end": 671}]}, {"trigger": {"text": "interactions", "start": 752, "end": 764}, "arguments": [{"role": "Theme", "text": "CD30", "start": 741, "end": 745}, {"role": "Theme2", "text": "CD30L", "start": 746, "end": 751}]}, {"trigger": {"text": "interactions", "start": 1058, "end": 1070}, "arguments": [{"role": "Theme", "text": "CD30", "start": 741, "end": 745}, {"role": "Theme2", "text": "CD30L", "start": 746, "end": 751}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 149, "end": 158}, "arguments": [{"role": "Theme", "text": "CD30", "start": 79, "end": 83}]}]}}, "schema": []}
{"input": "Integrin-mediated tyrosine phosphorylation and cytokine message induction in monocytic cells. A possible signaling role for the Syk tyrosine kinase. \nActivation of cytoplasmic tyrosine kinases is an important aspect of signal transduction mediated by integrins. In the human monocytic cell line THP-1, either integrin-dependent cell adhesion to fibronectin or ligation of beta 1 integrins with antibodies causes a rapid and intense tyrosine phosphorylation of two sets of proteins of about 65-75 and 120-125 kDa. In addition, integrin ligation leads to nuclear translocation of the p50 and p65 subunits of the NF-kappa B transcription factor, to activation of a reporter gene driven by a promoter containing NF-kappa B sites, and to increased levels of mRNAs for immediate-early genes, including the cytokine interleukin (IL)-1 beta. The tyrosine kinase inhibitors genistein and herbimycin A block both integrin-mediated tyrosine phosphorylation and increases in IL-1 beta message levels, indicating a causal relationship between the two events. The components tyrosine phosphorylated subsequent to cell adhesion include paxillin, pp125FAK, and the SH2 domain containing tyrosine kinase Syk. In contrast, integrin ligation with antibodies induces tyrosine phosphorylation of Syk but not of FAK or paxillin. In adhering cells, pre-treatment with cytochalasin D suppresses tyrosine phosphorylation of FAK and paxillin but not of Syk, while IL-1 beta message induction is unaffected. These observations indicate that the Syk tyrosine kinase may be an important component of an integrin signaling pathway in monocytic cells, leading to activation of NF-kappa B and to increased levels of cytokine messages. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 360, "end": 368}, "arguments": [{"role": "Theme", "text": "beta 1 integrin", "start": 372, "end": 387}]}], "localization": [{"trigger": {"text": "translocation", "start": 561, "end": 574}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 553, "end": 560}, {"role": "Theme", "text": "p50", "start": 582, "end": 585}]}, {"trigger": {"text": "translocation", "start": 561, "end": 574}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 553, "end": 560}, {"role": "Theme", "text": "p65", "start": 590, "end": 593}]}], "negative regulation": [{"trigger": {"text": "block", "start": 892, "end": 897}, "arguments": [{"role": "Theme", "text": "increases", "start": 950, "end": 959}]}, {"trigger": {"text": "suppresses", "start": 1360, "end": 1370}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1380, "end": 1395}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 1070, "end": 1084}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1061, "end": 1069}, {"role": "Theme", "text": "paxillin", "start": 1121, "end": 1129}]}, {"trigger": {"text": "phosphorylated", "start": 1070, "end": 1084}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1061, "end": 1069}, {"role": "Theme", "text": "pp125FAK", "start": 1131, "end": 1139}]}, {"trigger": {"text": "phosphorylated", "start": 1070, "end": 1084}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1061, "end": 1069}, {"role": "Theme", "text": "Syk", "start": 1187, "end": 1190}]}, {"trigger": {"text": "phosphorylation", "start": 1256, "end": 1271}, "arguments": [{"role": "Theme", "text": "pp125FAK", "start": 1131, "end": 1139}, {"role": "Site", "text": "tyrosine", "start": 1247, "end": 1255}]}, {"trigger": {"text": "phosphorylation", "start": 1256, "end": 1271}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1247, "end": 1255}, {"role": "Theme", "text": "Syk", "start": 1275, "end": 1278}]}, {"trigger": {"text": "phosphorylation", "start": 1256, "end": 1271}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1247, "end": 1255}, {"role": "Theme", "text": "paxillin", "start": 1297, "end": 1305}]}, {"trigger": {"text": "phosphorylation", "start": 1380, "end": 1395}, "arguments": [{"role": "Theme", "text": "pp125FAK", "start": 1131, "end": 1139}, {"role": "Site", "text": "tyrosine", "start": 1371, "end": 1379}]}, {"trigger": {"text": "phosphorylation", "start": 1380, "end": 1395}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1371, "end": 1379}, {"role": "Theme", "text": "paxillin", "start": 1407, "end": 1415}]}, {"trigger": {"text": "phosphorylation", "start": 1380, "end": 1395}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1371, "end": 1379}, {"role": "Theme", "text": "Syk", "start": 1427, "end": 1430}]}], "positive regulation": [{"trigger": {"text": "signaling role", "start": 105, "end": 119}, "arguments": [{"role": "Theme", "text": "Syk", "start": 128, "end": 131}]}, {"trigger": {"text": "leads", "start": 544, "end": 549}, "arguments": [{"role": "Theme", "text": "translocation", "start": 561, "end": 574}]}, {"trigger": {"text": "leads", "start": 544, "end": 549}, "arguments": [{"role": "Theme", "text": "increased", "start": 733, "end": 742}]}, {"trigger": {"text": "increased", "start": 733, "end": 742}, "arguments": [{"role": "Theme", "text": "interleukin (IL)-1 beta", "start": 809, "end": 832}]}, {"trigger": {"text": "increases", "start": 950, "end": 959}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 963, "end": 972}]}, {"trigger": {"text": "subsequent to", "start": 1085, "end": 1098}, "arguments": [{"role": "Theme", "text": "phosphorylated", "start": 1070, "end": 1084}]}, {"trigger": {"text": "subsequent to", "start": 1085, "end": 1098}, "arguments": [{"role": "Theme", "text": "induces", "start": 1239, "end": 1246}]}, {"trigger": {"text": "induces", "start": 1239, "end": 1246}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1256, "end": 1271}]}, {"trigger": {"text": "induction", "start": 1456, "end": 1465}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1438, "end": 1447}]}], "regulation": [{"trigger": {"text": "unaffected", "start": 1469, "end": 1479}, "arguments": [{"role": "Theme", "text": "induction", "start": 1456, "end": 1465}]}]}}, "schema": []}
{"input": "Nitric oxide decreases cytokine-induced endothelial activation. Nitric oxide selectively reduces endothelial expression of adhesion molecules and proinflammatory cytokines. \nTo test the hypothesis that nitric oxide (NO) limits endothelial activation, we treated cytokine-stimulated human saphenous vein endothelial cells with several NO donors and assessed their effects on the inducible expression of vascular cell adhesion molecule-1 (VCAM-1). In a concentration-dependent manner, NO inhibited interleukin (IL)-1 alpha-stimulated VCAM-1 expression by 35-55% as determined by cell surface enzyme immunoassays and flow cytometry. This inhibition was paralleled by reduced monocyte adhesion to endothelial monolayers in nonstatic assays, was unaffected by cGMP analogues, and was quantitatively similar after stimulation by either IL-1 alpha, IL-1 beta, IL-4, tumor necrosis factor (TNF alpha), or bacterial lipopolysaccharide. NO also decreased the endothelial expression of other leukocyte adhesion molecules (E-selectin and to a lesser extent, intercellular adhesion molecule-1) and secretable cytokines (IL-6 and IL-8). Inhibition of endogenous NO production by L-N-monomethyl-arginine also induced the expression of VCAM-1, but did not augment cytokine-induced VCAM-1 expression. Nuclear run-on assays, transfection studies using various VCAM-1 promoter reporter gene constructs, and electrophoretic mobility shift assays indicated that NO represses VCAM-1 gene transcription, in part, by inhibiting NF-kappa B. We propose that NO's ability to limit endothelial activation and inhibit monocyte adhesion may contribute to some of its antiatherogenic and antiinflammatory properties within the vessel wall. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 388, "end": 398}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 437, "end": 443}]}, {"trigger": {"text": "expression", "start": 539, "end": 549}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 532, "end": 538}]}, {"trigger": {"text": "expression", "start": 961, "end": 971}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1011, "end": 1021}]}, {"trigger": {"text": "expression", "start": 961, "end": 971}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 1046, "end": 1079}]}, {"trigger": {"text": "expression", "start": 961, "end": 971}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1107, "end": 1111}]}, {"trigger": {"text": "expression", "start": 961, "end": 971}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1116, "end": 1120}]}, {"trigger": {"text": "expression", "start": 1206, "end": 1216}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1220, "end": 1226}]}, {"trigger": {"text": "expression", "start": 1272, "end": 1282}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1265, "end": 1271}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 486, "end": 495}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 521, "end": 531}]}, {"trigger": {"text": "inhibition", "start": 635, "end": 645}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 808, "end": 819}]}, {"trigger": {"text": "decreased", "start": 935, "end": 944}, "arguments": [{"role": "Theme", "text": "expression", "start": 961, "end": 971}]}, {"trigger": {"text": "represses", "start": 1444, "end": 1453}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1466, "end": 1479}]}], "positive regulation": [{"trigger": {"text": "inducible", "start": 378, "end": 387}, "arguments": [{"role": "Theme", "text": "expression", "start": 388, "end": 398}]}, {"trigger": {"text": "stimulated", "start": 521, "end": 531}, "arguments": [{"role": "Cause", "text": "interleukin (IL)-1 alpha", "start": 496, "end": 520}, {"role": "Theme", "text": "expression", "start": 539, "end": 549}]}, {"trigger": {"text": "stimulation", "start": 808, "end": 819}, "arguments": [{"role": "Theme", "text": "expression", "start": 539, "end": 549}, {"role": "Cause", "text": "IL-1 alpha", "start": 830, "end": 840}]}, {"trigger": {"text": "stimulation", "start": 808, "end": 819}, "arguments": [{"role": "Theme", "text": "expression", "start": 539, "end": 549}, {"role": "Cause", "text": "IL-1 beta", "start": 842, "end": 851}]}, {"trigger": {"text": "stimulation", "start": 808, "end": 819}, "arguments": [{"role": "Theme", "text": "expression", "start": 539, "end": 549}, {"role": "Cause", "text": "IL-4", "start": 853, "end": 857}]}, {"trigger": {"text": "stimulation", "start": 808, "end": 819}, "arguments": [{"role": "Theme", "text": "expression", "start": 539, "end": 549}, {"role": "Cause", "text": "TNF alpha", "start": 882, "end": 891}]}, {"trigger": {"text": "stimulation", "start": 808, "end": 819}, "arguments": [{"role": "Theme", "text": "expression", "start": 539, "end": 549}]}, {"trigger": {"text": "induced", "start": 1194, "end": 1201}, "arguments": [{"role": "Theme", "text": "expression", "start": 1206, "end": 1216}]}, {"trigger": {"text": "augment", "start": 1240, "end": 1247}, "arguments": [{"role": "Theme", "text": "induced", "start": 1257, "end": 1264}]}, {"trigger": {"text": "induced", "start": 1257, "end": 1264}, "arguments": [{"role": "Theme", "text": "expression", "start": 1272, "end": 1282}]}], "regulation": [{"trigger": {"text": "effects", "start": 363, "end": 370}, "arguments": [{"role": "Theme", "text": "expression", "start": 388, "end": 398}]}, {"trigger": {"text": "unaffected", "start": 741, "end": 751}, "arguments": [{"role": "Theme", "text": "inhibited", "start": 486, "end": 495}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1466, "end": 1479}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1454, "end": 1460}]}]}}, "schema": []}
{"input": "Distinct signaling properties identify functionally different CD4 epitopes. \nThe CD4 coreceptor interacts with non-polymorphic regions of major histocompatibility complex class II molecules on antigen-presenting cells and contributes to T cell activation. We have investigated the effect of CD4 triggering on T cell activating signals in a lymphoma model using monoclonal antibodies (mAb) which recognize different CD4 epitopes. We demonstrate that CD4 triggering delivers signals capable of activating the NF-AT transcription factor which is required for interleukin-2 gene expression. Whereas different anti-CD4 mAb or HIV-1 gp120 could all trigger activation of the protein tyrosine kinases p56lck and p59fyn and phosphorylation of the Shc adaptor protein, which mediates signals to Ras, they differed significantly in their ability to activate NF-AT. Lack of full activation of NF-AT could be correlated to a dramatically reduced capacity to induce calcium flux and could be complemented with a calcium ionophore. The results identify functionally distinct epitopes on the CD4 coreceptor involved in activation of the Ras/protein kinase C and calcium pathways. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 96, "end": 105}, "arguments": [{"role": "Theme", "text": "CD4", "start": 81, "end": 84}]}, {"trigger": {"text": "recognize", "start": 395, "end": 404}, "arguments": [{"role": "Theme", "text": "CD4", "start": 415, "end": 418}, {"role": "Site", "text": "epitopes", "start": 419, "end": 427}]}], "gene expression": [{"trigger": {"text": "expression", "start": 575, "end": 585}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 556, "end": 569}]}], "positive regulation": [{"trigger": {"text": "triggering", "start": 295, "end": 305}, "arguments": [{"role": "Theme", "text": "CD4", "start": 291, "end": 294}]}, {"trigger": {"text": "triggering", "start": 453, "end": 463}, "arguments": [{"role": "Theme", "text": "CD4", "start": 449, "end": 452}]}, {"trigger": {"text": "required", "start": 543, "end": 551}, "arguments": [{"role": "Theme", "text": "expression", "start": 575, "end": 585}]}, {"trigger": {"text": "trigger", "start": 643, "end": 650}, "arguments": [{"role": "Cause", "text": "gp120", "start": 627, "end": 632}, {"role": "Theme", "text": "activation", "start": 651, "end": 661}]}, {"trigger": {"text": "trigger", "start": 643, "end": 650}, "arguments": [{"role": "Theme", "text": "activation", "start": 651, "end": 661}]}, {"trigger": {"text": "activation", "start": 651, "end": 661}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 694, "end": 700}]}, {"trigger": {"text": "activation", "start": 651, "end": 661}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 705, "end": 711}]}]}}, "schema": []}
{"input": "Lipopolysaccharide-induced E-selectin expression requires continuous presence of LPS and is inhibited by bactericidal/permeability-increasing protein. \nEndothelial cells stimulated by LPS express E-selectin, which plays an important role in mediating neutrophil adhesion during inflammation. E-selectin is induced within 1-2 h, peaks at 4-6 h, and gradually returns to basal level by 24 h. rBPI21, a recombinant N-terminal fragment of human bactericidal/permeability-increasing protein (BPI), inhibited LPS-induced E-selectin expression when added at the same time as, and up to 6 h after, LPS. Delayed administration of rBPI21 also affected LPS-mediated activation of the nuclear factor, NF-kappa B. Two to 4 h following LPS addition to endothelial cells, when NF-kappa B was already activated, addition of rBPI21 resulted in marked reduction of NF-kappa B detectable at 4 or 6 h. These results indicate that endothelial activation requires continuous presence of LPS, and rBPI21 acts to reverse LPS-mediated endothelial activation by interrupting the on-going LPS signal. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 38, "end": 48}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 27, "end": 37}]}, {"trigger": {"text": "express", "start": 188, "end": 195}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 196, "end": 206}]}, {"trigger": {"text": "expression", "start": 526, "end": 536}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 515, "end": 525}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 92, "end": 101}, "arguments": [{"role": "Theme", "text": "induced", "start": 19, "end": 26}]}, {"trigger": {"text": "inhibited", "start": 493, "end": 502}, "arguments": [{"role": "Theme", "text": "induced", "start": 507, "end": 514}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 19, "end": 26}, "arguments": [{"role": "Theme", "text": "expression", "start": 38, "end": 48}]}, {"trigger": {"text": "requires", "start": 49, "end": 57}, "arguments": [{"role": "Theme", "text": "induced", "start": 19, "end": 26}]}, {"trigger": {"text": "induced", "start": 306, "end": 313}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 292, "end": 302}]}, {"trigger": {"text": "induced", "start": 507, "end": 514}, "arguments": [{"role": "Theme", "text": "expression", "start": 526, "end": 536}]}]}}, "schema": []}
{"input": "Costimulation of human CD4+ T cells with LFA-3 and B7 induce distinct effects on AP-1 and NF-kappa B transcription factors. \nWe have earlier shown that stimulation of human CD4+ T cells with SEA presented on Chinese hamster ovary (CHO)-DR transfectants coexpressing either B7 or LFA-3 resulted in distinct cytokine profiles. We now demonstrate that B7, but not LFA-3, strongly costimulated IL-2 transcription and mRNA expression in CD4+ T cells. Maximal increase in IL-2 transcription was recorded with CHO-DR/B7/LFA-3, suggesting a cooperative effect of B7 and LFA-3 at the transcriptional level. Gel-shift analysis demonstrated that stimulation of CD4+ T cells with CHO-DR and staphylococcal enterotoxin A was sufficient to induce significant amounts of NF-kappa B binding proteins, whereas induction of AP-1 binding proteins required costimulation. LFA-3 induced moderate levels of AP-1, but did not influence the levels of NF-kappa B, while B7 costimulation strongly induced both AP-1 and substantially enhanced NF-kappa B binding proteins. The CHO-DR/B7/LFA-3 triple transfectant induced a further increase in AP-1 and NF-kappa B binding proteins compared with the double transfectants. The level of Oct-1 binding proteins remained similar in all samples. Super-shift analysis revealed that the NF-kappa B complex of costimulated CD4+ T cells contained large amounts of p50, substantial amounts of p65, and marginal levels of c-Rel proteins. The AP-1 binding proteins contained c-Jun, Jun-D, and Fra-1, but marginal amounts of Jun-B and c-Fos. Our results indicate distinct effects of B7 and LFA-3 costimulation on the activity of AP-1 and NF-kappa B. These may partly account for the differential effects of B7 and LFA-3 costimulation on IL-2 expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "coexpressing", "start": 253, "end": 265}, "arguments": [{"role": "Theme", "text": "B7", "start": 273, "end": 275}]}, {"trigger": {"text": "coexpressing", "start": 253, "end": 265}, "arguments": [{"role": "Theme", "text": "LFA-3", "start": 279, "end": 284}]}, {"trigger": {"text": "expression", "start": 1749, "end": 1759}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1744, "end": 1748}]}], "positive regulation": [{"trigger": {"text": "costimulated", "start": 377, "end": 389}, "arguments": [{"role": "Cause", "text": "B7", "start": 349, "end": 351}, {"role": "Theme", "text": "transcription", "start": 395, "end": 408}]}, {"trigger": {"text": "costimulated", "start": 377, "end": 389}, "arguments": [{"role": "Cause", "text": "B7", "start": 349, "end": 351}, {"role": "Theme", "text": "mRNA expression", "start": 413, "end": 428}]}, {"trigger": {"text": "costimulated", "start": 377, "end": 389}, "arguments": [{"role": "Cause", "text": "LFA-3", "start": 361, "end": 366}, {"role": "Theme", "text": "transcription", "start": 395, "end": 408}]}, {"trigger": {"text": "costimulated", "start": 377, "end": 389}, "arguments": [{"role": "Cause", "text": "LFA-3", "start": 361, "end": 366}, {"role": "Theme", "text": "mRNA expression", "start": 413, "end": 428}]}, {"trigger": {"text": "increase", "start": 454, "end": 462}, "arguments": [{"role": "Theme", "text": "transcription", "start": 471, "end": 484}]}], "regulation": [{"trigger": {"text": "effect", "start": 545, "end": 551}, "arguments": [{"role": "Theme", "text": "transcription", "start": 471, "end": 484}, {"role": "Cause", "text": "B7", "start": 555, "end": 557}]}, {"trigger": {"text": "effect", "start": 545, "end": 551}, "arguments": [{"role": "Theme", "text": "transcription", "start": 471, "end": 484}, {"role": "Cause", "text": "LFA-3", "start": 562, "end": 567}]}, {"trigger": {"text": "effects", "start": 1703, "end": 1710}, "arguments": [{"role": "Theme", "text": "expression", "start": 1749, "end": 1759}]}], "transcription": [{"trigger": {"text": "transcription", "start": 395, "end": 408}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 390, "end": 394}]}, {"trigger": {"text": "mRNA expression", "start": 413, "end": 428}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 390, "end": 394}]}, {"trigger": {"text": "transcription", "start": 471, "end": 484}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 466, "end": 470}]}]}}, "schema": []}
{"input": "Regulation of granulocyte-macrophage colony-stimulating factor and E-selectin expression in endothelial cells by cyclosporin A and the T-cell transcription factor NFAT. \nNuclear factor of activated T cells (NFAT) was originally described as a T-cell-specific transcription factor athat supported the activation of cytokine gene expression and mediated the immunoregulatory effects of cyclosporin A (CsA). As we observed that activated endothelial cells also expressed NFAT, we tested the antiinflammatory properties of CsA in endothelial cells. Significantly, CsA completely suppressed the induction of NFAT in endothelial cells and inhibited the activity of granulocyte-macrophage colony-stimulating factor (GM-CSF) gene regulatory elements that use NFAT by 60%. CsA similarly mediated a reduction of up to 65% in GM-CSF mRNA and protein expression in activated endothelial cells. CsA also suppressed E-selectin, but not vascular cell adhesion molecule-1 (VCAM-1) expression in endothelial cells, even though the E-selectin promoter is activated by NF-kappa B rather than NFAT. Hence, induction of cell surface expression of this leukocyte adhesion molecule by tumor necrosis factor (TNF)-alpha was reduced by 40% in the presence of CsA, and this was reflected by a 29% decrease in neutrophil adhesion. The effects of CsA on endothelial cells were also detected at the chromatin structure level, as DNasel hypersensitive sites within both the GM-CSF enhancer and the E-selectin promoter were suppressed by CsA. This represents the first report of NFAT in endothelial cells and suggests mechanisms by which CsA could function as an antiinflammatory agent. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 78, "end": 88}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 14, "end": 62}]}, {"trigger": {"text": "expression", "start": 78, "end": 88}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 67, "end": 77}]}, {"trigger": {"text": "expression", "start": 839, "end": 849}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 815, "end": 821}]}, {"trigger": {"text": "expression", "start": 965, "end": 975}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 902, "end": 912}]}, {"trigger": {"text": "expression", "start": 965, "end": 975}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 957, "end": 963}]}, {"trigger": {"text": "expression", "start": 1112, "end": 1122}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1014, "end": 1024}]}], "negative regulation": [{"trigger": {"text": "mediated a reduction", "start": 778, "end": 798}, "arguments": [{"role": "Theme", "text": "expression", "start": 839, "end": 849}]}, {"trigger": {"text": "suppressed", "start": 891, "end": 901}, "arguments": [{"role": "Theme", "text": "expression", "start": 965, "end": 975}]}, {"trigger": {"text": "reduced", "start": 1200, "end": 1207}, "arguments": [{"role": "Theme", "text": "induction", "start": 1086, "end": 1095}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 1037, "end": 1046}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1014, "end": 1024}, {"role": "Site", "text": "promoter", "start": 1025, "end": 1033}]}, {"trigger": {"text": "induction", "start": 1086, "end": 1095}, "arguments": [{"role": "Theme", "text": "expression", "start": 1112, "end": 1122}, {"role": "Cause", "text": "tumor necrosis factor (TNF)-alpha", "start": 1162, "end": 1195}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 78, "end": 88}]}], "transcription": [{"trigger": {"text": "expression", "start": 839, "end": 849}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 815, "end": 821}]}]}}, "schema": []}
{"input": "Signalling via CD28 of human naive neonatal T lymphocytes. \nAccessory molecules play a crucial role in the development of the T cell response to antigenic challenge. We have examined the role of CD28 in modulating the 'naive' neonatal T cell response to anti-CD2-mediated activation. To compare the role of CD28, neonatal and adult T cells were stimulated with a pair of mitogenic anti-CD2 antibodies in the presence or absence of anti-CD28 MoAb. With anti-CD2 alone, neonatal T cells proliferated slightly but produced no detectable IL-2, whereas adult T cells proliferated vigorously, with significant IL-2 production. Costimulation with anti-CD28 MoAb greatly enhanced the proliferative response of neonatal T cells to levels equivalent to those of adult T cells, whereas adult T cells showed only slight increases. Although IL-2 secretion was increased in the presence of anti-CD28 MoAb, neonatal T cell IL-2 production remained lower than in adults. In contrast, enhancement of IL-2 mRNA expression in neonates was similar to adult levels. Anti-CD28 MoAb costimulation increased NF kappa B levels in neonates, albeit to levels lower than that of adults. The cellular mechanism governing the diminished proliferative response of neonatal T lymphocytes to anti-CD2 may therefore be due to decreased NF kappa B induction, reduced IL-2 mRNA expression and deficient IL-2 production. Although anti-CD28 MoAb costimulation enhances all of the above signals, NF kappa B and IL-2 levels remain lower than in adults, suggesting the need for further activation requirements in the neonate. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "produced", "start": 511, "end": 519}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 534, "end": 538}]}, {"trigger": {"text": "production", "start": 609, "end": 619}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 604, "end": 608}]}, {"trigger": {"text": "production", "start": 913, "end": 923}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 908, "end": 912}]}, {"trigger": {"text": "production", "start": 1372, "end": 1382}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1367, "end": 1371}]}], "localization": [{"trigger": {"text": "secretion", "start": 833, "end": 842}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 828, "end": 832}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 1324, "end": 1331}, "arguments": [{"role": "Theme", "text": "expression", "start": 1342, "end": 1352}]}, {"trigger": {"text": "deficient", "start": 1357, "end": 1366}, "arguments": [{"role": "Theme", "text": "production", "start": 1372, "end": 1382}]}], "positive regulation": [{"trigger": {"text": "With", "start": 447, "end": 451}, "arguments": [{"role": "Theme", "text": "produced", "start": 511, "end": 519}]}, {"trigger": {"text": "With", "start": 447, "end": 451}, "arguments": [{"role": "Theme", "text": "production", "start": 609, "end": 619}]}, {"trigger": {"text": "increased", "start": 847, "end": 856}, "arguments": [{"role": "Theme", "text": "secretion", "start": 833, "end": 842}]}, {"trigger": {"text": "enhancement", "start": 968, "end": 979}, "arguments": [{"role": "Theme", "text": "expression", "start": 993, "end": 1003}]}, {"trigger": {"text": "enhances", "start": 1422, "end": 1430}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1367, "end": 1371}]}], "transcription": [{"trigger": {"text": "expression", "start": 993, "end": 1003}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 983, "end": 987}]}, {"trigger": {"text": "expression", "start": 1342, "end": 1352}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1332, "end": 1336}]}]}}, "schema": []}
{"input": "N- and C-terminal sequences control degradation of MAD3/I kappa B alpha in response to inducers of NF-kappa B activity. \nThe proteolytic degradation of the inhibitory protein MAD3/I kappa B alpha in response to extracellular stimulation is a prerequisite step in the activation of the transcription factor NF-kappa B. Analysis of the expression of human I kappa B alpha protein in stable transfectants of mouse 70Z/3 cells shows that, as for the endogenous murine protein, exogenous I kappa B alpha is degraded in response to inducers of NF-kappa B activity, such as phorbol myristate acetate or lipopolysaccharide. In addition, pretreatment of the cells with the proteasome inhibitor N-Ac-Leu-Leu-norleucinal inhibits this ligand-induced degradation and, in agreement with previous studies, stabilizes a hyperphosphorylated form of the human I kappa B alpha protein. By expressing mutant forms of the human protein in this cell line, we have been able to delineate the sequences responsible for both the ligand-induced phosphorylation and the degradation of I kappa B alpha. Our results show that deletion of the C terminus of the I kappa B alpha molecule up to amino acid 279 abolishes constitutive but not ligand-inducible phosphorylation and inhibits ligand-inducible degradation. Further analysis reveals that the inducible phosphorylation of I kappa B alpha maps to two serines in the N terminus of the protein (residues 32 and 36) and that the mutation of either residue is sufficient to abolish ligand-induced degradation, whereas both residues must be mutated to abolish inducible phosphorylation of the protein. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 334, "end": 344}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 354, "end": 369}]}], "negative regulation": [{"trigger": {"text": "abolish", "start": 1495, "end": 1502}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1518, "end": 1529}]}, {"trigger": {"text": "abolish", "start": 1572, "end": 1579}, "arguments": [{"role": "Theme", "text": "inducible", "start": 1580, "end": 1589}]}, {"trigger": {"text": "abolish", "start": 1572, "end": 1579}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1590, "end": 1605}]}], "phosphorylation": [{"trigger": {"text": "hyperphosphorylated", "start": 805, "end": 824}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 843, "end": 858}]}, {"trigger": {"text": "phosphorylation", "start": 1020, "end": 1035}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1059, "end": 1074}]}, {"trigger": {"text": "phosphorylation", "start": 1329, "end": 1344}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1348, "end": 1363}]}, {"trigger": {"text": "phosphorylation", "start": 1590, "end": 1605}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1348, "end": 1363}]}], "positive regulation": [{"trigger": {"text": "in response to", "start": 72, "end": 86}, "arguments": [{"role": "Theme", "text": "degradation", "start": 36, "end": 47}]}, {"trigger": {"text": "in response to", "start": 196, "end": 210}, "arguments": [{"role": "Theme", "text": "proteolytic degradation", "start": 125, "end": 148}]}, {"trigger": {"text": "in response to", "start": 511, "end": 525}, "arguments": [{"role": "Theme", "text": "degraded", "start": 502, "end": 510}]}, {"trigger": {"text": "stabilizes", "start": 792, "end": 802}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 843, "end": 858}]}, {"trigger": {"text": "induced", "start": 1012, "end": 1019}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1020, "end": 1035}]}, {"trigger": {"text": "induced", "start": 1012, "end": 1019}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1044, "end": 1055}]}, {"trigger": {"text": "inducible", "start": 1319, "end": 1328}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1329, "end": 1344}]}, {"trigger": {"text": "induced", "start": 1510, "end": 1517}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1518, "end": 1529}]}, {"trigger": {"text": "inducible", "start": 1580, "end": 1589}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1590, "end": 1605}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 36, "end": 47}, "arguments": [{"role": "Theme", "text": "MAD3", "start": 51, "end": 55}]}, {"trigger": {"text": "proteolytic degradation", "start": 125, "end": 148}, "arguments": [{"role": "Theme", "text": "MAD3", "start": 175, "end": 179}]}, {"trigger": {"text": "degraded", "start": 502, "end": 510}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 483, "end": 498}]}, {"trigger": {"text": "degradation", "start": 1044, "end": 1055}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1059, "end": 1074}]}, {"trigger": {"text": "degradation", "start": 1518, "end": 1529}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1348, "end": 1363}]}], "regulation": [{"trigger": {"text": "control", "start": 28, "end": 35}, "arguments": [{"role": "Theme", "text": "degradation", "start": 36, "end": 47}]}]}}, "schema": []}
{"input": "Transcriptional repression of the interleukin-2 gene by vitamin D3: direct inhibition of NFATp/AP-1 complex formation by a nuclear hormone receptor. \nT-lymphocyte proliferation is suppressed by 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], the active metabolite of vitamin D3, and is associated with a decrease in interleukin 2 (IL-2), gamma interferon, and granulocyte-macrophage colony-stimulating factor mRNA levels. We report here that 1,25(OH)2D3-mediated repression in Jurkat cells is cycloheximide resistant, suggesting that it is a direct transcriptional repressive effect on IL-2 expression by the vitamin D3 receptor (VDR). We therefore examined vitamin D3-mediated repression of activated IL-2 expression by cotransfecting Jurkat cells with IL-2 promoter/reporter constructs and a VDR overexpression vector and by DNA binding. We delineated an element conferring both DNA binding by the receptor in vitro and 1,25(OH)2D3-mediated repression in vivo to a short 40-bp region encompassing an important positive regulatory element, NF-AT-1, which is bound by a T-cell-specific transcription factor, NFATp, as well as by AP-1. VDR DNA-binding mutants were unable to either bind to this element in vitro or repress in vivo; the VDR DNA-binding domain alone, however, bound the element but also could not repress IL-2 expression. These results indicate that DNA binding by VDR is necessary but not sufficient to mediate IL-2 repression. By combining partially purified proteins in vitro, we observed the loss of the bound NFATp/AP-1-DNA complex upon inclusion of VDR or VDR-retinoid X receptor. Order of addition and off-rate experiments indicate that the VDR-retinoid X receptor heterodimer blocks NFATp/AP-1 complex formation and then stably associates with the NF-AT-1 element. This direct inhibition by a nuclear hormone receptor of transcriptional activators of the IL-2 gene may provide a mechanistic explanation of how vitamin derivatives can act as potent immunosuppressive agents. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complex formation", "start": 100, "end": 117}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 89, "end": 94}]}, {"trigger": {"text": "binding", "start": 877, "end": 884}, "arguments": [{"role": "Theme", "text": "VDR", "start": 786, "end": 789}]}, {"trigger": {"text": "bound", "start": 1051, "end": 1056}, "arguments": [{"role": "Theme", "text": "NF-AT-1", "start": 1033, "end": 1040}, {"role": "Theme2", "text": "NFATp", "start": 1100, "end": 1105}]}, {"trigger": {"text": "bound", "start": 1051, "end": 1056}, "arguments": [{"role": "Theme", "text": "NF-AT-1", "start": 1033, "end": 1040}]}, {"trigger": {"text": "binding mutants", "start": 1135, "end": 1150}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1127, "end": 1130}]}, {"trigger": {"text": "binding", "start": 1360, "end": 1367}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1371, "end": 1374}]}, {"trigger": {"text": "bound", "start": 1514, "end": 1519}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1520, "end": 1525}]}, {"trigger": {"text": "complex formation", "start": 1708, "end": 1725}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1697, "end": 1702}]}, {"trigger": {"text": "associates", "start": 1742, "end": 1752}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1654, "end": 1657}, {"role": "Theme2", "text": "NF-AT-1", "start": 1762, "end": 1769}]}], "gene expression": [{"trigger": {"text": "expression", "start": 699, "end": 709}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 694, "end": 698}]}, {"trigger": {"text": "cotransfecting", "start": 713, "end": 727}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 746, "end": 750}]}, {"trigger": {"text": "cotransfecting", "start": 713, "end": 727}, "arguments": [{"role": "Theme", "text": "VDR", "start": 786, "end": 789}]}, {"trigger": {"text": "expression", "start": 1316, "end": 1326}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1311, "end": 1315}]}], "negative regulation": [{"trigger": {"text": "Transcriptional repression", "start": 0, "end": 26}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 34, "end": 47}]}, {"trigger": {"text": "inhibition", "start": 75, "end": 85}, "arguments": [{"role": "Theme", "text": "complex formation", "start": 100, "end": 117}]}, {"trigger": {"text": "decrease", "start": 296, "end": 304}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 323, "end": 327}]}, {"trigger": {"text": "repressive effect", "start": 557, "end": 574}, "arguments": [{"role": "Theme", "text": "expression", "start": 583, "end": 593}, {"role": "Cause", "text": "VDR", "start": 622, "end": 625}]}, {"trigger": {"text": "repression", "start": 670, "end": 680}, "arguments": [{"role": "Theme", "text": "expression", "start": 699, "end": 709}, {"role": "Cause", "text": "cotransfecting", "start": 713, "end": 727}]}, {"trigger": {"text": "repress", "start": 1206, "end": 1213}, "arguments": [{"role": "Cause", "text": "binding mutants", "start": 1135, "end": 1150}, {"role": "Theme", "text": "expression", "start": 1316, "end": 1326}]}, {"trigger": {"text": "repress", "start": 1303, "end": 1310}, "arguments": [{"role": "Theme", "text": "expression", "start": 1316, "end": 1326}]}, {"trigger": {"text": "repression", "start": 1423, "end": 1433}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1418, "end": 1422}]}, {"trigger": {"text": "loss", "start": 1502, "end": 1506}, "arguments": [{"role": "Theme", "text": "bound", "start": 1514, "end": 1519}, {"role": "Cause", "text": "VDR", "start": 1561, "end": 1564}]}, {"trigger": {"text": "loss", "start": 1502, "end": 1506}, "arguments": [{"role": "Theme", "text": "bound", "start": 1514, "end": 1519}, {"role": "Cause", "text": "VDR", "start": 1568, "end": 1571}]}, {"trigger": {"text": "blocks", "start": 1690, "end": 1696}, "arguments": [{"role": "Cause", "text": "VDR", "start": 1654, "end": 1657}, {"role": "Theme", "text": "complex formation", "start": 1708, "end": 1725}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 684, "end": 693}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 694, "end": 698}]}, {"trigger": {"text": "necessary but not sufficient to mediate", "start": 1378, "end": 1417}, "arguments": [{"role": "Cause", "text": "binding", "start": 1360, "end": 1367}, {"role": "Theme", "text": "repression", "start": 1423, "end": 1433}]}, {"trigger": {"text": "transcriptional activators", "start": 1835, "end": 1861}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1869, "end": 1873}]}], "regulation": [{"trigger": {"text": "conferring", "start": 857, "end": 867}, "arguments": [{"role": "Theme", "text": "binding", "start": 877, "end": 884}]}], "transcription": [{"trigger": {"text": "expression", "start": 583, "end": 593}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 578, "end": 582}]}]}}, "schema": []}
{"input": "An interferon-gamma activation sequence mediates the transcriptional regulation of the IgG Fc receptor type IC gene by interferon-gamma. \nExpression of the IgG Fc receptor type I (Fc gamma RI) on myeloid cells is dramatically increased by treatment with interferon-gamma (IFN-gamma). We observed that Fc gamma RI transcript levels in monoblast-like U937 cells were elevated within 3 hr and peaked 12 hr after exposure to IFN-gamma. Treatment of U937 with IFN-gamma for 9 hr in the presence of cycloheximide led to super-induction of Fc gamma RI expression. Nuclear run-on analysis revealed that the rate of Fc gamma RI transcription was increased by IFN-gamma. Genomic sequence upstream of the Fc gamma RIC gene was cloned and subjected to primer extension analysis, which demonstrated a single transcription initiation site without a TATA box. Transient transfections of CAT reporter gene constructs containing various Fc gamma RIC promoter sequences into U937 cells revealed that a 20-bp region surrounding the transcription start site (-7 to +13) was capable of mediating transcription initiation and that an IFN-gamma responsive element (GIRE) was present within 74 bp upstream of the transcription initiation site. A 17-bp sequence between positions -51 and -35 conferred IFN-gamma responsiveness on a heterologous promoter. Double-stranded GIRE sequence, but not a scrambled sequence, was specifically bound by nuclear proteins from IFN-gamma treated U937 cells. Gel shift experiments further showed that the STAT1 alpha protein bound to the Fc gamma RIC GIRE in response to IFN-gamma treatment of U937 cells. The Fc gamma RIC GIRE is homologous to the IFN-gamma activation sequence (GAS) of the guanylate binding protein and to X box elements of class II MHC genes. Our results demonstrate that transcriptional regulation of the Fc gamma RIC gene by IFN-gamma involves the binding of STAT1 alpha to a 17-bp GAS homology in the proximal promoter. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 1535, "end": 1540}, "arguments": [{"role": "Theme", "text": "STAT1 alpha", "start": 1515, "end": 1526}]}, {"trigger": {"text": "binding", "start": 1880, "end": 1887}, "arguments": [{"role": "Theme", "text": "STAT1 alpha", "start": 1891, "end": 1902}]}], "gene expression": [{"trigger": {"text": "Expression", "start": 138, "end": 148}, "arguments": [{"role": "Theme", "text": "Fc gamma RI", "start": 180, "end": 191}]}, {"trigger": {"text": "expression", "start": 545, "end": 555}, "arguments": [{"role": "Theme", "text": "Fc gamma RI", "start": 533, "end": 544}]}], "positive regulation": [{"trigger": {"text": "mediates", "start": 40, "end": 48}, "arguments": [{"role": "Theme", "text": "transcriptional regulation", "start": 53, "end": 79}]}, {"trigger": {"text": "increased", "start": 226, "end": 235}, "arguments": [{"role": "Theme", "text": "Expression", "start": 138, "end": 148}]}, {"trigger": {"text": "elevated", "start": 365, "end": 373}, "arguments": [{"role": "Theme", "text": "Fc gamma RI", "start": 301, "end": 312}]}, {"trigger": {"text": "led", "start": 507, "end": 510}, "arguments": [{"role": "Theme", "text": "super", "start": 514, "end": 519}]}, {"trigger": {"text": "super", "start": 514, "end": 519}, "arguments": [{"role": "Theme", "text": "induction", "start": 520, "end": 529}]}, {"trigger": {"text": "induction", "start": 520, "end": 529}, "arguments": [{"role": "Theme", "text": "expression", "start": 545, "end": 555}]}, {"trigger": {"text": "increased", "start": 637, "end": 646}, "arguments": [{"role": "Theme", "text": "transcription", "start": 619, "end": 632}, {"role": "Cause", "text": "IFN-gamma", "start": 650, "end": 659}]}, {"trigger": {"text": "in response to", "start": 1566, "end": 1580}, "arguments": [{"role": "Theme", "text": "bound", "start": 1535, "end": 1540}]}], "regulation": [{"trigger": {"text": "transcriptional regulation", "start": 53, "end": 79}, "arguments": [{"role": "Theme", "text": "IgG Fc receptor type IC", "start": 87, "end": 110}, {"role": "Cause", "text": "interferon-gamma", "start": 119, "end": 135}]}, {"trigger": {"text": "transcriptional regulation", "start": 1802, "end": 1828}, "arguments": [{"role": "Theme", "text": "Fc gamma RIC", "start": 1836, "end": 1848}, {"role": "Cause", "text": "IFN-gamma", "start": 1857, "end": 1866}]}, {"trigger": {"text": "involves", "start": 1867, "end": 1875}, "arguments": [{"role": "Theme", "text": "transcriptional regulation", "start": 1802, "end": 1828}, {"role": "Cause", "text": "binding", "start": 1880, "end": 1887}]}], "transcription": [{"trigger": {"text": "transcription", "start": 619, "end": 632}, "arguments": [{"role": "Theme", "text": "Fc gamma RI", "start": 607, "end": 618}]}]}}, "schema": []}
{"input": "Immunosuppression by glucocorticoids: inhibition of NF-kappa B activity through induction of I kappa B synthesis [see comments] \nGlucocorticoids are among the most potent anti-inflammatory and immunosuppressive agents. They inhibit synthesis of almost all known cytokines and of several cell surface molecules required for immune function, but the mechanism underlying this activity has been unclear. Here it is shown that glucocorticoids are potent inhibitors of nuclear factor kappa B (NF-kappa B) activation in mice and cultured cells. This inhibition is mediated by induction of the I kappa B alpha inhibitory protein, which traps activated NF-kappa B in inactive cytoplasmic complexes. Because NF-kappa B activates many immunoregulatory genes in response to pro-inflammatory stimuli, the inhibition of its activity can be a major component of the anti-inflammatory activity of glucocorticoids. ", "output": {"json_structures": {}}, "schema": []}
{"input": "IFN-gamma priming of monocytes enhances LPS-induced TNF production by augmenting both transcription and MRNA stability. \nThe induction of cytokine expression in monocytes/macrophages by bacterial endotoxin or lipopolysaccharide is a critical, highly regulated host defence response. The augmentation of LPS responses by interferon gamma (IFN-gamma), referred to as priming, is well established. However, the mechanism(s) by which priming occurs is poorly defined. Using tumour necrosis factor (TNF) induction as a model, experiments were designed to analyse in detail the priming effect on the LPS response in human monocytes. Priming by IFN-gamma was primarily manifested at the level of TNF mRNA accumulation. IFN-gamma pre-treatment affected the magnitude rather than the sensitivity of the LPS response. Priming occurred after several hours of treatment, and the primed state was induced by either IFN-gamma or GM-CSF, but not M-CSF. Primed monocytes transcribed TNF mRNA at a higher rate than freshly isolated monocytes upon activation with LPS. The increased transcriptional rate correlated with a marked increase in nuclear factor-kappa B activity in these cells as determined by electrophoretic mobility shift assay using a consensus NF-kappa B oligonucleotide. An additional significant finding was than TNF mRNA induced in primed cells was much more stable than in unprimed cells (T1/2 increased 6-8-fold). Consistent with the increased mRNA stability, the duration of mRNA accumulation was longer following LPS stimulation in primed monocytes, in addition to being of greater magnitude. Finally, primed and unprimed cells possessed a differential sensitivity to the kinase inhibitor H-89. H-89 substantially suppressed LPS-induced TNF mRNA accumulation in unprimed cells, but had no effect on primed monocytes following LPS stimulation. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {}}, "schema": []}
{"input": "The myeloid zinc finger gene, MZF-1, regulates the CD34 promoter in vitro. \nMZF-1 is a C2H2 zinc finger gene encoding a putative transcriptional regulator of myeloid differentiation. The MZF-1 protein contains 13 C2H2 zinc fingers arranged in bipartite DNA binding domains containing zinc fingers through 4 and, in the carboxy-terminus, 5 through 13. We previously identified the DNA consensus binding site recognized by the two DNA binding domains. To assess the transcription regulatory function of MZF-1, the full-length MZF-1 coding region was fused to the DNA binding domain of the yeast transactivator GAL4. The expression vector was cotransfected with the chloramphenicol acetyl transferase (CAT) reporter gene regulated by the thymidine kinase promoter containing GAL4 DNA binding sites into NIH 3T3, 293, K562, and Jurkat cell lines. MZF-1 represses CAT reporter gene expression via GAL4 binding sites in the nonhematopoietic cell lines NIH 3T3 and 293. In contrast, MZF-1 activates CAT reporter gene expression in the hematopoietic cell lines K562 and Jurkat. The MZF-1 binding sites are present in the promoters of several genes expressed during myeloid differentiation, including the CD34 promoter. MZF-1 transcriptional regulation of this physiologically relevant promoter was assessed in both hematopoietic and nonhematopoietic cell lines. Recombinant MZF-1 protein specifically binds to the consensus binding sites in the CD34 promoter in mobility shift assays. MZF-1 expression vectors were cotransfected with the luciferase reporter plasmids regulated by the CD34 promoter into both nonhematopoietic and hematopoietic cell lines. As with the heterologous DNA binding domain, MZF-1 represses reporter gene expression in nonhematopoietic cell lines and activates expression in hematopoietic cell lines. Activation of CD34 expression in hematopoietic cell lines is dependent on the presence of intact MZF-1 binding sites. The cell type-specific regulation of the CD34 promoter by MZF-1 suggests the presence of tissue-specific regulators/adapters or differential MZF-1 modifications that determine MZF-1 transcriptional regulatory function. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 1393, "end": 1398}, "arguments": [{"role": "Theme", "text": "MZF-1", "start": 1366, "end": 1371}, {"role": "Site2", "text": "consensus binding sites", "start": 1406, "end": 1429}, {"role": "Theme2", "text": "CD34", "start": 1437, "end": 1441}]}], "gene expression": [{"trigger": {"text": "cotransfected", "start": 640, "end": 653}, "arguments": [{"role": "Theme", "text": "MZF-1", "start": 524, "end": 529}]}, {"trigger": {"text": "expression", "start": 877, "end": 887}, "arguments": [{"role": "Theme", "text": "CAT", "start": 859, "end": 862}]}, {"trigger": {"text": "expression", "start": 1010, "end": 1020}, "arguments": [{"role": "Theme", "text": "CAT", "start": 992, "end": 995}]}, {"trigger": {"text": "expressed", "start": 1140, "end": 1149}, "arguments": [{"role": "Theme", "text": "CD34", "start": 1196, "end": 1200}]}, {"trigger": {"text": "expression", "start": 1837, "end": 1847}, "arguments": [{"role": "Theme", "text": "CD34", "start": 1832, "end": 1836}]}], "negative regulation": [{"trigger": {"text": "represses", "start": 849, "end": 858}, "arguments": [{"role": "Cause", "text": "MZF-1", "start": 843, "end": 848}, {"role": "Theme", "text": "expression", "start": 877, "end": 887}]}], "positive regulation": [{"trigger": {"text": "cotransfected", "start": 640, "end": 653}, "arguments": [{"role": "Theme", "text": "cotransfected", "start": 640, "end": 653}]}, {"trigger": {"text": "via", "start": 888, "end": 891}, "arguments": [{"role": "Theme", "text": "represses", "start": 849, "end": 858}, {"role": "Cause", "text": "GAL4", "start": 892, "end": 896}]}, {"trigger": {"text": "activates", "start": 982, "end": 991}, "arguments": [{"role": "Cause", "text": "MZF-1", "start": 976, "end": 981}, {"role": "Theme", "text": "expression", "start": 1010, "end": 1020}]}, {"trigger": {"text": "Activation", "start": 1818, "end": 1828}, "arguments": [{"role": "Theme", "text": "expression", "start": 1837, "end": 1847}]}, {"trigger": {"text": "dependent", "start": 1879, "end": 1888}, "arguments": [{"role": "Theme", "text": "Activation", "start": 1818, "end": 1828}]}], "regulation": [{"trigger": {"text": "regulates", "start": 37, "end": 46}, "arguments": [{"role": "Cause", "text": "MZF-1", "start": 30, "end": 35}, {"role": "Theme", "text": "CD34", "start": 51, "end": 55}, {"role": "Site", "text": "promoter", "start": 56, "end": 64}]}, {"trigger": {"text": "regulated", "start": 718, "end": 727}, "arguments": [{"role": "Theme", "text": "CAT", "start": 699, "end": 702}, {"role": "Cause", "text": "thymidine kinase", "start": 735, "end": 751}, {"role": "CSite", "text": "promoter", "start": 752, "end": 760}]}, {"trigger": {"text": "transcriptional regulation", "start": 1217, "end": 1243}, "arguments": [{"role": "Theme", "text": "CD34", "start": 1196, "end": 1200}, {"role": "Site", "text": "promoter", "start": 1201, "end": 1209}, {"role": "Cause", "text": "MZF-1", "start": 1211, "end": 1216}]}, {"trigger": {"text": "regulation", "start": 1959, "end": 1969}, "arguments": [{"role": "Theme", "text": "CD34", "start": 1977, "end": 1981}, {"role": "Site", "text": "promoter", "start": 1982, "end": 1990}, {"role": "Cause", "text": "MZF-1", "start": 1994, "end": 1999}]}, {"trigger": {"text": "determine", "start": 2102, "end": 2111}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1959, "end": 1969}]}]}}, "schema": []}
{"input": "The normal cell cycle activation program is exploited during the infection of quiescent B lymphocytes by Epstein-Barr virus. \nB lymphocytes in the peripheral circulation are maintained in a non-proliferative state. Antigen recognition stimulates limited proliferation, whereas infection with Epstein-Barr virus (EBV) results in continual proliferation and the outgrowth of immortal cell lines. Because it is not clear at which point in cell cycle the peripheral B lymphocytes are arrested, we characterized the expression of several cell cycle-associated genes in quiescent and stimulated cells. We show that the expression of four cell genes, cdc-2, cyclin E, CD23, and cyclin D2, are up-regulated approximately 100-fold as a result of EBV-mediated immortalization. Because these genes play a positive role in cell proliferation, we suggest that this regulatory switch contributes to controlling entry into the cell cycle. Transient stimulation of quiescent B lymphocytes with either a cocktail of anti-CD40, anti-IgM, and IL4, or EBV results in the rapid expression of the same four genes, suggesting that, after infection, EBV exploits the normal program of B-lymphocyte cell cycle activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 613, "end": 623}, "arguments": [{"role": "Theme", "text": "cdc-2", "start": 644, "end": 649}]}, {"trigger": {"text": "expression", "start": 613, "end": 623}, "arguments": [{"role": "Theme", "text": "cyclin E", "start": 651, "end": 659}]}, {"trigger": {"text": "expression", "start": 613, "end": 623}, "arguments": [{"role": "Theme", "text": "CD23", "start": 661, "end": 665}]}, {"trigger": {"text": "expression", "start": 613, "end": 623}, "arguments": [{"role": "Theme", "text": "cyclin D2", "start": 671, "end": 680}]}, {"trigger": {"text": "expression", "start": 1057, "end": 1067}, "arguments": [{"role": "Theme", "text": "cdc-2", "start": 644, "end": 649}]}, {"trigger": {"text": "expression", "start": 1057, "end": 1067}, "arguments": [{"role": "Theme", "text": "cyclin E", "start": 651, "end": 659}]}, {"trigger": {"text": "expression", "start": 1057, "end": 1067}, "arguments": [{"role": "Theme", "text": "CD23", "start": 661, "end": 665}]}, {"trigger": {"text": "expression", "start": 1057, "end": 1067}, "arguments": [{"role": "Theme", "text": "cyclin D2", "start": 671, "end": 680}]}], "positive regulation": [{"trigger": {"text": "up-regulated", "start": 686, "end": 698}, "arguments": [{"role": "Theme", "text": "expression", "start": 613, "end": 623}]}, {"trigger": {"text": "results", "start": 1036, "end": 1043}, "arguments": [{"role": "Theme", "text": "expression", "start": 1057, "end": 1067}]}]}}, "schema": []}
{"input": "CD30 ligation induces nuclear factor-kappa B activation in human T cell lines. \nCD30 is a recently described member of the tumor necrosis factor/nerve growth factor receptor superfamily. In this report, we show that following incubation of L540 cells (Hodgkin's disease-derived, T cell-like, CD30+ cells) with the agonistic anti-CD30 monoclonal antibodies (mAb) M44 and M67, two nuclear factor (NF)-kappa B DNA binding activities were induced in nuclear extracts, as determined in gel retardation assays. The effect of the mAb towards NF-kappa B activation was rapid, as it occurred within 20 min, and was sustained for up to 6 h. By comparison, an isotype-matched antibody had no effect on NF-kappa B activation. Moreover, in human T helper (Th) clones functionally characterized as being of the type 0, type 1 and type 2 (28%, < 1% und 93% CD30+, respectively), the extent of CD30-mediated NF-kappa B activation correlated with the proportion of CD30+ cells. In all cell lines investigated, the NF-kappa B complexes induced following CD30 engagement were shown to contain p50 NF-kappa B1, p65 RelA, and possibly other transcription factors. Collectively, our results demonstrate that nuclear translocation and activation of NF-kappa B rank among the short-term cellular responses elicited following CD30 ligation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 5, "end": 13}, "arguments": [{"role": "Theme", "text": "CD30", "start": 0, "end": 4}]}, {"trigger": {"text": "engagement", "start": 1041, "end": 1051}, "arguments": [{"role": "Theme", "text": "CD30", "start": 1036, "end": 1040}]}, {"trigger": {"text": "ligation", "start": 1306, "end": 1314}, "arguments": [{"role": "Theme", "text": "CD30", "start": 1301, "end": 1305}]}]}}, "schema": []}
{"input": "Constitutive NF-kappa B activation, enhanced granulopoiesis, and neonatal lethality in I kappa B alpha-deficient mice. \nTranscription factors belonging to the NF-kappa B family are controlled by inhibitory I kappa B proteins, mainly I kappa B alpha and I kappa B beta. Apparently normal at birth, I kappa B alpha-/- mice exhibit severe runting, skin defects, and extensive granulopoiesis postnatally, typically dying by 8 days. Hematopoietic tissues from these mice display elevated levels of both nuclear NF-kappa B and mRNAs of some, but not all, genes thought to be regulated by NF-kappa B. NF-kappa B elevation results in these phenotypic abnormalities because mice lacking both I kappa B alpha and the p50 subunit of NF-kappa B show a dramatically delayed onset of abnormalities. In contrast to hematopoietic cells, I kappa B alpha-/- embryonic fibroblasts show minimal constitutive NF-kappa B, as well as normal signal-dependent NF-kappa B activation that is concomitant with I kappa B beta degradation. Our results indicate that I kappa b beta, but not I kappa B alpha, is required for the signal-dependent activation of NF-kappa B in fibroblasts. However, I kappa B alpha is required for the postinduction repression of NF-kappa B in fibroblasts. These results define distinct roles for the two forms of I kappa B and demonstrate the necessity for stringent control of NF-kappa B. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "deficient", "start": 103, "end": 112}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 87, "end": 102}]}], "negative regulation": [{"trigger": {"text": "lacking", "start": 670, "end": 677}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 683, "end": 698}]}, {"trigger": {"text": "lacking", "start": 670, "end": 677}, "arguments": [{"role": "Theme", "text": "p50", "start": 707, "end": 710}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 997, "end": 1008}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 982, "end": 996}]}]}}, "schema": []}
{"input": "Vitamin E therapy of acute CCl4-induced hepatic injury in mice is associated with inhibition of nuclear factor kappa B binding. \nOxidative stress, with reactive oxygen intermediate formation, may represent a common mechanism by which liver injury is induced by diverse etiologies. Oxidative stress enhances nuclear factor kappa B (NF-kappa B) activity, and NF-kappa B activity has been shown to enhance the expression of cytotoxic cytokines. Acute hepatic injury caused by reactive oxygen intermediate production was induced by an intraperitoneal injection of CCl4 in mice. This injury was significantly inhibited by intravenous pretreatment of the mice with a water-soluble emulsion of alpha-tocopherol. Alpha-tocopherol treatment of the mice given the CCl4 also reduced the NF-kappa B binding to levels approaching those found in normal mice. In vitro treatment of a monocyte/macrophage cell line with CCl4 led to enhanced NF-kappa B binding and an increase in tumor necrosis factor-alpha (TNF-alpha) messenger RNA levels. Liver specimens taken from patients with acute fulminant hepatitis had markedly increased NF-kappa B binding activity in comparison with the binding of normal livers. These data demonstrate that abolishing acute hepatic injury with alpha-tocopherol, a free radical scavenger, also eliminated increased NF-kappa B binding. It is tempting to speculate that enhanced NF-kappa B expression caused by free radical production/oxidative stress may modulate liver injury, perhaps through an effect on cytotoxic cytokine synthesis. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "increase", "start": 951, "end": 959}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 963, "end": 990}]}]}}, "schema": []}
{"input": "Activation of the signal transducer and transcription (STAT) signaling pathway in a primary T cell response. Critical role for IL-6. \nThe T cell activation is initiated by interaction of specific Ags with TCR, followed by activation of intracellular biochemical events leading to activation of several genes. The activation of signal transducer and activator of transcription (STAT) proteins in a primary TCR-mediated activation of T cells have been explored. In purified human peripheral blood T cells, nuclear STAT proteins were activated approximately 3 h after activation by cross-linked anti-CD3 Abs. These STAT proteins were detected by using the IFN-gamma-activated sequence (GAS) and related oligonucleotides as probes in electrophoretic mobility shift assay. Analysis of the nuclear extracts with anti-STAT Abs indicated that they contained STAT-3 and additional proteins crossreactive with the STAT family. The induction of STAT activity was inhibited completely by pretreatment with either cycloheximide or cyclosporin A, thus indicating that the induction was due to a secondary factor produced by the activated T cells. As neutralizing anti-IL-6 Abs effectively down-regulated the early induction of STAT proteins and as exogenously added IL-6 rapidly activated DNA binding similar to TCR-mediated bindings, it can be concluded that IL-6 is the factor responsible for the activation of STAT proteins in a primary T cell response. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 172, "end": 183}, "arguments": [{"role": "Theme", "text": "Ags", "start": 196, "end": 199}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 1265, "end": 1274}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1252, "end": 1256}]}], "regulation": [{"trigger": {"text": "followed", "start": 210, "end": 218}, "arguments": [{"role": "Theme", "text": "interaction", "start": 172, "end": 183}]}]}}, "schema": []}
{"input": "Regulation of IkB alpha phosphorylation by PKC- and Ca(2+)-dependent signal transduction pathways. \nThe Ca(2+)-dependent phosphatase calcineurin, a target of FK506 and CsA, synergizes with PKC-induced activation of nuclear factor (NF)-kappa B in T cell lines. We have investigated whether this synergy is present in other cell types and the mechanism(s) by which these two pathways lead to NF-kappa B activation. While this synergy is present in other cell types, in the monocytic cell line U937 calcineurin is also sufficient to activate NF-kappa B. Having previously shown that Ca(2+)- and PKC-dependent pathways synergize by accelerating the degradation of IkB alpha, we focused on the regulation of IkB alpha phosphorylation. While PKC-dependent pathways sequentially result in the phosphorylation and in an incomplete degradation of IkB alpha in T cell lines, co-activation of Ca(2+)-dependent pathways accelerates the rate of IkB alpha phosphorylation and results in its complete degradation. Activation of Ca(2+)-dependent pathways alone do not result in the phosphorylation and/or degradation of IkB alpha in Jurkat T or in U937 cells. Treatment of T cells with the selective PKC inhibitor GF109203X abrogates the PMA-induced IkB alpha phosphorylation/degradation irrespective of activation of Ca(2+)-dependent pathways, but not the phosphorylation and degradation of IkB alpha induced by TNF-alpha, a PKC-independent stimulus. Contrary to the interaction with PKC, Ca(2+)-dependent pathways synergize with TNF-alpha not at the level of IkB alpha phosphorylation, but at the level of its degradation. These results indicate that Ca(2+)-dependent pathways, including the phosphatase calcineurin, participate in the regulation of NF-kappa B in a cell specific fashion and synergize with PKC-dependent and -independent pathways at the level of IkB alpha phosphorylation and degradation. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "results", "start": 962, "end": 969}, "arguments": [{"role": "Theme", "text": "complete degradation", "start": 977, "end": 997}]}, {"trigger": {"text": "abrogates", "start": 1208, "end": 1217}, "arguments": [{"role": "Theme", "text": "induced", "start": 1226, "end": 1233}]}, {"trigger": {"text": "abrogates", "start": 1208, "end": 1217}, "arguments": [{"role": "Theme", "text": "induced", "start": 1386, "end": 1393}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 24, "end": 39}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 14, "end": 23}]}, {"trigger": {"text": "phosphorylation", "start": 713, "end": 728}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 703, "end": 712}]}, {"trigger": {"text": "phosphorylation", "start": 786, "end": 801}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 838, "end": 847}]}, {"trigger": {"text": "phosphorylation", "start": 942, "end": 957}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 932, "end": 941}]}, {"trigger": {"text": "phosphorylation", "start": 1066, "end": 1081}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1104, "end": 1113}]}, {"trigger": {"text": "phosphorylation", "start": 1244, "end": 1259}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1234, "end": 1243}]}, {"trigger": {"text": "phosphorylation", "start": 1341, "end": 1356}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1376, "end": 1385}]}, {"trigger": {"text": "phosphorylation", "start": 1555, "end": 1570}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1545, "end": 1554}]}, {"trigger": {"text": "phosphorylation", "start": 1859, "end": 1874}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1849, "end": 1858}]}], "positive regulation": [{"trigger": {"text": "pathways synergize", "start": 606, "end": 624}, "arguments": [{"role": "Theme", "text": "accelerating", "start": 628, "end": 640}]}, {"trigger": {"text": "accelerating", "start": 628, "end": 640}, "arguments": [{"role": "Theme", "text": "degradation", "start": 645, "end": 656}]}, {"trigger": {"text": "result", "start": 772, "end": 778}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 786, "end": 801}]}, {"trigger": {"text": "result", "start": 772, "end": 778}, "arguments": [{"role": "Theme", "text": "degradation", "start": 823, "end": 834}]}, {"trigger": {"text": "accelerates", "start": 908, "end": 919}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 942, "end": 957}]}, {"trigger": {"text": "result", "start": 1052, "end": 1058}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1066, "end": 1081}]}, {"trigger": {"text": "result", "start": 1052, "end": 1058}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1089, "end": 1100}]}, {"trigger": {"text": "induced", "start": 1226, "end": 1233}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1244, "end": 1259}]}, {"trigger": {"text": "induced", "start": 1226, "end": 1233}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1260, "end": 1271}]}, {"trigger": {"text": "induced", "start": 1386, "end": 1393}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1341, "end": 1356}, {"role": "Cause", "text": "TNF-alpha", "start": 1397, "end": 1406}]}, {"trigger": {"text": "induced", "start": 1386, "end": 1393}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1361, "end": 1372}, {"role": "Cause", "text": "TNF-alpha", "start": 1397, "end": 1406}]}, {"trigger": {"text": "synergize", "start": 1500, "end": 1509}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1515, "end": 1524}, {"role": "Theme", "text": "phosphorylation", "start": 1555, "end": 1570}]}, {"trigger": {"text": "synergize", "start": 1500, "end": 1509}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1515, "end": 1524}, {"role": "Theme", "text": "degradation", "start": 1596, "end": 1607}]}, {"trigger": {"text": "synergize", "start": 1778, "end": 1787}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1859, "end": 1874}]}, {"trigger": {"text": "synergize", "start": 1778, "end": 1787}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1879, "end": 1890}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 645, "end": 656}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 660, "end": 669}]}, {"trigger": {"text": "degradation", "start": 823, "end": 834}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 838, "end": 847}]}, {"trigger": {"text": "complete degradation", "start": 977, "end": 997}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 932, "end": 941}]}, {"trigger": {"text": "degradation", "start": 1089, "end": 1100}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1104, "end": 1113}]}, {"trigger": {"text": "degradation", "start": 1260, "end": 1271}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1234, "end": 1243}]}, {"trigger": {"text": "degradation", "start": 1361, "end": 1372}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1376, "end": 1385}]}, {"trigger": {"text": "degradation", "start": 1596, "end": 1607}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1545, "end": 1554}]}, {"trigger": {"text": "degradation", "start": 1879, "end": 1890}, "arguments": [{"role": "Theme", "text": "IkB alpha", "start": 1849, "end": 1858}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 24, "end": 39}]}, {"trigger": {"text": "regulation", "start": 689, "end": 699}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 713, "end": 728}]}]}}, "schema": []}
{"input": "Triggering of complement receptors CR1 (CD35) and CR3 (CD11b/CD18) induces nuclear translocation of NF-kappa B (p50/p65) in human monocytes and enhances viral replication in HIV-infected monocytic cells. \nMonocyte/macrophages may harbor HIV in a nonproductive fashion for prolonged periods of time. Viral gene expression may be reactivated by stimulation of the cells with LPS or cytokines such as TNF-alpha in vitro. The effect of LPS and TNF-alpha is mediated by their ability to induce nuclear translocation of the DNA-binding heterodimer NF-kappa B (p50/p65), which binds to a specific sequence in the HIV-long terminal repeat. The present study demonstrates that triggering of complement receptors CR1 (CD35) and CR3 (CD11b/CD18) enhances viral replication in HIV-infected human monocytic cells. Monocytic cell lines and normal peripheral blood monocytes were infected with HIV-1 in vitro and cultured in the presence or absence of F(ab')2 fragments of monoclonal anti-CR1 or anti-CR3 Abs or with C3 fragments. Stimulation of CR1 or CR3 induces a two- to fourfold increase in the amount of cell-associated and released p24 Ag in cell cultures that was equivalent to that observed in control cultures triggered with LPS. We further observed that stimulation of CR1 or CR3 induces the nuclear translocation of NF-kappa B p50/p65 in infected cells. Translocation of NF-kappa B p50/p65 was also observed following stimulation of CR1 or CR3 of uninfected peripheral blood monocytes from HIV-seronegative donors. The amount of protein translocated was similar to that observed when cells were stimulated with rhTNF-alpha. TNF-alpha did not mediate the translocation of NF-kappa B p50/p65 induced by triggering of complement receptors. Taken together, these observations suggest that HIV gene expression may be activated in infected monocytes through interaction of the cells with complement-opsonized particles and that enhanced viral replication is associated with C3 receptor-mediated nuclear translocation of the NF-kappa B complex. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 570, "end": 575}, "arguments": [{"role": "Theme", "text": "p50", "start": 554, "end": 557}]}, {"trigger": {"text": "binds", "start": 570, "end": 575}, "arguments": [{"role": "Theme", "text": "p65", "start": 558, "end": 561}]}], "localization": [{"trigger": {"text": "translocation", "start": 83, "end": 96}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 75, "end": 82}, {"role": "Theme", "text": "p50", "start": 112, "end": 115}]}, {"trigger": {"text": "translocation", "start": 83, "end": 96}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 75, "end": 82}, {"role": "Theme", "text": "p65", "start": 116, "end": 119}]}, {"trigger": {"text": "translocation", "start": 497, "end": 510}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 489, "end": 496}, {"role": "Theme", "text": "p50", "start": 554, "end": 557}]}, {"trigger": {"text": "translocation", "start": 497, "end": 510}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 489, "end": 496}, {"role": "Theme", "text": "p65", "start": 558, "end": 561}]}, {"trigger": {"text": "translocation", "start": 1296, "end": 1309}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1288, "end": 1295}, {"role": "Theme", "text": "p50", "start": 1324, "end": 1327}]}, {"trigger": {"text": "translocation", "start": 1296, "end": 1309}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1288, "end": 1295}, {"role": "Theme", "text": "p65", "start": 1328, "end": 1331}]}, {"trigger": {"text": "Translocation", "start": 1351, "end": 1364}, "arguments": [{"role": "Theme", "text": "p50", "start": 1379, "end": 1382}]}, {"trigger": {"text": "Translocation", "start": 1351, "end": 1364}, "arguments": [{"role": "Theme", "text": "p65", "start": 1383, "end": 1386}]}, {"trigger": {"text": "translocated", "start": 1534, "end": 1546}, "arguments": [{"role": "Theme", "text": "p50", "start": 1379, "end": 1382}]}, {"trigger": {"text": "translocated", "start": 1534, "end": 1546}, "arguments": [{"role": "Theme", "text": "p65", "start": 1383, "end": 1386}]}, {"trigger": {"text": "translocation", "start": 1651, "end": 1664}, "arguments": [{"role": "Theme", "text": "p50", "start": 1679, "end": 1682}]}, {"trigger": {"text": "translocation", "start": 1651, "end": 1664}, "arguments": [{"role": "Theme", "text": "p65", "start": 1683, "end": 1686}]}], "positive regulation": [{"trigger": {"text": "Triggering", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "CD35", "start": 40, "end": 44}]}, {"trigger": {"text": "Triggering", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "CD11b", "start": 55, "end": 60}]}, {"trigger": {"text": "Triggering", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "CD18", "start": 61, "end": 65}]}, {"trigger": {"text": "induces", "start": 67, "end": 74}, "arguments": [{"role": "Cause", "text": "Triggering", "start": 0, "end": 10}, {"role": "Theme", "text": "translocation", "start": 83, "end": 96}]}, {"trigger": {"text": "induce", "start": 482, "end": 488}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 440, "end": 449}, {"role": "Theme", "text": "translocation", "start": 497, "end": 510}]}, {"trigger": {"text": "induce", "start": 482, "end": 488}, "arguments": [{"role": "Theme", "text": "translocation", "start": 497, "end": 510}]}, {"trigger": {"text": "triggering", "start": 668, "end": 678}, "arguments": [{"role": "Theme", "text": "CD35", "start": 708, "end": 712}]}, {"trigger": {"text": "triggering", "start": 668, "end": 678}, "arguments": [{"role": "Theme", "text": "CD11b", "start": 723, "end": 728}]}, {"trigger": {"text": "triggering", "start": 668, "end": 678}, "arguments": [{"role": "Theme", "text": "CD18", "start": 729, "end": 733}]}, {"trigger": {"text": "Stimulation", "start": 1016, "end": 1027}, "arguments": [{"role": "Theme", "text": "CR1", "start": 1031, "end": 1034}]}, {"trigger": {"text": "increase", "start": 1069, "end": 1077}, "arguments": [{"role": "Cause", "text": "Stimulation", "start": 1016, "end": 1027}, {"role": "Theme", "text": "p24", "start": 1124, "end": 1127}]}, {"trigger": {"text": "increase", "start": 1069, "end": 1077}, "arguments": [{"role": "Theme", "text": "p24", "start": 1124, "end": 1127}]}, {"trigger": {"text": "stimulation", "start": 1250, "end": 1261}, "arguments": [{"role": "Theme", "text": "CR1", "start": 1265, "end": 1268}]}, {"trigger": {"text": "induces", "start": 1276, "end": 1283}, "arguments": [{"role": "Cause", "text": "stimulation", "start": 1250, "end": 1261}, {"role": "Theme", "text": "translocation", "start": 1296, "end": 1309}]}, {"trigger": {"text": "induces", "start": 1276, "end": 1283}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1296, "end": 1309}]}, {"trigger": {"text": "observed", "start": 1396, "end": 1404}, "arguments": [{"role": "Theme", "text": "Translocation", "start": 1351, "end": 1364}, {"role": "Cause", "text": "stimulation", "start": 1415, "end": 1426}]}, {"trigger": {"text": "observed", "start": 1396, "end": 1404}, "arguments": [{"role": "Theme", "text": "Translocation", "start": 1351, "end": 1364}]}, {"trigger": {"text": "stimulation", "start": 1415, "end": 1426}, "arguments": [{"role": "Theme", "text": "CR1", "start": 1430, "end": 1433}]}, {"trigger": {"text": "observed", "start": 1567, "end": 1575}, "arguments": [{"role": "Theme", "text": "translocated", "start": 1534, "end": 1546}]}, {"trigger": {"text": "mediate", "start": 1639, "end": 1646}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1621, "end": 1630}, {"role": "Theme", "text": "induced", "start": 1687, "end": 1694}]}, {"trigger": {"text": "induced", "start": 1687, "end": 1694}, "arguments": [{"role": "Theme", "text": "p50", "start": 1679, "end": 1682}]}, {"trigger": {"text": "induced", "start": 1687, "end": 1694}, "arguments": [{"role": "Theme", "text": "p65", "start": 1683, "end": 1686}]}]}}, "schema": []}
{"input": "Nuclear factor-IL6 activates the human IL-4 promoter in T cells. \nPositive regulatory element I (PRE-I) is a strong enhancer element essential for expression of the human IL-4 gene. To identify transcription factors binding to PRE-I, we screened a cDNA expression library from Jurkat T cells and isolated a cDNA encoding nuclear factor (NF)-IL6 (also known as C/EBP beta). NF-IL6 mRNA was found in human Jurkat T cells and in the mouse Th2 clone D10, but not in Th1 clone 29. rNF-IL6 expressed in bacteria was shown to specifically bind to PRE-I. PRE-I forms multiple DNA-protein complexes with nuclear extracts from Jurkat cells. Some of these complexes were demonstrated to contain NF-IL6 by using anti-C/EBP beta Abs. Overexpression of NF-IL6 enhanced expression of the chloramphenicol acetyl transferase reporter gene linked to the PRE-I-thymidine kinase or the human IL-4 promoter more than 10-fold in Jurkat cells. Promoter deletion studies revealed two additional NF-IL6 binding sites located at positions -44 to -36 (C/EBP proximal) and -87 to -79 (C/EBP medial), respectively. Our results demonstrate that NF-IL6 is involved in transcriptional activation of the human IL-4 promoter in T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 532, "end": 536}, "arguments": [{"role": "Theme", "text": "rNF-IL6", "start": 476, "end": 483}]}, {"trigger": {"text": "complexes", "start": 645, "end": 654}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 684, "end": 690}]}], "gene expression": [{"trigger": {"text": "expression", "start": 147, "end": 157}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 171, "end": 175}]}, {"trigger": {"text": "expressed", "start": 484, "end": 493}, "arguments": [{"role": "Theme", "text": "rNF-IL6", "start": 476, "end": 483}]}, {"trigger": {"text": "Overexpression", "start": 721, "end": 735}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 739, "end": 745}]}, {"trigger": {"text": "expression", "start": 755, "end": 765}, "arguments": [{"role": "Theme", "text": "chloramphenicol acetyl transferase", "start": 773, "end": 807}]}], "positive regulation": [{"trigger": {"text": "activates", "start": 19, "end": 28}, "arguments": [{"role": "Cause", "text": "Nuclear factor-IL6", "start": 0, "end": 18}, {"role": "Theme", "text": "IL-4", "start": 39, "end": 43}, {"role": "Site", "text": "promoter", "start": 44, "end": 52}]}, {"trigger": {"text": "essential", "start": 133, "end": 142}, "arguments": [{"role": "Theme", "text": "expression", "start": 147, "end": 157}]}, {"trigger": {"text": "Overexpression", "start": 721, "end": 735}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 721, "end": 735}]}, {"trigger": {"text": "enhanced", "start": 746, "end": 754}, "arguments": [{"role": "Cause", "text": "Overexpression", "start": 721, "end": 735}, {"role": "Theme", "text": "expression", "start": 755, "end": 765}]}, {"trigger": {"text": "transcriptional activation", "start": 1137, "end": 1163}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1177, "end": 1181}, {"role": "Site", "text": "promoter", "start": 1182, "end": 1190}]}], "regulation": [{"trigger": {"text": "involved", "start": 1125, "end": 1133}, "arguments": [{"role": "Cause", "text": "NF-IL6", "start": 1115, "end": 1121}, {"role": "Theme", "text": "transcriptional activation", "start": 1137, "end": 1163}]}], "transcription": [{"trigger": {"text": "found", "start": 389, "end": 394}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 373, "end": 379}]}]}}, "schema": []}
{"input": "The peri-kappa B site mediates human immunodeficiency virus type 2 enhancer activation in monocytes but not in T cells. \nHuman immunodeficiency virus type 2 (HIV-2), like HIV-1, causes AIDS and is associated with AIDS cases primarily in West Africa. HIV-1 and HIV-2 display significant differences in nucleic acid sequence and in the natural history of clinical disease. Consistent with these differences, we have previously demonstrated that the enhancer/promoter region of HIV-2 functions quite differently from that of HIV-1. Whereas activation of the HIV-1 enhancer following T-cell stimulation is mediated largely through binding of the transcription factor NF-kappa B to two adjacent kappa B sites in the HIV-1 long terminal repeat, activation of the HIV-2 enhancer in monocytes and T cells is dependent on four cis-acting elements: a single kappa B site, two purine-rich binding sites, PuB1 and PuB2, and a pets site. We have now identified a novel cis-acting element within the HIV-2 enhancer, immediately upstream of the kappa B site, designated peri-kappa B. This site is conserved among isolates of HIV-2 and the closely related simian immunodeficiency virus, and transfection assays show this site to mediate HIV-2 enhancer activation following stimulation of monocytic but not T-cell lines. This is the first description of an HIV-2 enhancer element which displays such monocyte specificity, and no comparable enhancer element has been clearly defined for HIV-1. While a nuclear factor(s) from both peripheral blood monocytes and T cells binds the peri-kappa B site, electrophoretic mobility shift assays suggest that either a different protein binds to this site in monocytes versus T cells or that the protein recognizing this enhancer element undergoes differential modification in monocytes and T cells, thus supporting the transfection data. Further, while specific constitutive binding to the peri-kappa B site is seen in monocytes, stimulation with phorbol esters induces additional, specific binding. Understanding the monocyte-specific function of the peri-kappa B factor may ultimately provide insight into the different role monocytes and T cells play in HIV pathogenesis. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Thapsigargin induces IL-2 receptor alpha-chain in human peripheral and Jurkat T cells via a protein kinase C-independent mechanism. \nThapsigargin (TG), an inhibitor of Ca(2+)-ATPase, depletes intracellular Ca2+ stores and induces a sustained Ca2+ influx without altering phosphatidyl inositol levels. TG plus phorbol myristate acetate (PMA) but not TG alone induced IL-2 in Jurkat T cells, suggesting that TG had no effect on protein kinase C (PKC). However, TG induced increases in IL-2R alpha protein as well as IL-2R alpha mRNA in Jurkat T cells in a dose-dependent manner. A similar increase in IL-2R alpha by TG was also observed in human peripheral T cells. Further, like PMA, TG markedly induced NF kappa B in Jurkat T cells. However, TG and PMA exhibited a synergistic action on IL-2R alpha expression, suggesting that TG and PMA induce IL-2R alpha through distinct pathways. PMA- but not TG-induced IL-2R alpha is inhibited by the PKC inhibitor H7, whereas TG- but not PMA-induced IL-2R alpha was inhibited by cholera toxin, forskolin and 1,9-dideoxy forskolin. In toto, these results suggest that TG induces IL-2R alpha in human T cells through a PKC-independent pathway. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 799, "end": 809}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 787, "end": 798}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 923, "end": 932}, "arguments": [{"role": "Theme", "text": "induced", "start": 900, "end": 907}]}, {"trigger": {"text": "inhibited", "start": 1006, "end": 1015}, "arguments": [{"role": "Theme", "text": "induced", "start": 982, "end": 989}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 13, "end": 20}, "arguments": [{"role": "Cause", "text": "induces", "start": 13, "end": 20}, {"role": "Theme", "text": "IL-2 receptor alpha-chain", "start": 21, "end": 46}]}, {"trigger": {"text": "induces", "start": 13, "end": 20}, "arguments": [{"role": "Theme", "text": "IL-2 receptor alpha-chain", "start": 21, "end": 46}, {"role": "Site", "text": "protein kinase C-independent mechanism", "start": 92, "end": 130}]}, {"trigger": {"text": "induced", "start": 358, "end": 365}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 366, "end": 370}]}, {"trigger": {"text": "increases", "start": 470, "end": 479}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 483, "end": 494}]}, {"trigger": {"text": "increases", "start": 470, "end": 479}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 514, "end": 525}]}, {"trigger": {"text": "increase", "start": 587, "end": 595}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 599, "end": 610}]}, {"trigger": {"text": "induce", "start": 838, "end": 844}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 845, "end": 856}]}, {"trigger": {"text": "induced", "start": 900, "end": 907}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 908, "end": 919}]}, {"trigger": {"text": "induced", "start": 982, "end": 989}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 990, "end": 1001}]}, {"trigger": {"text": "induces", "start": 1110, "end": 1117}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 1118, "end": 1129}]}], "regulation": [{"trigger": {"text": "synergistic action", "start": 765, "end": 783}, "arguments": [{"role": "Theme", "text": "expression", "start": 799, "end": 809}]}]}}, "schema": []}
{"input": "A functional T-cell receptor signaling pathway is required for p95vav activity. \nStimulation of the T-cell antigen receptor (TCR) induces activation of multiple tyrosine kinases, resulting in phosphorylation of numerous intracellular substrates. One substrate is p95vav, which is expressed exclusively in hematopoietic and trophoblast cells. It contains a number of structural motifs, including Src homology 2, Src homology 3, and pleckstrin homology domains and a putative guanine nucleotide exchange domain. The role of p95vav in TCR-mediated signaling processes is unclear. Here, we show that overexpression of p95vav alone in Jurkat T cells leads to activation of the nuclear factors, including NFAT, involved in interleukin-2 expression. Furthermore, p95vav synergizes with TCR stimulation in inducing NFAT- and interleukin-2-dependent transcription. In contrast, NFAT activation by a G-protein-coupled receptor is not modulated by p95vav overexpression, suggesting that the effect is specific to the TCR signaling pathways. Although removal of the first 67 amino acids of p95vav activates its transforming potential in NIH 3T3 cells, this region appears to be required for its function in T cells. We further demonstrate that the p95vav-induced NFAT activation is not mimicked by Ras activation, though its function is dependent upon Ras and Raf. Furthermore, the activating function of p95vav is blocked by FK506, suggesting that its activity also depends on calcineurin. To further dissect p95vav involvement in TCR signaling, we analyzed various Jurkat mutants deficient in TCR signaling function or TCR expression and showed that an intact TCR signaling pathway is required for p95vav to function. However, overexpression of p95vav does not appear to influence TCR-induced protein tyrosine phosphorylation or increases in cytoplasmic free calcium. Taken together, our data suggest that p95vav plays an important role at an yet unidentified proximal position in the TCR signaling cascade. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 280, "end": 289}, "arguments": [{"role": "Theme", "text": "p95vav", "start": 263, "end": 269}]}, {"trigger": {"text": "overexpression", "start": 596, "end": 610}, "arguments": [{"role": "Theme", "text": "p95vav", "start": 614, "end": 620}]}, {"trigger": {"text": "expression", "start": 731, "end": 741}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 717, "end": 730}]}, {"trigger": {"text": "overexpression", "start": 944, "end": 958}, "arguments": [{"role": "Theme", "text": "p95vav", "start": 937, "end": 943}]}, {"trigger": {"text": "overexpression", "start": 1717, "end": 1731}, "arguments": [{"role": "Theme", "text": "p95vav", "start": 1735, "end": 1741}]}], "positive regulation": [{"trigger": {"text": "required", "start": 50, "end": 58}, "arguments": [{"role": "Theme", "text": "p95vav", "start": 63, "end": 69}]}, {"trigger": {"text": "overexpression", "start": 596, "end": 610}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 596, "end": 610}]}, {"trigger": {"text": "overexpression", "start": 944, "end": 958}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 944, "end": 958}]}, {"trigger": {"text": "overexpression", "start": 1717, "end": 1731}, "arguments": [{"role": "Theme", "text": "p95vav", "start": 1735, "end": 1741}]}], "regulation": [{"trigger": {"text": "involved", "start": 705, "end": 713}, "arguments": [{"role": "Theme", "text": "expression", "start": 731, "end": 741}]}]}}, "schema": []}
{"input": "Activation of NF-kappa B by phosphatase inhibitors involves the phosphorylation of I kappa B alpha at phosphatase 2A-sensitive sites. \nActivation of NF-kappa B by various cellular stimuli involves the phosphorylation and subsequent degradation of its inhibitor, I kappa B alpha, although the underlying mechanism remains unclear. In the present study, the role of serine/threonine phosphatases in the regulation of I kappa B alpha phosphorylation was investigated. Our studies demonstrate that incubation of human T cells with low concentrations (approximately 1-5 nM) of calyculin A or okadaic acid, potent inhibitors of protein phosphatase type 1 (PP-1) and type 2A (PP-2A), induces the phosphorylation of I kappa B alpha even in the absence of any cellular stimulus. This action of the phosphatase inhibitors, which is associated with the activation of the RelA.p50 NF-kappa B heterodimer, is not affected by agents that block the induction of I kappa B alpha phosphorylation by tumor necrosis factor alpha (TNF-alpha). Furthermore, the phosphorylated I kappa B alpha from calyculin A-treated cells, but not that from TNF-alpha-stimulated cells, is sensitive to PP-2A in vitro, suggesting the existence of fundamental differences in the phosphorylation of I kappa B alpha induced by the two different NF-kappa B inducers. However, induction of I kappa B alpha phosphorylation by both TNF-alpha and the phosphatase inhibitors is associated with the subsequent degradation of I kappa B alpha. We further demonstrate that TNF-alpha- and calyculin A-induced I kappa B alpha degradation exhibits similar but not identical sensitivities to a proteasome inhibitor. Together, these results suggest that phosphorylation of I kappa B alpha, mediated through both the TNF-alpha-inducible and the PP-2A-opposing kinases, may serve to target I kappa B alpha for proteasome-mediated degradation. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "block", "start": 924, "end": 929}, "arguments": [{"role": "Theme", "text": "induction", "start": 934, "end": 943}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 64, "end": 79}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 83, "end": 98}]}, {"trigger": {"text": "phosphorylation", "start": 201, "end": 216}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 262, "end": 277}]}, {"trigger": {"text": "phosphorylation", "start": 431, "end": 446}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 415, "end": 430}]}, {"trigger": {"text": "phosphorylation", "start": 689, "end": 704}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 708, "end": 723}]}, {"trigger": {"text": "phosphorylation", "start": 963, "end": 978}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 947, "end": 962}]}, {"trigger": {"text": "phosphorylated", "start": 1040, "end": 1054}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1055, "end": 1070}]}, {"trigger": {"text": "phosphorylation", "start": 1240, "end": 1255}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1259, "end": 1274}]}, {"trigger": {"text": "phosphorylation", "start": 1363, "end": 1378}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1347, "end": 1362}]}, {"trigger": {"text": "phosphorylation", "start": 1698, "end": 1713}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1717, "end": 1732}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 677, "end": 684}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 689, "end": 704}]}, {"trigger": {"text": "activation", "start": 842, "end": 852}, "arguments": [{"role": "Theme", "text": "RelA", "start": 860, "end": 864}]}, {"trigger": {"text": "activation", "start": 842, "end": 852}, "arguments": [{"role": "Theme", "text": "p50", "start": 865, "end": 868}]}, {"trigger": {"text": "induction", "start": 934, "end": 943}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 963, "end": 978}, {"role": "Cause", "text": "TNF-alpha", "start": 1011, "end": 1020}]}, {"trigger": {"text": "induced", "start": 1275, "end": 1282}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1121, "end": 1130}, {"role": "Theme", "text": "phosphorylation", "start": 1240, "end": 1255}]}, {"trigger": {"text": "induced", "start": 1275, "end": 1282}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1240, "end": 1255}]}, {"trigger": {"text": "induction", "start": 1334, "end": 1343}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1363, "end": 1378}, {"role": "Cause", "text": "TNF-alpha", "start": 1387, "end": 1396}]}, {"trigger": {"text": "induction", "start": 1334, "end": 1343}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1363, "end": 1378}]}, {"trigger": {"text": "induced", "start": 1549, "end": 1556}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1522, "end": 1531}, {"role": "Theme", "text": "degradation", "start": 1573, "end": 1584}]}, {"trigger": {"text": "induced", "start": 1549, "end": 1556}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1573, "end": 1584}]}, {"trigger": {"text": "mediated", "start": 1734, "end": 1742}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1698, "end": 1713}]}, {"trigger": {"text": "mediated", "start": 1863, "end": 1871}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1872, "end": 1883}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 232, "end": 243}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 262, "end": 277}]}, {"trigger": {"text": "degradation", "start": 1462, "end": 1473}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1477, "end": 1492}]}, {"trigger": {"text": "degradation", "start": 1573, "end": 1584}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1557, "end": 1572}]}, {"trigger": {"text": "degradation", "start": 1872, "end": 1883}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1832, "end": 1847}]}], "regulation": [{"trigger": {"text": "regulation", "start": 401, "end": 411}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 431, "end": 446}]}, {"trigger": {"text": "absence", "start": 736, "end": 743}, "arguments": [{"role": "Theme", "text": "induces", "start": 677, "end": 684}]}, {"trigger": {"text": "affected", "start": 900, "end": 908}, "arguments": [{"role": "Theme", "text": "induces", "start": 677, "end": 684}]}, {"trigger": {"text": "serve to target", "start": 1816, "end": 1831}, "arguments": [{"role": "Cause", "text": "mediated", "start": 1734, "end": 1742}, {"role": "Theme", "text": "mediated", "start": 1863, "end": 1871}]}, {"trigger": {"text": "serve to target", "start": 1816, "end": 1831}, "arguments": [{"role": "Theme", "text": "mediated", "start": 1863, "end": 1871}]}]}}, "schema": []}
{"input": "Functional roles of the transcription factor Oct-2A and the high mobility group protein I/Y in HLA-DRA gene expression. \nThe class II major histocompatibility complex gene HLA-DRA is expressed in B cells, activated T lymphocytes, and in antigen-presenting cells. In addition, HLA-DRA gene expression is inducible in a variety of cell types by interferon-gamma (IFN-gamma). Here we show that the lymphoid-specific transcription factor Oct-2A plays a critical role in HLA-DRA gene expression in class II-positive B cell lines, and that the high mobility group protein (HMG) I/Y binds to multiple sites within the DRA promoter, including the Oct-2A binding site. Coexpression of HMG I/Y and Oct-2 in cell lines lacking Oct-2 results in high levels of HLA-DRA gene expression, and in vitro DNA-binding studies reveal that HMG I/Y stimulates Oct-2A binding to the HLA-DRA promoter. Thus, Oct-2A and HMG I/Y may synergize to activate HLA-DRA expression in B cells. By contrast, Oct-2A is not involved in the IFN-gamma induction of the HLA-DRA gene in HeLa cells, but antisense HMG I/Y dramatically decreases the level of induction. We conclude that distinct sets of transcription factors are involved in the two modes of HLA-DRA expression, and that HMG I/Y may be important for B cell-specific expression, and is essential for IFN-gamma induction. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 576, "end": 581}, "arguments": [{"role": "Theme", "text": "I/Y", "start": 572, "end": 575}]}, {"trigger": {"text": "binding", "start": 844, "end": 851}, "arguments": [{"role": "Theme", "text": "Oct-2A", "start": 837, "end": 843}]}], "gene expression": [{"trigger": {"text": "Coexpression", "start": 660, "end": 672}, "arguments": [{"role": "Theme", "text": "I/Y", "start": 680, "end": 683}]}, {"trigger": {"text": "Coexpression", "start": 660, "end": 672}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 688, "end": 693}]}], "positive regulation": [{"trigger": {"text": "stimulates", "start": 826, "end": 836}, "arguments": [{"role": "Cause", "text": "I/Y", "start": 822, "end": 825}, {"role": "Theme", "text": "binding", "start": 844, "end": 851}]}]}}, "schema": []}
{"input": "Interleukin 4 activates a signal transducer and activator of transcription (Stat) protein which interacts with an interferon-gamma activation site-like sequence upstream of the I epsilon exon in a human B cell line. Evidence for the involvement of Janus kinase 3 and interleukin-4 Stat. \nGerm line C transcripts can be induced by IL-4 in the human B cell line, BL-2. Utilizing a IFN-gamma activation site-like DNA sequence element located upstream of the I epsilon exon, we demonstrated by gel mobility shift assays that IL-4 induced a binding activity in the cytosol and nucleus of BL-2 cells. This factor was designated IL-4 NAF (IL-4-induced nuclear-activating factors) and was identified as a tyrosine phosphoprotein, which translocates from the cytosol to the nucleus upon IL-4 treatment. Because these are the characteristics of a signal transducer and activator of transcription (Stat) protein, we determined whether antibodies to Stat proteins will interfere with gel mobility shift and found that antibodies to IL-4 Stat, also known as Stat6, but not antibodies to other Stat proteins, interfere with the formation of the IL-4 NAF complex. Congruous with the involvement of a Stat protein, IL-4 induced robust Janus kinase 3 (JAK3) activity in BL-2 cells. Cotransfection of JAK3 with IL-4 Stat into COS-7 cells produced an intracellular activity which bound the same IFN-gamma activation site-like sequence and comigrated with IL-4 NAF in electrophoretic mobility shift assay. These results show that IL-4 NAF is IL-4 Stat, which is activated by JAK3 in response to IL-4 receptor engagement. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "comigrated", "start": 1420, "end": 1430}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1436, "end": 1440}]}], "gene expression": [{"trigger": {"text": "Cotransfection", "start": 1265, "end": 1279}, "arguments": [{"role": "Theme", "text": "JAK3", "start": 1283, "end": 1287}]}, {"trigger": {"text": "Cotransfection", "start": 1265, "end": 1279}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1293, "end": 1297}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1204, "end": 1211}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1199, "end": 1203}, {"role": "Theme", "text": "JAK3", "start": 1235, "end": 1239}]}, {"trigger": {"text": "Cotransfection", "start": 1265, "end": 1279}, "arguments": [{"role": "Theme", "text": "Cotransfection", "start": 1265, "end": 1279}]}, {"trigger": {"text": "activated", "start": 1542, "end": 1551}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1510, "end": 1514}, {"role": "Cause", "text": "JAK3", "start": 1555, "end": 1559}]}, {"trigger": {"text": "in response to", "start": 1560, "end": 1574}, "arguments": [{"role": "Theme", "text": "activated", "start": 1542, "end": 1551}]}]}}, "schema": []}
{"input": "An IRF-1-dependent pathway of DNA damage-induced apoptosis in mitogen-activated T lymphocytes. \nLymphocytes are particularly susceptible to DNA damage-induced apoptosis, a response which may serve as a form of 'altruistic suicide' to counter their intrinsic high potential for mutation and clonal expansion. The tumour suppressor p53 has been shown to regulate this type of apoptosis in thymocytes, but an as yet unknown, p53-independent pathway(s) appears to mediate the same event in mitogen-activated mature T lymphocytes. Here we show DNA damage-induced apoptosis in these T lymphocytes is dependent on the antioncogenic transcription factor interferon regulatory factor (IRF)-1. Thus two different anti-onco-genic transcription factors, p53 and IRF-1, are required for distinct apoptotic pathways in T lymphocytes. We also show that mitogen induction of the interleukin-1 beta converting enzyme (ICE) gene, a mammalian homologue of the Caenorhabditis elegans cell death gene ced-3, is IRF-1-dependent. Ectopic overexpression of IRF-1 results in the activation of the endogenous gene for ICE and enhances the sensitivity of cells to radiation-induced apoptosis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "overexpression", "start": 1015, "end": 1029}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1033, "end": 1038}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 846, "end": 855}, "arguments": [{"role": "Theme", "text": "ICE", "start": 901, "end": 904}]}, {"trigger": {"text": "overexpression", "start": 1015, "end": 1029}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1015, "end": 1029}]}, {"trigger": {"text": "results", "start": 1039, "end": 1046}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 1015, "end": 1029}, {"role": "Theme", "text": "activation", "start": 1054, "end": 1064}]}, {"trigger": {"text": "activation", "start": 1054, "end": 1064}, "arguments": [{"role": "Theme", "text": "ICE", "start": 1092, "end": 1095}]}], "regulation": [{"trigger": {"text": "dependent", "start": 996, "end": 1005}, "arguments": [{"role": "Theme", "text": "induction", "start": 846, "end": 855}, {"role": "Cause", "text": "IRF-1", "start": 990, "end": 995}]}]}}, "schema": []}
{"input": "Regulation of c-jun mRNA expression by hydroxyurea in human K562 cells during erythroid differentiation [published erratum appears in Biochim Biophys Acta 1995 Dec 27;1264(3):409] \nHydroxyurea (HU) is an antitumor agent which also induces hemoglobinization during erythroid differentiation. In addition, HU stimulates the synthesis of fetal hemoglobin in sickle cell anemia patients. To further understand its mechanism of action, we investigated the effects of HU on regulation of c-jun expression prior to the onset of erythroid differentiation of K562 cells. HU induced a dose-dependent stimulation of c-jun synthesis. The levels of c-jun mRNA was elevated 4 to 7.5-fold by HU within 2 h. This was followed by a gradual decline to the basal level by 24 h. Both nuclear run-on and actinomycin D pulse experiments strongly indicate that HU regulates c-jun mRNA expression by increasing the rate of synthesis as well as stabilizing the c-jun mRNA. In addition, the level of jun protein was elevated by 2 to 5-fold within 4 h in HU treated cells. Furthermore, concentrations of HU below 250 microM slightly increased the 5X AP-1/CAT activity. These results strongly suggest that HU induces both transcriptional and post-transcription regulation of c-jun during erythroid differentiation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 488, "end": 498}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 482, "end": 487}]}, {"trigger": {"text": "synthesis", "start": 611, "end": 620}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 605, "end": 610}]}, {"trigger": {"text": "post-transcription", "start": 1214, "end": 1232}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1247, "end": 1252}]}], "negative regulation": [{"trigger": {"text": "decline", "start": 723, "end": 730}, "arguments": [{"role": "Theme", "text": "elevated", "start": 651, "end": 659}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 565, "end": 572}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 590, "end": 601}]}, {"trigger": {"text": "stimulation", "start": 590, "end": 601}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 611, "end": 620}]}, {"trigger": {"text": "elevated", "start": 651, "end": 659}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 636, "end": 641}]}, {"trigger": {"text": "increasing", "start": 876, "end": 886}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 899, "end": 908}]}, {"trigger": {"text": "stabilizing", "start": 920, "end": 931}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 936, "end": 941}]}, {"trigger": {"text": "induces", "start": 1181, "end": 1188}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1233, "end": 1243}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 25, "end": 35}]}, {"trigger": {"text": "effects", "start": 451, "end": 458}, "arguments": [{"role": "Theme", "text": "regulation", "start": 468, "end": 478}]}, {"trigger": {"text": "regulation", "start": 468, "end": 478}, "arguments": [{"role": "Theme", "text": "expression", "start": 488, "end": 498}]}, {"trigger": {"text": "regulates", "start": 841, "end": 850}, "arguments": [{"role": "Theme", "text": "expression", "start": 862, "end": 872}, {"role": "Cause", "text": "increasing", "start": 876, "end": 886}]}, {"trigger": {"text": "regulation", "start": 1233, "end": 1243}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 1194, "end": 1209}]}, {"trigger": {"text": "regulation", "start": 1233, "end": 1243}, "arguments": [{"role": "Theme", "text": "post-transcription", "start": 1214, "end": 1232}]}], "transcription": [{"trigger": {"text": "expression", "start": 25, "end": 35}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 14, "end": 19}]}, {"trigger": {"text": "expression", "start": 862, "end": 872}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 851, "end": 856}]}, {"trigger": {"text": "synthesis", "start": 899, "end": 908}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 936, "end": 941}]}, {"trigger": {"text": "transcriptional", "start": 1194, "end": 1209}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1247, "end": 1252}]}]}}, "schema": []}
{"input": "Characterization of 5' end of human thromboxane receptor gene. Organizational analysis and mapping of protein kinase C--responsive elements regulating expression in platelets. \nPlatelet thromboxane receptors are acutely and reversibly upregulated after acute myocardial infarction. To determine if platelet thromboxane receptors are under transcriptional control, we isolated and characterized human genomic DNA clones containing the 5' flanking region of the thromboxane receptor gene. The exon-intron structure of the 5' portion of the thromboxane receptor gene was determined initially by comparing the nucleotide sequence of the 5' flanking genomic clone with that of a novel human uterine thromboxane receptor cDNA that extended the mRNA 141 bp further upstream than the previously identified human placental cDNA. A major transcription initiation site was located in three human tissues approximately 560 bp upstream from the translation initiation codon and 380 bp upstream from any previously identified transcription initiation site. The thromboxane receptor gene has neither a TATA nor a CAAT consensus site. Promoter function of the 5' flanking region of the thromboxane receptor gene was evaluated by transfection of thromboxane receptor gene promoter/chloramphenicol acetyltransferase (CAT) chimera plasmids into platelet-like K562 cells. Thromboxane receptor promoter activity, as assessed by CAT expression, was relatively weak but was significantly enhanced by phorbol ester treatment. Functional analysis of 5' deletion constructs in transfected K562 cells and gel mobility shift localized the major phorbol ester-responsive motifs in the thromboxane receptor gene promoter to a cluster of activator protein-2 (AP-2) binding consensus sites located approximately 1.8 kb 5' from the transcription initiation site. These studies are the first to determine the structure and organization of the 5' end of the thromboxane receptor gene and demonstrate that thromboxane receptor gene expression can be regulated by activation of protein kinase C via induction of an AP-2-like nuclear factor binding to upstream promoter elements. These findings strongly suggest that the mechanism for previously described upregulation of platelet thromboxane receptors after acute myocardial infarction is increased thromboxane receptor gene transcription in platelet-progenitor cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 151, "end": 161}, "arguments": [{"role": "Theme", "text": "thromboxane receptor", "start": 36, "end": 56}]}, {"trigger": {"text": "expression", "start": 1411, "end": 1421}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1407, "end": 1410}]}, {"trigger": {"text": "expression", "start": 1996, "end": 2006}, "arguments": [{"role": "Theme", "text": "thromboxane receptor", "start": 1970, "end": 1990}]}], "positive regulation": [{"trigger": {"text": "upregulated", "start": 235, "end": 246}, "arguments": [{"role": "Theme", "text": "thromboxane receptors", "start": 186, "end": 207}]}, {"trigger": {"text": "Promoter function", "start": 1119, "end": 1136}, "arguments": [{"role": "Site", "text": "5' flanking region", "start": 1144, "end": 1162}, {"role": "Theme", "text": "thromboxane receptor", "start": 1170, "end": 1190}]}, {"trigger": {"text": "enhanced", "start": 1465, "end": 1473}, "arguments": [{"role": "Theme", "text": "Thromboxane receptor", "start": 1352, "end": 1372}, {"role": "Site", "text": "promoter", "start": 1373, "end": 1381}]}, {"trigger": {"text": "mechanism", "start": 2183, "end": 2192}, "arguments": [{"role": "Theme", "text": "upregulation", "start": 2218, "end": 2230}, {"role": "Cause", "text": "increased", "start": 2302, "end": 2311}]}, {"trigger": {"text": "upregulation", "start": 2218, "end": 2230}, "arguments": [{"role": "Theme", "text": "thromboxane receptors", "start": 2243, "end": 2264}]}, {"trigger": {"text": "increased", "start": 2302, "end": 2311}, "arguments": [{"role": "Theme", "text": "transcription", "start": 2338, "end": 2351}]}], "regulation": [{"trigger": {"text": "regulating", "start": 140, "end": 150}, "arguments": [{"role": "Theme", "text": "expression", "start": 151, "end": 161}]}, {"trigger": {"text": "under transcriptional control", "start": 333, "end": 362}, "arguments": [{"role": "Theme", "text": "thromboxane receptors", "start": 307, "end": 328}]}, {"trigger": {"text": "regulated", "start": 2014, "end": 2023}, "arguments": [{"role": "Theme", "text": "expression", "start": 1996, "end": 2006}]}], "transcription": [{"trigger": {"text": "mRNA", "start": 738, "end": 742}, "arguments": [{"role": "Theme", "text": "thromboxane receptor", "start": 694, "end": 714}]}, {"trigger": {"text": "transcription", "start": 2338, "end": 2351}, "arguments": [{"role": "Theme", "text": "thromboxane receptor", "start": 2312, "end": 2332}]}]}}, "schema": []}
{"input": "IL-2 gene expression and NF-kappa B activation through CD28 requires reactive oxygen production by 5-lipoxygenase. \nActivation of the CD28 surface receptor provides a major costimulatory signal for T cell activation resulting in enhanced production of interleukin-2 (IL-2) and cell proliferation. In primary T lymphocytes we show that CD28 ligation leads to the rapid intracellular formation of reactive oxygen intermediates (ROIs) which are required for CD28-mediated activation of the NF-kappa B/CD28-responsive complex and IL-2 expression. Delineation of the CD28 signaling cascade was found to involve protein tyrosine kinase activity, followed by the activation of phospholipase A2 and 5-lipoxygenase. Our data suggest that lipoxygenase metabolites activate ROI formation which then induce IL-2 expression via NF-kappa B activation. These findings should be useful for therapeutic strategies and the development of immunosuppressants targeting the CD28 costimulatory pathway. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 10, "end": 20}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 0, "end": 4}]}, {"trigger": {"text": "production", "start": 238, "end": 248}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 267, "end": 271}]}, {"trigger": {"text": "expression", "start": 531, "end": 541}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 526, "end": 530}]}, {"trigger": {"text": "expression", "start": 800, "end": 810}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 795, "end": 799}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 36, "end": 46}, "arguments": [{"role": "Theme", "text": "expression", "start": 10, "end": 20}, {"role": "Cause", "text": "CD28", "start": 55, "end": 59}]}, {"trigger": {"text": "requires", "start": 60, "end": 68}, "arguments": [{"role": "Theme", "text": "activation", "start": 36, "end": 46}]}, {"trigger": {"text": "enhanced", "start": 229, "end": 237}, "arguments": [{"role": "Theme", "text": "production", "start": 238, "end": 248}]}, {"trigger": {"text": "required", "start": 442, "end": 450}, "arguments": [{"role": "Theme", "text": "activation", "start": 469, "end": 479}]}, {"trigger": {"text": "required", "start": 442, "end": 450}, "arguments": [{"role": "Theme", "text": "expression", "start": 531, "end": 541}]}, {"trigger": {"text": "activation", "start": 469, "end": 479}, "arguments": [{"role": "Cause", "text": "CD28", "start": 455, "end": 459}, {"role": "Theme", "text": "CD28", "start": 498, "end": 502}]}, {"trigger": {"text": "induce", "start": 788, "end": 794}, "arguments": [{"role": "Theme", "text": "expression", "start": 800, "end": 810}]}]}}, "schema": []}
{"input": "Infection and replication of Tat- human immunodeficiency viruses: genetic analyses of LTR and tat mutations in primary and long-term human lymphoid cells. \nTat is an essential regulatory protein for the replication of human immunodeficiency virus (HIV). Mutations in the tat gene have been shown to block HIV replication in human T cells. Several studies have established that Tat releases an elongation block to the transcription of HIV long terminal repeat (LTR); however, it is not known whether this mechanism alone is sufficient to explain the block to HIV replication in human T cells when Tat is absent. It is possible that Tat is also needed for other functions during HIV replication. To test these hypotheses, we studied several tat mutants, including two stop codon mutants and one deletion mutant using replication-competent HIV-1 constructs carrying wild-type or mutant LTRs with modifications in the NF-kappa B and/or Sp1 binding sites. In this study, we show that Tat- HIV-1 with wild-type LTRs can replicate in HeLa cells, and the virus produced from HeLa cells can infect primary peripheral blood lymphocytes and macrophages. It was found that the propagation of the Tat mutants containing wild-type LTRs was less efficient than that of the LTR-modified Tat mutants. Large amounts of viral RNA and particles were synthesized in infections established using the tat mutants that contain modified LTRs. However, this efficient propagation of the LTR-modified tat mutants was restricted to some lymphoid cell lines that have been transformed with other viruses. Thus, despite its essential role for releasing an elongation block, Tat is not otherwise absolutely required for synthesis of full-length HIV transcripts and assembly of virus particles. Direct sequencing of the viral genomes and reinfection kinetics showed no evidence of wild-type reversion even after prolonged infection with the Tat- virus. The implications for in vivo HIV-1 replication and potential application of this system to the study of alternative Tat function are discussed. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "absent", "start": 603, "end": 609}, "arguments": [{"role": "Theme", "text": "Tat", "start": 596, "end": 599}]}]}}, "schema": []}
{"input": "Activation and expression of the nuclear factors of activated T cells, NFATp and NFATc, in human natural killer cells: regulation upon CD16 ligand binding. \nThe putative factors that couple the signal transduction from surface receptors to the activation of cytokine synthesis in natural killer (NK) cells have not been elucidated. We report here that the nuclear factor of activated T cells (NFATp), a cyclosporin A (CsA)-sensitive factor that regulates the transcription of several cytokines, mediates CD16-induced activation of cytokine genes in human NK cells. CD16 (Fc gamma RIIIA)-induced expression of cytokine mRNA in NK cells occurs via a CsA-sensitive and Ca(2+)-dependent mechanism. Stimulation of NK cells with CD16 ligands induces NFAT-like DNA binding activity in the nuclear extracts from these cells, as detected in electrophoretic mobility shift assays. This occurs with fast kinetics after stimulation, via a CsA-sensitive and Ca(2+)-dependent mechanism that does not require de novo protein synthesis. NK cell NFAT is present in the cytosol of nonstimulated cells, migrates to the nucleus upon stimulation, and can associate with AP-1. Two distinct molecules, NFATp and NFATc, have been reported to mediate NFAT activity. The results of supershift assays using NFATp- and NFATc- specific antibodies indicate that NK cell activation early after CD16 ligand binding involves primarily, if not exclusively, NFATp, and Western blot analysis shows that this has the same electrophoretic mobility (approximately 120 kD) as that of T lymphocytes. NK cells do not express NFATc constitutively, but NFATc mRNA accumulation is induced in these cells within 2 h of stimulation with CD16 ligands. However, supershift assays using the available mAb recognizing the T cell NFATc revealed no detectable NFATc protein in nuclear and cytoplasmic extracts from CD16- or phorbol ester-stimulated cells at any time tested, up to 4 h. These results provide the first direct evidence that both CsA-sensitive transcription factors, NFATp and NFATc, are expressed in human NK cells, and that their activation and/or expression can be regulated in primary cells by a single stimulus, that, in the case of CD16 in NK cells, results in early activation of NFATp and subsequently induced expression of NFATc mRNA. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 15, "end": 25}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 71, "end": 76}]}, {"trigger": {"text": "expression", "start": 15, "end": 25}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 81, "end": 86}]}, {"trigger": {"text": "express", "start": 1575, "end": 1582}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 1583, "end": 1588}]}, {"trigger": {"text": "detectable", "start": 1796, "end": 1806}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 1807, "end": 1812}]}, {"trigger": {"text": "expressed", "start": 2049, "end": 2058}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 2028, "end": 2033}]}, {"trigger": {"text": "expressed", "start": 2049, "end": 2058}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 2038, "end": 2043}]}, {"trigger": {"text": "expression", "start": 2111, "end": 2121}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 2028, "end": 2033}]}, {"trigger": {"text": "expression", "start": 2111, "end": 2121}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 2038, "end": 2043}]}], "positive regulation": [{"trigger": {"text": "Activation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 71, "end": 76}]}, {"trigger": {"text": "Activation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 81, "end": 86}]}, {"trigger": {"text": "accumulation", "start": 1620, "end": 1632}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 1609, "end": 1614}]}, {"trigger": {"text": "induced", "start": 1636, "end": 1643}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1620, "end": 1632}]}, {"trigger": {"text": "activation", "start": 2093, "end": 2103}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 2028, "end": 2033}]}, {"trigger": {"text": "activation", "start": 2093, "end": 2103}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 2038, "end": 2043}]}, {"trigger": {"text": "results", "start": 2217, "end": 2224}, "arguments": [{"role": "Cause", "text": "regulated", "start": 2129, "end": 2138}, {"role": "Theme", "text": "activation", "start": 2234, "end": 2244}]}, {"trigger": {"text": "activation", "start": 2234, "end": 2244}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 2248, "end": 2253}]}, {"trigger": {"text": "induced", "start": 2271, "end": 2278}, "arguments": [{"role": "Cause", "text": "results", "start": 2217, "end": 2224}, {"role": "Theme", "text": "expression", "start": 2279, "end": 2289}]}], "regulation": [{"trigger": {"text": "regulation", "start": 119, "end": 129}, "arguments": [{"role": "Theme", "text": "Activation", "start": 0, "end": 10}]}, {"trigger": {"text": "regulation", "start": 119, "end": 129}, "arguments": [{"role": "Theme", "text": "expression", "start": 15, "end": 25}]}, {"trigger": {"text": "sensitive", "start": 423, "end": 432}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 393, "end": 398}]}, {"trigger": {"text": "sensitive", "start": 1995, "end": 2004}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 2028, "end": 2033}]}, {"trigger": {"text": "sensitive", "start": 1995, "end": 2004}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 2038, "end": 2043}]}, {"trigger": {"text": "regulated", "start": 2129, "end": 2138}, "arguments": [{"role": "Theme", "text": "activation", "start": 2093, "end": 2103}]}, {"trigger": {"text": "regulated", "start": 2129, "end": 2138}, "arguments": [{"role": "Theme", "text": "expression", "start": 2111, "end": 2121}]}], "transcription": [{"trigger": {"text": "expression", "start": 2279, "end": 2289}, "arguments": [{"role": "Theme", "text": "NFATc", "start": 2293, "end": 2298}]}]}}, "schema": []}
{"input": "Constitutive activation of different Jak tyrosine kinases in human T cell leukemia virus type 1 (HTLV-1) tax protein or virus-transformed cells. \nHTLV-1 infection causes an adult T cell leukemia in humans. The viral encoded protein tax, is thought to play an important role in oncogenesis. Our previous data obtained from a tax transgenic mouse model revealed that tax transforms mouse fibroblasts but not thymocytes, despite comparable levels of tax expression in both tissues. Constitutive tyrosine phosphorylation of a 130-kD protein(s) was observed in the tax transformed fibroblast B line and in HTLV-1 transformed human lymphoid lines, but not in thymocytes from Thy-tax transgenic mice. Phosphotyrosine immunoprecipitation followed by Western blot analysis with a set of Jak kinase specific antibodies, identified p130 as Jak2 in the tax transformed mouse fibroblastic cell line and Jak3 in HTLV-1 transformed human T cell lines. Phosphorylation of Jak2 in tax transformed cells resulted from high expression of IL-6. Tyrosine phosphorylation of this protein could also be induced in Balb/c3T3 cells using a supernatant from the B line, which was associated with induction of cell proliferation. Both phosphorylation and proliferation were inhibited by IL-6 neutralizing antibodies. Constitutive phosphorylation of Jak kinases may facilitate tumor growth in both HTLV-1 infected human T cells and the transgenic mouse model. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 451, "end": 461}, "arguments": [{"role": "Theme", "text": "tax", "start": 447, "end": 450}]}, {"trigger": {"text": "expression", "start": 1005, "end": 1015}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1019, "end": 1023}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1247, "end": 1256}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1034, "end": 1049}]}], "phosphorylation": [{"trigger": {"text": "Phosphorylation", "start": 937, "end": 952}, "arguments": [{"role": "Theme", "text": "Jak2", "start": 956, "end": 960}]}, {"trigger": {"text": "phosphorylation", "start": 1034, "end": 1049}, "arguments": [{"role": "Theme", "text": "Jak2", "start": 956, "end": 960}, {"role": "Site", "text": "Tyrosine", "start": 1025, "end": 1033}]}], "positive regulation": [{"trigger": {"text": "resulted", "start": 986, "end": 994}, "arguments": [{"role": "Theme", "text": "Phosphorylation", "start": 937, "end": 952}, {"role": "Cause", "text": "high", "start": 1000, "end": 1004}]}, {"trigger": {"text": "high", "start": 1000, "end": 1004}, "arguments": [{"role": "Theme", "text": "expression", "start": 1005, "end": 1015}]}, {"trigger": {"text": "induced", "start": 1080, "end": 1087}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1034, "end": 1049}]}]}}, "schema": []}
{"input": "Regulation of transcription of the human erythropoietin receptor gene by proteins binding to GATA-1 and Sp1 motifs. \nErythropoietin (Epo), the primary regulator of the production of erythroid cells, acts by binding to a cell surface receptor (EpoR) on erythroid progenitors. We used deletion analysis and transfection assays with reporter gene constructs to examine the transcription control elements in the 5' flanking region of the human EpoR gene. In erythroid cells most of the transcription activity was contained in a 150 bp promoter fragment with binding sites for transcription factors AP2, Sp1 and the erythroid-specific GATA-1. The 150 bp hEpoR promoter exhibited high and low activity in erythroid OCIM1 and K562 cells, respectively, reflecting the high and low levels of constitutive hEpoR expression. The GATA-1 and Sp1 binding sites in this promoter lacking a TATA sequence were necessary for a high level of transcription activation. Protein-DNA binding studies suggested that Sp1 and two other CCGCCC binding proteins from erythroid and non-erythroid cells could bind to the Sp1 binding motif. By increasing GATA-1 levels via co-transfection, we were able to transactivate the hEpoR promoter in K562 cells and non-erythroid cells, but not in the highly active OCIM1 cells, although GATA-1 mRNA levels were comparable in OCIM1 and K562. Interestingly, when we mutated the Sp1 site, resulting in a marked decrease in hEpoR promoter activity, we could restore transactivation by increasing GATA-1 levels in OCIM1 cells. These data suggest that while GATA-1 can transactivate the EpoR promoter, the level of hEpoR gene expression does not depend on GATA-1 alone. Rather, hEpoR transcription activity depends on coordination between Sp1 and GATA-1 with other cell-specific factors, including possibly other Sp1-like binding proteins, to provide high level, tissue-specific expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 207, "end": 214}, "arguments": [{"role": "Theme", "text": "Epo", "start": 133, "end": 136}, {"role": "Theme2", "text": "EpoR", "start": 243, "end": 247}]}, {"trigger": {"text": "bind", "start": 1079, "end": 1083}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 992, "end": 995}]}], "gene expression": [{"trigger": {"text": "expression", "start": 802, "end": 812}, "arguments": [{"role": "Theme", "text": "hEpoR", "start": 796, "end": 801}]}, {"trigger": {"text": "expression", "start": 1631, "end": 1641}, "arguments": [{"role": "Theme", "text": "hEpoR", "start": 1620, "end": 1625}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 1419, "end": 1427}, "arguments": [{"role": "Theme", "text": "hEpoR", "start": 1431, "end": 1436}, {"role": "Site", "text": "promoter", "start": 1437, "end": 1445}]}], "positive regulation": [{"trigger": {"text": "increasing", "start": 1113, "end": 1123}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1124, "end": 1130}]}, {"trigger": {"text": "transactivate", "start": 1175, "end": 1188}, "arguments": [{"role": "Cause", "text": "increasing", "start": 1113, "end": 1123}, {"role": "Theme", "text": "hEpoR", "start": 1193, "end": 1198}, {"role": "Site", "text": "promoter", "start": 1199, "end": 1207}]}, {"trigger": {"text": "resulting", "start": 1397, "end": 1406}, "arguments": [{"role": "Theme", "text": "decrease", "start": 1419, "end": 1427}]}, {"trigger": {"text": "restore", "start": 1465, "end": 1472}, "arguments": [{"role": "Theme", "text": "hEpoR", "start": 1431, "end": 1436}, {"role": "Site", "text": "promoter", "start": 1437, "end": 1445}]}, {"trigger": {"text": "transactivate", "start": 1574, "end": 1587}, "arguments": [{"role": "Cause", "text": "GATA-1", "start": 1563, "end": 1569}, {"role": "Theme", "text": "EpoR", "start": 1592, "end": 1596}, {"role": "Site", "text": "promoter", "start": 1597, "end": 1605}]}, {"trigger": {"text": "depend", "start": 1651, "end": 1657}, "arguments": [{"role": "Theme", "text": "expression", "start": 1631, "end": 1641}, {"role": "Cause", "text": "GATA-1", "start": 1661, "end": 1667}]}, {"trigger": {"text": "depends", "start": 1712, "end": 1719}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1689, "end": 1702}]}, {"trigger": {"text": "provide high level", "start": 1848, "end": 1866}, "arguments": [{"role": "Theme", "text": "expression", "start": 1631, "end": 1641}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "transcription", "start": 14, "end": 27}]}], "transcription": [{"trigger": {"text": "transcription", "start": 14, "end": 27}, "arguments": [{"role": "Theme", "text": "erythropoietin receptor", "start": 41, "end": 64}]}, {"trigger": {"text": "transcription", "start": 1689, "end": 1702}, "arguments": [{"role": "Theme", "text": "hEpoR", "start": 1683, "end": 1688}]}]}}, "schema": []}
{"input": "TCL1 oncogene activation in preleukemic T cells from a case of ataxia-telangiectasia. \nThe TCL1 oncogene on human chromosome 14q32.1 is involved in chromosome translocations [t(14;14)(q11;q32.1) and t(7;14)(q35;q32.1)] and inversions [inv14(q11;q32.1)] with TCR alpha/beta loci in T-cell leukemias, such as T-prolymphocytic (T-PLL). It is also involved in T- acute and- chronic leukemias arising in cases of ataxia-telangiectasia (AT), an immunodeficiency syndrome. Similar chromosomal rearrangements occur also in the clonally expanded T cells in AT patients before the appearance of the overt leukemia. We have analyzed the expression of TCL1 mRNA and protein in peripheral blood lymphocytes (PBLs) from four AT cases and from healthy controls. We found that the TCL1 gene was overexpressed in the PBLs of an AT patient with a large clonal T-cell population exhibiting the t(14;14) translocation but not in the lymphocytes of the other cases. Fluorescence in situ hybridization of the TCL1 genomic locus to lymphocyte metaphases from the AT patient with the T-cell clonal expansion showed that the breakpoint of the t(14;14) translocation lies within the TCL1 locus and is accompanied by an inverted duplication of the distal part of chromosome 14. These data indicate that TCL1 is activated in preleukemic clonal cells as a consequence of chromosome translocation involving sequences from the TCR locus at 14q11. Deregulation of TCL1 is the first event in the initiation of malignancy in these types of leukemias and represents a potential tool for clinical evaluation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 626, "end": 636}, "arguments": [{"role": "Theme", "text": "TCL1", "start": 640, "end": 644}]}, {"trigger": {"text": "overexpressed", "start": 779, "end": 792}, "arguments": [{"role": "Theme", "text": "TCL1", "start": 765, "end": 769}]}], "negative regulation": [{"trigger": {"text": "Deregulation", "start": 1416, "end": 1428}, "arguments": [{"role": "Theme", "text": "TCL1", "start": 1432, "end": 1436}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 14, "end": 24}, "arguments": [{"role": "Theme", "text": "TCL1", "start": 0, "end": 4}]}, {"trigger": {"text": "overexpressed", "start": 779, "end": 792}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 779, "end": 792}]}, {"trigger": {"text": "activated", "start": 1284, "end": 1293}, "arguments": [{"role": "Theme", "text": "TCL1", "start": 1276, "end": 1280}]}, {"trigger": {"text": "as a consequence of", "start": 1322, "end": 1341}, "arguments": [{"role": "Theme", "text": "activated", "start": 1284, "end": 1293}]}], "transcription": [{"trigger": {"text": "expression", "start": 626, "end": 636}, "arguments": [{"role": "Theme", "text": "TCL1", "start": 640, "end": 644}]}]}}, "schema": []}
{"input": "Interleukin-2 promoter activity in Epstein-Barr virus-transformed B lymphocytes is controlled by nuclear factor-chi B. \nThe regulation of interleukin (IL)-2 gene expression has been investigated mainly in T lymphocytes, the predominant producers of IL-2. However, B cells can also synthesize IL-2. In the present study we analyzed the control of IL-2 promoter activity in Epstein-Barr virus (EBV)-transformed B cell clones which are capable of secreting IL-2 at a low level after stimulation with phorbol 12-myristate 13-acetate and the Ca2+ ionophore ionomycin. Transient transfections using reporter constructs with multiples of transcription factor binding sites from the IL-2 promoter [distal nuclear factor (NF)-AT, proximal NF-AT, AP-1/Octamer (UPS) or NF-chi B (TCEd) sites] were performed. In EBV-transformed B clones, the chi B site exerted the strongest inducible activity; the NF-AT binding sites showed either no or only weak activity compared to Jurkat T cells. An IL-2 promoter bearing a defective NF-chi B site was completely inactive in EBV-transformed B cells, while it still had activity in Jurkat T cells. In seven EBV-B cell clones or lines differing in their capacity to secrete IL-2, the activity of the IL-2 promoter correlated well with the status of IL-2 secretion. Similarly, a human immunodeficiency virus promoter, whose activity is controlled through chi B factors, was found to be active in the IL-2 producing EBV-B cells, but inactive in the non-IL-2-producing cells. Electrophoretic mobility shift assays using protein extracts from EBV-B cells and the IL-2 NF-chi B probe revealed the constitutive generation of chi B complexes in IL-2-secreting cells consisting mainly of heterodimeric p50/p65 complexes. A weaker chi B complex formation and faster-migrating complexes were detected in non-IL-2-secreting cells. These results demonstrate that the IL-2 NF-chi B site is indispensable for the activity of the IL-2 promoter in EBV-transformed B cells, whereas other transcription factors appear to be less important for IL-2 expression in these cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 162, "end": 172}, "arguments": [{"role": "Theme", "text": "interleukin (IL)-2", "start": 138, "end": 156}]}, {"trigger": {"text": "producers", "start": 236, "end": 245}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 249, "end": 253}]}, {"trigger": {"text": "synthesize", "start": 281, "end": 291}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 292, "end": 296}]}, {"trigger": {"text": "producing", "start": 1430, "end": 1439}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1425, "end": 1429}]}, {"trigger": {"text": "producing", "start": 1482, "end": 1491}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1477, "end": 1481}]}, {"trigger": {"text": "expression", "start": 2056, "end": 2066}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 2051, "end": 2055}]}], "localization": [{"trigger": {"text": "secreting", "start": 444, "end": 453}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 454, "end": 458}]}, {"trigger": {"text": "secrete", "start": 1192, "end": 1199}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1200, "end": 1204}]}, {"trigger": {"text": "secretion", "start": 1280, "end": 1289}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1275, "end": 1279}]}, {"trigger": {"text": "secreting", "start": 1669, "end": 1678}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1664, "end": 1668}]}, {"trigger": {"text": "secreting", "start": 1829, "end": 1838}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1824, "end": 1828}]}], "positive regulation": [{"trigger": {"text": "after", "start": 474, "end": 479}, "arguments": [{"role": "Theme", "text": "secreting", "start": 444, "end": 453}]}, {"trigger": {"text": "activity", "start": 1210, "end": 1218}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1226, "end": 1230}, {"role": "Site", "text": "promoter", "start": 1231, "end": 1239}]}, {"trigger": {"text": "generation", "start": 1631, "end": 1641}, "arguments": [{"role": "Theme", "text": "p50", "start": 1720, "end": 1723}]}, {"trigger": {"text": "generation", "start": 1631, "end": 1641}, "arguments": [{"role": "Theme", "text": "p65", "start": 1724, "end": 1727}]}, {"trigger": {"text": "indispensable for the activity", "start": 1903, "end": 1933}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1941, "end": 1945}, {"role": "Site", "text": "promoter", "start": 1946, "end": 1954}]}], "regulation": [{"trigger": {"text": "regulation", "start": 124, "end": 134}, "arguments": [{"role": "Theme", "text": "expression", "start": 162, "end": 172}]}, {"trigger": {"text": "less important", "start": 2032, "end": 2046}, "arguments": [{"role": "Theme", "text": "expression", "start": 2056, "end": 2066}]}]}}, "schema": []}
{"input": "Ubiquitin-mediated processing of NF-kappa B transcriptional activator precursor p105. Reconstitution of a cell-free system and identification of the ubiquitin-carrier protein, E2, and a novel ubiquitin-protein ligase, E3, involved in conjugation. \nIn most cases, the transcriptional factor NF-kappa B is a heterodimer consisting of two subunits, p50 and p65, which are encoded by two distinct genes of the Rel family. p50 is translated as a precursor of 105 kDa. The C-terminal domain of the precursor is rapidly degraded, forming the mature p50 subunit consisted of the N-terminal region of the molecule. The mechanism of generation of p50 is not known. It has been suggested that the ubiquitin-proteasome system is involved in the process; however, the specific enzymes involved and the mechanism of limited proteolysis, in which half of the molecule is spared, have been obscure. Palombella and colleagues (Palombella, V.J., Rando, O.J., Goldberg, A.L., and Maniatis, T.(1994) Cell 78, 773-785) have shown that ubiquitin is required for the processing in a cell-free system of a truncated, artificially constructed, 60-kDa precursor. They have also shown that proteasome inhibitors block the processing both in vitro and in vivo. In this study, we demonstrate reconstitution of a cell-free processing system and demonstrate directly that: (a) the ubiquitin-proteasome system is involved in processing of the intact p105 precursor, (b) conjugation of ubiquitin to the precursor is an essential intermediate step in the processing, (c) the recently discovered novel species of the ubiquitin-carrier protein, E2-F1, that is involved in the conjugation and degradation of p53, is also required for the limited processing of the p105 precursor, and (d) a novel, approximately 320-kDa species of ubiquitin-protein ligase, is involved in the process. This novel enzyme is distinct from E6-AP, the p53-conjugating ligase, and from E3 alpha, the \"N-end rule\" ligase. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "heterodimer", "start": 306, "end": 317}, "arguments": [{"role": "Theme", "text": "p50", "start": 346, "end": 349}, {"role": "Theme2", "text": "p65", "start": 354, "end": 357}]}, {"trigger": {"text": "conjugation", "start": 1640, "end": 1651}, "arguments": [{"role": "Theme", "text": "p53", "start": 1671, "end": 1674}]}], "gene expression": [{"trigger": {"text": "generation", "start": 623, "end": 633}, "arguments": [{"role": "Theme", "text": "p50", "start": 637, "end": 640}]}], "positive regulation": [{"trigger": {"text": "forming", "start": 523, "end": 530}, "arguments": [{"role": "Cause", "text": "degraded", "start": 513, "end": 521}, {"role": "Theme", "text": "p50", "start": 542, "end": 545}]}], "protein catabolism": [{"trigger": {"text": "degraded", "start": 513, "end": 521}, "arguments": [{"role": "Theme", "text": "p105", "start": 80, "end": 84}]}, {"trigger": {"text": "degradation", "start": 1656, "end": 1667}, "arguments": [{"role": "Theme", "text": "p53", "start": 1671, "end": 1674}]}]}}, "schema": []}
{"input": "The hematopoietic transcription factor PU.1 is downregulated in human multiple myeloma cell lines. \nPU.1 is a hematopoietic transcription factor belonging to the Ets-family. It is identical to the Spi-1 oncogene, which is implicated in spleen focus-forming virus-induced murine erythroleukemias. PU.1 seems to be required for early development of multiple hematopoietic lineages, but its expression in mature cells is preferentially observed in cells of the B-cell-and monocyte/macrophage-differentiation lineage. It binds the so-called Pu box, an important tissue-specific regulatory DNA element present in a number of genes expressed in these cell lineages. We have analyzed the expression and activity of PU.1 during human B-cell development using a panel of B-cell lines representing different stages of maturation, from early precursors to differentiated plasma cells. PU.1 mRNA expression and PU.1 DNA binding activity, as measured by Northern blot analysis and electrophoretic mobility shift assay, respectively, were evident in cell lines representing pro-B, pre-B, and mature B cells. We could also show Pu box-dependent transactivation of a reporter gene in transient transfections in these cell lines. In contrast, in a number of multiple myeloma cell lines, representing differentiated, plasma cell-like B cells, PU.1 DNA binding activity, mRNA expression, and Pu box-dependent transactivation were absent or detectable at a very low level. In lymphoblastoid cell lines, which exemplify an intermediate stage of B-cell differentiation, a reduced expression and activity were observed. The findings in the human multiple myeloma cell lines represent the first examples of B cells with downregulated PU.1 expression and apparently contradict observations in the murine system in which PU.1 is expressed and active in plasmacytoma cell lines. At present, it is unclear whether the lack of PU.1 expression and activity in human multiple myeloma cell lines represents a malignancy-associated defect in these cells or exemplifies a normal developmental regulation in terminally differentiated B cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 517, "end": 522}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 296, "end": 300}]}, {"trigger": {"text": "binding activity", "start": 908, "end": 924}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 899, "end": 903}]}], "gene expression": [{"trigger": {"text": "expression", "start": 388, "end": 398}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 296, "end": 300}]}, {"trigger": {"text": "expression", "start": 681, "end": 691}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 708, "end": 712}]}, {"trigger": {"text": "expression", "start": 1558, "end": 1568}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1325, "end": 1329}]}, {"trigger": {"text": "expression", "start": 1715, "end": 1725}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1710, "end": 1714}]}, {"trigger": {"text": "expressed", "start": 1803, "end": 1812}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1795, "end": 1799}]}, {"trigger": {"text": "expression", "start": 1903, "end": 1913}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1898, "end": 1902}]}], "negative regulation": [{"trigger": {"text": "downregulated", "start": 47, "end": 60}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 39, "end": 43}]}, {"trigger": {"text": "absent or detectable at a very low level", "start": 1411, "end": 1451}, "arguments": [{"role": "Theme", "text": "expression", "start": 884, "end": 894}]}, {"trigger": {"text": "absent or detectable at a very low level", "start": 1411, "end": 1451}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 908, "end": 924}]}, {"trigger": {"text": "reduced", "start": 1550, "end": 1557}, "arguments": [{"role": "Theme", "text": "expression", "start": 1558, "end": 1568}]}, {"trigger": {"text": "reduced", "start": 1550, "end": 1557}, "arguments": [{"role": "Theme", "text": "activity", "start": 1573, "end": 1581}]}, {"trigger": {"text": "downregulated", "start": 1696, "end": 1709}, "arguments": [{"role": "Theme", "text": "expression", "start": 1715, "end": 1725}]}, {"trigger": {"text": "lack", "start": 1890, "end": 1894}, "arguments": [{"role": "Theme", "text": "expression", "start": 1903, "end": 1913}]}, {"trigger": {"text": "lack", "start": 1890, "end": 1894}, "arguments": [{"role": "Theme", "text": "activity", "start": 1918, "end": 1926}]}], "positive regulation": [{"trigger": {"text": "activity", "start": 696, "end": 704}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 708, "end": 712}]}, {"trigger": {"text": "activity", "start": 1573, "end": 1581}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1325, "end": 1329}]}, {"trigger": {"text": "active", "start": 1817, "end": 1823}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1795, "end": 1799}]}, {"trigger": {"text": "activity", "start": 1918, "end": 1926}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1898, "end": 1902}]}], "regulation": [{"trigger": {"text": "associated", "start": 1988, "end": 1998}, "arguments": [{"role": "Theme", "text": "lack", "start": 1890, "end": 1894}]}, {"trigger": {"text": "developmental regulation", "start": 2045, "end": 2069}, "arguments": [{"role": "Theme", "text": "lack", "start": 1890, "end": 1894}]}], "transcription": [{"trigger": {"text": "expression", "start": 884, "end": 894}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 874, "end": 878}]}]}}, "schema": []}
{"input": "A regulatory element in the human interleukin 2 gene promoter is a binding site for the zinc finger proteins Sp1 and EGR-1. \nActivation of the interleukin 2 (IL-2) gene after antigen recognition is a critical event for T cell proliferation and effector function. Prior studies have identified several transcription factors that contribute to the activity of the IL-2 promoter in stimulated T lymphocytes. Here we describe a novel regulatory element within the IL-2 promoter located immediately upstream of the nuclear factor of activated T cell (NFAT) domain. This region (termed the zinc finger protein binding region (ZIP)) serves as binding site for two differently regulated zinc finger proteins: the constitutively expressed transcription factor Sp1 and the inducible early growth response protein EGR-1. In unstimulated cells which do not secrete IL-2, only Sp1 binds to this region, while in stimulated IL-2 secreting cells the inducible EGR-1 protein recognizes this element. In Jurkat T cells, the ZIP site serves as an activator for IL-2 gene expression, and a combination of ZIP and NFAT binding sites is required for maximal IL-2 promoter activity. These results suggest a critical role of the ZIP site for IL-2 promoter activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 67, "end": 74}, "arguments": [{"role": "Site", "text": "regulatory element", "start": 2, "end": 20}, {"role": "Theme", "text": "interleukin 2", "start": 34, "end": 47}, {"role": "Theme2", "text": "Sp1", "start": 109, "end": 112}]}, {"trigger": {"text": "binding", "start": 67, "end": 74}, "arguments": [{"role": "Site", "text": "regulatory element", "start": 2, "end": 20}, {"role": "Theme", "text": "interleukin 2", "start": 34, "end": 47}, {"role": "Theme2", "text": "EGR-1", "start": 117, "end": 122}]}, {"trigger": {"text": "binding", "start": 636, "end": 643}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 751, "end": 754}]}, {"trigger": {"text": "binding", "start": 636, "end": 643}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 803, "end": 808}]}, {"trigger": {"text": "binds", "start": 868, "end": 873}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 864, "end": 867}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 720, "end": 729}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 751, "end": 754}]}, {"trigger": {"text": "expression", "start": 1053, "end": 1063}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1043, "end": 1047}]}], "localization": [{"trigger": {"text": "secrete", "start": 845, "end": 852}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 853, "end": 857}]}, {"trigger": {"text": "secreting", "start": 915, "end": 924}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 910, "end": 914}]}], "positive regulation": [{"trigger": {"text": "Activation", "start": 125, "end": 135}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 158, "end": 162}]}, {"trigger": {"text": "contribute", "start": 328, "end": 338}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 362, "end": 366}, {"role": "Site", "text": "promoter", "start": 367, "end": 375}]}, {"trigger": {"text": "inducible", "start": 763, "end": 772}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 803, "end": 808}]}, {"trigger": {"text": "stimulated", "start": 899, "end": 909}, "arguments": [{"role": "Theme", "text": "secreting", "start": 915, "end": 924}]}, {"trigger": {"text": "inducible", "start": 935, "end": 944}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 945, "end": 950}]}, {"trigger": {"text": "activator", "start": 1029, "end": 1038}, "arguments": [{"role": "Theme", "text": "expression", "start": 1053, "end": 1063}]}, {"trigger": {"text": "required", "start": 1116, "end": 1124}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1137, "end": 1141}, {"role": "Site", "text": "promoter", "start": 1142, "end": 1150}]}], "regulation": [{"trigger": {"text": "role", "start": 1194, "end": 1198}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1219, "end": 1223}, {"role": "Site", "text": "promoter", "start": 1224, "end": 1232}]}]}}, "schema": []}
{"input": "Functional antagonism between vitamin D3 and retinoic acid in the regulation of CD14 and CD23 expression during monocytic differentiation of U-937 cells. \n1,25 alpha-Dihydroxicholecalciferol (VitD3) and retinoic acid (RA) are important regulators of the proliferation and differentiation of several cell types. This paper describes how the expression of the monocyte-macrophage Ag, CD14, and the low affinity Fc receptor for IgE, CD23, were inversely regulated during VitD3- and RA-induced monocytic differentiation of human U-937 monoblasts. PMA induced the expression of both CD14 and CD23 mRNA and protein. Exposure to VitD3 rapidly induced the de novo expression of CD14 mRNA and protein. The addition of cycloheximide completely blocked the VitD3 induction of CD14 mRNA expression, indicating that the induction was dependent on ongoing protein synthesis. While inducing CD14 expression, VitD3 concomitantly suppressed the basal, PMA-, and RA-inducible CD23 expression in a dose-dependent manner. In contrast, U-937 cells induced by RA strongly increased their expression of CD23 mRNA and protein, whereas they completely lacked detectable CD14 cell surface or mRNA expression. Furthermore, the VitD3- and the PMA-induced CD14 expression was inhibited as a temporal consequence of the RA-induced differentiation. The results suggest that there exists a functional antagonism between VitD3 and RA that may have important implications for the regulation of certain immune and inflammatory responses through their inverse effects on CD14 and CD23 gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 94, "end": 104}, "arguments": [{"role": "Theme", "text": "CD14", "start": 80, "end": 84}]}, {"trigger": {"text": "expression", "start": 94, "end": 104}, "arguments": [{"role": "Theme", "text": "CD23", "start": 89, "end": 93}]}, {"trigger": {"text": "expression", "start": 340, "end": 350}, "arguments": [{"role": "Theme", "text": "CD14", "start": 382, "end": 386}]}, {"trigger": {"text": "expression", "start": 340, "end": 350}, "arguments": [{"role": "Theme", "text": "CD23", "start": 430, "end": 434}]}, {"trigger": {"text": "expression", "start": 559, "end": 569}, "arguments": [{"role": "Theme", "text": "CD14", "start": 578, "end": 582}]}, {"trigger": {"text": "expression", "start": 559, "end": 569}, "arguments": [{"role": "Theme", "text": "CD23", "start": 587, "end": 591}]}, {"trigger": {"text": "expression", "start": 656, "end": 666}, "arguments": [{"role": "Theme", "text": "CD14", "start": 670, "end": 674}]}, {"trigger": {"text": "expression", "start": 881, "end": 891}, "arguments": [{"role": "Theme", "text": "CD14", "start": 876, "end": 880}]}, {"trigger": {"text": "expression", "start": 963, "end": 973}, "arguments": [{"role": "Theme", "text": "CD23", "start": 958, "end": 962}]}, {"trigger": {"text": "expression", "start": 1066, "end": 1076}, "arguments": [{"role": "Theme", "text": "CD23", "start": 1080, "end": 1084}]}, {"trigger": {"text": "expression", "start": 1171, "end": 1181}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1145, "end": 1149}]}, {"trigger": {"text": "expression", "start": 1232, "end": 1242}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1227, "end": 1231}]}, {"trigger": {"text": "gene expression", "start": 1549, "end": 1564}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1535, "end": 1539}]}, {"trigger": {"text": "gene expression", "start": 1549, "end": 1564}, "arguments": [{"role": "Theme", "text": "CD23", "start": 1544, "end": 1548}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 734, "end": 741}, "arguments": [{"role": "Theme", "text": "induction", "start": 752, "end": 761}]}, {"trigger": {"text": "suppressed", "start": 913, "end": 923}, "arguments": [{"role": "Theme", "text": "inducible", "start": 948, "end": 957}]}, {"trigger": {"text": "suppressed", "start": 913, "end": 923}, "arguments": [{"role": "Theme", "text": "expression", "start": 963, "end": 973}]}, {"trigger": {"text": "inhibited", "start": 1247, "end": 1256}, "arguments": [{"role": "Theme", "text": "induced", "start": 1219, "end": 1226}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 547, "end": 554}, "arguments": [{"role": "Theme", "text": "expression", "start": 559, "end": 569}]}, {"trigger": {"text": "induced", "start": 636, "end": 643}, "arguments": [{"role": "Theme", "text": "expression", "start": 656, "end": 666}]}, {"trigger": {"text": "induction", "start": 752, "end": 761}, "arguments": [{"role": "Theme", "text": "expression", "start": 775, "end": 785}]}, {"trigger": {"text": "inducing", "start": 867, "end": 875}, "arguments": [{"role": "Theme", "text": "expression", "start": 881, "end": 891}]}, {"trigger": {"text": "inducible", "start": 948, "end": 957}, "arguments": [{"role": "Theme", "text": "expression", "start": 963, "end": 973}]}, {"trigger": {"text": "increased", "start": 1050, "end": 1059}, "arguments": [{"role": "Theme", "text": "expression", "start": 1066, "end": 1076}]}, {"trigger": {"text": "induced", "start": 1219, "end": 1226}, "arguments": [{"role": "Theme", "text": "expression", "start": 1232, "end": 1242}]}, {"trigger": {"text": "as a temporal consequence of", "start": 1257, "end": 1285}, "arguments": [{"role": "Theme", "text": "inhibited", "start": 1247, "end": 1256}]}], "regulation": [{"trigger": {"text": "regulation", "start": 66, "end": 76}, "arguments": [{"role": "Theme", "text": "expression", "start": 94, "end": 104}]}, {"trigger": {"text": "regulated", "start": 451, "end": 460}, "arguments": [{"role": "Theme", "text": "expression", "start": 340, "end": 350}]}, {"trigger": {"text": "dependent", "start": 821, "end": 830}, "arguments": [{"role": "Theme", "text": "induction", "start": 752, "end": 761}]}, {"trigger": {"text": "effects", "start": 1524, "end": 1531}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 1549, "end": 1564}]}], "transcription": [{"trigger": {"text": "expression", "start": 559, "end": 569}, "arguments": [{"role": "Theme", "text": "CD14", "start": 578, "end": 582}]}, {"trigger": {"text": "expression", "start": 559, "end": 569}, "arguments": [{"role": "Theme", "text": "CD23", "start": 587, "end": 591}]}, {"trigger": {"text": "expression", "start": 656, "end": 666}, "arguments": [{"role": "Theme", "text": "CD14", "start": 670, "end": 674}]}, {"trigger": {"text": "expression", "start": 775, "end": 785}, "arguments": [{"role": "Theme", "text": "CD14", "start": 765, "end": 769}]}, {"trigger": {"text": "expression", "start": 1066, "end": 1076}, "arguments": [{"role": "Theme", "text": "CD23", "start": 1080, "end": 1084}]}, {"trigger": {"text": "expression", "start": 1171, "end": 1181}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1145, "end": 1149}]}]}}, "schema": []}
{"input": "Cytokine modulation of HIV expression. \nCytokines, the peptide hormones which control the homeostasis of the immune system and also play a fundamental role in inflammatory and immune mediated reactions, have been involved at multiple levels in the pathogenesis of the acquired immune deficiency syndrome (AIDS). Infection with the human immunodeficiency virus (HIV) has been shown to induce production of several cytokines both in vitro and in vivo. Conversely, several cytokines modulate the levels of HIV expression in infected cells of both T lymphocytic and mononuclear phagocytic lineage. Activated mononuclear cells, particularly B cells which are in a state of chronic activation in HIV infected individuals, release HIV-inductive cytokines and thus play a potentially important role in the pathogenesis of HIV infection. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Inhibition of HIV-1 latency reactivation by dehydroepiandrosterone (DHEA) and an analog of DHEA. \nThe initial infection with human immunodeficiency virus type 1 (HIV-1) in most individuals usually results in the establishment of a latent or chronic infection before eventual progression toward acquired immunodeficiency syndrome. HIV-1 can also establish a latent or persistent infection in some T cell lines that show minimal constitutive virus expression. However, activation of the T cell lines leading to enhanced HIV-1 replication can be induced by antigens, mitogens, and cytokines (tumor necrosis factor alpha [TNF-alpha], interleukin 1, and interleukin-2). Various gene products from other viruses (HTLV-1, HSV, EBV, CMV, HBV, and HHV-6) can also enhance HIV-1 long terminal repeat (LTR)-driven reporter gene activity. On the basis of these observations, it has been proposed that reactivation of latent HIV-1 harbored in chronically infected T lymphocytes, monocytes, or macrophages plays an important role in the pathogenesis of AIDS. So far, there are no drugs or therapy available that can provide protection against HIV-1 latency reactivation. ACH-2, derived from a human T cell line (CEM), is chronically infected with HIV-1, with low levels of constitutive virus expression. ACH-2 can be converted to productive infection by stimulation of the cells with 12-O-tetradecanoylphorbol-13-acetate (TPA), mitogen or cytokines (TNF-alpha), or infection with HSV. Therefore the ACH-2 cell line is a good candidate for studying the effects of drugs on HIV-1 activation. Previously, we have reported that DHEA and synthetic analogs of DHEA can be modest inhibitors of HIV-1 IIIB replication in phytohemagglutinin-stimulated peripheral blood lymphocyte cultures. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {}}, "schema": []}
{"input": "Nitric oxide-stimulated guanine nucleotide exchange on p21ras. \nThe protooncogene p21ras, a monomeric G protein family member, plays a critical role in converting extracellular signals into intracellular biochemical events. Here, we report that nitric oxide (NO) activates p21ras in human T cells as evidenced by an increase in GTP-bound p21ras. In vitro studies using pure recombinant p21ras demonstrate that the activation is direct and reversible. Circular dichroism analysis reveals that NO induces a profound conformational change in p21ras in association with GDP/GTP exchange. The mechanism of activation is due to S-nitrosylation of a critical cysteine residue which stimulates guanine nucleotide exchange. Furthermore, we demonstrate that p21ras is essential for NO-induced downstream signaling, such as NF-kappa B activation, and that endogenous NO can activate p21ras in the same cell. These studies identify p21ras as a target of the same cell. These studies identify p21ras as a target of NO in T cells and suggest that NO activates p21ras by an action which mimics that of guanine nucleotide exchange factors. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "activates", "start": 263, "end": 272}, "arguments": [{"role": "Theme", "text": "p21ras", "start": 273, "end": 279}]}, {"trigger": {"text": "increase", "start": 316, "end": 324}, "arguments": [{"role": "Theme", "text": "p21ras", "start": 338, "end": 344}]}, {"trigger": {"text": "activate", "start": 863, "end": 871}, "arguments": [{"role": "Theme", "text": "p21ras", "start": 872, "end": 878}]}, {"trigger": {"text": "activates", "start": 1036, "end": 1045}, "arguments": [{"role": "Theme", "text": "p21ras", "start": 1046, "end": 1052}]}], "regulation": [{"trigger": {"text": "target", "start": 992, "end": 998}, "arguments": [{"role": "Theme", "text": "p21ras", "start": 980, "end": 986}]}]}}, "schema": []}
{"input": "Transcriptional regulation of the vacuolar H(+)-ATPase B2 subunit gene in differentiating THP-1 cells. \nMonocyte-macrophage differentiation was used as a model system for studying gene regulation of the human vacuolar H(+)-ATPase (V-ATPase). We examined mRNA levels of various V-ATPase subunits during differentiation of both native monocytes and the cell line THP-1, and found that transcriptional and post-transcriptional mechanisms could account for increases in cell V-ATPase content. From nuclear runoff experiments, we found that one subunit in particular, the B2 isoform (Mr = 56,000), was amplified primarily by transcriptional means. We have begun to examine the structure of the B2 subunit promoter region. Isolation and sequencing of the first exon and 5'-flanking region of this gene reveal a TATA-less promoter with a high G + C content. Primer extension and ribonuclease protection analyses indicate a single major transcriptional start site. We transfected promoter-luciferase reporter plasmids into THP-1 cells to define sequences that mediate transcriptional control during monocyte differentiation. We found that sequences downstream from the transcriptional start site were sufficient to confer increased expression during THP-1 differentiation. DNase I footprinting and sequence analysis revealed the existence of multiple AP2 and Sp1 binding sites in the 5'-untranslated and proximal coding regions. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1355, "end": 1362}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1351, "end": 1354}]}], "positive regulation": [{"trigger": {"text": "amplified", "start": 597, "end": 606}, "arguments": [{"role": "Theme", "text": "B2", "start": 567, "end": 569}]}]}}, "schema": []}
{"input": "Functional characterization of novel IL-2 transcriptional inhibitors. \nIL-2-mediated T cell proliferation is a critical early event in the inflammatory process. Formation of the NFAT-1 transcriptional complex on the IL-2 promoter is essential for IL-2 transcription. Using a cell line that is stably transfected with a trimer of the NFAT-1 regulatory element linked to a lac-Z reporter gene, we screened for inhibitors of NFAT-1-mediated beta-galactosidase activity. WIN 61058 and WIN 53071 were identified as microM inhibitors. These compounds also inhibited beta-galactosidase mRNA levels. Similar inhibition of NFAT-1-mediated gene expression was observed in a second cell line, which is stably transfected with NFAT-1 regulatory elements linked to the reporter gene for sCD8. At 10 microM, both compounds inhibited IL-2 mRNA and protein levels in the NFAT-1-linked lac-Z transfectants, and in human lymphocytes. Both compounds inhibited the mixed lymphocyte reaction, and this inhibition was reversed by exogenous IL-2. WIN 53071 inhibited IL-2 production induced in the calcium-dependent PMA and ionomycin pathway. Conversely, calcium-independent anti-CD28 Ab and PMA-induced IL-2 production was resistant. Both compounds altered the NFAT-1 transcriptional complex, causing its retarded mobility on gels. By these functional criteria, we believe we have identified two structurally distinct, novel inhibitors of NFAT-1-mediated transcription. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complex", "start": 201, "end": 208}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 178, "end": 184}, {"role": "Theme2", "text": "IL-2", "start": 216, "end": 220}, {"role": "Site2", "text": "promoter", "start": 221, "end": 229}]}, {"trigger": {"text": "transcriptional complex", "start": 1246, "end": 1269}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1239, "end": 1245}]}], "gene expression": [{"trigger": {"text": "transfected", "start": 698, "end": 709}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 715, "end": 721}]}, {"trigger": {"text": "levels", "start": 841, "end": 847}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 819, "end": 823}]}, {"trigger": {"text": "production", "start": 1049, "end": 1059}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1044, "end": 1048}]}, {"trigger": {"text": "production", "start": 1186, "end": 1196}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1181, "end": 1185}]}], "negative regulation": [{"trigger": {"text": "transcriptional inhibitors", "start": 42, "end": 68}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 37, "end": 41}]}, {"trigger": {"text": "inhibitors", "start": 408, "end": 418}, "arguments": [{"role": "Theme", "text": "beta-galactosidase", "start": 438, "end": 456}]}, {"trigger": {"text": "inhibitors", "start": 517, "end": 527}, "arguments": [{"role": "Theme", "text": "beta-galactosidase", "start": 438, "end": 456}]}, {"trigger": {"text": "inhibited", "start": 550, "end": 559}, "arguments": [{"role": "Theme", "text": "levels", "start": 584, "end": 590}]}, {"trigger": {"text": "inhibited", "start": 809, "end": 818}, "arguments": [{"role": "Theme", "text": "levels", "start": 841, "end": 847}]}, {"trigger": {"text": "inhibited", "start": 1034, "end": 1043}, "arguments": [{"role": "Theme", "text": "production", "start": 1049, "end": 1059}]}], "positive regulation": [{"trigger": {"text": "essential", "start": 233, "end": 242}, "arguments": [{"role": "Cause", "text": "complex", "start": 201, "end": 208}, {"role": "Theme", "text": "transcription", "start": 252, "end": 265}]}, {"trigger": {"text": "screened", "start": 395, "end": 403}, "arguments": [{"role": "Theme", "text": "inhibitors", "start": 408, "end": 418}]}, {"trigger": {"text": "mediated", "start": 429, "end": 437}, "arguments": [{"role": "Cause", "text": "NFAT-1", "start": 422, "end": 428}, {"role": "Theme", "text": "beta-galactosidase", "start": 438, "end": 456}]}, {"trigger": {"text": "transfected", "start": 698, "end": 709}, "arguments": [{"role": "Theme", "text": "transfected", "start": 698, "end": 709}]}, {"trigger": {"text": "induced", "start": 1060, "end": 1067}, "arguments": [{"role": "Theme", "text": "production", "start": 1049, "end": 1059}]}, {"trigger": {"text": "induced", "start": 1173, "end": 1180}, "arguments": [{"role": "Theme", "text": "production", "start": 1186, "end": 1196}]}], "regulation": [{"trigger": {"text": "altered", "start": 1227, "end": 1234}, "arguments": [{"role": "Theme", "text": "transcriptional complex", "start": 1246, "end": 1269}]}], "transcription": [{"trigger": {"text": "transcription", "start": 252, "end": 265}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 247, "end": 251}]}, {"trigger": {"text": "levels", "start": 584, "end": 590}, "arguments": [{"role": "Theme", "text": "beta-galactosidase", "start": 560, "end": 578}]}, {"trigger": {"text": "levels", "start": 841, "end": 847}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 819, "end": 823}]}]}}, "schema": []}
{"input": "cDNA cloning of a NGFI-B/nur77-related transcription factor from an apoptotic human T cell line. \nA human T lymphoid cell line, PEER, dies by apoptosis in the presence of PMA and calcium ionophore. A new gene, TINUR, was cloned from apoptotic PEER cells. The expression of the TINUR gene is induced within 1 h after the cross-linking of the T cell Ag receptor complex. TINUR belongs to the NGFI-B/nur77 family of the steroid receptor superfamily and is an orphan receptor. TINUR binds to the same DNA sequence as NGFI-B/nur77. We also propose that the NGFI-B/nur77 family can be classified into two subtypes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 479, "end": 484}, "arguments": [{"role": "Theme", "text": "TINUR", "start": 473, "end": 478}]}, {"trigger": {"text": "binds", "start": 479, "end": 484}, "arguments": [{"role": "Theme", "text": "NGFI-B", "start": 513, "end": 519}]}], "gene expression": [{"trigger": {"text": "expression", "start": 259, "end": 269}, "arguments": [{"role": "Theme", "text": "TINUR", "start": 277, "end": 282}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 291, "end": 298}, "arguments": [{"role": "Theme", "text": "expression", "start": 259, "end": 269}]}]}}, "schema": []}
{"input": "Platelet-activating factor stimulates transcription of the heparin-binding epidermal growth factor-like growth factor in monocytes. Correlation with an increased kappa B binding activity. \nHuman peripheral blood monocytes responded to stimulation of platelet-activating factor (PAF) with up-regulation of the transcript for heparin-binding epidermal growth factor-like growth factor (HB-EGF), a potent mitogen for vascular smooth muscle cells. This function of PAF was observed at nanomolar concentrations of the ligand, starting at 30 min after stimulation. The PAF-induced up-regulation of HB-EGF mRNA was accompanied by an increase in kappa B binding activity. These functions of PAF appeared to be mediated through the cell surface PAF receptors, as two PAF receptor antagonists, WEB 2086 and L-659,989, blocked both the up-regulation of HB-EGF mRNA and kappa B binding activity induced by PAF. The antagonists, however, had no effect on phorbol ester-induced up-regulation of HB-EGF mRNA and kappa B binding activity. Pretreatment of monocytes with pertussis toxin inhibited these functions of PAF, whereas cholera toxin had no inhibitory effect. Pyrrolidine dithiocarbamate, an inhibitor for NF-kappa B activation, markedly reduced PAF-stimulated kappa B binding activity as well as up-regulation of HB-EGF mRNA. These results suggest a potential role of PAF in HB-EGF expression and provide evidence that this stimulation may occur through increased kappa B binding activity. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1375, "end": 1385}, "arguments": [{"role": "Theme", "text": "HB-EGF", "start": 1368, "end": 1374}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 808, "end": 815}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 825, "end": 838}]}, {"trigger": {"text": "inhibited", "start": 1070, "end": 1079}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 575, "end": 588}]}, {"trigger": {"text": "inhibitory effect", "start": 1133, "end": 1150}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 575, "end": 588}]}, {"trigger": {"text": "reduced", "start": 1230, "end": 1237}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 1289, "end": 1302}]}], "positive regulation": [{"trigger": {"text": "stimulates", "start": 27, "end": 37}, "arguments": [{"role": "Theme", "text": "transcription", "start": 38, "end": 51}]}, {"trigger": {"text": "up-regulation", "start": 288, "end": 301}, "arguments": [{"role": "Theme", "text": "heparin-binding epidermal growth factor-like growth factor", "start": 324, "end": 382}]}, {"trigger": {"text": "up-regulation", "start": 575, "end": 588}, "arguments": [{"role": "Theme", "text": "HB-EGF", "start": 592, "end": 598}]}, {"trigger": {"text": "mediated", "start": 702, "end": 710}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 575, "end": 588}]}, {"trigger": {"text": "up-regulation", "start": 825, "end": 838}, "arguments": [{"role": "Theme", "text": "HB-EGF", "start": 842, "end": 848}]}, {"trigger": {"text": "up-regulation", "start": 964, "end": 977}, "arguments": [{"role": "Theme", "text": "HB-EGF", "start": 981, "end": 987}]}, {"trigger": {"text": "up-regulation", "start": 1289, "end": 1302}, "arguments": [{"role": "Theme", "text": "HB-EGF", "start": 1306, "end": 1312}]}, {"trigger": {"text": "potential role", "start": 1343, "end": 1357}, "arguments": [{"role": "Theme", "text": "expression", "start": 1375, "end": 1385}]}, {"trigger": {"text": "occur", "start": 1433, "end": 1438}, "arguments": [{"role": "Theme", "text": "potential role", "start": 1343, "end": 1357}]}], "regulation": [{"trigger": {"text": "effect", "start": 932, "end": 938}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 964, "end": 977}]}], "transcription": [{"trigger": {"text": "transcription", "start": 38, "end": 51}, "arguments": [{"role": "Theme", "text": "heparin-binding epidermal growth factor-like growth factor", "start": 59, "end": 117}]}]}}, "schema": []}
{"input": "IL-1 receptor and TCR signals synergize to activate NF-kappa B-mediated gene transcription. \nPrevious studies have demonstrated that IL-1 receptor (IL-1R)- and TCR-initiated signals can interact synergistically to increase the rate of transcription of several lymphokine and lymphokine receptor genes during the competence phase of the activation program in T helper lymphocytes. In this report we describe how signals initiated through the type I IL-1R interact with signals from the antigen receptor to synergistically augment the transactivating properties of NF-kappa B. The synergistic antigen receptor initiated signals are mediated through protein kinase C because they can be mimicked by the phorbol ester, 12-O-tetradecanoylphorbol-13-acetate, but not with calcium ionophores; and are staurosporine sensitive but cyclosporine resistant. Gel shift analyses demonstrate that NF-kappa B nuclear translocation is stimulated primarily by IL-1 rather than by antigen receptor signals. Western blot and phosphorylation analyses demonstrate that the synergistic effect on NF-kappa B functional activity is independent of I kappa B alpha (MAD3)-NF-kappa B dissociation in the cytosol and is not associated with I kappa B nuclear translocation. The IL-1-induced NF-kappa B DNA nuclear localization is transient and can be prolonged either by an antigen receptor-initiated signal or by inhibiting protein synthesis. These results suggest that IL-1 induces both NF-kappa B nuclear translocation and the synthesis of a protein(s) responsible for terminating NF-kappa B-DNA interaction in the nucleus. Antigen receptor signals prolong NF-kappa B-DNA interaction, probably by functionally antagonizing the IL-1-induced synthesis of a protein(s) responsible for the transient NF-kappa B-DNA interaction and consequently synergistically enhance IL-1-induced NF-kappa B-dependent gene transcription. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Induction of transcription factors in human T lymphocytes by aspirin-like drugs. \nAspirin-like drugs (ALD) induce calcium mobilization, an essential component of T cell activation, but do not induce the biosynthesis of IL-2. To understand the extent to which ALD may mimic mitogenic stimulation, we studied cytoplasmic and nuclear signaling steps in ALD-treated T cells. We found that ALD induce a transient activation of protein kinase (PKC) but have no effect (in comparison to anti-CD3 antibodies) on protein tyrosine phosphorylation nor on PCL gamma 1 tyrosine phosphorylation. ALD-induced calcium mobilization and PKC activation are independent of tyrosine protein kinase activity as shown by the lack of effect of herbimycin, a tyrosine-protein kinase-specific inhibitor. Although we detected no IL-2 mRNA in ALD-treated cells, the nuclei of these cells contain proteins capable of binding to three regulatory sequences in the IL-2 promoter region: NFAT, NF kappa B, and AP-1. These binding activities are expressed only in activated T cells. The expression of AP-1 depended on calcium mobilization and PKC activation. These data suggest that ALD cause transient but significant changes in T cell transmembrane signaling, although some events induced by stimulation with anti-CD3 antibodies are not induced by ALD. The signal is transmitted to the nucleus and induces DNA-binding activity by several transcription factors. However, the ALD stimulus is not capable of causing complete T cell activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 888, "end": 895}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 933, "end": 937}, {"role": "Site", "text": "promoter region", "start": 938, "end": 953}]}], "gene expression": [{"trigger": {"text": "biosynthesis", "start": 203, "end": 215}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 219, "end": 223}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 565, "end": 580}, "arguments": [{"role": "Theme", "text": "PCL gamma 1", "start": 544, "end": 555}, {"role": "Site", "text": "tyrosine", "start": 556, "end": 564}]}], "positive regulation": [{"trigger": {"text": "induce", "start": 192, "end": 198}, "arguments": [{"role": "Theme", "text": "biosynthesis", "start": 203, "end": 215}]}, {"trigger": {"text": "expressed", "start": 1012, "end": 1021}, "arguments": [{"role": "Theme", "text": "binding", "start": 888, "end": 895}]}], "regulation": [{"trigger": {"text": "effect", "start": 455, "end": 461}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 565, "end": 580}]}], "transcription": [{"trigger": {"text": "detected", "start": 790, "end": 798}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 802, "end": 806}]}]}}, "schema": []}
{"input": "Interleukin (IL)-10 inhibits nuclear factor kappa B (NF kappa B) activation in human monocytes. IL-10 and IL-4 suppress cytokine synthesis by different mechanisms. \nOur previous studies in human monocytes have demonstrated that interleukin (IL)-10 inhibits lipopolysaccharide (LPS)-stimulated production of inflammatory cytokines, IL-1 beta, IL-6, IL-8, and tumor necrosis factor (TNF)-alpha by blocking gene transcription. Using electrophoretic mobility shift assays (EMSA), we now show that, in monocytes stimulated with LPS or TNF alpha, IL-10 inhibits nuclear stimulation of nuclear factor kappa B (NF kappa B), a transcription factor involved in the expression of inflammatory cytokine genes. Several other transcription factors including NF-IL-6, AP-1, AP-2, GR, CREB, Oct-1, and Sp-1 are not affected by IL-10. This selective inhibition by IL-10 of NF kappa B activation occurs rapidly and in a dose-dependent manner and correlates well with IL-10's cytokine synthesis inhibitory activity in terms of both kinetics and dose responsiveness. Furthermore, compounds such as tosylphenylalanyl chloromethyl ketone and pyrrolidinedithiocarbamate that are known to selectively inhibit NF kappa B activation block cytokine gene transcription in LPS-stimulated monocytes. Taken together, these results suggest that inhibition of NF kappa B activation may be an important mechanism for IL-10 suppression of cytokine gene transcription in human monocytes. IL-4, another cytokine that inhibits cytokine mRNA accumulation in monocytes, shows little inhibitory effect on LPS-induced NF kappa B activation. Further examination reveals that, unlike IL-10, IL-4 enhances mRNA degradation and does not suppress cytokine gene transcription. These data indicate that IL-10 and IL-4 inhibit cytokine production by different mechanisms. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 293, "end": 303}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 331, "end": 340}]}, {"trigger": {"text": "production", "start": 293, "end": 303}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 342, "end": 346}]}, {"trigger": {"text": "production", "start": 293, "end": 303}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 348, "end": 352}]}, {"trigger": {"text": "production", "start": 293, "end": 303}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor (TNF)-alpha", "start": 358, "end": 391}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 248, "end": 256}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 282, "end": 292}]}], "positive regulation": [{"trigger": {"text": "stimulated", "start": 282, "end": 292}, "arguments": [{"role": "Theme", "text": "production", "start": 293, "end": 303}]}], "regulation": [{"trigger": {"text": "affected", "start": 799, "end": 807}, "arguments": [{"role": "Theme", "text": "NF-IL-6", "start": 744, "end": 751}, {"role": "Cause", "text": "IL-10", "start": 811, "end": 816}]}, {"trigger": {"text": "affected", "start": 799, "end": 807}, "arguments": [{"role": "Theme", "text": "AP-1", "start": 753, "end": 757}, {"role": "Cause", "text": "IL-10", "start": 811, "end": 816}]}, {"trigger": {"text": "affected", "start": 799, "end": 807}, "arguments": [{"role": "Theme", "text": "AP-2", "start": 759, "end": 763}, {"role": "Cause", "text": "IL-10", "start": 811, "end": 816}]}, {"trigger": {"text": "affected", "start": 799, "end": 807}, "arguments": [{"role": "Theme", "text": "GR", "start": 765, "end": 767}, {"role": "Cause", "text": "IL-10", "start": 811, "end": 816}]}, {"trigger": {"text": "affected", "start": 799, "end": 807}, "arguments": [{"role": "Theme", "text": "CREB", "start": 769, "end": 773}, {"role": "Cause", "text": "IL-10", "start": 811, "end": 816}]}, {"trigger": {"text": "affected", "start": 799, "end": 807}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 775, "end": 780}, {"role": "Cause", "text": "IL-10", "start": 811, "end": 816}]}, {"trigger": {"text": "affected", "start": 799, "end": 807}, "arguments": [{"role": "Theme", "text": "Sp-1", "start": 786, "end": 790}, {"role": "Cause", "text": "IL-10", "start": 811, "end": 816}]}]}}, "schema": []}
{"input": "Activation of transcription by binding of NF-E1 (YY1) to a newly identified element in the first exon of the human DR alpha gene. \nA previously unrecognized element, located downstream of the start site of transcription in the first exon of the DR alpha gene, has been defined that enhances promoter activity up to eightfold in a position-dependent manner. Mutations in this DNA-binding site abolished binding of a nuclear factor in human B cell nuclear extract and decreased the activity of the DR alpha promoter to a basal level. Significant sequence homology of this element was found in the DNA of the DR beta, DP alpha and -beta, and DQ alpha genes, always located downstream of the transcriptional start site. The nuclear factor binds to the DR alpha and DP alpha element but not to the element in the DQ alpha gene. It was identified as NF-E1 (YY1). This protein, previously identified by its binding to the Ig kappa 3' enhancer and the Ig heavy chain mu E1 site, thus also appears to be quite important in the regulation of MHC class II gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 31, "end": 38}, "arguments": [{"role": "Theme", "text": "NF-E1", "start": 42, "end": 47}, {"role": "Theme2", "text": "DR alpha", "start": 115, "end": 123}]}, {"trigger": {"text": "binds", "start": 735, "end": 740}, "arguments": [{"role": "Site", "text": "element", "start": 793, "end": 800}, {"role": "Theme", "text": "DQ alpha", "start": 808, "end": 816}]}, {"trigger": {"text": "binding", "start": 900, "end": 907}, "arguments": [{"role": "Theme", "text": "NF-E1", "start": 844, "end": 849}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 466, "end": 475}, "arguments": [{"role": "Theme", "text": "DR alpha", "start": 496, "end": 504}, {"role": "Site", "text": "promoter", "start": 505, "end": 513}]}]}}, "schema": []}
{"input": "Coupling of a signal response domain in I kappa B alpha to multiple pathways for NF-kappa B activation. \nThe eukaryotic transcription factor NF-kappa B plays a central role in the induced expression of human immunodeficiency virus type 1 and in many aspects of the genetic program mediating normal T-cell activation and growth. The nuclear activity of NF-kappa B is tightly regulated from the cytoplasmic compartment by an inhibitory subunit called I kappa B alpha. This cytoplasmic inhibitor is rapidly phosphorylated and degraded in response to a diverse set of NF-kappa B-inducing agents, including T-cell mitogens, proinflammatory cytokines, and viral transactivators such as the Tax protein of human T-cell leukemia virus type 1. To explore these I kappa B alpha-dependent mechanisms for NF-kappa B induction, we identified novel mutants of I kappa B alpha that uncouple its inhibitory and signal-transducing functions in human T lymphocytes. Specifically, removal of the N-terminal 36 amino acids of I kappa B alpha failed to disrupt its ability to form latent complexes with NF-kappa B in the cytoplasm. However, this deletion mutation prevented the induced phosphorylation, degradative loss, and functional release of I kappa B alpha from NF-kappa B in Tax-expressing cells. Alanine substitutions introduced at two serine residues positioned within this N-terminal regulatory region of I kappa B alpha also yielded constitutive repressors that escaped from Tax-induced turnover and that potently inhibited immune activation pathways for NF-kappa B induction, including those initiated from antigen and cytokine receptors. In contrast, introduction of a phosphoserine mimetic at these sites rectified this functional defect, a finding consistent with a causal linkage between the phosphorylation status and proteolytic stability of this cytoplasmic inhibitor. Together, these in vivo studies define a critical signal response domain in I kappa B alpha that coordinately controls the biologic activities of I kappa B alpha and NF-kappa B in response to viral and immune stimuli. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "prevented", "start": 1143, "end": 1152}, "arguments": [{"role": "Cause", "text": "I kappa B alpha", "start": 846, "end": 861}, {"role": "Theme", "text": "induced", "start": 1157, "end": 1164}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 504, "end": 518}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 449, "end": 464}]}, {"trigger": {"text": "phosphorylation", "start": 1165, "end": 1180}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1226, "end": 1241}]}, {"trigger": {"text": "phosphorylation", "start": 1787, "end": 1802}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1226, "end": 1241}]}], "positive regulation": [{"trigger": {"text": "in response to", "start": 532, "end": 546}, "arguments": [{"role": "Theme", "text": "phosphorylated", "start": 504, "end": 518}, {"role": "Cause", "text": "Tax", "start": 684, "end": 687}]}, {"trigger": {"text": "in response to", "start": 532, "end": 546}, "arguments": [{"role": "Theme", "text": "degraded", "start": 523, "end": 531}, {"role": "Cause", "text": "Tax", "start": 684, "end": 687}]}, {"trigger": {"text": "in response to", "start": 532, "end": 546}, "arguments": [{"role": "Theme", "text": "phosphorylated", "start": 504, "end": 518}]}, {"trigger": {"text": "in response to", "start": 532, "end": 546}, "arguments": [{"role": "Theme", "text": "degraded", "start": 523, "end": 531}]}, {"trigger": {"text": "induced", "start": 1157, "end": 1164}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1165, "end": 1180}]}, {"trigger": {"text": "induced", "start": 1157, "end": 1164}, "arguments": [{"role": "Theme", "text": "degradative loss", "start": 1182, "end": 1198}]}, {"trigger": {"text": "in response to", "start": 2044, "end": 2058}, "arguments": [{"role": "Theme", "text": "controls", "start": 1977, "end": 1985}]}], "protein catabolism": [{"trigger": {"text": "degraded", "start": 523, "end": 531}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 449, "end": 464}]}, {"trigger": {"text": "degradative loss", "start": 1182, "end": 1198}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1226, "end": 1241}]}, {"trigger": {"text": "proteolytic", "start": 1814, "end": 1825}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1226, "end": 1241}]}], "regulation": [{"trigger": {"text": "controls", "start": 1977, "end": 1985}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 2013, "end": 2028}]}]}}, "schema": []}
{"input": "HIV type 1 protease activation of NF-kappa B within T lymphoid cells. \nNF-kappa B is a nuclear protein of the rel oncogene family capable of enhancing transcription of several cellular genes, including IL-2 and the IL-2 receptor, and viral genes transcribed from the HIV-1 LTR. It has been reported that HIV-1 protease may cleave the NF-kappa B precursor to its active form in vitro. In this study the effects of HIV protease on NF-kappa B precursor activation were examined in Jurkat T cells by introducing a protease expression vector into the cells. Increased NF-kappa B activity was observed and this increased activity was blocked by a specific inhibitor of the viral protease. Viral transcription, as measured using LTR-CAT assays, was only slightly enhanced in the HIV-protease expressing cells, while secretion of IL-2 and expression of the IL-2 receptor were not affected. The limited activation of NF-kappa B by HIV protease appears unlikely to have a significant effect on virus expression or T cell function. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 519, "end": 529}, "arguments": [{"role": "Theme", "text": "HIV protease", "start": 413, "end": 425}]}, {"trigger": {"text": "expressing", "start": 785, "end": 795}, "arguments": [{"role": "Theme", "text": "HIV-protease", "start": 772, "end": 784}]}], "localization": [{"trigger": {"text": "secretion", "start": 809, "end": 818}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 822, "end": 826}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 650, "end": 659}, "arguments": [{"role": "Theme", "text": "HIV protease", "start": 413, "end": 425}]}], "positive regulation": [{"trigger": {"text": "enhancing", "start": 141, "end": 150}, "arguments": [{"role": "Theme", "text": "transcription", "start": 151, "end": 164}]}, {"trigger": {"text": "introducing", "start": 496, "end": 507}, "arguments": [{"role": "Theme", "text": "expression", "start": 519, "end": 529}]}], "regulation": [{"trigger": {"text": "affected", "start": 872, "end": 880}, "arguments": [{"role": "Theme", "text": "secretion", "start": 809, "end": 818}]}], "transcription": [{"trigger": {"text": "transcription", "start": 151, "end": 164}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 202, "end": 206}]}]}}, "schema": []}
{"input": "Expression of Ah receptor (TCDD receptor) during human monocytic differentiation. \nWe have previously found a high expression of human Ah receptor (TCDD receptor) mRNA in peripheral blood cells of individuals. In this paper, the expression of this gene in blood cells was first investigated in fractions of nucleated cells, revealing predominant expression of the Ah receptor gene in the monocyte fraction. Then the expression levels of AhR mRNA in various hematopoietic cell lines were examined together with those of Arnt and P450IA1. AhR was expressed at high levels in monocytoid U937, THP1, and HEL/S cells, and at moderate levels in promyelocytic HL60 cells and erythroblastic HEL cells. However, it was not detected in lymphoid cells MOLT4 (T cell) and BALL1 (B cell), nor in K562 erythroblasts. Furthermore, a specific induction of AhR during monocytic differentiation was investigated in HL60 and HEL cells. HL60 cells were induced to differentiate toward monocytes-macrophages by incubation with phorbol ester, showing a 5- to 2-fold increase of AhR mRNA. The incubation with transforming growth factor beta 1 and 1 alpha,25-dihydroxyvitamin D3 resulted in a 5- to 7-fold increase of AhR mRNA. The HEL cells also exhibited a similar elevation of AhR mRNA level, when they had differentiated toward monocyte-macrophage cells by these combined inducers, but little change in the mRNA level was observed when the cells were induced to differentiate into other cell types. Treatment of the differentiated HL60 cells with 3-methylcholanthrene, a ligand of AhR, induced the expression of the P450IA1 gene. These results indicated that expression of AhR mRNA was significantly induced during monocytic differentiation and that the differentiated cells were responsive to xenobiotics. Our results suggest that AhR may play an important role in the function of monocytes and also in the eventual activation of environmental carcinogens. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligand", "start": 1551, "end": 1557}, "arguments": [{"role": "Theme", "text": "AhR", "start": 1561, "end": 1564}]}], "gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "Ah receptor", "start": 14, "end": 25}]}, {"trigger": {"text": "expression", "start": 229, "end": 239}, "arguments": [{"role": "Theme", "text": "TCDD receptor", "start": 148, "end": 161}]}, {"trigger": {"text": "expression", "start": 346, "end": 356}, "arguments": [{"role": "Theme", "text": "Ah receptor", "start": 364, "end": 375}]}, {"trigger": {"text": "expression", "start": 416, "end": 426}, "arguments": [{"role": "Theme", "text": "P450IA1", "start": 528, "end": 535}]}, {"trigger": {"text": "expressed", "start": 545, "end": 554}, "arguments": [{"role": "Theme", "text": "AhR", "start": 537, "end": 540}]}, {"trigger": {"text": "detected", "start": 714, "end": 722}, "arguments": [{"role": "Theme", "text": "AhR", "start": 537, "end": 540}]}, {"trigger": {"text": "expression", "start": 1578, "end": 1588}, "arguments": [{"role": "Theme", "text": "P450IA1", "start": 1596, "end": 1603}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 827, "end": 836}, "arguments": [{"role": "Theme", "text": "AhR", "start": 840, "end": 843}]}, {"trigger": {"text": "increase", "start": 1044, "end": 1052}, "arguments": [{"role": "Theme", "text": "AhR", "start": 1056, "end": 1059}]}, {"trigger": {"text": "increase", "start": 1182, "end": 1190}, "arguments": [{"role": "Theme", "text": "AhR", "start": 1194, "end": 1197}]}, {"trigger": {"text": "elevation", "start": 1243, "end": 1252}, "arguments": [{"role": "Theme", "text": "AhR", "start": 1256, "end": 1259}]}, {"trigger": {"text": "induced", "start": 1566, "end": 1573}, "arguments": [{"role": "Theme", "text": "expression", "start": 1578, "end": 1588}]}, {"trigger": {"text": "induced", "start": 1680, "end": 1687}, "arguments": [{"role": "Theme", "text": "expression", "start": 1639, "end": 1649}]}], "regulation": [{"trigger": {"text": "change", "start": 1373, "end": 1379}, "arguments": [{"role": "Theme", "text": "AhR", "start": 1256, "end": 1259}]}], "transcription": [{"trigger": {"text": "expression", "start": 115, "end": 125}, "arguments": [{"role": "Theme", "text": "TCDD receptor", "start": 148, "end": 161}]}, {"trigger": {"text": "expression", "start": 416, "end": 426}, "arguments": [{"role": "Theme", "text": "AhR", "start": 437, "end": 440}]}, {"trigger": {"text": "expression", "start": 1639, "end": 1649}, "arguments": [{"role": "Theme", "text": "AhR", "start": 1653, "end": 1656}]}]}}, "schema": []}
{"input": "Platelet-activating factor (PAF) positively auto-regulates the expression of human PAF receptor transcript 1 (leukocyte-type) through NF-kappa B. \nThe human platelet-activating factor receptor (PAFR) gene is transcribed by two distinct promoters (promoter 1 and promoter 2) to generate two transcripts (designated as PAFR transcript 1 and PAFR transcript 2), though their open reading frames are identical. By primer extension analysis to discriminate two transcripts, we found that the levels of PAFR transcript 1 (leukocyte-type), but not PAFR transcript 2 (tissue-type), are upregulated by PAF as well as by 12-O-tetradecanoylphorbol-13-acetate (TPA) in the human stomach cancer cell line (JR-St cells) which expresses both functional PAFR transcript 1 and PAFR transcript 2 endogenously. Functional analysis of the promoter 1 with a transient expression assay using chloramphenicol acetyltransferase (CAT) gene as a reporter showed that both PAF and TPA activated the promoter 1 but not the deleted promoter lacking the three consensus binding sites for NF-kappa B located from -571 bp to -459 bp. These findings suggest a molecular mechanism of positive regulation of PAFR gene expression by PAF through NF-kappa B, possibly by a phosphorylation reaction involving protein kinase C by PAF. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expresses", "start": 712, "end": 721}, "arguments": [{"role": "Theme", "text": "PAFR", "start": 738, "end": 742}]}, {"trigger": {"text": "expresses", "start": 712, "end": 721}, "arguments": [{"role": "Theme", "text": "PAFR", "start": 760, "end": 764}]}, {"trigger": {"text": "expression", "start": 1183, "end": 1193}, "arguments": [{"role": "Theme", "text": "PAFR", "start": 1173, "end": 1177}]}], "positive regulation": [{"trigger": {"text": "expression", "start": 63, "end": 73}, "arguments": [{"role": "Theme", "text": "PAF receptor", "start": 83, "end": 95}]}, {"trigger": {"text": "by", "start": 220, "end": 222}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 208, "end": 219}]}, {"trigger": {"text": "upregulated", "start": 578, "end": 589}, "arguments": [{"role": "Theme", "text": "PAFR", "start": 541, "end": 545}]}, {"trigger": {"text": "positive regulation", "start": 1150, "end": 1169}, "arguments": [{"role": "Theme", "text": "expression", "start": 1183, "end": 1193}]}], "transcription": [{"trigger": {"text": "transcribed", "start": 208, "end": 219}, "arguments": [{"role": "Theme", "text": "PAFR", "start": 194, "end": 198}]}]}}, "schema": []}
{"input": "Distinct roles of the molecular chaperone hsp90 in modulating dioxin receptor function via the basic helix-loop-helix and PAS domains. \nThe intracellular dioxin receptor mediates signal transduction by dioxin and functions as a ligand-activated transcription factor. It contains a basic helix-loop-helix (bHLH) motif contiguous with a Per-Arnt-Sim (PAS) homology region. In extracts from nonstimulated cells the receptor is recovered in an inducible cytoplasmic form associated with the 90-kDa heat shock protein (hsp90), a molecular chaperone. We have reconstituted ligand-dependent activation of the receptor to a DNA-binding form by using the dioxin receptor and its bHLH-PAS partner factor Arnt expressed by in vitro translation in reticulocyte lysate. Deletion of the PAS domain of the receptor resulted in constitutive dimerization with Arnt. In contrast, this receptor mutant showed low levels of xenobiotic response element-binding activity, indicating that the PAS domain may be important for DNA-binding affinity and/or specificity of the receptor. It was not possible to reconstitute dioxin receptor function with proteins expressed in wheat germ lysate. In line with these observations, reticulocyte lysate but not wheat germ lysate promoted the association of de novo synthesized dioxin receptor with hsp90. At least two distinct domains of the receptor mediated interaction with hsp90: the ligand-binding domain located within the PAS region and, surprisingly, the bHLH domain. Whereas ligand-binding activity correlated with association with hsp90, bHLH-hsp90 interaction appeared to be important for DNA-binding activity but not for dimerization of the receptor. Several distinct roles for hsp90 in modulating dioxin receptor function are therefore likely: correct folding of the ligand-binding domain, interference with Arnt heterodimerization, and folding of a DNA-binding conformation of the bHLH domain. Thus, the dioxin receptor system provides a complex and interesting model of the regulation of transcription factors by hsp90. ", "output": {"json_structures": {}}, "schema": []}
{"input": "T-cell functional regions of the human IL-3 proximal promoter. \nThe human interleukin-3 (IL-3) gene is expressed almost exclusively in activated T cells. Its expression is regulated at both the transcriptional and post-transcriptional level. We have previously shown that treatment of Jurkat T cells with phytohemaglutinin (PHA) and the phorbol ester, PMA, activated transcription initiation from the IL-3 gene. To define the regions of the gene required for transcription activation, we generated a series of reporter constructs containing different regions of the IL-3 gene 5' and 3' flanking sequences. Both positive and negative regulatory elements were identified in the proximal 5' flanking region of the IL-3 gene. The promoter region between -173 and -60 contained the strongest activating elements. The transcription factor AP-1 could bind to this positive activator region of the promoter. We also examined the function of the IL-3 CK-1/CK-2 elements that are present in many cytokine genes and found that they acted as a repressor of basal level expression when cloned upstream of a heterologous promoter but were also inducible by PMA/PHA. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 103, "end": 112}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 89, "end": 93}]}, {"trigger": {"text": "expression", "start": 158, "end": 168}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 89, "end": 93}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 357, "end": 366}, "arguments": [{"role": "Theme", "text": "transcription initiation", "start": 367, "end": 391}]}, {"trigger": {"text": "required", "start": 446, "end": 454}, "arguments": [{"role": "Theme", "text": "activated", "start": 357, "end": 366}, {"role": "Cause", "text": "IL-3", "start": 566, "end": 570}]}], "regulation": [{"trigger": {"text": "regulated", "start": 172, "end": 181}, "arguments": [{"role": "Theme", "text": "expression", "start": 158, "end": 168}]}, {"trigger": {"text": "regulated", "start": 172, "end": 181}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 194, "end": 209}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 194, "end": 209}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 89, "end": 93}]}, {"trigger": {"text": "transcription initiation", "start": 367, "end": 391}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 401, "end": 405}]}]}}, "schema": []}
{"input": "Two distinct signalling pathways are involved in the control of the biphasic junB transcription induced by interleukin-6 in the B cell hybridoma 7TD1. \nWe have measured the level of junB mRNA in the B hybridoma cell line 7TD1, under interleukin-6 (IL-6) stimulation. IL-6 increases junB mRNA in a biphasic fashion. The first early-induced peak was transient and likely corresponds to the well documented typical junB mRNA, stimulated in response to numerous growth factors, including IL-6. At variance, the second peak which has never been reported previously, lasted several hours. As a consequence of its effect on junB mRNA, IL-6 stimulated, in a biphasic fashion, the nuclear accumulation of the JunB protein. In this study, we demonstrated that IL-6 regulation occurred exclusively at the transcriptional level and that the bimodal increase of junB mRNA and JunB protein can be accounted for by a biphasic stimulation of junB transcription. Furthermore, our data point to two major differences between the mechanism of control of the early and the late IL-6-induced junB transcription waves. First, cycloheximide strongly potentiated the transcription of the second wave, whereas it failed to affect the early-induced burst. Second, tyrphostin, a tyrosine kinase inhibitor, impaired the expression of the first but not the second junB mRNA peak. Conversely, genistein, another tyrosine kinase inhibitor, totally abolished the expression of the second peak of junB mRNA whereas it did not affect the expression of the first peak. Altogether these data indicate that, in 7TD1 cells, IL-6 controls junB transcription in a biphasic fashion by means of two separate transduction pathways. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "accumulation", "start": 680, "end": 692}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 672, "end": 679}, {"role": "Theme", "text": "JunB", "start": 700, "end": 704}]}], "negative regulation": [{"trigger": {"text": "impaired", "start": 1279, "end": 1287}, "arguments": [{"role": "Theme", "text": "expression", "start": 1292, "end": 1302}]}, {"trigger": {"text": "abolished", "start": 1417, "end": 1426}, "arguments": [{"role": "Theme", "text": "expression", "start": 1431, "end": 1441}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 96, "end": 103}, "arguments": [{"role": "Theme", "text": "transcription", "start": 82, "end": 95}, {"role": "Cause", "text": "interleukin-6", "start": 107, "end": 120}]}, {"trigger": {"text": "increases", "start": 272, "end": 281}, "arguments": [{"role": "Cause", "text": "IL-6", "start": 267, "end": 271}, {"role": "Theme", "text": "junB", "start": 282, "end": 286}]}, {"trigger": {"text": "stimulated", "start": 423, "end": 433}, "arguments": [{"role": "Theme", "text": "junB", "start": 412, "end": 416}, {"role": "Cause", "text": "IL-6", "start": 484, "end": 488}]}, {"trigger": {"text": "stimulated", "start": 633, "end": 643}, "arguments": [{"role": "Cause", "text": "effect", "start": 607, "end": 613}, {"role": "Theme", "text": "accumulation", "start": 680, "end": 692}]}, {"trigger": {"text": "increase", "start": 837, "end": 845}, "arguments": [{"role": "Theme", "text": "junB", "start": 849, "end": 853}, {"role": "Cause", "text": "stimulation", "start": 911, "end": 922}]}, {"trigger": {"text": "increase", "start": 837, "end": 845}, "arguments": [{"role": "Theme", "text": "JunB", "start": 863, "end": 867}, {"role": "Cause", "text": "stimulation", "start": 911, "end": 922}]}, {"trigger": {"text": "stimulation", "start": 911, "end": 922}, "arguments": [{"role": "Cause", "text": "IL-6", "start": 750, "end": 754}, {"role": "Theme", "text": "transcription", "start": 931, "end": 944}]}, {"trigger": {"text": "induced", "start": 1063, "end": 1070}, "arguments": [{"role": "Cause", "text": "IL-6", "start": 1058, "end": 1062}, {"role": "Theme", "text": "transcription", "start": 1076, "end": 1089}]}, {"trigger": {"text": "by means of", "start": 1641, "end": 1652}, "arguments": [{"role": "Theme", "text": "controls", "start": 1591, "end": 1599}]}], "regulation": [{"trigger": {"text": "control", "start": 53, "end": 60}, "arguments": [{"role": "Theme", "text": "transcription", "start": 82, "end": 95}]}, {"trigger": {"text": "under", "start": 227, "end": 232}, "arguments": [{"role": "Theme", "text": "level", "start": 173, "end": 178}]}, {"trigger": {"text": "effect", "start": 607, "end": 613}, "arguments": [{"role": "Theme", "text": "junB", "start": 617, "end": 621}, {"role": "Cause", "text": "IL-6", "start": 628, "end": 632}]}, {"trigger": {"text": "control", "start": 1024, "end": 1031}, "arguments": [{"role": "Theme", "text": "induced", "start": 1063, "end": 1070}]}, {"trigger": {"text": "affect", "start": 1493, "end": 1499}, "arguments": [{"role": "Theme", "text": "expression", "start": 1431, "end": 1441}]}, {"trigger": {"text": "controls", "start": 1591, "end": 1599}, "arguments": [{"role": "Cause", "text": "IL-6", "start": 1586, "end": 1590}, {"role": "Theme", "text": "transcription", "start": 1605, "end": 1618}]}], "transcription": [{"trigger": {"text": "transcription", "start": 82, "end": 95}, "arguments": [{"role": "Theme", "text": "junB", "start": 77, "end": 81}]}, {"trigger": {"text": "level", "start": 173, "end": 178}, "arguments": [{"role": "Theme", "text": "junB", "start": 182, "end": 186}]}, {"trigger": {"text": "transcription", "start": 931, "end": 944}, "arguments": [{"role": "Theme", "text": "junB", "start": 926, "end": 930}]}, {"trigger": {"text": "transcription", "start": 1076, "end": 1089}, "arguments": [{"role": "Theme", "text": "junB", "start": 1071, "end": 1075}]}, {"trigger": {"text": "expression", "start": 1292, "end": 1302}, "arguments": [{"role": "Theme", "text": "junB", "start": 1335, "end": 1339}]}, {"trigger": {"text": "expression", "start": 1431, "end": 1441}, "arguments": [{"role": "Theme", "text": "junB", "start": 1464, "end": 1468}]}, {"trigger": {"text": "transcription", "start": 1605, "end": 1618}, "arguments": [{"role": "Theme", "text": "junB", "start": 1600, "end": 1604}]}]}}, "schema": []}
{"input": "Biphasic control of nuclear factor-kappa B activation by the T cell receptor complex: role of tumor necrosis factor alpha. \nThe regulation of nuclear factor (NF)-kappa B activation by the T cell receptor (TcR)/CD3 complex in primary human T cells has been studied at various times after activation. Only p50 NF-kappa B protein bound the kappa B element of interleukin-2 receptor (IL-2R) alpha chain promoter on resting T cells. However, immediately after TcR/CD3 cross-linking (after approximately 1 h; immediate) binding of p50.p65 heterodimers was observed. p50.c-rel heterodimers were also detected bound to this sequence at early time points (7-16 h; early), and both remained active at later time points (40 h; late) after activation. This regulation takes place mainly at the level of nuclear translocation of p65 and c-rel, at immediate and early time points. Activation also induced c-rel and p105/p50 mRNA synthesis, but not p65 mRNA whose expression was constitutive. Interestingly, all those early and late events, but not the immediate ones, were inhibited by a neutralizing anti-tumor necrosis factor alpha (TNF-alpha) monoclonal antibody. Similarly, cycloheximide prevented the p65 and c-rel translocation and consequent formation of active binding heterodimers, at early and late times. Cyclosporin A impaired not only early and late, but also immediate events; however, addition of TNF-alpha prevented all inhibition. These results indicate that the regulation of NF-kappa B activation during T cell activation by TcR/CD3 signals is biphasic: TcR/CD3 triggers its immediate translocation, which is transient if no TNF-alpha is present. TNF-alpha, therefore, emerges as the main factor responsible for a second phase of NF-kappa B regulation, controlling both translocation of p65 and c-rel, and new mRNA synthesis for c-rel and p105/p50. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 327, "end": 332}, "arguments": [{"role": "Theme", "text": "p50", "start": 304, "end": 307}]}, {"trigger": {"text": "binding", "start": 514, "end": 521}, "arguments": [{"role": "Theme", "text": "p50", "start": 525, "end": 528}]}, {"trigger": {"text": "binding", "start": 514, "end": 521}, "arguments": [{"role": "Theme", "text": "p65", "start": 529, "end": 532}]}, {"trigger": {"text": "heterodimers", "start": 533, "end": 545}, "arguments": [{"role": "Theme", "text": "p50", "start": 525, "end": 528}, {"role": "Theme2", "text": "p65", "start": 529, "end": 532}]}, {"trigger": {"text": "heterodimers", "start": 570, "end": 582}, "arguments": [{"role": "Theme", "text": "p50", "start": 560, "end": 563}, {"role": "Theme2", "text": "c-rel", "start": 564, "end": 569}]}, {"trigger": {"text": "bound", "start": 602, "end": 607}, "arguments": [{"role": "Theme", "text": "p50", "start": 560, "end": 563}]}, {"trigger": {"text": "bound", "start": 602, "end": 607}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 564, "end": 569}]}, {"trigger": {"text": "heterodimers", "start": 1263, "end": 1275}, "arguments": [{"role": "Theme", "text": "p65", "start": 1192, "end": 1195}, {"role": "Theme2", "text": "c-rel", "start": 1200, "end": 1205}]}], "localization": [{"trigger": {"text": "translocation", "start": 799, "end": 812}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 791, "end": 798}, {"role": "Theme", "text": "p65", "start": 816, "end": 819}]}, {"trigger": {"text": "translocation", "start": 799, "end": 812}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 791, "end": 798}, {"role": "Theme", "text": "c-rel", "start": 824, "end": 829}]}, {"trigger": {"text": "translocation", "start": 1206, "end": 1219}, "arguments": [{"role": "Theme", "text": "p65", "start": 1192, "end": 1195}]}, {"trigger": {"text": "translocation", "start": 1206, "end": 1219}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 1200, "end": 1205}]}, {"trigger": {"text": "translocation", "start": 1775, "end": 1788}, "arguments": [{"role": "Theme", "text": "p65", "start": 1792, "end": 1795}]}, {"trigger": {"text": "translocation", "start": 1775, "end": 1788}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 1800, "end": 1805}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1059, "end": 1068}, "arguments": [{"role": "Theme", "text": "binding", "start": 514, "end": 521}]}, {"trigger": {"text": "inhibited", "start": 1059, "end": 1068}, "arguments": [{"role": "Theme", "text": "bound", "start": 602, "end": 607}]}, {"trigger": {"text": "inhibited", "start": 1059, "end": 1068}, "arguments": [{"role": "Theme", "text": "translocation", "start": 799, "end": 812}]}, {"trigger": {"text": "prevented", "start": 1178, "end": 1187}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1206, "end": 1219}]}, {"trigger": {"text": "prevented", "start": 1178, "end": 1187}, "arguments": [{"role": "Theme", "text": "heterodimers", "start": 1263, "end": 1275}]}, {"trigger": {"text": "impaired", "start": 1316, "end": 1324}, "arguments": [{"role": "Theme", "text": "binding", "start": 514, "end": 521}]}, {"trigger": {"text": "impaired", "start": 1316, "end": 1324}, "arguments": [{"role": "Theme", "text": "bound", "start": 602, "end": 607}]}, {"trigger": {"text": "impaired", "start": 1316, "end": 1324}, "arguments": [{"role": "Theme", "text": "translocation", "start": 799, "end": 812}]}, {"trigger": {"text": "prevented", "start": 1408, "end": 1417}, "arguments": [{"role": "Theme", "text": "impaired", "start": 1316, "end": 1324}, {"role": "Cause", "text": "TNF-alpha", "start": 1398, "end": 1407}]}], "positive regulation": [{"trigger": {"text": "after", "start": 449, "end": 454}, "arguments": [{"role": "Theme", "text": "binding", "start": 514, "end": 521}]}, {"trigger": {"text": "induced", "start": 883, "end": 890}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 915, "end": 924}]}], "regulation": [{"trigger": {"text": "controlling", "start": 1758, "end": 1769}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1652, "end": 1661}, {"role": "Theme", "text": "translocation", "start": 1775, "end": 1788}]}, {"trigger": {"text": "controlling", "start": 1758, "end": 1769}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1652, "end": 1661}, {"role": "Theme", "text": "mRNA synthesis", "start": 1815, "end": 1829}]}], "transcription": [{"trigger": {"text": "synthesis", "start": 915, "end": 924}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 891, "end": 896}]}, {"trigger": {"text": "synthesis", "start": 915, "end": 924}, "arguments": [{"role": "Theme", "text": "p50", "start": 906, "end": 909}]}, {"trigger": {"text": "synthesis", "start": 915, "end": 924}, "arguments": [{"role": "Theme", "text": "p65", "start": 934, "end": 937}]}, {"trigger": {"text": "mRNA synthesis", "start": 1815, "end": 1829}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 1834, "end": 1839}]}, {"trigger": {"text": "mRNA synthesis", "start": 1815, "end": 1829}, "arguments": [{"role": "Theme", "text": "p50", "start": 1849, "end": 1852}]}]}}, "schema": []}
{"input": "Protein kinase C is not a downstream effector of p21ras in activated T cells. \nThe aim of this present study was to investigate the role of protein kinase C (PKC), downstream of p21ras, in activating interleukin-2 (IL-2) gene expression. It has been reported that PKC is an effector of p21ras in T cells. Data is presented, using the potent and selective PKC inhibitor Ro 31-8425 and transient expression of a constitutively active ras mutant, which clearly shows that PKC is not downstream of p21ras in the induction of NF-AT and AP-1 transcriptional activity and in the expression of IL-2 in human Jurkat T cells. Reporter gene experiments demonstrated that NF-kappa B transcriptional activity is not affected by expression of activated p21ras. The signaling pathways involving PKC activation, calcium mobilization and ras activation combine to provide the necessary components for production of IL-2 during T cell activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 226, "end": 236}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 215, "end": 219}]}, {"trigger": {"text": "expression", "start": 572, "end": 582}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 586, "end": 590}]}, {"trigger": {"text": "production", "start": 884, "end": 894}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 898, "end": 902}]}], "positive regulation": [{"trigger": {"text": "activating", "start": 189, "end": 199}, "arguments": [{"role": "Theme", "text": "expression", "start": 226, "end": 236}]}, {"trigger": {"text": "activated", "start": 729, "end": 738}, "arguments": [{"role": "Theme", "text": "p21ras", "start": 739, "end": 745}]}, {"trigger": {"text": "during", "start": 903, "end": 909}, "arguments": [{"role": "Theme", "text": "production", "start": 884, "end": 894}]}]}}, "schema": []}
{"input": "Association of alterations in NF-kappa B moieties with HIV type 1 proviral latency in certain monocytic cells. \nHuman immunodeficiency virus type 1 (HIV-1) replication is controlled by a complex array of virally encoded and cellular proteins. A wide spectrum of levels of HIV-1 expression have been demonstrated in various cells, both in cell culture and in vivo. Molecular mechanisms leading to restricted HIV-1 replication may differ between certain cell types. It is now demonstrated that HIV-1 proviral latency in the monocytic cell line U1, in which only extremely low levels of HIV-1 expression are detected in the baseline unstimulated state, is associated with alterations in nuclear factor-kappa B (NF-kappa B) moieties demonstrated in these cells by electrophoretic mobility shift assays (EMSAs) and in situ UV cross-linking studies. A predominance of p50 NF-kappa B moieties and possibly p50 homodimers or closely related species, rather than the p50-p56 heterodimer of NF-kappa B that is the predominant NF-kappa B species in most T lymphocytic and monocytic cells, is demonstrated in the nuclei of U1 cells. This pattern of NF-kappa B-related moieties differs from the latently infected T lymphocytic cell line ACH-2, and from the U937 monocytic line, the parental cell line of the U1 cellular clone. As such, these data suggest that different proximal mechanisms may lead to restricted HIV-1 replication in various cell types. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "homodimers", "start": 903, "end": 913}, "arguments": [{"role": "Theme", "text": "p50", "start": 899, "end": 902}]}, {"trigger": {"text": "heterodimer", "start": 966, "end": 977}, "arguments": [{"role": "Theme", "text": "p50", "start": 958, "end": 961}, {"role": "Theme2", "text": "p56", "start": 962, "end": 965}]}]}}, "schema": []}
{"input": "Overexpression of protein kinase C-zeta stimulates leukemic cell differentiation. \nA function for protein kinase C-zeta (PKC-zeta), a member of the phorbol ester nonresponsive atypical protein kinase C subfamily, in modulating differentiation was examined in the leukemic U937 cell. Transfected U937 cells stably overexpressing PKC-zeta displayed a longer doubling time, lower saturation density at confluency, and an increase in adherence to plastic as compared to control cells. PKC-zeta cells expressed a more differentiated phenotype as assessed by changes in morphology, surface antigen expression, and lysosomal enzyme activities and were distinct from parental U937 cells stimulated to differentiate by exposure to phorbol esters. In contrast to parental U937 cells, PKC-zeta cells constitutively expressed mRNA transcripts for c-jun and a low mobility AP-1 binding activity. Thus, PKC-zeta overexpression stimulates a type of phenotypic differentiation that differs significantly from maturation occurring upon activation of other PKC subfamilies induced by phorbol ester treatment. Increased expression of the c-jun protooncogene and an increase in AP-1 binding activity in PKC-zeta cells provides a potential mechanism for explaining the altered differentiation status of this cell. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Overexpression", "start": 0, "end": 14}, "arguments": [{"role": "Theme", "text": "protein kinase C-zeta", "start": 18, "end": 39}]}, {"trigger": {"text": "overexpressing", "start": 313, "end": 327}, "arguments": [{"role": "Theme", "text": "PKC-zeta", "start": 328, "end": 336}]}, {"trigger": {"text": "overexpression", "start": 898, "end": 912}, "arguments": [{"role": "Theme", "text": "PKC-zeta", "start": 889, "end": 897}]}, {"trigger": {"text": "expression", "start": 1101, "end": 1111}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1119, "end": 1124}]}], "positive regulation": [{"trigger": {"text": "Overexpression", "start": 0, "end": 14}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 0, "end": 14}]}, {"trigger": {"text": "overexpressing", "start": 313, "end": 327}, "arguments": [{"role": "Theme", "text": "overexpressing", "start": 313, "end": 327}]}, {"trigger": {"text": "overexpression", "start": 898, "end": 912}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 898, "end": 912}]}, {"trigger": {"text": "Increased", "start": 1091, "end": 1100}, "arguments": [{"role": "Theme", "text": "expression", "start": 1101, "end": 1111}]}], "regulation": [{"trigger": {"text": "nonresponsive", "start": 162, "end": 175}, "arguments": [{"role": "Theme", "text": "PKC-zeta", "start": 121, "end": 129}]}], "transcription": [{"trigger": {"text": "expressed", "start": 804, "end": 813}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 835, "end": 840}]}]}}, "schema": []}
{"input": "Posttranscriptional regulation of macrophage tissue factor expression by antioxidants. \nTissue factor (TF) expression by cells of monocyte/macrophage lineage represents an important mechanism underlying the initiation of fibrin deposition at sites of extravascular inflammation. Recent evidence suggests a role for oxidant stress in the signalling pathway of various cell types by virtue of its ability to induce DNA binding of various transcription factors, including nuclear factor kappa B and AP-1. The effect of antioxidant treatment on lipopolysaccharide (LPS)-induced TF expression was examined in murine peritoneal macrophages and human monocytes. Both pyrrolidine dithiocarbamate, an oxidant scavenger, and N-acetyl-cysteine, a precursor of the endogenous antioxidant glutathione, inhibited stimulation of macrophage procoagulant activity by LPS. Northern blot analysis showed that neither of these agents reduced LPS-stimulated TF mRNA accumulation, thereby suggesting a posttranscriptional mechanism for the effect. Immunofluorescence studies of human monocytes using polyclonal anti-TF antibody showed that N-acetyl-cysteine treatment prevented the characteristic plasmalemmal localization of TF antigen that occurs in response to LPS. Western blot analysis showed that N-acetyl-cysteine reduced the accumulation of the 47-kD mature glycoprotein in LPS-treated cells, a finding consistent with the results of the immunofluorescence studies. Furthermore, these conditions did not result in an accumulation of the less mature forms of TF. When considered together, these data suggest that antioxidants exert their effects by impairing translation and/or by causing degradation of newly translated protein. The effect of antioxidants on tumor necrosis factor appeared to be species specific, with no effect on LPS-induced tumor necrosis factor in murine cells, but with inhibition in human monocytes. The posttranscriptional effect of antioxidants on TF expression data suggests a novel mechanism whereby these agents might modulate monocyte/macrophage activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 59, "end": 69}, "arguments": [{"role": "Theme", "text": "tissue factor", "start": 45, "end": 58}]}, {"trigger": {"text": "expression", "start": 107, "end": 117}, "arguments": [{"role": "Theme", "text": "TF", "start": 103, "end": 105}]}, {"trigger": {"text": "expression", "start": 577, "end": 587}, "arguments": [{"role": "Theme", "text": "TF", "start": 574, "end": 576}]}, {"trigger": {"text": "expression", "start": 1962, "end": 1972}, "arguments": [{"role": "Theme", "text": "TF", "start": 1959, "end": 1961}]}], "localization": [{"trigger": {"text": "localization", "start": 1188, "end": 1200}, "arguments": [{"role": "ToLoc", "text": "plasmalemmal", "start": 1175, "end": 1187}, {"role": "Theme", "text": "TF", "start": 1204, "end": 1206}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 914, "end": 921}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 926, "end": 936}]}, {"trigger": {"text": "prevented", "start": 1146, "end": 1155}, "arguments": [{"role": "Theme", "text": "occurs", "start": 1220, "end": 1226}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 566, "end": 573}, "arguments": [{"role": "Theme", "text": "expression", "start": 577, "end": 587}]}, {"trigger": {"text": "stimulated", "start": 926, "end": 936}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 945, "end": 957}]}, {"trigger": {"text": "accumulation", "start": 945, "end": 957}, "arguments": [{"role": "Theme", "text": "TF", "start": 937, "end": 939}]}, {"trigger": {"text": "occurs", "start": 1220, "end": 1226}, "arguments": [{"role": "Theme", "text": "localization", "start": 1188, "end": 1200}]}, {"trigger": {"text": "result", "start": 1490, "end": 1496}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1503, "end": 1515}]}, {"trigger": {"text": "accumulation", "start": 1503, "end": 1515}, "arguments": [{"role": "Theme", "text": "TF", "start": 1544, "end": 1546}]}], "regulation": [{"trigger": {"text": "Posttranscriptional regulation", "start": 0, "end": 30}, "arguments": [{"role": "Theme", "text": "expression", "start": 59, "end": 69}]}, {"trigger": {"text": "effect", "start": 506, "end": 512}, "arguments": [{"role": "Theme", "text": "induced", "start": 566, "end": 573}]}, {"trigger": {"text": "posttranscriptional effect", "start": 1913, "end": 1939}, "arguments": [{"role": "Theme", "text": "expression", "start": 1962, "end": 1972}]}]}}, "schema": []}
{"input": "Regulation of I kappa B alpha and p105 in monocytes and macrophages persistently infected with human immunodeficiency virus. \nThe mechanisms regulating human immunodeficiency virus (HIV) persistence in human monocytes/macrophages are partially understood. Persistent HIV infection of U937 monocytic cells results in NF-kappa B activation. Whether virus-induced NF-kappa B activation is a mechanism that favors continuous viral replication in macrophages remains unknown. To further delineate the molecular mechanisms involved in the activation of NF-kappa B in HIV-infected monocytes and macrophages, we have focused on the regulation of the I kappa B molecules. First, we show that persistent HIV infection results in the activation of NF-kappa B not only in monocytic cells but also in macrophages. In HIV-infected cells, I kappa B alpha protein levels are decreased secondary to enhanced protein degradation. This parallels the increased I kappa B alpha synthesis secondary to increased I kappa B alpha gene transcription, i.e., increased RNA and transcriptional activity of its promoter-enhancer. Another protein with I kappa B function, p105, is also modified in HIV-infected cells: p105 and p50 steady-state protein levels are increased as a result of increased synthesis and proteolytic processing of p105. Transcriptional activity of p105 is also increased in infected cells and is also mediated by NF-kappa B through a specific kappa B motif. These results demonstrate the existence of a triple autoregulatory loop in monocytes and macrophages involving HIV, p105 and p50, and MAD3, with the end result of persistent NF-kappa B activation and viral persistence. Furthermore, persistent HIV infection of monocytes and macrophages provides a useful model with which to study concomitant modifications of different I kappa B molecules. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "decreased", "start": 859, "end": 868}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 824, "end": 839}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 980, "end": 989}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1011, "end": 1024}]}, {"trigger": {"text": "increased", "start": 1032, "end": 1041}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 1050, "end": 1074}]}, {"trigger": {"text": "increased", "start": 1032, "end": 1041}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 990, "end": 1005}]}, {"trigger": {"text": "increased", "start": 1233, "end": 1242}, "arguments": [{"role": "Theme", "text": "p105", "start": 1188, "end": 1192}]}, {"trigger": {"text": "increased", "start": 1233, "end": 1242}, "arguments": [{"role": "Theme", "text": "p50", "start": 1197, "end": 1200}]}, {"trigger": {"text": "increased", "start": 1355, "end": 1364}, "arguments": [{"role": "Theme", "text": "Transcriptional activity", "start": 1314, "end": 1338}]}, {"trigger": {"text": "mediated", "start": 1395, "end": 1403}, "arguments": [{"role": "Theme", "text": "Transcriptional activity", "start": 1314, "end": 1338}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 14, "end": 29}]}, {"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "p105", "start": 34, "end": 38}]}, {"trigger": {"text": "modified", "start": 1156, "end": 1164}, "arguments": [{"role": "Theme", "text": "p105", "start": 1142, "end": 1146}]}, {"trigger": {"text": "triple autoregulatory loop", "start": 1497, "end": 1523}, "arguments": [{"role": "Theme", "text": "p105", "start": 1568, "end": 1572}]}, {"trigger": {"text": "triple autoregulatory loop", "start": 1497, "end": 1523}, "arguments": [{"role": "Theme", "text": "p50", "start": 1577, "end": 1580}]}, {"trigger": {"text": "triple autoregulatory loop", "start": 1497, "end": 1523}, "arguments": [{"role": "Theme", "text": "MAD3", "start": 1586, "end": 1590}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1011, "end": 1024}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 990, "end": 1005}]}, {"trigger": {"text": "transcriptional activity", "start": 1050, "end": 1074}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 990, "end": 1005}]}, {"trigger": {"text": "Transcriptional activity", "start": 1314, "end": 1338}, "arguments": [{"role": "Theme", "text": "p105", "start": 1342, "end": 1346}]}]}}, "schema": []}
{"input": "Expression and genomic configuration of GM-CSF, IL-3, M-CSF receptor (C-FMS), early growth response gene-1 (EGR-1) and M-CSF genes in primary myelodysplastic syndromes. \nPeripheral blood mononuclear cells from seventeen patients with primary myelodysplastic syndromes (MDS) in advanced stage were enriched for blasts and tested for (1) karyotype, (2) genomic configuration and (3) expression of IL-3, GM-CSF, FMS and EGR-1 genes which are all located on the long arm of chromosome 5. The expression of the M-CSF gene, that has been recently reassigned to the short arm of chromosome 1 (lp), was also investigated. Aims of the study were to (1) assess the potential role of the expression of these genes in the maintenance and expansion of the neoplastic clones and (2) search for constitutional losses or rearrangements of one allele followed by a deletion of the second allele of the same genes in the leukemic cells. The latter issue was investigated by comparing, in 8 cases, constitutive DNA from skin fibroblasts with leukemic DNA. Eleven of the 17 patients had abnormal karyotypes. The M-CSF gene was expressed in 6 cases and the FMS and the EGR-1 genes were expressed in 2 of the latter cases. An autocrine mechanism of growth could be hypothesized only for the 2 patients whose cells expressed both the M-CSF and FMS genes. No germline changes or rearrangements were observed in any of the genes studied. Thus, deregulation of genes encoding for certain hemopoietic growth factors or receptors does not seem to represent a major mechanism of MDS progression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 108, "end": 113}]}, {"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 119, "end": 124}]}, {"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 40, "end": 46}]}, {"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 48, "end": 52}]}, {"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "C-FMS", "start": 70, "end": 75}]}, {"trigger": {"text": "expression", "start": 381, "end": 391}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 395, "end": 399}]}, {"trigger": {"text": "expression", "start": 381, "end": 391}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 401, "end": 407}]}, {"trigger": {"text": "expression", "start": 381, "end": 391}, "arguments": [{"role": "Theme", "text": "FMS", "start": 409, "end": 412}]}, {"trigger": {"text": "expression", "start": 381, "end": 391}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 417, "end": 422}]}, {"trigger": {"text": "expression", "start": 488, "end": 498}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 506, "end": 511}]}, {"trigger": {"text": "expression", "start": 677, "end": 687}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 395, "end": 399}]}, {"trigger": {"text": "expression", "start": 677, "end": 687}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 401, "end": 407}]}, {"trigger": {"text": "expression", "start": 677, "end": 687}, "arguments": [{"role": "Theme", "text": "FMS", "start": 409, "end": 412}]}, {"trigger": {"text": "expression", "start": 677, "end": 687}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 417, "end": 422}]}, {"trigger": {"text": "expression", "start": 677, "end": 687}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 506, "end": 511}]}, {"trigger": {"text": "expressed", "start": 1107, "end": 1116}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 1092, "end": 1097}]}, {"trigger": {"text": "expressed", "start": 1165, "end": 1174}, "arguments": [{"role": "Theme", "text": "FMS", "start": 1136, "end": 1139}]}, {"trigger": {"text": "expressed", "start": 1165, "end": 1174}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 1148, "end": 1153}]}, {"trigger": {"text": "expressed", "start": 1292, "end": 1301}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 1311, "end": 1316}]}, {"trigger": {"text": "expressed", "start": 1292, "end": 1301}, "arguments": [{"role": "Theme", "text": "FMS", "start": 1321, "end": 1324}]}], "regulation": [{"trigger": {"text": "changes", "start": 1344, "end": 1351}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 395, "end": 399}]}, {"trigger": {"text": "changes", "start": 1344, "end": 1351}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 401, "end": 407}]}, {"trigger": {"text": "changes", "start": 1344, "end": 1351}, "arguments": [{"role": "Theme", "text": "FMS", "start": 409, "end": 412}]}, {"trigger": {"text": "changes", "start": 1344, "end": 1351}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 417, "end": 422}]}, {"trigger": {"text": "changes", "start": 1344, "end": 1351}, "arguments": [{"role": "Theme", "text": "M-CSF", "start": 506, "end": 511}]}]}}, "schema": []}
{"input": "OBF-1, a novel B cell-specific coactivator that stimulates immunoglobulin promoter activity through association with octamer-binding proteins. \nRecent biochemical and genetic studies indicate that in addition to the octamer-binding proteins Oct-1 and Oct-2, other B cell components are required for lymphoid-restricted, octamer site-mediated immunoglobulin gene promoter activity. Using a genetic screen in yeast, we have isolated B cell-derived cDNAs encoding Oct-binding factor 1 (OBF-1), a novel protein that specifically associates with Oct-1 and Oct-2. Biochemical studies demonstrate that OBF-1 has no intrinsic DNA-binding activity and recognizes the POU domains of Oct-1 and Oct-2, but not those of Oct-4 and Oct-6. The OBF-1 mRNA is expressed in a highly cell-specific manner, being most abundant in B cells and essentially absent in most of the other cells or tissues tested. Furthermore, expression of OBF-1 in HeLa cells selectively stimulates the activity of a natural immunoglobulin promoter in an octamer site-dependent manner. Thus, OBF-1 has all the properties expected for a B cell-specific transcriptional coactivator protein. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "association", "start": 100, "end": 111}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 0, "end": 5}]}, {"trigger": {"text": "associates", "start": 525, "end": 535}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 483, "end": 488}, {"role": "Theme2", "text": "Oct-1", "start": 541, "end": 546}]}, {"trigger": {"text": "associates", "start": 525, "end": 535}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 483, "end": 488}, {"role": "Theme2", "text": "Oct-2", "start": 551, "end": 556}]}, {"trigger": {"text": "binding", "start": 622, "end": 629}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 595, "end": 600}]}, {"trigger": {"text": "recognizes", "start": 643, "end": 653}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 595, "end": 600}, {"role": "Site2", "text": "POU domains", "start": 658, "end": 669}, {"role": "Theme2", "text": "Oct-1", "start": 673, "end": 678}]}, {"trigger": {"text": "recognizes", "start": 643, "end": 653}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 595, "end": 600}, {"role": "Site2", "text": "POU domains", "start": 658, "end": 669}, {"role": "Theme2", "text": "Oct-2", "start": 683, "end": 688}]}, {"trigger": {"text": "recognizes", "start": 643, "end": 653}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 595, "end": 600}, {"role": "Site2", "text": "POU domains", "start": 658, "end": 669}, {"role": "Theme2", "text": "Oct-4", "start": 707, "end": 712}]}, {"trigger": {"text": "recognizes", "start": 643, "end": 653}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 595, "end": 600}, {"role": "Site2", "text": "POU domains", "start": 658, "end": 669}, {"role": "Theme2", "text": "Oct-6", "start": 717, "end": 722}]}], "gene expression": [{"trigger": {"text": "expression", "start": 899, "end": 909}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 913, "end": 918}]}], "transcription": [{"trigger": {"text": "expressed", "start": 742, "end": 751}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 728, "end": 733}]}]}}, "schema": []}
{"input": "Glucocorticoid-induced apoptosis of human leukemic cells is caused by the repressive function of the glucocorticoid receptor. \nInduction of apoptosis in lymphocytes, which may account for the therapeutic effects of glucocorticoids in various diseases including leukemia, depends on the glucocorticoid receptor. However, the events leading from the activated receptor to cell lysis are not understood. A prevailing hypothesis postulates induction of so-called 'lysis genes' by the activated receptor. In this study, we show that an activation-deficient glucocorticoid receptor mutant is as effective as the wild-type receptor in repression of AP-1 activity, inhibition of interleukin-2 production, inhibition of c-myc expression and induction of apoptosis. Furthermore, we show that retinoic acid can also induce apoptosis in these cells through the retinoic acid receptor, whose repressive functions but not target site specificity, are similar to those of the glucocorticoid receptor. Therefore, the primary effect of the receptor in glucocorticoid-mediated apoptosis correlates with transcriptional repression rather than activation and could be mediated by interference with other transcription factors required for cell survival. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 685, "end": 695}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 671, "end": 684}]}, {"trigger": {"text": "expression", "start": 717, "end": 727}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 711, "end": 716}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 657, "end": 667}, "arguments": [{"role": "Cause", "text": "glucocorticoid receptor", "start": 552, "end": 575}, {"role": "Theme", "text": "production", "start": 685, "end": 695}]}, {"trigger": {"text": "inhibition", "start": 697, "end": 707}, "arguments": [{"role": "Cause", "text": "glucocorticoid receptor", "start": 552, "end": 575}, {"role": "Theme", "text": "expression", "start": 717, "end": 727}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 348, "end": 357}, "arguments": [{"role": "Theme", "text": "glucocorticoid receptor", "start": 286, "end": 309}]}, {"trigger": {"text": "activated", "start": 480, "end": 489}, "arguments": [{"role": "Theme", "text": "glucocorticoid receptor", "start": 286, "end": 309}]}]}}, "schema": []}
{"input": "HIV-1 Tat potentiates TNF-induced NF-kappa B activation and cytotoxicity by altering the cellular redox state. \nThis study demonstrates that human immunodeficiency virus type 1 (HIV-1) Tat protein amplifies the activity of tumor necrosis factor (TNF), a cytokine that stimulates HIV-1 replication through activation of NF-kappa B. In HeLa cells stably transfected with the HIV-1 tat gene (HeLa-tat cells), expression of the Tat protein enhanced both TNF-induced activation of NF-kappa B and TNF-mediated cytotoxicity. A similar potentiation of TNF effects was observed in Jurkat T cells and HeLa cells treated with soluble Tat protein. TNF-mediated activation of NF-kappa B and cytotoxicity involves the intracellular formation of reactive oxygen intermediates. Therefore, Tat-mediated effects on the cellular redox state were analyzed. In both T cells and HeLa cells HIV-1 Tat suppressed the expression of Mn-dependent superoxide dismutase (Mn-SOD), a mitochondrial enzyme that is part of the cellular defense system against oxidative stress. Thus, Mn-SOD RNA protein levels and activity were markedly reduced in the presence of Tat. Decreased Mn-SOD expression was associated with decreased levels of glutathione and a lower ratio of reduced:oxidized glutathione. A truncated Tat protein (Tat1-72), known to transactivate the HIV-1 long terminal repeat (LTR), no longer affected Mn-SOD expression, the cellular redox state or TNF-mediated cytotoxicity. Thus, our experiments demonstrate that the C-terminal region of HIV-1 Tat is required to suppress Mn-SOD expression and to induce pro-oxidative conditions reflected by a drop in reduced glutathione (GSH) and the GSH:oxidized GSH (GSSG) ratio. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 406, "end": 416}, "arguments": [{"role": "Theme", "text": "Tat", "start": 424, "end": 427}]}, {"trigger": {"text": "expression", "start": 893, "end": 903}, "arguments": [{"role": "Theme", "text": "Mn-SOD", "start": 942, "end": 948}]}, {"trigger": {"text": "protein levels", "start": 1061, "end": 1075}, "arguments": [{"role": "Theme", "text": "Mn-SOD", "start": 1050, "end": 1056}]}, {"trigger": {"text": "expression", "start": 1152, "end": 1162}, "arguments": [{"role": "Theme", "text": "Mn-SOD", "start": 1145, "end": 1151}]}, {"trigger": {"text": "expression", "start": 1388, "end": 1398}, "arguments": [{"role": "Theme", "text": "Mn-SOD", "start": 1381, "end": 1387}]}, {"trigger": {"text": "expression", "start": 1560, "end": 1570}, "arguments": [{"role": "Theme", "text": "Mn-SOD", "start": 1553, "end": 1559}]}], "negative regulation": [{"trigger": {"text": "suppressed", "start": 878, "end": 888}, "arguments": [{"role": "Cause", "text": "Tat", "start": 874, "end": 877}, {"role": "Theme", "text": "expression", "start": 893, "end": 903}]}, {"trigger": {"text": "reduced", "start": 1103, "end": 1110}, "arguments": [{"role": "Theme", "text": "Mn-SOD", "start": 1050, "end": 1056}, {"role": "Cause", "text": "Tat", "start": 1130, "end": 1133}]}, {"trigger": {"text": "reduced", "start": 1103, "end": 1110}, "arguments": [{"role": "Theme", "text": "RNA", "start": 1057, "end": 1060}, {"role": "Cause", "text": "Tat", "start": 1130, "end": 1133}]}, {"trigger": {"text": "reduced", "start": 1103, "end": 1110}, "arguments": [{"role": "Theme", "text": "protein levels", "start": 1061, "end": 1075}, {"role": "Cause", "text": "Tat", "start": 1130, "end": 1133}]}, {"trigger": {"text": "Decreased", "start": 1135, "end": 1144}, "arguments": [{"role": "Theme", "text": "expression", "start": 1152, "end": 1162}]}, {"trigger": {"text": "suppress", "start": 1544, "end": 1552}, "arguments": [{"role": "Theme", "text": "expression", "start": 1560, "end": 1570}]}], "regulation": [{"trigger": {"text": "affected", "start": 1372, "end": 1380}, "arguments": [{"role": "Cause", "text": "Tat", "start": 1278, "end": 1281}, {"role": "Theme", "text": "expression", "start": 1388, "end": 1398}]}], "transcription": [{"trigger": {"text": "RNA", "start": 1057, "end": 1060}, "arguments": [{"role": "Theme", "text": "Mn-SOD", "start": 1050, "end": 1056}]}]}}, "schema": []}
{"input": "Expression of the Runt domain-encoding PEBP2 alpha genes in T cells during thymic development. \nThe PEBP2 alpha A and PEBP2 alpha B genes encode the DNA-binding subunit of a murine transcription factor, PEBP2, which is implicated as a T-cell-specific transcriptional regulator. These two related genes share the evolutionarily conserved region encoding the Runt domain. PEBP2 alpha B is the murine counterpart of human AML1, which is located at the breakpoints of the 8;21 and 3;21 chromosome translocations associated with acute myeloid leukemia. Northern (RNA) blots of various adult mouse tissues revealed that the levels of expression of both genes were most prominent in the thymus. Furthermore, transcripts of PEBP2 alpha A and mouse AML1/PEBP2 alpha B were detected in T lymphocytes in the thymuses from day 16 embryos and newborns, as well as 4-week-old adult mice, by in situ hybridization. The expression of the genes persisted in peripheral lymph nodes of adult mice. The transcripts were detected in all the CD4- CD8-, CD4+ CD8+, CD4+ CD8-, and CD4- CD8+ cell populations. The results indicated that both genes are expressed in T cells throughout their development, supporting the notion that PEBP2 is a T-cell-specific transcription factor. Transcripts of mouse AML1/PEBP2 alpha B were also detected in day 12 fetal hematopoietic liver and in the bone marrow cells of newborn mice. The implication of mouse AML1/PEBP2 alpha B expression in hematopoietic cells other than those of T-cell lineage is discussed in relation to myeloid leukemogenesis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 628, "end": 638}, "arguments": [{"role": "Theme", "text": "PEBP2 alpha A", "start": 100, "end": 113}]}, {"trigger": {"text": "expression", "start": 628, "end": 638}, "arguments": [{"role": "Theme", "text": "PEBP2 alpha B", "start": 118, "end": 131}]}, {"trigger": {"text": "expression", "start": 904, "end": 914}, "arguments": [{"role": "Theme", "text": "PEBP2 alpha A", "start": 716, "end": 729}]}, {"trigger": {"text": "expression", "start": 904, "end": 914}, "arguments": [{"role": "Theme", "text": "AML1/PEBP2 alpha B", "start": 740, "end": 758}]}, {"trigger": {"text": "expressed", "start": 1127, "end": 1136}, "arguments": [{"role": "Theme", "text": "PEBP2 alpha A", "start": 716, "end": 729}]}, {"trigger": {"text": "expressed", "start": 1127, "end": 1136}, "arguments": [{"role": "Theme", "text": "AML1/PEBP2 alpha B", "start": 740, "end": 758}]}, {"trigger": {"text": "expression", "start": 1439, "end": 1449}, "arguments": [{"role": "Theme", "text": "AML1/PEBP2 alpha B", "start": 1420, "end": 1438}]}], "positive regulation": [{"trigger": {"text": "prominent", "start": 663, "end": 672}, "arguments": [{"role": "Theme", "text": "expression", "start": 628, "end": 638}]}, {"trigger": {"text": "persisted", "start": 928, "end": 937}, "arguments": [{"role": "Theme", "text": "expression", "start": 904, "end": 914}]}], "transcription": [{"trigger": {"text": "detected", "start": 764, "end": 772}, "arguments": [{"role": "Theme", "text": "PEBP2 alpha A", "start": 716, "end": 729}]}, {"trigger": {"text": "detected", "start": 764, "end": 772}, "arguments": [{"role": "Theme", "text": "AML1/PEBP2 alpha B", "start": 740, "end": 758}]}, {"trigger": {"text": "detected", "start": 1000, "end": 1008}, "arguments": [{"role": "Theme", "text": "PEBP2 alpha A", "start": 716, "end": 729}]}, {"trigger": {"text": "detected", "start": 1000, "end": 1008}, "arguments": [{"role": "Theme", "text": "AML1/PEBP2 alpha B", "start": 740, "end": 758}]}, {"trigger": {"text": "detected", "start": 1304, "end": 1312}, "arguments": [{"role": "Theme", "text": "AML1/PEBP2 alpha B", "start": 1275, "end": 1293}]}]}}, "schema": []}
{"input": "Regulation of cell-type-specific interleukin-2 receptor alpha-chain gene expression: potential role of physical interactions between Elf-1, HMG-I(Y), and NF-kappa B family proteins. \nThe interleukin 2 receptor alpha-chain (IL-2R alpha) gene is rapidly and potently induced in T cells in response to mitogenic stimuli. Previously, an inducible enhancer between nucleotides -299 and -228 that contains NF-kappa B and CArG motifs was identified. We now report the characterization of a second essential positive regulatory element located between nucleotides -137 and -64 that binds Elf-1 and HMG-I(Y). This element had maximal activity in lymphoid cells, paralleling the cell type specificity of Elf-1 expression. Transcription from the IL-2R alpha promoter was inhibited when either the Elf-1 or the HMG-I(Y) binding site was mutated. Coexpression of both proteins activated transcription of the -137 to -64 element in COS-7 cells. Elf-1 physically associated with HMG-I and with NF-kappa B p50 and c-Rel in vitro, suggesting that protein-protein interactions might functionally coordinate the actions of the upstream and downstream positive regulatory elements. This is the first report of a physical interaction between an Ets family member and NF-kappa B family proteins. These findings provide significant new insights into the protein-protein and protein-DNA interactions that regulate cell-type-specific and inducible IL-2R alpha gene expression and also have implications for other genes regulated by Elf-1 and NF-kappa B family proteins. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interactions", "start": 112, "end": 124}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 133, "end": 138}]}, {"trigger": {"text": "interactions", "start": 112, "end": 124}, "arguments": [{"role": "Theme", "text": "HMG-I(Y)", "start": 140, "end": 148}]}, {"trigger": {"text": "binds", "start": 574, "end": 579}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 580, "end": 585}]}, {"trigger": {"text": "binds", "start": 574, "end": 579}, "arguments": [{"role": "Theme", "text": "HMG-I(Y)", "start": 590, "end": 598}]}, {"trigger": {"text": "associated", "start": 948, "end": 958}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 931, "end": 936}, {"role": "Theme2", "text": "HMG-I", "start": 964, "end": 969}]}, {"trigger": {"text": "associated", "start": 948, "end": 958}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 931, "end": 936}, {"role": "Theme2", "text": "p50", "start": 990, "end": 993}]}, {"trigger": {"text": "associated", "start": 948, "end": 958}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 931, "end": 936}, {"role": "Theme2", "text": "c-Rel", "start": 998, "end": 1003}]}], "gene expression": [{"trigger": {"text": "expression", "start": 73, "end": 83}, "arguments": [{"role": "Theme", "text": "interleukin-2 receptor alpha-chain", "start": 33, "end": 67}]}, {"trigger": {"text": "induced", "start": 265, "end": 272}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 223, "end": 234}]}, {"trigger": {"text": "expression", "start": 700, "end": 710}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 694, "end": 699}]}, {"trigger": {"text": "Coexpression", "start": 834, "end": 846}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 786, "end": 791}]}, {"trigger": {"text": "Coexpression", "start": 834, "end": 846}, "arguments": [{"role": "Theme", "text": "HMG-I(Y)", "start": 799, "end": 807}]}, {"trigger": {"text": "expression", "start": 1440, "end": 1450}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 1423, "end": 1434}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 760, "end": 769}, "arguments": [{"role": "Theme", "text": "from", "start": 726, "end": 730}]}], "positive regulation": [{"trigger": {"text": "response", "start": 287, "end": 295}, "arguments": [{"role": "Theme", "text": "induced", "start": 265, "end": 272}]}, {"trigger": {"text": "from", "start": 726, "end": 730}, "arguments": [{"role": "Theme", "text": "Transcription", "start": 712, "end": 725}, {"role": "Cause", "text": "IL-2R alpha", "start": 735, "end": 746}, {"role": "CSite", "text": "promoter", "start": 747, "end": 755}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 73, "end": 83}]}, {"trigger": {"text": "regulate", "start": 1381, "end": 1389}, "arguments": [{"role": "Theme", "text": "expression", "start": 1440, "end": 1450}]}], "transcription": [{"trigger": {"text": "Transcription", "start": 712, "end": 725}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 735, "end": 746}]}]}}, "schema": []}
{"input": "Effects of glucocorticoids on transcription factor activation in human peripheral blood mononuclear cells. \nGlucocorticoids have an inhibitory effect on inflammatory and immune responses, and this may be through the modulation of transcription factor binding to DNA. The interaction of the transcription factors, activator protein-1 (AP-1), nuclear factor kappa B (NF kappa B), and cAMP-responsive element binding protein (CREB) with DNA and glucocorticoid receptors (GR) was analyzed in human peripheral blood mononuclear cells by gel mobility shift assays. TNF-alpha, IL-1 beta and phorbol myristate acetate (PMA) treatment increased AP-1 and NF kappa B DNA binding by up to 200% but decreased CREB binding (38%) over a 60-min time course. Dexamethasone produced a rapid and sustained increase in glucocorticoid response element binding and a concomitant 40-50% decrease in AP-1, NF kappa B, and CREB DNA binding that was blocked by combined dexamethasone and cytokine or PMA treatment. These latter effects were due to increases in the nuclear localization of GR, not to reduced amounts of the other transcription factors. This suggests that in these cells GR within the nucleus interacts with cytokine-stimulated transcription factors by the process of cross coupling. This may be an important molecular site of steroid action. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 271, "end": 282}, "arguments": [{"role": "Theme", "text": "GR", "start": 468, "end": 470}]}, {"trigger": {"text": "interacts", "start": 1182, "end": 1191}, "arguments": [{"role": "Theme", "text": "GR", "start": 1160, "end": 1162}]}], "localization": [{"trigger": {"text": "localization", "start": 1047, "end": 1059}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 1039, "end": 1046}, {"role": "Theme", "text": "GR", "start": 1063, "end": 1065}]}]}}, "schema": []}
{"input": "Isolation of cDNA clones for 42 different Kruppel-related zinc finger proteins expressed in the human monoblast cell line U-937. \nTo study the complexity and structural characteristics of zinc finger proteins expressed during human hematopoiesis and to isolate novel regulators of blood cell development, a degenerate oligonucleotide probe specific for a consensus zinc finger peptide domain was used to isolate 63 cDNA clones for Kruppel-related zinc finger genes from the human monoblast cell line U-937. By extensive nucleotide sequence and Northern blot analysis, these cDNA clones were found to originate from approximately 42 different genes (HZF 1-42) of which only 8 have previously been described. Northern blot analysis showed that a majority of these genes were expressed at comparable levels in U-937 and HeLa cells. The large number of individual genes represented among the 63 clones and their apparent non-cell-type-specific expression suggest that the majority of the Kruppel-related zinc finger genes are likely to be expressed in most human tissues. In contrast, some of the genes displayed a restricted expression pattern, indicating that they represent potential regulators of monocyte differentiation or proliferation. Detailed structural analysis of the first 12 cDNAs (HZF 1-10) and a partial characterization of HZF 11-42 revealed that a common feature of human Kruppel-related zinc finger proteins is the presence of tandem arrays of zinc fingers ranging in number from 3 to over 20 that are preferentially located in the carboxy-terminal regions of the proteins. In addition, several novel KRAB-containing zinc finger genes and a novel conserved sequence element were identified. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 773, "end": 782}, "arguments": [{"role": "Theme", "text": "HZF 1", "start": 649, "end": 654}]}, {"trigger": {"text": "expressed", "start": 773, "end": 782}, "arguments": [{"role": "Theme", "text": "42", "start": 655, "end": 657}]}, {"trigger": {"text": "expression", "start": 940, "end": 950}, "arguments": [{"role": "Theme", "text": "HZF 1", "start": 649, "end": 654}]}, {"trigger": {"text": "expression", "start": 940, "end": 950}, "arguments": [{"role": "Theme", "text": "42", "start": 655, "end": 657}]}, {"trigger": {"text": "expression", "start": 1122, "end": 1132}, "arguments": [{"role": "Theme", "text": "HZF 1", "start": 649, "end": 654}]}]}}, "schema": []}
{"input": "Calcium/calmodulin-dependent protein kinase II downregulates both calcineurin and protein kinase C-mediated pathways for cytokine gene transcription in human T cells. \nEngagement of the T cell receptor for antigen activates phospholipase C resulting in an increase in intracellular free calcium concentration ([Ca2+]i) and activation of protein kinase C (PKC). Increased [Ca2+]i activates Ca2+/calmodulin-dependent kinases including the multifunctional Ca2+/calmodulin-dependent protein kinase II (CaM-K II), as well as calcineurin, a type 2B protein phosphatase. Recent studies have identified calcineurin as a key enzyme for interleukin (IL)-2 and IL-4 promoter activation. However, the role of CaM-K II remains unknown. We have used mutants of these kinases and phosphatases (gamma B*CaM-K and delta CaM-AI, respectively) to explore their relative role in cytokine gene transcription and their interactions with PKC-dependent signaling systems. gamma B*CaM-K and delta CaM-AI, known to exhibit constitutive Ca(2+)-independent activity, were cotransfected (alone or in combination) in Jurkat T cells with a plasmid containing the intact IL-2 promoter driving the expression of the chloramphenicol acetyltransferase reporter gene. Cotransfection of gamma B*CaM-K with the IL-2 promoter construct downregulated its transcription in response to stimulation with ionomycin and phorbol myristate acetate (PMA). The inhibitory effect of CaM-K II on IL-2 promoter was associated with decreased transcription of its AP-1 and NF-AT transactivating pathways. Under the same conditions, delta CaM-AI superinduced IL-2 promoter activity (approximately twofold increase). When both mutants were used in combination, gamma B*CaM-K inhibited the induction of the IL-2 promoter by delta CaM-AI. Similar results were obtained when a construct containing the IL-4 promoter also was used. gamma B*CaM-K also downregulated the activation of AP-1 in response to transfection with a constitutively active mutant of PKC or stimulation with PMA. These results suggest that CaM-K II may exert negative influences on cytokine gene transcription in human T cells, and provide preliminary evidence for negative cross-talk with the calcineurin- and PKC- dependent signaling systems. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitory effect", "start": 1412, "end": 1429}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1445, "end": 1449}, {"role": "Site", "text": "promoter", "start": 1450, "end": 1458}]}, {"trigger": {"text": "decreased", "start": 1479, "end": 1488}, "arguments": [{"role": "Theme", "text": "transactivating pathways", "start": 1525, "end": 1549}]}, {"trigger": {"text": "inhibited", "start": 1719, "end": 1728}, "arguments": [{"role": "Theme", "text": "induction", "start": 1733, "end": 1742}]}], "positive regulation": [{"trigger": {"text": "key enzyme", "start": 612, "end": 622}, "arguments": [{"role": "Theme", "text": "activation", "start": 664, "end": 674}]}, {"trigger": {"text": "activation", "start": 664, "end": 674}, "arguments": [{"role": "Theme", "text": "interleukin (IL)-2", "start": 627, "end": 645}, {"role": "Site", "text": "promoter", "start": 655, "end": 663}]}, {"trigger": {"text": "activation", "start": 664, "end": 674}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 650, "end": 654}, {"role": "Site", "text": "promoter", "start": 655, "end": 663}]}, {"trigger": {"text": "transactivating pathways", "start": 1525, "end": 1549}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1489, "end": 1502}]}, {"trigger": {"text": "superinduced", "start": 1591, "end": 1603}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1604, "end": 1608}, {"role": "Site", "text": "promoter", "start": 1609, "end": 1617}]}, {"trigger": {"text": "induction", "start": 1733, "end": 1742}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1750, "end": 1754}, {"role": "Site", "text": "promoter", "start": 1755, "end": 1763}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1489, "end": 1502}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1445, "end": 1449}]}]}}, "schema": []}
{"input": "Control of I kappa B-alpha proteolysis by site-specific, signal-induced phosphorylation. \nI kappa B-alpha inhibits transcription factor NF-kappa B by retaining it in the cytoplasm. Various stimuli, typically those associated with stress or pathogens, rapidly inactivate I kappa B-alpha. This liberates NF-kappa B to translocate to the nucleus and initiate transcription of genes important for the defense of the organism. Activation of NF-kappa B correlates with phosphorylation of I kappa B-alpha and requires the proteolysis of this inhibitor. When either serine-32 or serine-36 of I kappa B-alpha was mutated, the protein did not undergo signal-induced phosphorylation or degradation, and NF-kappa B could not be activated. These results suggest that phosphorylation at one or both of these residues is critical for activation of NF-kappa B. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inactivate", "start": 259, "end": 269}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 270, "end": 285}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 72, "end": 87}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 11, "end": 26}]}, {"trigger": {"text": "phosphorylation", "start": 463, "end": 478}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 482, "end": 497}]}, {"trigger": {"text": "phosphorylation", "start": 656, "end": 671}, "arguments": [{"role": "Site", "text": "serine-32", "start": 558, "end": 567}, {"role": "Theme", "text": "I kappa B-alpha", "start": 584, "end": 599}]}, {"trigger": {"text": "phosphorylation", "start": 656, "end": 671}, "arguments": [{"role": "Site", "text": "serine-36", "start": 571, "end": 580}, {"role": "Theme", "text": "I kappa B-alpha", "start": 584, "end": 599}]}, {"trigger": {"text": "phosphorylation", "start": 754, "end": 769}, "arguments": [{"role": "Site", "text": "serine-32", "start": 558, "end": 567}, {"role": "Theme", "text": "I kappa B-alpha", "start": 584, "end": 599}]}, {"trigger": {"text": "phosphorylation", "start": 754, "end": 769}, "arguments": [{"role": "Site", "text": "serine-36", "start": 571, "end": 580}, {"role": "Theme", "text": "I kappa B-alpha", "start": 584, "end": 599}]}], "protein catabolism": [{"trigger": {"text": "proteolysis", "start": 27, "end": 38}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 11, "end": 26}]}, {"trigger": {"text": "proteolysis", "start": 515, "end": 526}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 482, "end": 497}]}, {"trigger": {"text": "degradation", "start": 675, "end": 686}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 584, "end": 599}]}], "regulation": [{"trigger": {"text": "Control", "start": 0, "end": 7}, "arguments": [{"role": "Theme", "text": "proteolysis", "start": 27, "end": 38}, {"role": "Cause", "text": "phosphorylation", "start": 72, "end": 87}]}, {"trigger": {"text": "requires", "start": 502, "end": 510}, "arguments": [{"role": "Theme", "text": "proteolysis", "start": 515, "end": 526}]}]}}, "schema": []}
{"input": "HIV-1 Nef leads to inhibition or activation of T cells depending on its intracellular localization. \nNef of primate lentiviruses is required for viremia and progression to AIDS in monkeys. Negative, positive, and no effects of Nef have also been reported on viral replication in cells. To reconcile these observations, we expressed a hybrid CD8-Nef protein in Jurkat cells. Two opposite phenotypes were found, which depended on the intracellular localization of Nef. Expressed in the cytoplasm or on the cell surface, the chimera inhibited or activated early signaling events from the T cell antigen receptor. Activated Jurkat cells died by apoptosis, and only cells with mutated nef genes expressing truncated Nefs survived, which rendered Nef nonfunctional. These mutations paralleled those in other viral strains passaged in vitro. Not only do these positional effects of Nef reconcile diverse phenotypes of Nef and suggest a role for its N-terminal myristylation, but they also explain effects of Nef in HIV infection and progression to AIDS. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 690, "end": 700}, "arguments": [{"role": "Theme", "text": "Nef", "start": 711, "end": 714}]}], "localization": [{"trigger": {"text": "localization", "start": 86, "end": 98}, "arguments": [{"role": "Theme", "text": "Nef", "start": 6, "end": 9}, {"role": "AtLoc", "text": "intracellular", "start": 72, "end": 85}]}, {"trigger": {"text": "localization", "start": 446, "end": 458}, "arguments": [{"role": "AtLoc", "text": "intracellular", "start": 432, "end": 445}, {"role": "Theme", "text": "Nef", "start": 462, "end": 465}]}]}}, "schema": []}
{"input": "LMP-1 activates NF-kappa B by targeting the inhibitory molecule I kappa B alpha. \nLMP-1, an Epstein-Barr virus membrane protein expressed during latent infection, has oncogenic properties, as judged from its ability to transform B lymphocytes and rodent fibroblasts. LMP-1 induces the expression of bcl2, an oncogene which protects cells from apoptosis, as well as of genes encoding other proteins involved in cell regulation and growth control. The mechanisms by which LMP-1 upregulates these proteins is unknown, but it is plausible that LMP-1 modifies signal transduction pathways that result in the activation of one or more transcription factors that ultimately regulate transcription of oncogenic genes. NF-kappa B, a transcription factor controlling the expression of genes involved in cell activation and growth control, has been shown to be activated by LMP-1. The mechanism(s) regulating this activation remains unknown. Our data indicate that increased NF-kappa B DNA binding and functional activity are present in B-lymphoid cells stably or transiently expressing LMP-1. I kappa B alpha is selectively modified in LMP-1-expressing B cells. A phosphorylated form of I kappa B alpha and increased protein turnover-degradation correlate with increased NF-kappa B nuclear translocation. This results in increased transcription of NF-kappa B-dependent-genes, including those encoding p105 and I kappa B alpha (MAD3). These results indicate that LMP-1 activates NF-kappa B in B-cell lines by targeting I kappa B alpha. Identification of the pathways activated by LMP-1 to result in posttranslational modifications of I kappa B alpha will aid in determining the role of this virus-host cell protein interaction in Epstein-Barr virus-mediated oncogenesis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 128, "end": 137}, "arguments": [{"role": "Theme", "text": "LMP-1", "start": 82, "end": 87}]}, {"trigger": {"text": "expression", "start": 285, "end": 295}, "arguments": [{"role": "Theme", "text": "bcl2", "start": 299, "end": 303}]}, {"trigger": {"text": "expressing", "start": 1065, "end": 1075}, "arguments": [{"role": "Theme", "text": "LMP-1", "start": 1076, "end": 1081}]}, {"trigger": {"text": "expressing", "start": 1132, "end": 1142}, "arguments": [{"role": "Theme", "text": "LMP-1", "start": 1126, "end": 1131}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated form", "start": 1154, "end": 1173}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1177, "end": 1192}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 273, "end": 280}, "arguments": [{"role": "Cause", "text": "LMP-1", "start": 267, "end": 272}, {"role": "Theme", "text": "expression", "start": 285, "end": 295}]}, {"trigger": {"text": "upregulates", "start": 476, "end": 487}, "arguments": [{"role": "Theme", "text": "bcl2", "start": 299, "end": 303}, {"role": "Cause", "text": "LMP-1", "start": 470, "end": 475}]}, {"trigger": {"text": "increased", "start": 1311, "end": 1320}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1321, "end": 1334}]}], "regulation": [{"trigger": {"text": "targeting", "start": 30, "end": 39}, "arguments": [{"role": "Cause", "text": "LMP-1", "start": 0, "end": 5}, {"role": "Theme", "text": "I kappa B alpha", "start": 64, "end": 79}]}, {"trigger": {"text": "targeting", "start": 1498, "end": 1507}, "arguments": [{"role": "Cause", "text": "LMP-1", "start": 1452, "end": 1457}, {"role": "Theme", "text": "I kappa B alpha", "start": 1508, "end": 1523}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1321, "end": 1334}, "arguments": [{"role": "Theme", "text": "p105", "start": 1391, "end": 1395}]}, {"trigger": {"text": "transcription", "start": 1321, "end": 1334}, "arguments": [{"role": "Theme", "text": "MAD3", "start": 1417, "end": 1421}]}]}}, "schema": []}
{"input": "The regulation of HIV by retinoic acid correlates with cellular expression of the retinoic acid receptors. \nOBJECTIVES: To analyze the effect of retinoic acids (RA) on HIV-1 expression and correlate this effect with expression levels of RA receptors (RARs) in T-lymphoid and monocytoid cell lines. DESIGN AND METHODS: The effect of all-trans and 9-cis RA on HIV-1 production in T-lymphoid (H9, CEM) and monocytoid (U937,THP-1) cell lines was measured during acute and chronic infection. The expression levels of human RAR alpha (hRAR alpha, receptor for all-trans RA) and the human retinoid-X receptor alpha (hRXR alpha receptor for 9-cis RA) were determined by Northern blot analysis. RESULTS: Both all-trans and 9-cis RA inhibited virus replication in HIV-1 IIIB-infected monocytoid cells, in the presence and absence of the co-stimulatory agent phorbol myristate acetate (PMA). The retinoids had weak or no stimulatory effects on HIV production by T-cell lines. HIV production by PMA-stimulated T-cell lines was inhibited by these retinoids. The 9-cis RA was generally more effective than all-trans RA in inhibiting HIV production and in combination generally more effective than the single agents alone. Human RAR alpha was expressed in H9, U937 and THP-1 cells, but almost undetectable in CEM cells. Human RXR alpha was significantly expressed in U937 and THP-1 cells, weakly expressed in H9 cells and not detectable in CEM cells. After stimulation by PMA, RXR alpha expression increased in H9 and U937 cells but not in CEM cells. Human RAR alpha expression was unchanged in H9 and CEM cells, and elevated in U937 cells, after PMA stimulation. CONCLUSION: The effect of RA on HIV-1 expression was cell-type-dependent and partially correlated with cellular expression of RARs. Endogenous or exogenously administered RA may have a significant role in HIV regulation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "receptor", "start": 541, "end": 549}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 518, "end": 527}]}, {"trigger": {"text": "receptor", "start": 620, "end": 628}, "arguments": [{"role": "Theme", "text": "hRXR alpha", "start": 609, "end": 619}]}], "gene expression": [{"trigger": {"text": "expression", "start": 491, "end": 501}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 518, "end": 527}]}, {"trigger": {"text": "expression", "start": 491, "end": 501}, "arguments": [{"role": "Theme", "text": "hRXR alpha", "start": 609, "end": 619}]}, {"trigger": {"text": "expressed", "start": 1339, "end": 1348}, "arguments": [{"role": "Theme", "text": "RXR alpha", "start": 1311, "end": 1320}]}, {"trigger": {"text": "expressed", "start": 1381, "end": 1390}, "arguments": [{"role": "Theme", "text": "RXR alpha", "start": 1311, "end": 1320}]}, {"trigger": {"text": "detectable", "start": 1411, "end": 1421}, "arguments": [{"role": "Theme", "text": "RXR alpha", "start": 1311, "end": 1320}]}, {"trigger": {"text": "expression", "start": 1472, "end": 1482}, "arguments": [{"role": "Theme", "text": "RXR alpha", "start": 1462, "end": 1471}]}, {"trigger": {"text": "expression", "start": 1552, "end": 1562}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 1542, "end": 1551}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 1483, "end": 1492}, "arguments": [{"role": "Theme", "text": "expression", "start": 1472, "end": 1482}]}, {"trigger": {"text": "elevated", "start": 1602, "end": 1610}, "arguments": [{"role": "Theme", "text": "expression", "start": 1552, "end": 1562}]}], "regulation": [{"trigger": {"text": "unchanged", "start": 1567, "end": 1576}, "arguments": [{"role": "Theme", "text": "expression", "start": 1552, "end": 1562}]}]}}, "schema": []}
{"input": "Identification of human TR2 orphan receptor response element in the transcriptional initiation site of the simian virus 40 major late promoter [published erratum appears in J Biol Chem 1995 Nov 3;270(44):26721] \nA DNA response element (TR2RE-SV40) for the TR2 orphan receptor, a member of the steroid-thyroid hormone receptor superfamily, has been identified in the simian virus 40 (SV40) +55 region (nucleotide numbers 368-389, 5'-GTTAAGGTTCGTAGGTCATGGA-3'). Electrophoretic mobility shift assay, using in vitro translated TR2 orphan receptor with a molecular mass of 67 kilodaltons, showed a specific binding with high affinity (dissociation constant = 9 nM) for this DNA sequence. DNA-swap experiments using chloramphenicol acetyl-transferase assay demonstrated that androgen can suppress the transcriptional activities of SV40 early promoter via the interaction between this TR2RE-SV40 and the chimeric receptor AR/TR2/AR with the DNA-binding domain of the TR2 orphan receptor flanked by the N-terminal and androgen-binding domains of the androgen receptor. In addition, this TR2RE-SV40 can function as a repressor to suppress the transcriptional activities of both SV40 early and late promoters. Together, these data suggest the TR2RE-SV40 may represent the first identified natural DNA response element for the TR2 orphan receptor that may function as a repressor for the SV40 gene expression. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Mapping of the interaction site of the defective transcription factor in the class II major histocompatibility complex mutant cell line clone-13 to the divergent X2-box. \nWe have previously described a mutant B lymphoblastoid cell line, Clone-13, that expresses HLA-DQ in the absence of HLA-DR and -DP. Several criteria indicated that the defect in this cell line influences the activity of an isotype-specific transcription factor. Indeed, transient transfection of HLA-DRA and DQB reporter constructs indicated that the affected factor operates via cis-elements located between -141 base pairs and the transcription initiation site. A series of hybrid DRA/DQB reporter constructs was generated to further map the relevant cis-elements in this system. Insertion of oligonucleotides spanning the DQB X-box (but not the DQB-W region or the DQB Y-box) upstream of -141 in a DRA reporter plasmid rescued expression to nearly wild-type levels. Substitution promoters were then generated where the entire X-box, or only the X1- or X2-boxes of HLA-DRA were replaced with the analogous regions of HLA-DQB. The DQB X2-box was able to restore expression to the silent DRA reporter construct. Moreover, replacement of the DQB X2-box with the DRA X2-box markedly diminished the activity of the DQB promoter in the mutant cell. None of the hybrid reporter constructs were defective when transfected into the wild-type, HLA-DR/-DQ positive parental cell line, Jijoye. These studies suggest that the divergent X2-box of the class II major histocompatibility complex promoters plays an important role in influencing differential expression of the human class II isotypes. ", "output": {"json_structures": {}}, "schema": []}
{"input": "[Regulation of transcription of the interleukin-2 gene in B-lymphocytes] \nSince most B cell clones immortalized with EBV virus can be induced to produce interleukin-2, a typical T cell cytokine, we studied the role of different elements of the IL-2 promoter in such clones by transfection. It was found, in particular, that the element TCEd, which binds the transcription factor NF-kB, is very active in all three B clones tested. This element has no activity in T cells of the Jurkat line. The NFATd element, which binds the transcription factor NFAT-1 and is very active in T cells, is only weakly active in one B clone and not at all in another. Different elements thus contribute to IL-2 promoter activity in different cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 516, "end": 521}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 547, "end": 553}]}], "gene expression": [{"trigger": {"text": "produce", "start": 145, "end": 152}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 153, "end": 166}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 134, "end": 141}, "arguments": [{"role": "Theme", "text": "produce", "start": 145, "end": 152}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 1, "end": 11}, "arguments": [{"role": "Theme", "text": "transcription", "start": 15, "end": 28}]}], "transcription": [{"trigger": {"text": "transcription", "start": 15, "end": 28}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 36, "end": 49}]}]}}, "schema": []}
{"input": "Effects of CD45 on NF-kappa B. Implications for replication of HIV-1. \nIncreased levels of replication of the HIV type 1 are observed after the activation of infected T cells through the TCR. However, anti-CD45 antibodies inhibit these effects in cells from infected individuals. In this study, we examined interrelationships between CD45 and HIV-1 further. We measured effects on the HIV-1 LTR in T cell lines that were stimulated with antibodies against CD45 and in those that lacked the expression of CD45 on their surfaces. First, anti-CD45 antibodies did not affect basal but decreased activated levels of expression from the HIV-1 LTR. Second, T cells, which lack CD45 and cannot signal via the TCR, supported higher levels of viral replication and gene expression. This was due to the presence of active NF-kappa B complexes in the nucleus of CD45- T cells. Additionally, infected T cells displayed lower levels of CD45 on their surfaces. Thus, CD45 plays an active role in the physiology of T cells and in the replication of HIV-1. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 490, "end": 500}, "arguments": [{"role": "Theme", "text": "CD45", "start": 504, "end": 508}]}], "negative regulation": [{"trigger": {"text": "lack", "start": 665, "end": 669}, "arguments": [{"role": "Theme", "text": "CD45", "start": 670, "end": 674}]}, {"trigger": {"text": "displayed lower levels", "start": 896, "end": 918}, "arguments": [{"role": "Theme", "text": "CD45", "start": 922, "end": 926}]}]}}, "schema": []}
{"input": "ERP, a new member of the ets transcription factor/oncoprotein family: cloning, characterization, and differential expression during B-lymphocyte development. \nThe ets gene family encodes a group of proteins which function as transcription factors under physiological conditions and, if aberrantly expressed, can cause cellular transformation. We have recently identified two regulatory elements in the murine immunoglobulin heavy-chain (IgH) enhancer, pi and microB, which exhibit striking similarity to binding sites for ets-related proteins. To identify ets-related transcriptional regulators expressed in pre-B lymphocytes that may interact with either the pi or the microB site, we have used a PCR approach with degenerate oligonucleotides encoding conserved sequences in all members of the ets family. We have cloned the gene for a new ets-related transcription factor, ERP (ets-related protein), from the murine pre-B cell line BASC 6C2 and from mouse lung tissue. The ERP protein contains a region of high homology with the ETS DNA-binding domain common to all members of the ets transcription factor/oncoprotein family. Three additional smaller regions show homology to the ELK-1 and SAP-1 genes, a subgroup of the ets gene family that interacts with the serum response factor. Full-length ERP expresses only negligible DNA-binding activity by itself. Removal of the carboxy terminus enables ERP to interact with a variety of ets-binding sites including the E74 site, the IgH enhancer pi site, and the lck promoter ets site, suggesting a carboxy-terminal negative regulatory domain. At least three ERP-related transcripts are expressed in a variety of tissues. However, within the B-cell lineage, ERP is highly expressed primarily at early stages of B-lymphocyte development, and expression declines drastically upon B-cell maturation, correlating with the enhancer activity of the IgH pi site. These data suggest that ERP might play a role in B-cell development and in IgH gene regulation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 1244, "end": 1253}, "arguments": [{"role": "Theme", "text": "ELK-1", "start": 1182, "end": 1187}, {"role": "Theme2", "text": "serum response factor", "start": 1263, "end": 1284}]}, {"trigger": {"text": "interacts", "start": 1244, "end": 1253}, "arguments": [{"role": "Theme", "text": "SAP-1", "start": 1192, "end": 1197}, {"role": "Theme2", "text": "serum response factor", "start": 1263, "end": 1284}]}, {"trigger": {"text": "binding activity", "start": 1332, "end": 1348}, "arguments": [{"role": "Theme", "text": "ERP", "start": 1298, "end": 1301}]}, {"trigger": {"text": "interact", "start": 1407, "end": 1415}, "arguments": [{"role": "Theme", "text": "ERP", "start": 1400, "end": 1403}, {"role": "Theme2", "text": "lck", "start": 1510, "end": 1513}, {"role": "Site2", "text": "promoter ets site", "start": 1514, "end": 1531}]}, {"trigger": {"text": "interact", "start": 1407, "end": 1415}, "arguments": [{"role": "Theme", "text": "ERP", "start": 1400, "end": 1403}]}], "gene expression": [{"trigger": {"text": "expression", "start": 114, "end": 124}, "arguments": [{"role": "Theme", "text": "ERP", "start": 0, "end": 3}]}, {"trigger": {"text": "expressed", "start": 1719, "end": 1728}, "arguments": [{"role": "Theme", "text": "ERP", "start": 1705, "end": 1708}]}], "negative regulation": [{"trigger": {"text": "declines", "start": 1799, "end": 1807}, "arguments": [{"role": "Theme", "text": "expressed", "start": 1719, "end": 1728}]}], "positive regulation": [{"trigger": {"text": "enables", "start": 1392, "end": 1399}, "arguments": [{"role": "Theme", "text": "interact", "start": 1407, "end": 1415}]}]}}, "schema": []}
{"input": "Pentoxifylline for the treatment of infection with human immunodeficiency virus. \nCytokine dysregulation in human immunodeficiency virus type 1 (HIV-1) infection has been documented in numerous studies and has been cited as an important component in the pathogenesis of this retroviral infection. Pharmacological modification of cytokine dysregulation, therefore, has been suggested as a therapeutic modality for HIV-1 infection. Dr. Dezube of Beth Israel Hospital (Boston) concisely reviews the state of our knowledge regarding the effects of pentoxifylline on expression of tumor necrosis factor-alpha, a cytokine known to influence HIV-1 replication and to play a possible role in the clinical manifestations of advanced infection with this virus. Pentoxifylline, a trisubstituted xanthine derivative, has been used to decrease blood viscosity and is reasonably well tolerated by most recipients of the drug. Results of preliminary studies, many of which were conducted by Dr. Dezube, suggest that use of this agent in combination with antiretroviral compounds may prove useful in the treatment of patients with HIV-1 infection. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 562, "end": 572}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 576, "end": 603}]}], "regulation": [{"trigger": {"text": "effects", "start": 533, "end": 540}, "arguments": [{"role": "Theme", "text": "expression", "start": 562, "end": 572}]}]}}, "schema": []}
{"input": "Signals transduced through the CD4 molecule on T lymphocytes activate NF-kappa B. \nWe have demonstrated that native envelope glycoproteins of HIV-1, gp160 can induce activation of the transcription factor, NF-kappa B. The stimulatory effects of gp160 are mediated through the CD4 molecule, since pretreatment with soluble CD4 abrogates its activity. The gp160-induced NF-kappa B complex consists of p65, p50 and c-rel proteins. The stimulatory effect of gp160 on NF-kappa B activation is protein synthesis independent, is dependent upon protein tyrosine phosphorylation, and abrogated by inhibitors of protein kinase C. The gp160-mediated activation of NF-kappa B in CD4 positive T cells may be involved in biological effects, e.g., enhanced HIV replication, hypergammaglobulinemia, increased cytokine secretion, hypercellularity in bone marrow and apoptosis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complex", "start": 379, "end": 386}, "arguments": [{"role": "Theme", "text": "p65", "start": 399, "end": 402}, {"role": "Theme2", "text": "p50", "start": 404, "end": 407}, {"role": "Theme3", "text": "c-rel", "start": 412, "end": 417}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 360, "end": 367}, "arguments": [{"role": "Cause", "text": "gp160", "start": 354, "end": 359}, {"role": "Theme", "text": "complex", "start": 379, "end": 386}]}]}}, "schema": []}
{"input": "Role of HIV-1 Nef expression in activation pathways in CD4+ T cells. \nThe role of the human immunodeficiency virus (HIV-1) Nef protein in T cell activation pathways was investigated using a Jurkat CD4+ cell line stably transfected with a Nef expression vector. Secretion of IL-2 and TNF-alpha, surface expression of IL-2R, and DNA-binding activity of NF-kappa B and AP-1 (Fos/Jun) complex in response to phorbol myristate acetate, TNF-alpha, or immobilized antibodies to CD3 were monitored. These parameters were not modified by Nef expression in Jurkat cells, whereas stimulation with the same stimuli resulted in partial inhibition of LTR activation in Nef+ Jurkat cells. This inhibition was not mediated through Nef phosphorylation on Thr-15 or GTP-binding activity because mutations in critical sites did not alter this inhibition. Analysis of truncated LTRs confirmed that inhibition of LTR activation was not mediated through NF-kappa B-binding activity but through the region containing the negative responding elements (NREs). These results suggest that Nef downmodulates LTR activation without significantly inhibiting the capacity of T cells to respond to immunological activations. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 331, "end": 347}, "arguments": [{"role": "Theme", "text": "Fos", "start": 372, "end": 375}]}, {"trigger": {"text": "binding activity", "start": 331, "end": 347}, "arguments": [{"role": "Theme", "text": "Jun", "start": 376, "end": 379}]}, {"trigger": {"text": "binding activity", "start": 752, "end": 768}, "arguments": [{"role": "Theme", "text": "Nef", "start": 715, "end": 718}]}], "gene expression": [{"trigger": {"text": "expression", "start": 18, "end": 28}, "arguments": [{"role": "Theme", "text": "Nef", "start": 14, "end": 17}]}, {"trigger": {"text": "expression", "start": 242, "end": 252}, "arguments": [{"role": "Theme", "text": "Nef", "start": 238, "end": 241}]}, {"trigger": {"text": "expression", "start": 533, "end": 543}, "arguments": [{"role": "Theme", "text": "Nef", "start": 529, "end": 532}]}], "localization": [{"trigger": {"text": "Secretion", "start": 261, "end": 270}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 274, "end": 278}]}, {"trigger": {"text": "Secretion", "start": 261, "end": 270}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 283, "end": 292}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 719, "end": 734}, "arguments": [{"role": "Theme", "text": "Nef", "start": 715, "end": 718}, {"role": "Site", "text": "Thr-15", "start": 738, "end": 744}]}], "positive regulation": [{"trigger": {"text": "transfected", "start": 219, "end": 230}, "arguments": [{"role": "Theme", "text": "expression", "start": 242, "end": 252}]}, {"trigger": {"text": "response", "start": 392, "end": 400}, "arguments": [{"role": "Theme", "text": "Secretion", "start": 261, "end": 270}, {"role": "Cause", "text": "TNF-alpha", "start": 431, "end": 440}]}, {"trigger": {"text": "response", "start": 392, "end": 400}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 331, "end": 347}, {"role": "Cause", "text": "TNF-alpha", "start": 431, "end": 440}]}, {"trigger": {"text": "response", "start": 392, "end": 400}, "arguments": [{"role": "Theme", "text": "Secretion", "start": 261, "end": 270}]}, {"trigger": {"text": "response", "start": 392, "end": 400}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 331, "end": 347}]}], "regulation": [{"trigger": {"text": "modified", "start": 517, "end": 525}, "arguments": [{"role": "Theme", "text": "Secretion", "start": 261, "end": 270}, {"role": "Cause", "text": "expression", "start": 533, "end": 543}]}, {"trigger": {"text": "modified", "start": 517, "end": 525}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 331, "end": 347}, {"role": "Cause", "text": "expression", "start": 533, "end": 543}]}]}}, "schema": []}
{"input": "A low NM23.H1 gene expression identifying high malignancy human melanomas. \nThe NM23 gene has been proposed as a metastasis-suppressor gene, and its use has been suggested as prognostic factor. NM23 was identified in a system of murine melanoma cell lines, in which an inverse relationship was found between NM23 expression and metastatic ability. In a human malignant melanoma study NM23 expression was found to be significantly lower in metastases that developed less than 24 months after diagnosis of the primary tumours. The present paper studies the expression of the NM23.H1 gene in cell lines which derive from primary or metastatic human malignant melanomas in relation to staging, infiltration degree, lymphocytic infiltration, cell morphology, cell pigmentation, karyotype, and disease-free survival. The level of mRNA expression of the NM23 gene is significantly lower in cell lines that derive from more infiltrating primary melanomas than in cell lines obtained from less infiltrating tumours. Moreover, cell lines derived from tumours of patients with a disease-free survival of more than 24 months (24-58 months) express the NM23 gene at higher levels than cell lines obtained from melanomas of patients with a disease-free survival of less than 24 months (6-15 months). ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 19, "end": 29}, "arguments": [{"role": "Theme", "text": "NM23.H1", "start": 6, "end": 13}]}, {"trigger": {"text": "expression", "start": 555, "end": 565}, "arguments": [{"role": "Theme", "text": "NM23.H1", "start": 573, "end": 580}]}]}}, "schema": []}
{"input": "T cells from renal cell carcinoma patients exhibit an abnormal pattern of kappa B-specific DNA-binding activity: a preliminary report. \nRecent data suggest that the poor induction of a T-cell response to human renal cell carcinoma (RCC) may be related to alterations in signal transduction pathways. We report that T cells from RCC patients have two alterations in kappa B motif-specific DNA-binding activity. The first alteration involves the constitutive expression of substantial kappa B-binding activity in nuclear extracts, which was observed in the electrophoretic mobility shift assay. The magnitude of kappa B activity in unstimulated patient T cells was similar to that observed in T cells from normal individuals that had been activated in vitro. On the basis of Western blotting experiments using antibodies to kappa B/Rel family proteins, the kappa B-binding activity constitutively expressed in T cells from RCC patients is composed mostly of the NF-kappa B1 (p50) subunit. The second abnormality in kappa B-binding activity in T cells from these patients is that RelA, a member of the Rel homology family which is part of the normal NF-kappa B complex, was not induced in the nucleus following activation. Western blotting analysis did not detect any RelA in nuclear extracts either before or after stimulation of T cells. The altered kappa B-binding activity in T cells from RCC patients may impair their capacity to respond normally to various stimuli. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 863, "end": 879}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 960, "end": 971}]}], "localization": [{"trigger": {"text": "detect", "start": 1254, "end": 1260}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1265, "end": 1269}, {"role": "AtLoc", "text": "nuclear extracts", "start": 1273, "end": 1289}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1175, "end": 1182}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1077, "end": 1081}]}]}}, "schema": []}
{"input": "Activation of NF-kappa B in vivo is regulated by multiple phosphorylations. \nThe activation of nuclear factor kappa B (NF-kappa B) in intact cells is mechanistically not well understood. Therefore we investigated the modifications imposed on NF-kappa B/I kappa B components following stimulation and show that the final step of NF-kappa B induction in vivo involves phosphorylation of several members of the NF-kappa B/I kappa B protein families. In HeLa cells as well as in B cells, TNF-alpha rapidly induced nuclear translocation primarily of p50-p65, but not of c-rel. Both NF-kappa B precursors and I kappa B alpha became strongly phosphorylated with the same kinetics. In addition to the inducible phosphorylation after stimulation, B lymphocytes containing constitutive nuclear NF-kappa B revealed constitutively phosphorylated p65 and I kappa B alpha. Phosphorylation was accompanied by induced processing of the precursors p100 and p105 and by degradation of I kappa B alpha. As an in vitro model we show that phosphorylation of p105 impedes its ability to interact with NF-kappa B, as has been shown before for I kappa B alpha. Surprisingly, even p65, but not c-rel, was phosphorylated after induction in vivo, suggesting that TNF-alpha selectively activates only specific NF-kappa B heteromers and that modifications regulate not only I kappa B molecules but also NF-kappa B molecules. In fact, cellular NF-kappa B activity was phosphorylation-dependent and the DNA binding activity of p65-containing NF-kappa B was enhanced by phosphorylation in vitro. Furthermore, we found that the induction by hydrogen peroxide of NF-kappa B translocation to the nucleus, which is assumed to be triggered by reactive oxygen intermediates, also coincided with incorporation of phosphate into the same subunits that were modified after stimulation by TNF-alpha. Thus, phosphorylation appears to be a general mechanism for activation of NF-kappa B in vivo. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 1065, "end": 1073}, "arguments": [{"role": "Theme", "text": "p105", "start": 1037, "end": 1041}]}, {"trigger": {"text": "interact", "start": 1065, "end": 1073}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1120, "end": 1135}]}, {"trigger": {"text": "binding activity", "start": 1476, "end": 1492}, "arguments": [{"role": "Theme", "text": "p65", "start": 1496, "end": 1499}]}], "localization": [{"trigger": {"text": "translocation", "start": 518, "end": 531}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 510, "end": 517}, {"role": "Theme", "text": "p50", "start": 545, "end": 548}]}, {"trigger": {"text": "translocation", "start": 518, "end": 531}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 510, "end": 517}, {"role": "Theme", "text": "p65", "start": 549, "end": 552}]}, {"trigger": {"text": "translocation", "start": 518, "end": 531}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 510, "end": 517}, {"role": "Theme", "text": "c-rel", "start": 565, "end": 570}]}], "negative regulation": [{"trigger": {"text": "impedes", "start": 1042, "end": 1049}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 1018, "end": 1033}, {"role": "Theme", "text": "interact", "start": 1065, "end": 1073}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 635, "end": 649}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 603, "end": 618}]}, {"trigger": {"text": "phosphorylated", "start": 819, "end": 833}, "arguments": [{"role": "Theme", "text": "p65", "start": 834, "end": 837}]}, {"trigger": {"text": "phosphorylated", "start": 819, "end": 833}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 842, "end": 857}]}, {"trigger": {"text": "phosphorylation", "start": 1018, "end": 1033}, "arguments": [{"role": "Theme", "text": "p105", "start": 1037, "end": 1041}]}, {"trigger": {"text": "phosphorylation", "start": 1018, "end": 1033}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1120, "end": 1135}]}, {"trigger": {"text": "phosphorylated", "start": 1180, "end": 1194}, "arguments": [{"role": "Theme", "text": "p65", "start": 1156, "end": 1159}]}, {"trigger": {"text": "phosphorylated", "start": 1180, "end": 1194}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 1169, "end": 1174}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 502, "end": 509}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 484, "end": 493}, {"role": "Theme", "text": "translocation", "start": 518, "end": 531}]}, {"trigger": {"text": "induction", "start": 1201, "end": 1210}, "arguments": [{"role": "Theme", "text": "p65", "start": 1156, "end": 1159}]}, {"trigger": {"text": "induction", "start": 1201, "end": 1210}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 1169, "end": 1174}]}, {"trigger": {"text": "enhanced", "start": 1526, "end": 1534}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 1476, "end": 1492}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 952, "end": 963}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 967, "end": 982}]}]}}, "schema": []}
{"input": "An active v-abl protein tyrosine kinase blocks immunoglobulin light-chain gene rearrangement. \nLymphoid cells transformed by Abelson murine leukemia virus have provided one of the classic models for study of early B-cell development and immunoglobulin rearrangement. Most of these cells have rearranged their heavy-chain locus but not their light chain genes, suggesting that an active v-abl protein interferes with this differentiation step. To test this hypothesis, light-chain gene structure was examined in pre-B cells transformed by temperature-sensitive mutants of the Abelson virus and in derivatives that survive at the nonpermissive temperature because they express a human BCL-2 gene. Our studies reveal that inactivation of the v-abl protein tyrosine kinase triggers high-frequency rearrangement of kappa and lambda light-chain genes. These events are accompanied by marked increases in the expression of RAG-1 and RAG-2 RNAs. These increases occur in the absence of protein synthesis but are dependent on inactivation of the v-abl protein tyrosine kinase. As documented in the accompanying paper (Klug et al., this issue), an active v-abl protein also suppresses the activity of NF-kappa B/rel and expression controlled by the kappa intron enhancer. Together these data demonstrate that the v-abl protein specifically interferes with light-chain gene rearrangement by suppressing at least two pathways essential for this stage of B-cell differentiation and suggest that tyrosine phosphorylation is important in regulating RAG gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "express", "start": 667, "end": 674}, "arguments": [{"role": "Theme", "text": "BCL-2", "start": 683, "end": 688}]}], "negative regulation": [{"trigger": {"text": "inactivation", "start": 719, "end": 731}, "arguments": [{"role": "Theme", "text": "v-abl", "start": 739, "end": 744}]}, {"trigger": {"text": "inactivation", "start": 1017, "end": 1029}, "arguments": [{"role": "Theme", "text": "v-abl", "start": 1037, "end": 1042}]}], "positive regulation": [{"trigger": {"text": "increases", "start": 885, "end": 894}, "arguments": [{"role": "Theme", "text": "expression", "start": 902, "end": 912}]}, {"trigger": {"text": "dependent", "start": 1004, "end": 1013}, "arguments": [{"role": "Theme", "text": "increases", "start": 885, "end": 894}, {"role": "Cause", "text": "inactivation", "start": 1017, "end": 1029}]}], "transcription": [{"trigger": {"text": "expression", "start": 902, "end": 912}, "arguments": [{"role": "Theme", "text": "RAG-1", "start": 916, "end": 921}]}, {"trigger": {"text": "expression", "start": 902, "end": 912}, "arguments": [{"role": "Theme", "text": "RAG-2", "start": 926, "end": 931}]}]}}, "schema": []}
{"input": "[An overexpression of retinoic acid receptor alpha blocks myeloid cell differentiation at the promyelocyte stage] \nRetinoic acid (RA), a vitamin A derivative, exerts a wide range of biological effects related to cell proliferation and differentiation. The pleiotropic effects of RA are thought to be mediated through specific nuclear RA receptors (RARs). RARs are members of the steroid/thyroid hormone receptor superfamily and exhibit a molecular structure that possess discrete DNA-binding and RA (ligand)-binding domains. In hematopoietic system, RA and RARs, predominantly RAR alpha may play key roles for the proliferation and differentiation of hematopoietic progenitors. However, it is currently unknown how RA and RARs are involved in regulating normal hematopoietic differentiation. To make clear the roles of RA and RAR alpha in the normal hematopoiesis, I have introduced the construct of human RAR alpha (hRAR alpha) into murine bone marrow cells with retroviral vector, and selected infected cells with drug resistant marker (Neo(r)) cultured on the stroma cell line (PA6-neo), and analyzed the behavior of infected cells. All of procedure were done in vitro. Most cells infected with hRAR alpha exhibited promyelocytic morphology and were thought to be blocked at the promyelocytic stage in their myeloid differentiation. Furthermore, these immature cells differentiated terminally into mature granulocytes by adding with RA (10(-6) M). RAR alpha infected cells were also able to differentiate into mature macrophages in the both of long term culture and IL3 colony. These observations suggest that an overexpression of RAR alpha alone is effective to suppress myeloid cell differentiation and RAR alpha plays a crucial role in the terminal differentiation of myeloid precursors. The system described here may serve as a model for studying the the essential genes for differentiation of normal bone marrow cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "overexpression", "start": 4, "end": 18}, "arguments": [{"role": "Theme", "text": "retinoic acid receptor alpha", "start": 22, "end": 50}]}, {"trigger": {"text": "overexpression", "start": 1616, "end": 1630}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 1634, "end": 1643}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 4, "end": 18}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 4, "end": 18}]}, {"trigger": {"text": "overexpression", "start": 1616, "end": 1630}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1616, "end": 1630}]}]}}, "schema": []}
{"input": "Regulation of interleukin-2 receptor alpha chain expression and nuclear factor.kappa B activation by protein kinase C in T lymphocytes. Autocrine role of tumor necrosis factor alpha. \nThe regulation of interleukin-2 receptor alpha chain (IL-2R alpha) expression and nuclear factor (NF) activation by protein kinase C (PKC) in resting T cells, has been studied. Treatment of human resting T cells with phorbol esters strongly induced the expression of IL-2R alpha and the activation of NF.kappa B. This activation was due to the translocation of p65 and c-Rel NF.kappa B proteins from cytoplasmic stores to the nucleus, where they bound the kappa B sequence of the IL-2R alpha promoter either as p50.p65 or as p50.c-Rel heterodimers. Interestingly, all of those events were largely indirect and mediated by endogenously secreted tumor necrosis factor alpha (TNF alpha), as they were strongly inhibited by a neutralizing anti-TNF alpha monoclonal antibody. Furthermore, cyclosporin A, which blocked TNF alpha production induced by PKC, strongly inhibited IL-2R alpha and NF.kappa B activation. The addition of either TNF alpha or IL-2 partially recovered cyclosporin A-induced IL-2R alpha inhibition, but only TNF alpha completely recovered NF.kappa B activation. Those results indicate that, in resting T cells, PKC activation has only a triggering role, whereas the endogenously secreted TNF alpha plays an essential role in the quantitative control of the expression of IL-2R alpha chain or NF.kappa B activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 630, "end": 635}, "arguments": [{"role": "Theme", "text": "p65", "start": 545, "end": 548}, {"role": "Theme2", "text": "IL-2R alpha", "start": 664, "end": 675}]}, {"trigger": {"text": "bound", "start": 630, "end": 635}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 553, "end": 558}, {"role": "Theme2", "text": "IL-2R alpha", "start": 664, "end": 675}]}, {"trigger": {"text": "heterodimers", "start": 719, "end": 731}, "arguments": [{"role": "Theme", "text": "p50", "start": 695, "end": 698}, {"role": "Theme2", "text": "p65", "start": 699, "end": 702}]}, {"trigger": {"text": "heterodimers", "start": 719, "end": 731}, "arguments": [{"role": "Theme", "text": "p50", "start": 709, "end": 712}, {"role": "Theme2", "text": "c-Rel", "start": 713, "end": 718}]}], "gene expression": [{"trigger": {"text": "expression", "start": 49, "end": 59}, "arguments": [{"role": "Theme", "text": "interleukin-2 receptor alpha chain", "start": 14, "end": 48}]}, {"trigger": {"text": "expression", "start": 251, "end": 261}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 238, "end": 249}]}, {"trigger": {"text": "expression", "start": 437, "end": 447}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 451, "end": 462}]}, {"trigger": {"text": "production", "start": 1007, "end": 1017}, "arguments": [{"role": "Theme", "text": "TNF alpha", "start": 997, "end": 1006}]}, {"trigger": {"text": "expression", "start": 1457, "end": 1467}, "arguments": [{"role": "Theme", "text": "IL-2R alpha chain", "start": 1471, "end": 1488}]}], "localization": [{"trigger": {"text": "translocation", "start": 528, "end": 541}, "arguments": [{"role": "Theme", "text": "p65", "start": 545, "end": 548}, {"role": "ToLoc", "text": "nucleus", "start": 610, "end": 617}]}, {"trigger": {"text": "translocation", "start": 528, "end": 541}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 553, "end": 558}, {"role": "ToLoc", "text": "nucleus", "start": 610, "end": 617}]}, {"trigger": {"text": "secreted", "start": 819, "end": 827}, "arguments": [{"role": "Theme", "text": "TNF alpha", "start": 857, "end": 866}]}, {"trigger": {"text": "secreted", "start": 1379, "end": 1387}, "arguments": [{"role": "Theme", "text": "TNF alpha", "start": 1388, "end": 1397}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 891, "end": 900}, "arguments": [{"role": "Theme", "text": "translocation", "start": 528, "end": 541}]}, {"trigger": {"text": "inhibited", "start": 891, "end": 900}, "arguments": [{"role": "Theme", "text": "bound", "start": 630, "end": 635}]}, {"trigger": {"text": "blocked", "start": 989, "end": 996}, "arguments": [{"role": "Theme", "text": "induced", "start": 1018, "end": 1025}]}, {"trigger": {"text": "inhibited", "start": 1043, "end": 1052}, "arguments": [{"role": "Theme", "text": "activation", "start": 1080, "end": 1090}]}, {"trigger": {"text": "recovered", "start": 1143, "end": 1152}, "arguments": [{"role": "Cause", "text": "TNF alpha", "start": 1115, "end": 1124}, {"role": "Theme", "text": "inhibition", "start": 1187, "end": 1197}]}, {"trigger": {"text": "recovered", "start": 1143, "end": 1152}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1128, "end": 1132}, {"role": "Theme", "text": "inhibition", "start": 1187, "end": 1197}]}, {"trigger": {"text": "inhibition", "start": 1187, "end": 1197}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 1175, "end": 1186}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 425, "end": 432}, "arguments": [{"role": "Theme", "text": "expression", "start": 437, "end": 447}]}, {"trigger": {"text": "mediated", "start": 794, "end": 802}, "arguments": [{"role": "Theme", "text": "translocation", "start": 528, "end": 541}, {"role": "Cause", "text": "TNF alpha", "start": 857, "end": 866}]}, {"trigger": {"text": "mediated", "start": 794, "end": 802}, "arguments": [{"role": "Theme", "text": "bound", "start": 630, "end": 635}, {"role": "Cause", "text": "TNF alpha", "start": 857, "end": 866}]}, {"trigger": {"text": "induced", "start": 1018, "end": 1025}, "arguments": [{"role": "Theme", "text": "production", "start": 1007, "end": 1017}]}, {"trigger": {"text": "activation", "start": 1080, "end": 1090}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 1053, "end": 1064}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 49, "end": 59}]}, {"trigger": {"text": "regulation", "start": 188, "end": 198}, "arguments": [{"role": "Theme", "text": "expression", "start": 251, "end": 261}]}, {"trigger": {"text": "control", "start": 1442, "end": 1449}, "arguments": [{"role": "Cause", "text": "TNF alpha", "start": 1388, "end": 1397}, {"role": "Theme", "text": "expression", "start": 1457, "end": 1467}]}]}}, "schema": []}
{"input": "Protease inhibitors block lipopolysaccharide induction of tissue factor gene expression in human monocytic cells by preventing activation of c-Rel/p65 heterodimers. \nTissue factor (TF) is expressed rapidly by human monocytes exposed to bacterial endotoxin (lipopolysaccharide, or LPS). Transcriptional regulation is mediated by binding of c-Rel/p65 heterodimers to a kappa B-like site in the TF promoter. Nuclear translocation of cytosolic c-Rel/p65 heterodimers and other members of the NF-kappa B/Rel family requires dissociation and proteolytic degradation of the inhibitor protein, I kappa B alpha. The protease inhibitors N alpha-tosylphenylalanyl chloromethyl ketone (TPCK) and N alpha-tosyl-L-lysine chloromethyl ketone (TLCK) block activation of NF-kappa B/Rel proteins by preventing degradation of I kappa B alpha. To determine if TPCK and TLCK inhibited LPS induction of TF expression, freshly isolated human monocytes and monocytic THP-1 cells were pretreated with these inhibitors for 30 min before LPS stimulation. Both TPCK and TLCK inhibited LPS induction of TF protein, TF mRNA and TF promoter activity in a dose-dependent manner. These inhibitors specifically prevented degradation of I kappa B alpha and nuclear translocation of c-Rel/p65 heterodimers. In contrast, TPCK and TLCK did not block induction of an immediate-early gene encoding the transcription factor, Egr-1. Taken together, these data indicated that inhibiting nuclear translocation of c-Rel/p65 heterodimers prevented LPS induction of TF gene transcription in monocytic cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 328, "end": 335}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 339, "end": 344}, {"role": "Site2", "text": "kappa B-like site", "start": 367, "end": 384}, {"role": "Theme2", "text": "TF", "start": 392, "end": 394}]}, {"trigger": {"text": "binding", "start": 328, "end": 335}, "arguments": [{"role": "Theme", "text": "p65", "start": 345, "end": 348}, {"role": "Site2", "text": "kappa B-like site", "start": 367, "end": 384}, {"role": "Theme2", "text": "TF", "start": 392, "end": 394}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 188, "end": 197}, "arguments": [{"role": "Theme", "text": "TF", "start": 181, "end": 183}]}, {"trigger": {"text": "expression", "start": 884, "end": 894}, "arguments": [{"role": "Theme", "text": "TF", "start": 881, "end": 883}]}], "localization": [{"trigger": {"text": "translocation", "start": 413, "end": 426}, "arguments": [{"role": "ToLoc", "text": "Nuclear", "start": 405, "end": 412}, {"role": "Theme", "text": "c-Rel", "start": 440, "end": 445}]}, {"trigger": {"text": "translocation", "start": 413, "end": 426}, "arguments": [{"role": "ToLoc", "text": "Nuclear", "start": 405, "end": 412}, {"role": "Theme", "text": "p65", "start": 446, "end": 449}]}, {"trigger": {"text": "translocation", "start": 1230, "end": 1243}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1222, "end": 1229}, {"role": "Theme", "text": "c-Rel", "start": 1247, "end": 1252}]}, {"trigger": {"text": "translocation", "start": 1230, "end": 1243}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1222, "end": 1229}, {"role": "Theme", "text": "p65", "start": 1253, "end": 1256}]}, {"trigger": {"text": "translocation", "start": 1452, "end": 1465}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1444, "end": 1451}, {"role": "Theme", "text": "c-Rel", "start": 1469, "end": 1474}]}, {"trigger": {"text": "translocation", "start": 1452, "end": 1465}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1444, "end": 1451}, {"role": "Theme", "text": "p65", "start": 1475, "end": 1478}]}], "negative regulation": [{"trigger": {"text": "preventing", "start": 116, "end": 126}, "arguments": [{"role": "Theme", "text": "activation", "start": 127, "end": 137}]}, {"trigger": {"text": "preventing", "start": 781, "end": 791}, "arguments": [{"role": "Theme", "text": "degradation", "start": 792, "end": 803}]}, {"trigger": {"text": "inhibited", "start": 854, "end": 863}, "arguments": [{"role": "Theme", "text": "induction", "start": 868, "end": 877}]}, {"trigger": {"text": "inhibited", "start": 1047, "end": 1056}, "arguments": [{"role": "Theme", "text": "induction", "start": 1061, "end": 1070}]}, {"trigger": {"text": "prevented", "start": 1177, "end": 1186}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1187, "end": 1198}]}, {"trigger": {"text": "prevented", "start": 1177, "end": 1186}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1230, "end": 1243}]}, {"trigger": {"text": "block", "start": 1306, "end": 1311}, "arguments": [{"role": "Theme", "text": "induction", "start": 1312, "end": 1321}]}, {"trigger": {"text": "inhibiting", "start": 1433, "end": 1443}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1452, "end": 1465}]}, {"trigger": {"text": "prevented", "start": 1492, "end": 1501}, "arguments": [{"role": "Cause", "text": "inhibiting", "start": 1433, "end": 1443}, {"role": "Theme", "text": "induction", "start": 1506, "end": 1515}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 127, "end": 137}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 141, "end": 146}]}, {"trigger": {"text": "activation", "start": 127, "end": 137}, "arguments": [{"role": "Theme", "text": "p65", "start": 147, "end": 150}]}, {"trigger": {"text": "exposed to", "start": 225, "end": 235}, "arguments": [{"role": "Theme", "text": "expressed", "start": 188, "end": 197}]}, {"trigger": {"text": "requires", "start": 510, "end": 518}, "arguments": [{"role": "Theme", "text": "translocation", "start": 413, "end": 426}, {"role": "Cause", "text": "proteolytic degradation", "start": 536, "end": 559}]}, {"trigger": {"text": "requires", "start": 510, "end": 518}, "arguments": [{"role": "Theme", "text": "translocation", "start": 413, "end": 426}]}, {"trigger": {"text": "induction", "start": 868, "end": 877}, "arguments": [{"role": "Theme", "text": "expression", "start": 884, "end": 894}]}, {"trigger": {"text": "induction", "start": 1061, "end": 1070}, "arguments": [{"role": "Theme", "text": "TF", "start": 1098, "end": 1100}, {"role": "Site", "text": "promoter", "start": 1101, "end": 1109}]}, {"trigger": {"text": "induction", "start": 1061, "end": 1070}, "arguments": [{"role": "Theme", "text": "TF", "start": 1074, "end": 1076}]}, {"trigger": {"text": "induction", "start": 1061, "end": 1070}, "arguments": [{"role": "Theme", "text": "TF", "start": 1086, "end": 1088}]}, {"trigger": {"text": "induction", "start": 1312, "end": 1321}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1384, "end": 1389}]}, {"trigger": {"text": "induction", "start": 1506, "end": 1515}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1527, "end": 1540}]}], "protein catabolism": [{"trigger": {"text": "proteolytic degradation", "start": 536, "end": 559}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 586, "end": 601}]}, {"trigger": {"text": "degradation", "start": 792, "end": 803}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 807, "end": 822}]}, {"trigger": {"text": "degradation", "start": 1187, "end": 1198}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1202, "end": 1217}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1527, "end": 1540}, "arguments": [{"role": "Theme", "text": "TF", "start": 1519, "end": 1521}]}]}}, "schema": []}
{"input": "A family of serine proteases expressed exclusively in myelo-monocytic cells specifically processes the nuclear factor-kappa B subunit p65 in vitro and may impair human immunodeficiency virus replication in these cells. \nTwo groups of U937 promonocytic cells were obtained by limiting dilution cloning which differed strikingly in their ability to support human immunodeficiency virus 1 (HIV-1) replication. \"Plus\" clones replicated the virus efficiently, whereas \"minus\" clones did not. We examined these clones for differences in nuclear factor (NF)-kappa B activity which might account for the observed phenomenon. Stimulation of plus clones liberated the classical p50-p65 complex from cytoplasmic pools, whereas minus clones produced an apparently novel, faster-migrating complex, as judged by electrophoretic mobility shift assays. It is surprising that the faster-migrating complex was composed also of p50 and p65. However, the p65 subunit was COOH-terminally truncated, as shown by immunoprecipitation. The truncation resulted from limited proteolysis of p65 during cellular extraction which released particular lysosomal serine proteases, such as elastase, cathepsin G, and proteinase 3. These specific proteases are coordinately expressed and were present exclusively in the minus U937 clones, but not in the plus clones, as demonstrated in the case of cathepsin G. In addition, these proteases were detected in certain subclones of THP-1 and HL-60 cells and in primary monocytes, in each case correlating with the truncated from of p65. We demonstrate in vitro cleavage of p65 by purified elastase and cathepsin G. It is possible that particular serine proteases may have inhibiting effects on the replication of HIV-1 in myelo-monocytic cells. The data also demonstrate that special precautions must be taken when making extracts from myelo-monocytic cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 1239, "end": 1248}, "arguments": [{"role": "Theme", "text": "cathepsin G", "start": 1166, "end": 1177}]}, {"trigger": {"text": "expressed", "start": 1239, "end": 1248}, "arguments": [{"role": "Theme", "text": "proteinase 3", "start": 1183, "end": 1195}]}, {"trigger": {"text": "detected", "start": 1410, "end": 1418}, "arguments": [{"role": "Theme", "text": "cathepsin G", "start": 1166, "end": 1177}]}, {"trigger": {"text": "detected", "start": 1410, "end": 1418}, "arguments": [{"role": "Theme", "text": "proteinase 3", "start": 1183, "end": 1195}]}], "localization": [{"trigger": {"text": "liberated", "start": 644, "end": 653}, "arguments": [{"role": "Theme", "text": "p50", "start": 668, "end": 671}]}, {"trigger": {"text": "liberated", "start": 644, "end": 653}, "arguments": [{"role": "Theme", "text": "p65", "start": 672, "end": 675}]}], "positive regulation": [{"trigger": {"text": "liberated", "start": 644, "end": 653}, "arguments": [{"role": "Theme", "text": "liberated", "start": 644, "end": 653}]}]}}, "schema": []}
{"input": "Human T-cell leukemia virus type I Tax activation of NF-kappa B/Rel involves phosphorylation and degradation of I kappa B alpha and RelA (p65)-mediated induction of the c-rel gene. \nThe tax gene product of human T-cell leukemia virus type I (HTLV-I) is a potent transcriptional activator that both stimulates viral gene expression and activates an array of cellular genes involved in T-cell growth. Tax acts indirectly by inducing or modifying the action of various host transcription factors, including members of the NF-kappa B/Rel family of enhancer-binding proteins. In resting T cells, many of these NF-kappa B/Rel factors are sequestered in the cytoplasm by various ankyrin-rich inhibitory proteins, including I kappa B alpha. HTLV-I Tax expression leads to the constitutive nuclear expression of biologically active NF-kappa B and c-Rel complexes; however, the biochemical mechanism(s) underlying this response remains poorly understood. In this study, we demonstrate that Tax-stimulated nuclear expression of NF-kappa B in both HTLV-I-infected and Tax-transfected human T cells is associated with the phosphorylation and rapid proteolytic degradation of I kappa B alpha. In contrast to prior in vitro studies, at least a fraction of the phosphorylated form of I kappa B alpha remains physically associated with the NF-kappa B complex in vivo but is subject to rapid degradation, thereby promoting the nuclear translocation of the active NF-kappa B complex. We further demonstrate that Tax induction of nuclear c-Rel expression is activated by the RelA (p65) subunit of NF-kappa B, which activates transcription of the c-rel gene through an intrinsic kappa B enhancer element. In normal cells, the subsequent accumulation of nuclear c-Rel acts to inhibit its own continued production, indicating the presence of an autoregulatory loop. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associated", "start": 1303, "end": 1313}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1268, "end": 1283}]}], "gene expression": [{"trigger": {"text": "expression", "start": 744, "end": 754}, "arguments": [{"role": "Theme", "text": "Tax", "start": 740, "end": 743}]}, {"trigger": {"text": "expression", "start": 789, "end": 799}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 838, "end": 843}]}, {"trigger": {"text": "expression", "start": 1524, "end": 1534}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1518, "end": 1523}]}, {"trigger": {"text": "production", "start": 1780, "end": 1790}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1740, "end": 1745}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 1754, "end": 1761}, "arguments": [{"role": "Cause", "text": "accumulation", "start": 1716, "end": 1728}, {"role": "Theme", "text": "production", "start": 1780, "end": 1790}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 77, "end": 92}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 112, "end": 127}]}, {"trigger": {"text": "phosphorylation", "start": 1109, "end": 1124}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1162, "end": 1177}]}], "positive regulation": [{"trigger": {"text": "leads", "start": 755, "end": 760}, "arguments": [{"role": "Cause", "text": "expression", "start": 744, "end": 754}, {"role": "Theme", "text": "expression", "start": 789, "end": 799}]}, {"trigger": {"text": "induction", "start": 1497, "end": 1506}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1493, "end": 1496}, {"role": "Theme", "text": "expression", "start": 1524, "end": 1534}]}, {"trigger": {"text": "activated", "start": 1538, "end": 1547}, "arguments": [{"role": "Theme", "text": "induction", "start": 1497, "end": 1506}, {"role": "Cause", "text": "p65", "start": 1561, "end": 1564}]}, {"trigger": {"text": "activates", "start": 1595, "end": 1604}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1605, "end": 1618}, {"role": "Cause", "text": "c-rel", "start": 1626, "end": 1631}]}, {"trigger": {"text": "accumulation", "start": 1716, "end": 1728}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1740, "end": 1745}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 97, "end": 108}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 112, "end": 127}]}, {"trigger": {"text": "degradation", "start": 1147, "end": 1158}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1162, "end": 1177}]}, {"trigger": {"text": "degradation", "start": 1374, "end": 1385}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1268, "end": 1283}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1605, "end": 1618}, "arguments": [{"role": "Theme", "text": "c-rel", "start": 1626, "end": 1631}]}]}}, "schema": []}
{"input": "Arrested development: understanding v-abl. \nThe protein tyrosine kinase activity of the v-abl oncogene has been demonstrated to subvert the normal second messenger systems used by lymphoid cells for growth and differentiation. Transformation of bone marrow with the Abelson murine leukemia virus results in the appearance of B cell lineage cells arrested at the pre-B cell stage. Recent reports have characterized these cells expressing high v-abl kinase activity as deficient in detectable NF-kappaB DNA binding activity and low level RAG gene expression. These observations suggest that v-abl may be inhibiting the differentiation of B cells by blocking these two crucial elements in the maturation pathway. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Distinct DNase-I hypersensitive sites are associated with TAL-1 transcription in erythroid and T-cell lines. \nThe tal-1 gene, frequently activated in human T-cell acute lymphoblastic leukemia (T-ALL), is expressed in the erythroid, megakaryocytic, and mast cell lineages during normal hematopoiesis. To gain further insight into the molecular mechanisms that control tal-1 expression, we investigated tal-1 chromatin structure in erythroid/megakaryocytic cell lines and in T-cell lines either with or without tal-1 rearrangements. Tal-1 transcription was shown to be monoallelic in Jurkat, a T-cell line that expresses tal-1 in the absence of apparent genomic alteration of the locus. Methylation studies indicated that the tal-15' GC-rich region behaves like a CpG island, hypomethylated in normal cells, and methylated de novo on transcriptionally inactive alleles in established cell lines. Five major DNase-I hypersensitive sites (HS) were mapped in the tal-1 locus. HS I, IV, and V were exclusively observed in the erythroid/megakaryocytic cell lines that express tal-1 from the promoters 1a and 1b. HS II was weak in hematopoietic cell lines, absent in Hela, and greatly enhanced in Jurkat, suggesting that this region might be implicated in the cis-activation of tal-1 promoter 1b in this cell line. HS III was weak in HEL and Jurkat, and greatly enhanced in DU528, a T-cell line that bears a t (1;14) and initiates tal-1 transcription within exon 4. These results suggest that distinct regulatory elements are associated with the use of the different tal-1 promoters. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 204, "end": 213}, "arguments": [{"role": "Theme", "text": "tal-1", "start": 114, "end": 119}]}, {"trigger": {"text": "expression", "start": 373, "end": 383}, "arguments": [{"role": "Theme", "text": "tal-1", "start": 367, "end": 372}]}, {"trigger": {"text": "expresses", "start": 609, "end": 618}, "arguments": [{"role": "Theme", "text": "tal-1", "start": 619, "end": 624}]}, {"trigger": {"text": "express", "start": 1061, "end": 1068}, "arguments": [{"role": "Theme", "text": "tal-1", "start": 1069, "end": 1074}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 137, "end": 146}, "arguments": [{"role": "Theme", "text": "tal-1", "start": 114, "end": 119}]}, {"trigger": {"text": "from", "start": 1075, "end": 1079}, "arguments": [{"role": "Theme", "text": "express", "start": 1061, "end": 1068}]}, {"trigger": {"text": "cis-activation", "start": 1252, "end": 1266}, "arguments": [{"role": "Theme", "text": "tal-1", "start": 1270, "end": 1275}, {"role": "Site", "text": "promoter 1b", "start": 1276, "end": 1287}]}], "regulation": [{"trigger": {"text": "control", "start": 359, "end": 366}, "arguments": [{"role": "Theme", "text": "expression", "start": 373, "end": 383}]}], "transcription": [{"trigger": {"text": "transcription", "start": 64, "end": 77}, "arguments": [{"role": "Theme", "text": "TAL-1", "start": 58, "end": 63}]}, {"trigger": {"text": "transcription", "start": 537, "end": 550}, "arguments": [{"role": "Theme", "text": "Tal-1", "start": 531, "end": 536}]}, {"trigger": {"text": "transcription", "start": 1429, "end": 1442}, "arguments": [{"role": "Theme", "text": "tal-1", "start": 1423, "end": 1428}]}]}}, "schema": []}
{"input": "Functions of glutathione and glutathione disulfide in immunology and immunopathology. \nEven a moderate increase in the cellular cysteine supply elevates the intracellular glutathione (GSH) and glutathione disulfide (GSSG) levels and potentiates immunological functions of lymphocytes in vitro. At low GSSG levels, T cells cannot optimally activate the immunologically important transcription factor NF kappa B, whereas high GSSG levels inhibit the DNA binding activity of NF kappa B. The effects of GSSG are antagonized by reduced thioredoxin (TRX). As the protein tyrosine kinase activities p56lck and p59fyn are activated in intact cells by hydrogen peroxide, they are likely targets for GSSG action. These redox-regulated enzymes trigger signal cascades for NF kappa B activation and transduce signals from the T cell antigen receptor, from CD4 and CD8 molecules, and from the IL-2 receptor beta-chain. The effector phase of cytotoxic T cell responses and IL-2-dependent functions are inhibited even by a partial depletion of the intracellular GSH pool. As signal transduction is facilitated by prooxidant conditions, we propose that the well-known immunological consequences of GSH depletion ultimately may be results of the accompanying GSSG deficiency. As HIV-infected patients and SIV-infected rhesus macaques have, on the average, significantly decreased plasma cyst(e)ine and intracellular GSH levels, we also hypothesize that AIDS may be the consequence of a GSSG deficiency as well. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "activated", "start": 614, "end": 623}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 592, "end": 598}]}, {"trigger": {"text": "activated", "start": 614, "end": 623}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 603, "end": 609}]}, {"trigger": {"text": "trigger signal cascades", "start": 733, "end": 756}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 592, "end": 598}]}, {"trigger": {"text": "trigger signal cascades", "start": 733, "end": 756}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 603, "end": 609}]}], "regulation": [{"trigger": {"text": "targets", "start": 678, "end": 685}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 592, "end": 598}]}, {"trigger": {"text": "targets", "start": 678, "end": 685}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 603, "end": 609}]}]}}, "schema": []}
{"input": "Erythropoietin-dependent induction of hemoglobin synthesis in a cytokine-dependent cell line M-TAT. \nM-TAT is a cytokine-dependent cell line with the potential to differentiate along the erythroid and megakaryocytic lineages. We cultured M-TAT cells long term (> 1 year) in the continuous presence of erythropoietin (EPO), granulocyte-macrophage colony-stimulating factor (GM-CSF), or stem cell factor (SCF). These long term cultures are referred to as M-TAT/EPO, M-TAT/GM-CSF, and M-TAT/SCF cells, respectively. Hemoglobin concentration and gamma-globin and erythroid delta-aminolevulinate synthase mRNA levels were significantly higher in M-TAT/EPO cells than in M-TAT/GM-CSF cells. When the supplemented cytokine was switched from GM-CSF to EPO, hemoglobin synthesis in M-TAT/GM-CSF cells increased rapidly (within 5 h), and the level of GATA-1 mRNA increased. In contrast, the addition of GM-CSF to the M-TAT/EPO cell culture decreased the amount of hemoglobin, even in the presence of EPO, indicating that the EPO signal for erythroid differentiation is suppressed by GM-CSF. Thus, erythroid development of M-TAT cells is promoted by EPO and suppressed by GM-CSF. These results support the hypothesis that EPO actively influences the programming of gene expression required for erythroid progenitor cell differentiation. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "increased", "start": 853, "end": 862}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 841, "end": 847}]}], "transcription": [{"trigger": {"text": "mRNA levels", "start": 600, "end": 611}, "arguments": [{"role": "Theme", "text": "erythroid delta-aminolevulinate synthase", "start": 559, "end": 599}]}, {"trigger": {"text": "levels", "start": 605, "end": 611}, "arguments": [{"role": "Theme", "text": "erythroid delta-aminolevulinate synthase", "start": 559, "end": 599}]}]}}, "schema": []}
{"input": "One gene, two transcripts: isolation of an alternative transcript encoding for the autoantigen La/SS-B from a cDNA library of a patient with primary Sjogrens' syndrome. \nA cDNA library was prepared from peripheral blood lymphocytes of an autoimmune patient with primary Sjogrens' syndrome. The cDNA library was screened with the patients own autoimmune serum being monospecific for the nuclear autoantigen La/SS-B. Thereby an alternative type of La mRNA was identified that differed from the known La mRNA due to an exchange of the exon 1. Sequencing of the genomic region between the exons 1 and 2 showed that the alternative 5'-end is a part of the intron. In addition, the presence of an alternative promoter site, which exists within the intron downstream of the exon 1, became evident. In consequence, the alternative La mRNA is the result of a promoter switching combined with an alternative splicing mechanism. In the intron, further transcription factor binding sites, including a NF-kappa B element, were identified leading to the suggestion that the expression of the gene encoding for the nuclear autoantigen La/SS-B alters in dependence on disease conditions. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1060, "end": 1070}, "arguments": [{"role": "Theme", "text": "autoantigen La", "start": 1108, "end": 1122}]}], "positive regulation": [{"trigger": {"text": "result", "start": 838, "end": 844}, "arguments": [{"role": "Theme", "text": "La", "start": 823, "end": 825}]}], "regulation": [{"trigger": {"text": "alters", "start": 1128, "end": 1134}, "arguments": [{"role": "Theme", "text": "expression", "start": 1060, "end": 1070}]}]}}, "schema": []}
{"input": "Functional Myc-Max heterodimer is required for activation-induced apoptosis in T cell hybridomas. \nT cell hybridomas respond to activation signals by undergoing apoptotic cell death, and this is likely to represent comparable events related to tolerance induction in immature and mature T cells in vivo. Previous studies using antisense oligonucleotides implicated the c-Myc protein in the phenomenon of activation-induced apoptosis. This role for c-Myc in apoptosis is now confirmed in studies using a dominant negative form of its heterodimeric binding partner, Max, which we show here inhibits activation-induced apoptosis. Further, coexpression of a reciprocally mutant Myc protein capable of forming functional heterodimers with the mutant Max can compensate for the dominant negative activity and restore activation-induced apoptosis. These results imply that Myc promotes activation-induced apoptosis by obligatory heterodimerization with Max, and therefore, by regulating gene transcription. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding partner", "start": 547, "end": 562}, "arguments": [{"role": "Theme", "text": "c-Myc", "start": 448, "end": 453}, {"role": "Theme2", "text": "Max", "start": 564, "end": 567}]}, {"trigger": {"text": "capable of forming functional heterodimers", "start": 686, "end": 728}, "arguments": [{"role": "Theme", "text": "Myc", "start": 674, "end": 677}, {"role": "Theme2", "text": "Max", "start": 745, "end": 748}]}, {"trigger": {"text": "heterodimerization", "start": 922, "end": 940}, "arguments": [{"role": "Theme", "text": "Myc", "start": 866, "end": 869}, {"role": "Theme2", "text": "Max", "start": 946, "end": 949}]}], "gene expression": [{"trigger": {"text": "coexpression", "start": 636, "end": 648}, "arguments": [{"role": "Theme", "text": "Myc", "start": 674, "end": 677}]}, {"trigger": {"text": "coexpression", "start": 636, "end": 648}, "arguments": [{"role": "Theme", "text": "Max", "start": 745, "end": 748}]}]}}, "schema": []}
{"input": "DNA-binding studies of the Epstein-Barr virus nuclear antigen 2 (EBNA-2): evidence for complex formation by latent membrane protein gene promoter-binding proteins in EBNA-2-positive cell lines. \nThe Epstein-Barr virus (EBV) nuclear antigen 2 (EBNA-2) protein is essential for the immortalization of human primary B cells by EBV. EBNA-2 trans-activates cellular and viral genes like CD23, c-fgr, latent membrane protein 1 (LMP1) and terminal protein 1 (TP1). Trans-activation of the TP1 promoter and of the BamHI C promoter has already been investigated in detail and appears to be mediated via protein-protein interactions and not by direct binding of EBNA-2 type A (of EBV type 1) to the DNA. EBNA-2 is able to trans-activate the expression of the LMP gene in several cell lines. Various reports have delineated the cis-acting elements of the LMP promoter through which EBNA-2 mediates trans-activation. To determine whether EBNA-2 also trans-activates the LMP promoter by protein-protein interactions, we performed a series of gel retardation assays and competition experiments with LMP promoter fragments of different sizes. We determined that the protein-binding region on the LMP promoter was within a 42 bp fragment encompassing nucleotides -135 to -176 relative to the LMP transcriptional start site. None of the DNA fragments investigated indicated interaction of EBNA-2 with the DNA via protein-protein interactions. No significant differences between EBNA-2-positive and EBNA-2-negative nuclear extracts could be seen in the gel retardation assay under conditions that clearly showed binding of EBNA-2A to the TP1 promoter. However, analysis of sucrose gradient fractions in the gel retardation assay provided evidence that the LMP promoter-binding proteins form a complex of higher M(r) in EBNA-2-positive cell extracts. These complexes were destroyed by detergent. We deduce from these results that EBNA-2-positive cells might indeed contain specific complexes bound to the LMP promoter which are, however, too labile to be detected in a standard gel retardation assay. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 4, "end": 11}, "arguments": [{"role": "Theme", "text": "EBNA-2", "start": 65, "end": 71}]}, {"trigger": {"text": "interactions", "start": 990, "end": 1002}, "arguments": [{"role": "Theme", "text": "EBNA-2", "start": 926, "end": 932}]}, {"trigger": {"text": "binding", "start": 1159, "end": 1166}, "arguments": [{"role": "Theme", "text": "LMP", "start": 1181, "end": 1184}, {"role": "Site", "text": "promoter", "start": 1185, "end": 1193}]}, {"trigger": {"text": "interaction", "start": 1357, "end": 1368}, "arguments": [{"role": "Theme", "text": "EBNA-2", "start": 1372, "end": 1378}]}, {"trigger": {"text": "interactions", "start": 1412, "end": 1424}, "arguments": [{"role": "Theme", "text": "EBNA-2", "start": 1372, "end": 1378}]}, {"trigger": {"text": "binding", "start": 1594, "end": 1601}, "arguments": [{"role": "Theme", "text": "EBNA-2A", "start": 1605, "end": 1612}, {"role": "Theme2", "text": "TP1", "start": 1620, "end": 1623}, {"role": "Site2", "text": "promoter", "start": 1624, "end": 1632}]}, {"trigger": {"text": "binding", "start": 1751, "end": 1758}, "arguments": [{"role": "Theme", "text": "LMP", "start": 1738, "end": 1741}, {"role": "Site", "text": "promoter", "start": 1742, "end": 1750}]}, {"trigger": {"text": "bound", "start": 1973, "end": 1978}, "arguments": [{"role": "Theme", "text": "LMP", "start": 1986, "end": 1989}, {"role": "Site", "text": "promoter", "start": 1990, "end": 1998}]}], "gene expression": [{"trigger": {"text": "expression", "start": 731, "end": 741}, "arguments": [{"role": "Theme", "text": "LMP", "start": 749, "end": 752}]}], "positive regulation": [{"trigger": {"text": "trans-activates", "start": 336, "end": 351}, "arguments": [{"role": "Cause", "text": "EBNA-2", "start": 329, "end": 335}, {"role": "Theme", "text": "CD23", "start": 382, "end": 386}]}, {"trigger": {"text": "trans-activates", "start": 336, "end": 351}, "arguments": [{"role": "Cause", "text": "EBNA-2", "start": 329, "end": 335}, {"role": "Theme", "text": "c-fgr", "start": 388, "end": 393}]}, {"trigger": {"text": "trans-activates", "start": 336, "end": 351}, "arguments": [{"role": "Cause", "text": "EBNA-2", "start": 329, "end": 335}, {"role": "Theme", "text": "LMP1", "start": 422, "end": 426}]}, {"trigger": {"text": "trans-activates", "start": 336, "end": 351}, "arguments": [{"role": "Cause", "text": "EBNA-2", "start": 329, "end": 335}, {"role": "Theme", "text": "TP1", "start": 452, "end": 455}]}, {"trigger": {"text": "Trans-activation", "start": 458, "end": 474}, "arguments": [{"role": "Theme", "text": "TP1", "start": 482, "end": 485}, {"role": "Site", "text": "promoter", "start": 486, "end": 494}]}, {"trigger": {"text": "Trans-activation", "start": 458, "end": 474}, "arguments": [{"role": "Theme", "text": "BamHI C", "start": 506, "end": 513}, {"role": "Site", "text": "promoter", "start": 514, "end": 522}]}, {"trigger": {"text": "mediated", "start": 581, "end": 589}, "arguments": [{"role": "Theme", "text": "Trans-activation", "start": 458, "end": 474}]}, {"trigger": {"text": "trans-activate", "start": 712, "end": 726}, "arguments": [{"role": "Cause", "text": "EBNA-2", "start": 694, "end": 700}, {"role": "Theme", "text": "expression", "start": 731, "end": 741}]}, {"trigger": {"text": "mediates", "start": 878, "end": 886}, "arguments": [{"role": "Site", "text": "cis-acting elements", "start": 817, "end": 836}, {"role": "Theme", "text": "LMP", "start": 844, "end": 847}, {"role": "Cause", "text": "EBNA-2", "start": 871, "end": 877}]}, {"trigger": {"text": "trans-activates", "start": 938, "end": 953}, "arguments": [{"role": "Theme", "text": "LMP", "start": 958, "end": 961}, {"role": "Site", "text": "promoter", "start": 962, "end": 970}, {"role": "Cause", "text": "interactions", "start": 990, "end": 1002}]}]}}, "schema": []}
{"input": "Enhanced responsiveness to nuclear factor kappa B contributes to the unique phenotype of simian immunodeficiency virus variant SIVsmmPBj14. \nInfection with a variant of simian immunodeficiency virus, SIVsmmPBj14, leads to severe acute disease in macaques. This study was designed to investigate the functional significance of previously described mutations in the viral long terminal repeat (LTR) and to elucidate their contribution to the unique phenotype of SIVsmmPBj14. LTR-directed transcription was measured by using luciferase reporter constructs that were transiently transfected into cultured cells. In a wide range of cell types, the basal transcriptional activity of the LTR from SIVsmmPBj14 was found to be 2- to 4.5-fold higher than that of an LTR from a non-acutely pathogenic strain. These LTRs differ by five point mutations and a 22-bp duplication in SIVsmmPBj14, which includes a nuclear factor kappa B (NF kappa B) site. Transcriptional differences between these LTRs were further enhanced by two- to threefold upon treatment of cells with phorbol ester or tumor necrosis factor alpha or by cotransfection with plasmids expressing NF kappa B subunits. Mutagenesis studies, and the use of a reporter construct containing an enhancerless promoter, indicate that these transcriptional effects are due principally to the 22-bp sequence duplication and the NF kappa B site contained within it. Finally, infectious virus stocks that were isogenic except for the LTR were generated. The LTR from SIVsmmPBj14 was found to confer an increase in the kinetics of virus replication in cultured cells. Inclusion of this LTR in recombinant SIVs also resulted in a two- to threefold rise in the extent of cellular proliferation that was induced in quiescent simian peripheral blood mononuclear cells. These studies are consistent with the hypothesis that LTR mutations assist SIVsmmPBj14 in responding efficiently to cellular stimulation and allow it to replicate to high titers during the acute phase of viral infection. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Identification of a region which directs the monocytic activity of the colony-stimulating factor 1 (macrophage colony-stimulating factor) receptor promoter and binds PEBP2/CBF (AML1). \nThe receptor for the macrophage colony-stimulating factor (or colony-stimulating factor 1 [CSF-1]) is expressed from different promoters in monocytic cells and placental trophoblasts. We have demonstrated that the monocyte-specific expression of the CSF-1 receptor is regulated at the level of transcription by a tissue-specific promoter whose activity is stimulated by the monocyte/B-cell-specific transcription factor PU.1 (D.-E.Zhang, C.J.Hetherington, H.-M.Chen, and D.G.Tenen, Mol.Cell. Biol.14:373-381, 1994). Here we report that the tissue specificity of this promoter is also mediated by sequences in a region II (bp -88 to - 59), which lies 10 bp upstream from the PU.1-binding site. When analyzed by DNase footprinting, region II was protected preferentially in monocytic cells. Electrophoretic mobility shift assays confirmed that region II interacts specifically with nuclear proteins from monocytic cells. Two gel shift complexes (Mono A and Mono B) were formed with separate sequence elements within this region. Competition and supershift experiments indicate that Mono B contains a member of the polyomavirus enhancer-binding protein 2/core-binding factor (PEBP2/CBF) family, which includes the AML1 gene product, while Mono A is a distinct complex preferentially expressed in monocytic cells. Promoter constructs with mutations in these sequence elements were no longer expressed specifically in monocytes. Furthermore, multimerized region II sequence elements enhanced the activity of a heterologous thymidine kinase promoter in monocytic cells but not other cell types tested. These results indicate that the monocyte/B-cell-specific transcription factor PU.1 and the Mono A and Mono B protein complexes act in concert to regulate monocyte-specific transcription of the CSF-1 receptor. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 160, "end": 165}, "arguments": [{"role": "Theme", "text": "AML1", "start": 177, "end": 181}]}, {"trigger": {"text": "contains", "start": 1272, "end": 1280}, "arguments": [{"role": "Theme", "text": "AML1", "start": 1396, "end": 1400}]}], "gene expression": [{"trigger": {"text": "expression", "start": 417, "end": 427}, "arguments": [{"role": "Theme", "text": "CSF-1 receptor", "start": 435, "end": 449}]}], "regulation": [{"trigger": {"text": "directs", "start": 33, "end": 40}, "arguments": [{"role": "Theme", "text": "colony-stimulating factor 1 (macrophage colony-stimulating factor) receptor", "start": 71, "end": 146}, {"role": "Site", "text": "promoter", "start": 147, "end": 155}]}, {"trigger": {"text": "regulated", "start": 453, "end": 462}, "arguments": [{"role": "Theme", "text": "expression", "start": 417, "end": 427}]}, {"trigger": {"text": "in concert to regulate", "start": 1912, "end": 1934}, "arguments": [{"role": "Cause", "text": "PU.1", "start": 1859, "end": 1863}, {"role": "Theme", "text": "transcription", "start": 1953, "end": 1966}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1953, "end": 1966}, "arguments": [{"role": "Theme", "text": "CSF-1 receptor", "start": 1974, "end": 1988}]}]}}, "schema": []}
{"input": "A factor that regulates the class II major histocompatibility complex gene DPA is a member of a subfamily of zinc finger proteins that includes a Drosophila developmental control protein. \nA novel DNA sequence element termed the J element involved in the regulated expression of class II major histocompatibility complex genes was recently described. To study this element and its role in class II gene regulation further, a cDNA library was screened with oligonucleotide probes containing both the S element and the nearby J element of the human DPA gene. Several DNA clones were obtained by this procedure, one of which, clone 18, is reported and characterized here. It encodes a protein predicted to contain 688 amino acid residues, including 11 zinc finger motifs of the C2H2 type in the C-terminal region, that are Kruppel-like in the conservation of the H/C link sequence connecting them. The 160 N-terminal amino acids in the nonfinger region of clone 18 are highly homologous with similar regions of several other human, mouse, and Drosophila sequences, defining a subfamily of Kruppel-like zinc finger proteins termed TAB (tramtrack [ttk]-associated box) here. One of the Drosophila sequences, ttk, is a developmental control gene, while a second does not contain a zinc finger region but encodes a structure important in oocyte development. An acidic activation domain is located between the N-terminal conserved region of clone 18 and its zinc fingers. This protein appears to require both the S and J elements, which are separated by 10 bp for optimal binding. Antisense cDNA to clone 18 inhibited the expression of a reporter construct containing the DPA promoter, indicating its functional importance in the expression of this class II gene. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1722, "end": 1732}, "arguments": [{"role": "Theme", "text": "DPA", "start": 75, "end": 78}]}], "positive regulation": [{"trigger": {"text": "importance", "start": 1704, "end": 1714}, "arguments": [{"role": "Theme", "text": "expression", "start": 1722, "end": 1732}]}], "regulation": [{"trigger": {"text": "regulates", "start": 14, "end": 23}, "arguments": [{"role": "Theme", "text": "DPA", "start": 75, "end": 78}]}]}}, "schema": []}
{"input": "Glucocorticoid-induced apoptosis of lymphoid cells. \nThe induction of cell death in lymphoid cells by glucocorticoids is one of the earliest and most thoroughly studied models of apoptosis. Although the exact mechanism by which apoptosis occurs in lymphocytes is unknown many biochemical and molecular changes have been shown to occur in these cells in response to glucocorticoids. The role of chromatin degradation and endonucleases in the apoptotic process has been closely studied, as well as the involvement of several oncogenes in glucocorticoid-induced cell lysis. In addition, the clinical importance of glucocorticoid-induced apoptosis in the treatment of lymphoid neoplasms has recently received increased attention. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Inhibition of human immunodeficiency virus type 1 replication by a Tat-activated, transduced interferon gene: targeted expression to human immunodeficiency virus type 1-infected cells. \nWe have examined the feasibility of using interferon (IFN) gene transfer as a novel approach to anti-human immunodeficiency virus type 1 (HIV-1) therapy in this study. To limit expression of a transduced HIV-1 long terminal repeat (LTR)-IFNA2 (the new approved nomenclature for IFN genes is used throughout this article) hybrid gene to the HIV-1-infected cells, HIV-1 LTR was modified. Deletion of the NF-kappa B elements of the HIV-1 LTR significantly inhibited Tat-mediated transactivation in T-cell lines, as well as in a monocyte line, U937. Replacement of the NF-kappa B elements in the HIV-1 LTR by a DNA fragment derived from the 5'-flanking region of IFN-stimulated gene 15 (ISG15), containing the IFN-stimulated response element, partially restored Tat-mediated activation of LTR in T cells as well as in monocytes. Insertion of this chimeric promoter (ISG15 LTR) upstream of the human IFNA2 gene directed high levels of IFN synthesis in Tat-expressing cells, while this promoter was not responsive to tumor necrosis factor alpha-mediated activation. ISG15-LTR-IFN hybrid gene inserted into the retrovirus vector was transduced into Jurkat and U937 cells. Selected transfected clones produced low levels of IFN A (IFNA) constitutively, and their abilities to express interleukin-2 and interleukin-2 receptor upon stimulation with phytohemagglutinin and phorbol myristate acetate were retained. Enhancement of IFNA synthesis observed upon HIV-1 infection resulted in significant inhibition of HIV-1 replication for a period of at least 30 days. Virus isolated from IFNA-producing cells was able to replicate in the U937 cells but did not replicate efficiently in U937 cells transduced with the IFNA gene. These results suggest that targeting IFN synthesis to HIV-1-infected cells is an attainable goal and that autocrine IFN synthesis results in a long-lasting and permanent suppression of HIV-1 replication. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 1137, "end": 1147}, "arguments": [{"role": "Theme", "text": "Tat", "start": 1133, "end": 1136}]}, {"trigger": {"text": "produced", "start": 1379, "end": 1387}, "arguments": [{"role": "Theme", "text": "IFNA", "start": 1409, "end": 1413}]}, {"trigger": {"text": "express", "start": 1454, "end": 1461}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 1462, "end": 1475}]}, {"trigger": {"text": "synthesis", "start": 1609, "end": 1618}, "arguments": [{"role": "Theme", "text": "IFNA", "start": 1604, "end": 1608}]}, {"trigger": {"text": "producing", "start": 1764, "end": 1773}, "arguments": [{"role": "Theme", "text": "IFNA", "start": 1759, "end": 1763}]}], "positive regulation": [{"trigger": {"text": "stimulation", "start": 1508, "end": 1519}, "arguments": [{"role": "Theme", "text": "express", "start": 1454, "end": 1461}, {"role": "Cause", "text": "phytohemagglutinin", "start": 1525, "end": 1543}]}, {"trigger": {"text": "stimulation", "start": 1508, "end": 1519}, "arguments": [{"role": "Theme", "text": "express", "start": 1454, "end": 1461}]}, {"trigger": {"text": "Enhancement", "start": 1589, "end": 1600}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1609, "end": 1618}]}]}}, "schema": []}
{"input": "Pyrrolidine dithiocarbamate, a potent inhibitor of nuclear factor kappa B (NF-kappa B) activation, prevents apoptosis in human promyelocytic leukemia HL-60 cells and thymocytes. \nWe examined the effect of pyrrolidine dithiocarbamate (PDTC), which potently blocks the activation of nuclear factor kappa B (NF-kappa B), on the induction of apoptosis by a variety of agents. Treatment of a human promyelocytic leukemia cell line, HL-60, with 10 micrograms/mL etoposide or 2 microM 1-beta-D-arabinofuranosylcytosine induced NF-kappa B activation within 1 hr and subsequently caused apoptosis within 3-4 hr. The simultaneous addition of 50-500 microM PDTC with these agents blocked NF-kappa B activation and completely abrogated both morphologically apoptotic changes and internucleosomal DNA fragmentation for up to 6 hr. However, PDTC failed to inhibit the endonuclease activity contained in the whole cell lysates. The inhibitory effect of PDTC was also observed in etoposide- and dexamethasone-induced apoptosis in human thymocytes at a concentration of 1-10 microM. Since PDTC has both antioxidant and metal-ion chelating activities, we tested the effects of N-acetyl-L-cysteine (NAC) (antioxidant) or o-phenanthroline (OP) (metal-ion chelator) on the induction of apoptosis. Pretreatment of HL-60 cells or thymocytes with 100-500 microM OP for 2 hr, but not 10-60 mM NAC, suppressed subsequent occurrence of apoptosis induced by etoposide. These results suggest that the activation of NF-kappa B plays an important role in the apoptotic process of human hematopoietic cells. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Differential regulation of proto-oncogenes c-jun and c-fos in T lymphocytes activated through CD28. \nThe T cell surface molecule CD28 binds to ligands on accessory cells and APCs, playing an important costimulatory role in the response of T cells to Ags. Our knowledge of the intracellular signaling pathways coupled to this receptor is incomplete. In addition to activation of phospholipase C gamma 1, ligation of this receptor also seems to activate a calcium-independent, CD28-specific pathway. In this paper, we report that cross-linking of CD28 (but not CD2, CD5, LFA-1, or CD7) leads to an elevation of c-jun mRNA, with only minimal activation of c-fos expression. CD28-dependent induction of c-jun expression requires protein tyrosine kinase activity, but does not depend on activation of a phorbol ester-responsive protein kinase C or elevation of cytosolic calcium. Furthermore, CD28-dependent elevation of c-jun mRNA does not appear to be mediated at the level of mRNA stability. A mechanism is suggested whereby expression of c-jun and junB, in the absence of members of the fos family, can prevent inappropriate activation of T cells caused by ligation of CD28 in the absence of a specific antigenic stimulus. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 134, "end": 139}, "arguments": [{"role": "Theme", "text": "CD28", "start": 129, "end": 133}]}, {"trigger": {"text": "ligation", "start": 403, "end": 411}, "arguments": [{"role": "Theme", "text": "CD28", "start": 475, "end": 479}]}, {"trigger": {"text": "cross-linking", "start": 528, "end": 541}, "arguments": [{"role": "Theme", "text": "CD28", "start": 545, "end": 549}]}, {"trigger": {"text": "cross-linking", "start": 528, "end": 541}, "arguments": [{"role": "Theme", "text": "CD5", "start": 564, "end": 567}]}, {"trigger": {"text": "cross-linking", "start": 528, "end": 541}, "arguments": [{"role": "Theme", "text": "CD7", "start": 579, "end": 582}]}, {"trigger": {"text": "ligation", "start": 1156, "end": 1164}, "arguments": [{"role": "Theme", "text": "CD28", "start": 1168, "end": 1172}]}], "gene expression": [{"trigger": {"text": "expression", "start": 659, "end": 669}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 653, "end": 658}]}, {"trigger": {"text": "expression", "start": 705, "end": 715}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 699, "end": 704}]}, {"trigger": {"text": "expression", "start": 1023, "end": 1033}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1037, "end": 1042}]}, {"trigger": {"text": "expression", "start": 1023, "end": 1033}, "arguments": [{"role": "Theme", "text": "junB", "start": 1047, "end": 1051}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 364, "end": 374}, "arguments": [{"role": "Theme", "text": "phospholipase C gamma 1", "start": 378, "end": 401}, {"role": "Cause", "text": "ligation", "start": 403, "end": 411}]}, {"trigger": {"text": "leads", "start": 584, "end": 589}, "arguments": [{"role": "Cause", "text": "cross-linking", "start": 528, "end": 541}, {"role": "Theme", "text": "elevation", "start": 596, "end": 605}]}, {"trigger": {"text": "leads", "start": 584, "end": 589}, "arguments": [{"role": "Theme", "text": "elevation", "start": 596, "end": 605}]}, {"trigger": {"text": "elevation", "start": 596, "end": 605}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 609, "end": 614}]}, {"trigger": {"text": "activation", "start": 639, "end": 649}, "arguments": [{"role": "Cause", "text": "cross-linking", "start": 528, "end": 541}, {"role": "Theme", "text": "expression", "start": 659, "end": 669}]}, {"trigger": {"text": "induction", "start": 686, "end": 695}, "arguments": [{"role": "Cause", "text": "CD28", "start": 671, "end": 675}, {"role": "Theme", "text": "expression", "start": 705, "end": 715}]}, {"trigger": {"text": "requires", "start": 716, "end": 724}, "arguments": [{"role": "Theme", "text": "induction", "start": 686, "end": 695}]}, {"trigger": {"text": "elevation", "start": 903, "end": 912}, "arguments": [{"role": "Cause", "text": "CD28", "start": 888, "end": 892}, {"role": "Theme", "text": "c-jun", "start": 916, "end": 921}]}, {"trigger": {"text": "mediated", "start": 949, "end": 957}, "arguments": [{"role": "Theme", "text": "elevation", "start": 903, "end": 912}, {"role": "Cause", "text": "stability", "start": 979, "end": 988}]}], "regulation": [{"trigger": {"text": "regulation", "start": 13, "end": 23}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 43, "end": 48}]}, {"trigger": {"text": "regulation", "start": 13, "end": 23}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 53, "end": 58}]}, {"trigger": {"text": "depend", "start": 772, "end": 778}, "arguments": [{"role": "Theme", "text": "induction", "start": 686, "end": 695}]}, {"trigger": {"text": "stability", "start": 979, "end": 988}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 916, "end": 921}]}]}}, "schema": []}
{"input": "Constitutive nuclear NF-kappa B in cells of the monocyte lineage. \nIn monocytes, the nuclear factor NF-kappa B has been invoked as an important transcription factor in the expression of cytokine genes, of cell-surface receptors and in the expression of human immunodeficiency virus. In such cells, DNA binding activity of NF-kappa B can be detected without intentional stimulation. In our studies, cells of the human monocytic line Mono Mac 6, cultured in medium containing fetal-calf serum and low levels of lipopolysaccharide (LPS), also exhibit such 'constitutive' NF-kappa B, as demonstrated by mobility-shift analysis of nuclear extracts. This nuclear NF-kappa B was still present when contaminant LPS was removed by ultrafiltration and when serum was omitted. Protein-DNA complexes of constitutive NF-kappa B are similar in mobility to the LPS-induced NF-kappa B and both are recognized by an antibody specific to the p50 subunit of NF-kappa B. By contrast, treatment of cells with pyrrolidine dithiocarbamate (PDTC) will only block LPS-induced NF-kappa B, but not the constitutive binding protein. Using LPS-free and serum-free conditions, constitutive NF-kappa B can be detected in different cell lines of the monocytic lineage (HL60, U937, THP-1, Mono Mac 1 and Mono Mac 6), but not in Molt 4 T cells or K562 stem cells. When ordered according to stage of maturation, the amount of constitutive NF-kappa B was not increased in more mature cell lines. Furthermore, when inducing differentiation in Mono Mac 6 cells, with vitamin D3, no change in constitutive or inducible NF-kappa B can be detected. Analysis of primary cells revealed substantial constitutive NF-kappa B-binding activity in blood monocytes, pleural macrophages and alveolar macrophages. The constitutive NF-kappa B appears to be functionally active, since a low level of tumour necrosis factor (TNF) transcript is detectable in monocytes, and this level can be increased by blocking transcript degradation using cycloheximide. The level of constitutive NF-kappa B in these cells is variable and is frequently found to be lower in the more mature macrophages. Constitutive NF-kappa B was not maintained by autocrine action of cytokines TNF, interleukin 6, interleukin 10, granulocyte-macrophage colony-stimulating factor or macrophage colony-stimulating factor, since neutralizing antibodies did not reduce constitutive DNA-binding activity. Furthermore, blockade of prostaglandin or leukotriene biosynthesis did not affect constitutive NF-kappa B. (ABSTRACT TRUNCATED AT 400 WORDS) ", "output": {"json_structures": {}}, "schema": []}
{"input": "Function and activation of NF-kappa B in the immune system. \nNF-kappa B is a ubiquitous transcription factor. Nevertheless, its properties seem to be most extensively exploited in cells of the immune system. Among these properties are NF-kappa B's rapid posttranslational activation in response to many pathogenic signals, its direct participation in cytoplasmic/nuclear signaling, and its potency to activate transcription of a great variety of genes encoding immunologically relevant proteins. In vertebrates, five distinct DNA binding subunits are currently known which might extensively heterodimerize, thereby forming complexes with distinct transcriptional activity, DNA sequence specificity, and cell type- and cell stage-specific distribution. The activity of DNA binding NF-kappa B dimers is tightly controlled by accessory proteins called I kappa B subunits of which there are also five different species currently known in vertebrates. I kappa B proteins inhibit DNA binding and prevent nuclear uptake of NF-kappa B complexes. An exception is the Bcl-3 protein which in addition can function as a transcription activating subunit in th nucleus. Other I kappa B proteins are rather involved in terminating NF-kappa B's activity in the nucleus. The intracellular events that lead to the inactivation of I kappa B, i.e. the activation of NF-kappa B, are complex. They involve phosphorylation and proteolytic reactions and seem to be controlled by the cells' redox status. Interference with the activation or activity of NF-kappa B may be beneficial in suppressing toxic/septic shock, graft-vs-host reactions, acute inflammatory reactions, acute phase response, and radiation damage. The inhibition of NF-kappa B activation by antioxidants and specific protease inhibitors may provide a pharmacological basis for interfering with these acute processes. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Increased interleukin 2 transcription in murine lymphocytes by ciprofloxacin. \nThe fluoroquinolone antibiotic, ciprofloxacin (cipro), induces hyperproduction of interleukin 2 (IL-2) and interferon-gamma (IFN-gamma) in stimulated human peripheral blood lymphocytes. In this investigation an enhanced and prolonged IL-2 and IL-2 mRNA response was also detected in both stimulated (T cell mitogens or alloantigens) murine splenocytes and in the stimulated murine T cell line EL-4 in the presence of ciprofloxacin (5-80 micrograms/ml) as compared to control cells without antibiotics. However, in contrast to human lymphocytes, IFN-gamma production was inhibited and IFN-gamma mRNA levels were unaffected at 24 h and only slightly upregulated at 48 and 72 h of culture in murine splenocytes incubated with cipro (20 micrograms/ml). EL-4 cells were transfected with a plasmid containing the IL-2 promoter and enhancer region linked to the chloramphenicol acetyltransferase (CAT) reporter gene. Analysis of CAT activity revealed that cipro enhanced IL-2 gene induction. In addition, EL-4 cells incubated with ciprofloxacin showed an early peak and more activated nuclear factor of activated T cells (NFAT-1) as compared to control cells without antibiotics. Cipro did not affect the nuclear transcription factors AP-1 or NFIL-2A. Taken together, cipro inhibited IFN-gamma synthesis, but enhanced IL-2 production in murine lymphocytes by means of influencing NFAT-1 and causing an increased IL-2 transcription. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 147, "end": 157}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 176, "end": 180}]}, {"trigger": {"text": "production", "start": 147, "end": 157}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 204, "end": 213}]}, {"trigger": {"text": "production", "start": 634, "end": 644}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 624, "end": 633}]}, {"trigger": {"text": "induction", "start": 1053, "end": 1062}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1043, "end": 1047}]}, {"trigger": {"text": "synthesis", "start": 1366, "end": 1375}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1356, "end": 1365}]}, {"trigger": {"text": "production", "start": 1395, "end": 1405}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1390, "end": 1394}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 649, "end": 658}, "arguments": [{"role": "Theme", "text": "production", "start": 634, "end": 644}]}, {"trigger": {"text": "inhibited", "start": 1346, "end": 1355}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1366, "end": 1375}]}], "positive regulation": [{"trigger": {"text": "Increased", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "transcription", "start": 24, "end": 37}]}, {"trigger": {"text": "induces hyper", "start": 134, "end": 147}, "arguments": [{"role": "Theme", "text": "production", "start": 147, "end": 157}]}, {"trigger": {"text": "enhanced and prolonged", "start": 290, "end": 312}, "arguments": [{"role": "Theme", "text": "response", "start": 332, "end": 340}]}, {"trigger": {"text": "upregulated", "start": 727, "end": 738}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 663, "end": 672}]}, {"trigger": {"text": "enhanced", "start": 1034, "end": 1042}, "arguments": [{"role": "Theme", "text": "induction", "start": 1053, "end": 1062}]}, {"trigger": {"text": "showed an early peak and more activated", "start": 1117, "end": 1156}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1194, "end": 1200}]}, {"trigger": {"text": "enhanced", "start": 1381, "end": 1389}, "arguments": [{"role": "Theme", "text": "production", "start": 1395, "end": 1405}, {"role": "Cause", "text": "influencing", "start": 1440, "end": 1451}]}, {"trigger": {"text": "enhanced", "start": 1381, "end": 1389}, "arguments": [{"role": "Theme", "text": "production", "start": 1395, "end": 1405}, {"role": "Cause", "text": "causing an increased", "start": 1463, "end": 1483}]}, {"trigger": {"text": "causing an increased", "start": 1463, "end": 1483}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1484, "end": 1488}, {"role": "Theme", "text": "transcription", "start": 1489, "end": 1502}]}], "regulation": [{"trigger": {"text": "response", "start": 332, "end": 340}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 313, "end": 317}]}, {"trigger": {"text": "response", "start": 332, "end": 340}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 322, "end": 326}]}, {"trigger": {"text": "unaffected", "start": 690, "end": 700}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 663, "end": 672}]}, {"trigger": {"text": "affect", "start": 1266, "end": 1272}, "arguments": [{"role": "Theme", "text": "NFIL-2A", "start": 1315, "end": 1322}]}, {"trigger": {"text": "influencing", "start": 1440, "end": 1451}, "arguments": [{"role": "Theme", "text": "NFAT-1", "start": 1452, "end": 1458}]}], "transcription": [{"trigger": {"text": "transcription", "start": 24, "end": 37}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 10, "end": 23}]}, {"trigger": {"text": "transcription", "start": 1489, "end": 1502}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1484, "end": 1488}]}]}}, "schema": []}
{"input": "Multiple prolactin-responsive elements mediate G1 and S phase expression of the interferon regulatory factor-1 gene. \nThe interferon regulatory factor-1 (IRF-1) gene is both an immediate-early G1 phase gene and an S phase gene inducible by PRL in rat Nb2 T lymphocytes. To understand the mechanism by which PRL regulates the biphasic expression of IRF-1, we cloned the rat IRF-1 gene and functionally characterized the IRF-1 promoter. Upon transfection into Nb2 T cells, 1.7 kilobases (kb) of IRF-1 5'-flanking DNA linked to a chloramphenicol acetyl transferase (CAT) reporter gene mediated a 30-fold induction of CAT enzyme activity in response to 24 h of PRL stimulation. Deletion mutants containing 1.3, 0.6, and 0.2 kb 5'-flanking DNA were incrementally less transcriptionally active, although 0.2 kb still mediated a 12-fold induction by PRL. The sequence between -1.7 and -0.2 kb linked to a heterologous thymidine kinase promoter failed to respond to PRL stimulation, suggesting that the activity of upstream PRL response elements may require an interaction with promoter-proximal elements. By assaying CAT enzyme activity across a 24-h PRL induction time course, we were able to assign G1 vs. S phase PRL responses of the IRF-1 gene to different regions of the IRF-1 5'-flanking and promoter DNA. The 0.2-kb IRF-CAT construct was induced by PRL stimulation during the G1 phase of the cell cycle. In contrast, the 1.7-kb IRF-CAT construct was inducible by PRL during both G1 and S phase of the cell cycle. Hence, the PRL-induced biphasic expression of the IRF-1 gene appears to be controlled by separate PRL-responsive elements: elements in the first 0.2 kb of the IRF-1 promoter region act during early activation, and elements between 0.2 and 1.7 kb act in concert with the proximal 0.2-kb region during S phase progression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 62, "end": 72}, "arguments": [{"role": "Theme", "text": "interferon regulatory factor-1", "start": 80, "end": 110}]}, {"trigger": {"text": "expression", "start": 334, "end": 344}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 373, "end": 378}]}, {"trigger": {"text": "expression", "start": 1545, "end": 1555}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1563, "end": 1568}]}], "positive regulation": [{"trigger": {"text": "mediate", "start": 39, "end": 46}, "arguments": [{"role": "Theme", "text": "expression", "start": 62, "end": 72}]}, {"trigger": {"text": "inducible", "start": 227, "end": 236}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 154, "end": 159}, {"role": "Cause", "text": "PRL", "start": 240, "end": 243}]}, {"trigger": {"text": "mediated", "start": 582, "end": 590}, "arguments": [{"role": "Theme", "text": "induction", "start": 601, "end": 610}]}, {"trigger": {"text": "induction", "start": 601, "end": 610}, "arguments": [{"role": "Theme", "text": "CAT", "start": 614, "end": 617}, {"role": "Cause", "text": "PRL", "start": 657, "end": 660}]}, {"trigger": {"text": "induced", "start": 1528, "end": 1535}, "arguments": [{"role": "Cause", "text": "PRL", "start": 1524, "end": 1527}, {"role": "Theme", "text": "expression", "start": 1545, "end": 1555}]}, {"trigger": {"text": "act", "start": 1694, "end": 1697}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1672, "end": 1677}, {"role": "Site", "text": "promoter region", "start": 1678, "end": 1693}]}], "regulation": [{"trigger": {"text": "regulates", "start": 311, "end": 320}, "arguments": [{"role": "Cause", "text": "PRL", "start": 307, "end": 310}, {"role": "Theme", "text": "expression", "start": 334, "end": 344}]}, {"trigger": {"text": "responses", "start": 1213, "end": 1222}, "arguments": [{"role": "Cause", "text": "PRL", "start": 1209, "end": 1212}, {"role": "Theme", "text": "IRF-1", "start": 1230, "end": 1235}]}, {"trigger": {"text": "controlled", "start": 1588, "end": 1598}, "arguments": [{"role": "Theme", "text": "induced", "start": 1528, "end": 1535}, {"role": "Cause", "text": "IRF-1", "start": 1672, "end": 1677}, {"role": "CSite", "text": "promoter region", "start": 1678, "end": 1693}]}, {"trigger": {"text": "controlled", "start": 1588, "end": 1598}, "arguments": [{"role": "Theme", "text": "induced", "start": 1528, "end": 1535}]}]}}, "schema": []}
{"input": "Nonpituitary human prolactin gene transcription is independent of Pit-1 and differentially controlled in lymphocytes and in endometrial stroma. \nExpression of the human PRL (hPRL) gene in extrapituitary sites such as the uterus (decidualized endometrial stroma and myometrium) and cells of the hematopoietic lineage is directed by an alternative promoter which is located approximately 6 kilobases (kb) upstream of the pituitary-specific start site. In order to delineate the tissue-specific mechanisms governing the control of nonpituitary PRL gene expression, we have cloned and sequenced 3 kb 5'-flanking DNA of the upstream decidual/lymphoid (dPRL) promoter. Based on sequence homology we identified two binding motifs for Pit-1 and seven half-sites for glucocorticoid receptor/progesterone receptor (PR) binding. We focused our studies on the role of Pit-1 and of PR as potential transcriptional regulators, since the POU domain protein Pit-1 is essential in the control of pituitary PRL expression, and progesterone induces decidual transformation of the endometrial stroma, a differentiation process during which the decidual PRL gene is activated. We demonstrate in a variety of cell types, including lymphocytes and endometrial stroma, that Pit-1 is not involved in the regulation of dPRL promoter/reporter gene constructs carrying 3 kb 5'-flanking DNA. Our experiments also show that activated PR does not confer direct transcriptional control on the dPRL promoter. When we compared the activity of the transfected dPRL promoter in PRL-secreting and nonsecreting lymphoid cells, we found that the 3 kb 5'-flanking region of the dPRL promoter did not contain elements restricting expression to only those lymphocytes that produce PRL but allowed expression of fusion reporter genes irrespective of the status of the endogenous PRL gene. This was in sharp contrast to endometrial cells where 3 kb 5'-flanking DNA conferred strong transcriptional activation on the dPRL promoter in decidualized endometrial stromal cells actively secreting PRL, but did not allow transcription in undifferentiated non-PRL-secreting endometrial stromal cells. Activation of the dPRL promoter construct in these undifferentiated cells could however be induced by the addition of cAMP, in the absence of progesterone, suggesting that a signal transduced through the cAMP signaling pathway is a primary inducer of decidual PRL gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 145, "end": 155}, "arguments": [{"role": "Theme", "text": "hPRL", "start": 174, "end": 178}]}, {"trigger": {"text": "expression", "start": 550, "end": 560}, "arguments": [{"role": "Theme", "text": "PRL", "start": 541, "end": 544}]}, {"trigger": {"text": "expression", "start": 993, "end": 1003}, "arguments": [{"role": "Theme", "text": "PRL", "start": 989, "end": 992}]}, {"trigger": {"text": "secreting", "start": 1546, "end": 1555}, "arguments": [{"role": "Theme", "text": "PRL", "start": 1542, "end": 1545}]}, {"trigger": {"text": "nonsecreting", "start": 1560, "end": 1572}, "arguments": [{"role": "Theme", "text": "PRL", "start": 1542, "end": 1545}]}, {"trigger": {"text": "expression", "start": 1689, "end": 1699}, "arguments": [{"role": "Theme", "text": "PRL", "start": 1739, "end": 1742}]}, {"trigger": {"text": "produce", "start": 1731, "end": 1738}, "arguments": [{"role": "Theme", "text": "PRL", "start": 1739, "end": 1742}]}, {"trigger": {"text": "secreting", "start": 2037, "end": 2046}, "arguments": [{"role": "Theme", "text": "PRL", "start": 2047, "end": 2050}]}, {"trigger": {"text": "secreting", "start": 2112, "end": 2121}, "arguments": [{"role": "Theme", "text": "PRL", "start": 2108, "end": 2111}]}, {"trigger": {"text": "expression", "start": 2418, "end": 2428}, "arguments": [{"role": "Theme", "text": "PRL", "start": 2409, "end": 2412}]}], "positive regulation": [{"trigger": {"text": "directed", "start": 319, "end": 327}, "arguments": [{"role": "Theme", "text": "Expression", "start": 145, "end": 155}]}, {"trigger": {"text": "activated", "start": 1145, "end": 1154}, "arguments": [{"role": "Theme", "text": "PRL", "start": 1133, "end": 1136}]}, {"trigger": {"text": "activated", "start": 1394, "end": 1403}, "arguments": [{"role": "Theme", "text": "PR", "start": 1404, "end": 1406}]}, {"trigger": {"text": "restricting", "start": 1677, "end": 1688}, "arguments": [{"role": "Theme", "text": "expression", "start": 1689, "end": 1699}]}, {"trigger": {"text": "conferred strong transcriptional activation", "start": 1921, "end": 1964}, "arguments": [{"role": "Theme", "text": "dPRL", "start": 1972, "end": 1976}, {"role": "Site", "text": "promoter", "start": 1977, "end": 1985}]}, {"trigger": {"text": "allow", "start": 2064, "end": 2069}, "arguments": [{"role": "Theme", "text": "transcription", "start": 2070, "end": 2083}]}, {"trigger": {"text": "inducer", "start": 2389, "end": 2396}, "arguments": [{"role": "Theme", "text": "expression", "start": 2418, "end": 2428}]}], "regulation": [{"trigger": {"text": "independent", "start": 51, "end": 62}, "arguments": [{"role": "Theme", "text": "transcription", "start": 34, "end": 47}, {"role": "Cause", "text": "Pit-1", "start": 66, "end": 71}]}, {"trigger": {"text": "controlled", "start": 91, "end": 101}, "arguments": [{"role": "Theme", "text": "transcription", "start": 34, "end": 47}]}, {"trigger": {"text": "control", "start": 517, "end": 524}, "arguments": [{"role": "Theme", "text": "expression", "start": 550, "end": 560}]}, {"trigger": {"text": "essential in the control", "start": 951, "end": 975}, "arguments": [{"role": "Cause", "text": "Pit-1", "start": 942, "end": 947}, {"role": "Theme", "text": "expression", "start": 993, "end": 1003}]}, {"trigger": {"text": "confer direct transcriptional control", "start": 1416, "end": 1453}, "arguments": [{"role": "Cause", "text": "activated", "start": 1394, "end": 1403}, {"role": "Theme", "text": "dPRL", "start": 1461, "end": 1465}, {"role": "Site", "text": "promoter", "start": 1466, "end": 1474}]}], "transcription": [{"trigger": {"text": "transcription", "start": 34, "end": 47}, "arguments": [{"role": "Theme", "text": "prolactin", "start": 19, "end": 28}]}, {"trigger": {"text": "transcription", "start": 2070, "end": 2083}, "arguments": [{"role": "Theme", "text": "PRL", "start": 2108, "end": 2111}]}]}}, "schema": []}
{"input": "Activation of early growth response 1 gene transcription and pp90rsk during induction of monocytic differentiation. \nThe present work has studied mechanisms responsible for induction of early growth response 1 (EGR-1) gene expression during monocytic differentiation of U-937 myeloid leukemia cells. Differentiation of U-937 cells with 12-O-tetradecanoylphorbol-13-acetate (TPA), an activator of the serine/threonine protein kinase C, was associated with transcriptional activation of EGR-1 promoter-reporter constructs. The EGR-1 promoter contains six CC(A/T)6GG (CArG) motifs. The two 5'-most distal CArG sequences conferred TPA inducibility. In contrast, there was little effect of TPA on EGR-1 transcription in a TPA-resistant U-937 cell variant, designated TUR. Treatment of both U-937 and TUR cells with okadaic acid, an inhibitor of serine/threonine protein phosphatases 1 and 2A, was associated with induction of monocytic differentiation and EGR-1 transcription through the 5'-most CArG element. Since these findings supported the involvement of serine/threonine protein phosphorylation in the regulation of EGR-1 expression, we studied activation of the 40S ribosomal protein S6 serine/threonine kinases, pp70S6K and pp90rsk. Although both kinases participate in regulating cell growth, there was no detectable activation of pp70S6K during TPA- or okadaic acid-induced monocytic differentiation. Moreover, rapamycin, an inhibitor of pp70S6K activation, had no effect on induction of EGR-1 expression. In contrast, analysis of pp90rsk activity by phosphorylation of a peptide derived from S6 protein demonstrated stimulation of this kinase in TPA-treated U-937, and not TUR, cells. Okadaic acid treatment of both cell types was associated with activation of pp90rsk. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 223, "end": 233}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 211, "end": 216}]}, {"trigger": {"text": "expression", "start": 1123, "end": 1133}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 1117, "end": 1122}]}, {"trigger": {"text": "expression", "start": 1499, "end": 1509}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 1493, "end": 1498}]}], "positive regulation": [{"trigger": {"text": "Activation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "transcription", "start": 43, "end": 56}]}, {"trigger": {"text": "induction", "start": 173, "end": 182}, "arguments": [{"role": "Theme", "text": "expression", "start": 223, "end": 233}]}, {"trigger": {"text": "induction", "start": 908, "end": 917}, "arguments": [{"role": "Theme", "text": "transcription", "start": 957, "end": 970}]}, {"trigger": {"text": "induction", "start": 1480, "end": 1489}, "arguments": [{"role": "Theme", "text": "expression", "start": 1499, "end": 1509}]}], "regulation": [{"trigger": {"text": "effect", "start": 675, "end": 681}, "arguments": [{"role": "Theme", "text": "transcription", "start": 698, "end": 711}]}, {"trigger": {"text": "regulation", "start": 1103, "end": 1113}, "arguments": [{"role": "Theme", "text": "expression", "start": 1123, "end": 1133}]}, {"trigger": {"text": "effect", "start": 1470, "end": 1476}, "arguments": [{"role": "Theme", "text": "induction", "start": 1480, "end": 1489}]}], "transcription": [{"trigger": {"text": "transcription", "start": 43, "end": 56}, "arguments": [{"role": "Theme", "text": "early growth response 1", "start": 14, "end": 37}]}, {"trigger": {"text": "transcription", "start": 698, "end": 711}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 692, "end": 697}]}, {"trigger": {"text": "transcription", "start": 957, "end": 970}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 951, "end": 956}]}]}}, "schema": []}
{"input": "Effects of prostaglandin E2 on Th0-type human T cell clones: modulation of functions of nuclear proteins involved in cytokine production. \nThe effects of prostaglandin E2 (PGE2) on cytokine production and proliferation of the CD4+ human helper T cell clone SP-B21 were investigated. In cells stimulated with anti-CD3 mAb, PGE2 inhibited cell proliferation and the production of all the cytokines examined. Addition of rIL-2 fully restored the proliferative response and partially restored the production of IL-4 and IL-5, but not that of other cytokines. In contrast, in cells stimulated with phorbol myristate acetate (PMA)/A23187, PGE2 enhanced the production of IL-4 and IL-5, and only partially inhibited the production of other cytokines. Therefore, the effects of PGE2 vary depending on the mode of T cell activation, and the IL-4 and IL-5 are regulated differently from other cytokines. In a mobility shift assay, only the NF-kappa B (p50/p50) homodimer was observed in a complex formed with the kappa B sequence in unstimulated SP-B21 cells. When cells were stimulated with anti-CD3 mAb or PMA/A23187, a complex formation of NF-kappa B (p50/p65) heterodimer with the kappa B sequence was induced. Interestingly, PGE2 or di-butyryl (Bt2)cAMP abolished the binding of NF-kappa B (p50/p65) heterodimer to the kappa B sequence in cells stimulated with anti-CD3 mAb but not with PMA/A23187. Our results suggest that the target of PGE2 action is a component in the signal transduction pathway leading to the activation of protein kinase C. However, the inhibition of the T cell activation signals by PGE2 is selective. PGE2 enhanced the complex formation with NF-AT, AP-1 and CLE0 sequences when the cells were activated by either anti-CD3 mAb or PMA/A23187 stimulation. It seems therefore that PGE2, by elevating cAMP levels, interferes with the activation pathway for NF-kappa B but not for NF-AT, AP-1 or CLE0 binding protein. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complex formed", "start": 979, "end": 993}, "arguments": [{"role": "Theme", "text": "p50", "start": 942, "end": 945}]}, {"trigger": {"text": "complex formation", "start": 1112, "end": 1129}, "arguments": [{"role": "Theme", "text": "p50", "start": 1145, "end": 1148}]}, {"trigger": {"text": "complex formation", "start": 1112, "end": 1129}, "arguments": [{"role": "Theme", "text": "p65", "start": 1149, "end": 1152}]}, {"trigger": {"text": "binding", "start": 1263, "end": 1270}, "arguments": [{"role": "Theme", "text": "p50", "start": 1286, "end": 1289}]}, {"trigger": {"text": "binding", "start": 1263, "end": 1270}, "arguments": [{"role": "Theme", "text": "p65", "start": 1290, "end": 1293}]}], "gene expression": [{"trigger": {"text": "production", "start": 493, "end": 503}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 507, "end": 511}]}, {"trigger": {"text": "production", "start": 493, "end": 503}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 516, "end": 520}]}, {"trigger": {"text": "production", "start": 651, "end": 661}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 665, "end": 669}]}, {"trigger": {"text": "production", "start": 651, "end": 661}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 674, "end": 678}]}], "negative regulation": [{"trigger": {"text": "abolished", "start": 1249, "end": 1258}, "arguments": [{"role": "Theme", "text": "binding", "start": 1263, "end": 1270}]}], "positive regulation": [{"trigger": {"text": "restored", "start": 480, "end": 488}, "arguments": [{"role": "Theme", "text": "production", "start": 493, "end": 503}]}, {"trigger": {"text": "enhanced", "start": 638, "end": 646}, "arguments": [{"role": "Theme", "text": "production", "start": 651, "end": 661}]}, {"trigger": {"text": "induced", "start": 1196, "end": 1203}, "arguments": [{"role": "Theme", "text": "complex formation", "start": 1112, "end": 1129}]}], "regulation": [{"trigger": {"text": "regulated", "start": 850, "end": 859}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 832, "end": 836}]}, {"trigger": {"text": "regulated", "start": 850, "end": 859}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 841, "end": 845}]}]}}, "schema": []}
{"input": "IL-4 down-regulates IL-2-, IL-3-, and GM-CSF-induced cytokine gene expression in peripheral blood monocytes. \nIL-4, a product of the T-helper 0 (Th0) and 2 (Th2) subset, was originally described as a B-cell stimulatory factor and has subsequently been found to suppress IL-1 alpha, IL-1 beta, IL-6, IL-8, and TNF-alpha gene expression in monocytes stimulated with LPS, and to upregulate IL-1 receptor antagonist (IL1-RA) gene expression. In this study we investigated the effect of IL-4 on the expression of cytokine genes in monocytes evoked by other T-helper cell cytokines: IL-2, IL-3, and GM-CSF. IL-4 down-regulated mRNA accumulation of the proinflammatory cytokines IL-1 beta, IL-8, and TNF-alpha in monocytes stimulated with IL-2, IL-3, and GM-CSF. IL-4 also suppressed the IL-2-induced IL-6 mRNA expression. Temporal analysis of the IL-4 down-regulatory effect on the IL-2-, IL-3-, or GM-CSF-induced proinflammatory cytokine gene expression in monocytes provided evidence that IL-4 acts predominantly on the post-transcriptional level. This was supported by the observation that the down-regulatory capacity of IL-4 appeared to be dependent on de novo protein synthesis. IL-4 did not exert significant influence on the induction of expression of IL-1-RA or various CSFs by IL-2, IL-3, and GM-CSF. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "product", "start": 118, "end": 125}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 110, "end": 114}]}, {"trigger": {"text": "expression", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "IL-1 alpha", "start": 270, "end": 280}]}, {"trigger": {"text": "expression", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 282, "end": 291}]}, {"trigger": {"text": "expression", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 293, "end": 297}]}, {"trigger": {"text": "expression", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 299, "end": 303}]}, {"trigger": {"text": "expression", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 309, "end": 318}]}, {"trigger": {"text": "expression", "start": 426, "end": 436}, "arguments": [{"role": "Theme", "text": "(IL1-RA", "start": 412, "end": 419}]}, {"trigger": {"text": "expression", "start": 1240, "end": 1250}, "arguments": [{"role": "Theme", "text": "IL-1-RA", "start": 1254, "end": 1261}]}], "negative regulation": [{"trigger": {"text": "suppress", "start": 261, "end": 269}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 110, "end": 114}, {"role": "Theme", "text": "stimulated", "start": 348, "end": 358}]}, {"trigger": {"text": "down-regulated", "start": 606, "end": 620}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 601, "end": 605}, {"role": "Theme", "text": "mRNA accumulation", "start": 621, "end": 638}]}, {"trigger": {"text": "suppressed", "start": 766, "end": 776}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 756, "end": 760}, {"role": "Theme", "text": "induced", "start": 786, "end": 793}]}], "positive regulation": [{"trigger": {"text": "stimulated", "start": 348, "end": 358}, "arguments": [{"role": "Theme", "text": "expression", "start": 324, "end": 334}]}, {"trigger": {"text": "upregulate", "start": 376, "end": 386}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 110, "end": 114}, {"role": "Theme", "text": "expression", "start": 426, "end": 436}]}, {"trigger": {"text": "mRNA accumulation", "start": 621, "end": 638}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 672, "end": 681}]}, {"trigger": {"text": "mRNA accumulation", "start": 621, "end": 638}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 683, "end": 687}]}, {"trigger": {"text": "mRNA accumulation", "start": 621, "end": 638}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 693, "end": 702}]}, {"trigger": {"text": "induced", "start": 786, "end": 793}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 781, "end": 785}, {"role": "Theme", "text": "expression", "start": 804, "end": 814}]}, {"trigger": {"text": "induction", "start": 1227, "end": 1236}, "arguments": [{"role": "Theme", "text": "expression", "start": 1240, "end": 1250}, {"role": "Cause", "text": "IL-2", "start": 1281, "end": 1285}]}, {"trigger": {"text": "induction", "start": 1227, "end": 1236}, "arguments": [{"role": "Theme", "text": "expression", "start": 1240, "end": 1250}, {"role": "Cause", "text": "IL-3", "start": 1287, "end": 1291}]}, {"trigger": {"text": "induction", "start": 1227, "end": 1236}, "arguments": [{"role": "Theme", "text": "expression", "start": 1240, "end": 1250}, {"role": "Cause", "text": "GM-CSF", "start": 1297, "end": 1303}]}], "regulation": [{"trigger": {"text": "influence", "start": 1210, "end": 1219}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1179, "end": 1183}, {"role": "Theme", "text": "induction", "start": 1227, "end": 1236}]}], "transcription": [{"trigger": {"text": "expression", "start": 804, "end": 814}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 794, "end": 798}]}]}}, "schema": []}
{"input": "Long-term inositol phosphate release, but not tyrosine kinase activity, correlates with IL-2 secretion and NF-AT induction in anti-CD3-activated peripheral human T lymphocytes. \nThe cascade of events within the first few minutes of T cell stimulation has been well characterized. Although many second messengers have been shown to be necessary and sufficient for T cell activation in a number of model systems, the rate-limiting step in peripheral T cells has not been demonstrated. To model effective versus ineffective CD3-mediated stimulation in peripheral T cells, we used two anti-CD3 mAbs that differ in their ability to stimulate purified T cells: OKT3, which causes early second messenger generation but is unable to activate T cells without a second signal, and 64.1, which stimulates T cell proliferation on its own. We found that tyrosine kinase activity was similar for both mAbs over a period of hours. However, the inositol phosphate response was stronger for 64.1 than for OKT3. To tie these events to gene activation, we measured NF-kappa B and NF-AT activity in the nucleus after anti-CD3 stimulation. Both stimuli induced the appearance of the NF-kappa B components (c-Rel, p65 (RelA), and p50 (NF-kappa B1)) and NF-kappa B DNA binding activity in the nucleus. However, only 64.1 induced NF-AT in the nucleus, correlating with its ability to activate T cells. Thus, NF-AT induction and IL-2 secretion were correlated with the levels of inositol phosphate release but not with gross levels of tyrosine kinase activity induced late following the response. On the other hand, NF-kappa B induction and IL-2 receptor expression occurred even with the smaller second messenger response generated by OKT3. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "secretion", "start": 93, "end": 102}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 88, "end": 92}]}, {"trigger": {"text": "appearance", "start": 1144, "end": 1154}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1185, "end": 1190}, {"role": "AtLoc", "text": "nucleus", "start": 1270, "end": 1277}]}, {"trigger": {"text": "appearance", "start": 1144, "end": 1154}, "arguments": [{"role": "Theme", "text": "p65", "start": 1192, "end": 1195}, {"role": "AtLoc", "text": "nucleus", "start": 1270, "end": 1277}]}, {"trigger": {"text": "appearance", "start": 1144, "end": 1154}, "arguments": [{"role": "Theme", "text": "p50", "start": 1208, "end": 1211}, {"role": "AtLoc", "text": "nucleus", "start": 1270, "end": 1277}]}, {"trigger": {"text": "secretion", "start": 1409, "end": 1418}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1404, "end": 1408}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1132, "end": 1139}, "arguments": [{"role": "Theme", "text": "appearance", "start": 1144, "end": 1154}]}, {"trigger": {"text": "appearance", "start": 1144, "end": 1154}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1185, "end": 1190}]}]}}, "schema": []}
{"input": "ZAP-70 tyrosine kinase, CD45, and T cell receptor involvement in UV- and H2O2-induced T cell signal transduction. \nSeveral mammalian responses to UV irradiation, including the activation of NF-kappa B, are believed to involve tyrosine phosphorylation. UV irradiation and H2O2 treatment of T lymphocytes induce protein tyrosine phosphorylation and Ca2+ signals similar to those observed following biological stimulation. We have examined the role of cell surface molecules in these responses. Normal T lymphocytes whose surface expression of CD3 was depleted showed impaired UV-induced tyrosine phosphorylation and Ca2+ signals. Similarly, Jurkat T cell lines deficient in CD3 or CD45 expression also gave impaired UV responses. However, all these cell types still gave strong Ca2+ and tyrosine phosphorylation responses to H2O2. The T cell tyrosine kinase ZAP-70 was found to be highly responsive to UV and H2O2 treatment. ZAP-70 responsiveness to UV required expression of both CD3 and CD45, whereas only CD3 was required for the response to H2O2. UV-induced activation of NF-kappa B was blocked by CD3 depletion, indicating the importance of such cell surface molecules in biological responses to UV. In nonlymphoid cells, the epidermal growth factor receptor displayed increased tyrosine phosphorylation within seconds of UV irradiation. These results suggest that UV-induced signal transduction is mediated via cell surface receptors that normally respond to biological stimulation, whereas H2O2 is able to partially bypass this requirement. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 684, "end": 694}, "arguments": [{"role": "Theme", "text": "CD45", "start": 679, "end": 683}]}, {"trigger": {"text": "expression", "start": 960, "end": 970}, "arguments": [{"role": "Theme", "text": "CD45", "start": 987, "end": 991}]}], "negative regulation": [{"trigger": {"text": "deficient", "start": 659, "end": 668}, "arguments": [{"role": "Theme", "text": "expression", "start": 684, "end": 694}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1291, "end": 1306}, "arguments": [{"role": "Theme", "text": "epidermal growth factor receptor", "start": 1229, "end": 1261}, {"role": "Site", "text": "tyrosine", "start": 1282, "end": 1290}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 1272, "end": 1281}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1291, "end": 1306}]}], "regulation": [{"trigger": {"text": "responsive", "start": 886, "end": 896}, "arguments": [{"role": "Theme", "text": "ZAP-70", "start": 856, "end": 862}]}, {"trigger": {"text": "responsive", "start": 886, "end": 896}, "arguments": [{"role": "Theme", "text": "ZAP-70", "start": 923, "end": 929}]}, {"trigger": {"text": "responsiveness", "start": 930, "end": 944}, "arguments": [{"role": "Theme", "text": "ZAP-70", "start": 923, "end": 929}]}, {"trigger": {"text": "response", "start": 1031, "end": 1039}, "arguments": [{"role": "Theme", "text": "ZAP-70", "start": 923, "end": 929}]}]}}, "schema": []}
{"input": "Inhibition of NF-kappa B by sodium salicylate and aspirin [see comments] \nThe transcription factor nuclear factor-kappa B (NF-kappa B) is critical for the inducible expression of multiple cellular and viral genes involved in inflammation and infection including interleukin-1 (IL-1), IL-6, and adhesion molecules. The anti-inflammatory drugs sodium salicylate and aspirin inhibited the activation of NF-kappa B, which further explains the mechanism of action of these drugs. This inhibition prevented the degradation of the NF-kappa B inhibitor, I kappa B, and therefore NF-kappa B was retained in the cytosol. Sodium salicylate and aspirin also inhibited NF-kappa B-dependent transcription from the Ig kappa enhancer and the human immunodeficiency virus (HIV) long terminal repeat (LTR) in transfected T cells. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibited", "start": 646, "end": 655}, "arguments": [{"role": "Theme", "text": "dependent", "start": 667, "end": 676}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 667, "end": 676}, "arguments": [{"role": "Theme", "text": "transcription", "start": 677, "end": 690}]}], "transcription": [{"trigger": {"text": "transcription", "start": 677, "end": 690}, "arguments": [{"role": "Theme", "text": "Ig kappa", "start": 700, "end": 708}]}]}}, "schema": []}
{"input": "Positive and negative regulation of IL-2 gene expression: role of multiple regulatory sites. \nInterleukin 2 (IL-2) is an important lymphokine required in the process of T cell activation, proliferation, clonal expansion and differentiation. The IL-2 gene displays both T cell specific and inducible expression: it is only expressed in CD4+ T cells after antigenic or mitogenic stimulation. Several cis-acting regulatory sites are required for induction of the IL-2 gene after stimulation. In this study, we have analysed the function of these cis-acting regulatory sites in the context of the native IL-2 enhancer and promoter sequence. The results of this study suggest that the NFAT (-276 to -261), the distal octamer (-256 to -248) and the proximal octamer (-75 to -66) sites not only act as enhancers of IL-2 gene transcription in the presence of cellular stimulation, but also have a silencing effect on IL-2 gene expression in resting cells. Two other sites display disparate effects on IL-2 gene expression in different T leukemia cell lines: the distal purine box (-291 to -277) and the proximal purine box sites (-145 to -128). Finally, the AP-1 (-186 to -176) and the kappa B sites (-206 to -195) respond to different cellular activation in EL4 cells. The AP-1 site mediated the response to PMA stimulation while the kappa B site responded to IL-1 stimulation. These data suggest that the regulation of IL-2 gene expression is a complex process and multiple cis-acting regulatory sites interact to exert different effects in T cells representative of alternative stages of differentiation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 46, "end": 56}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 36, "end": 40}]}, {"trigger": {"text": "expression", "start": 299, "end": 309}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 245, "end": 249}]}, {"trigger": {"text": "expression", "start": 919, "end": 929}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 909, "end": 913}]}, {"trigger": {"text": "expression", "start": 1003, "end": 1013}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 993, "end": 997}]}, {"trigger": {"text": "expression", "start": 1423, "end": 1433}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1413, "end": 1417}]}], "negative regulation": [{"trigger": {"text": "negative regulation", "start": 13, "end": 32}, "arguments": [{"role": "Theme", "text": "expression", "start": 46, "end": 56}]}, {"trigger": {"text": "have a silencing effect", "start": 882, "end": 905}, "arguments": [{"role": "Theme", "text": "expression", "start": 919, "end": 929}]}], "positive regulation": [{"trigger": {"text": "Positive", "start": 0, "end": 8}, "arguments": [{"role": "Theme", "text": "expression", "start": 46, "end": 56}]}, {"trigger": {"text": "inducible", "start": 289, "end": 298}, "arguments": [{"role": "Theme", "text": "expression", "start": 299, "end": 309}]}, {"trigger": {"text": "expressed", "start": 322, "end": 331}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 245, "end": 249}]}, {"trigger": {"text": "required", "start": 430, "end": 438}, "arguments": [{"role": "Theme", "text": "induction", "start": 443, "end": 452}]}, {"trigger": {"text": "induction", "start": 443, "end": 452}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 460, "end": 464}]}, {"trigger": {"text": "act as enhancers", "start": 788, "end": 804}, "arguments": [{"role": "Theme", "text": "in the presence of", "start": 832, "end": 850}]}, {"trigger": {"text": "in the presence of", "start": 832, "end": 850}, "arguments": [{"role": "Theme", "text": "transcription", "start": 818, "end": 831}]}], "regulation": [{"trigger": {"text": "role", "start": 58, "end": 62}, "arguments": [{"role": "Theme", "text": "Positive", "start": 0, "end": 8}]}, {"trigger": {"text": "role", "start": 58, "end": 62}, "arguments": [{"role": "Theme", "text": "negative regulation", "start": 13, "end": 32}]}, {"trigger": {"text": "display disparate effects", "start": 964, "end": 989}, "arguments": [{"role": "Theme", "text": "expression", "start": 1003, "end": 1013}]}, {"trigger": {"text": "regulation", "start": 1399, "end": 1409}, "arguments": [{"role": "Theme", "text": "expression", "start": 1423, "end": 1433}]}, {"trigger": {"text": "interact to exert different effects", "start": 1496, "end": 1531}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1399, "end": 1409}]}], "transcription": [{"trigger": {"text": "transcription", "start": 818, "end": 831}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 808, "end": 812}]}]}}, "schema": []}
{"input": "Superantigens activate HIV-1 gene expression in monocytic cells. \nBinding of superantigens to MHC class II molecules results in transduction of biochemical signals leading to cellular activation and gene expression. We demonstrate that the staphylococcal superantigens toxic shock syndrome toxin-1 (TSST-1) and staphylococcal enterotoxin A (SEA) activate HIV-1-LTR-driven transcription of chloramphenicol acetyl transferase in the human monocytic cell line THP-1. Induction of HIV-1-LTR-driven transcription in THP-1 cells by superantigens was associated with the induction of nuclear factor-kappa B DNA-binding activity. Superantigens also increased viral protein secretion from the granulocyte-macrophage colony-stimulating factor-pretreated chronically infected human monocytic cell line U1. Induction of HIV-1 gene expression in monocytic cells by superantigens occurred via tumor necrosis factor-alpha-dependent and -independent mechanisms. Our results suggest that superantigens and other MHC class II ligands may activate HIV-1 gene expression in monocytes/macrophages. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "activate", "start": 346, "end": 354}, "arguments": [{"role": "Cause", "text": "TSST-1", "start": 299, "end": 305}, {"role": "Theme", "text": "driven", "start": 365, "end": 371}]}, {"trigger": {"text": "activate", "start": 346, "end": 354}, "arguments": [{"role": "Cause", "text": "SEA", "start": 341, "end": 344}, {"role": "Theme", "text": "driven", "start": 365, "end": 371}]}, {"trigger": {"text": "driven", "start": 365, "end": 371}, "arguments": [{"role": "Theme", "text": "transcription", "start": 372, "end": 385}]}], "transcription": [{"trigger": {"text": "transcription", "start": 372, "end": 385}, "arguments": [{"role": "Theme", "text": "chloramphenicol acetyl transferase", "start": 389, "end": 423}]}]}}, "schema": []}
{"input": "Inhibition of activation of transcription factor AP-1 by CD28 signalling in human T-cells. \nCo-stimulation of T-lymphocytes by T-cell receptor (TcR) occupancy and activation of the CD28 surface molecule results in enhanced proliferation and interleukin 2 (IL-2) production. The increase in IL-2 gene expression triggered by CD28 involves a kappa B-like sequence in the 5'-regulatory region of the IL-2 promoter, called CD28-responsive element. Stimulation of T-cells by agonistic anti-CD28 antibodies in conjunction with phorbol 12-myristate 13-acetate (PMA)- or TcR-derived signals induces the enhanced activation of the transcription factor NF-kappa B. Here we report that CD28 engagement, however, exerts opposite effects on the transcription factor AP-1. Whereas anti-CD28 together with PMA increased the DNA binding and trans-activation activity of NF-kappa B, PMA-induced activation of AP-1 was significantly suppressed. The inhibitory effect exerted by anti-CD28 was observed at the level of DNA binding as well as in functional reporter-gene assays. These results suggest that the two transcription factors are independently regulated and may perform different functions during T-cell activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "engagement", "start": 680, "end": 690}, "arguments": [{"role": "Theme", "text": "CD28", "start": 675, "end": 679}]}], "gene expression": [{"trigger": {"text": "production", "start": 262, "end": 272}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 256, "end": 260}]}, {"trigger": {"text": "expression", "start": 300, "end": 310}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 290, "end": 294}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 163, "end": 173}, "arguments": [{"role": "Theme", "text": "CD28", "start": 181, "end": 185}]}, {"trigger": {"text": "increase", "start": 278, "end": 286}, "arguments": [{"role": "Theme", "text": "expression", "start": 300, "end": 310}, {"role": "Cause", "text": "CD28", "start": 324, "end": 328}]}]}}, "schema": []}
{"input": "Induction of IL-8 expression in T cells uses the CD28 costimulatory pathway. \nIL-8, a potent chemotactic factor for neutrophil granulocytes and lymphocytes, is a proinflammatory cytokine secreted by a variety of cell types, including T cells. Stimulation of the CD28 cell surface molecule delivers costimulatory signals essential for lymphokine production in activated T cells via a conserved sequence element found in the promoter of several lymphokine genes. Anti-CD28-stimulated T cells produced significant amounts of IL-8; additionally, costimulation with anti-CD3 and anti-CD28 Abs resulted in a synergistic induction of IL-8 secretion. Sequence homology, single nucleotide mutations, and anti-CD28 Ab stimulation studies established that the NF-kappa B-like sequence in the promoter of the IL-8 gene functioned as a CD28 response element. Furthermore, cyclosporin A, but not rapamycin, blocked the synergistic induction of IL-8 expression achieved with anti-CD3 and anti-CD28 costimulation. The involvement of a CD28 response element in the induction of IL-8 expression in activated T cells may provide new insights into the pathogenesis and persistence of immune disorders characterized by increased levels of IL-8, such as psoriasis and rheumatoid arthritis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 18, "end": 28}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 13, "end": 17}]}, {"trigger": {"text": "produced", "start": 490, "end": 498}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 522, "end": 526}]}, {"trigger": {"text": "expression", "start": 935, "end": 945}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 930, "end": 934}]}, {"trigger": {"text": "expression", "start": 1066, "end": 1076}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1061, "end": 1065}]}, {"trigger": {"text": "levels", "start": 1208, "end": 1214}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1218, "end": 1222}]}], "localization": [{"trigger": {"text": "secreted", "start": 187, "end": 195}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 78, "end": 82}]}, {"trigger": {"text": "secretion", "start": 632, "end": 641}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 627, "end": 631}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 893, "end": 900}, "arguments": [{"role": "Theme", "text": "synergistic induction", "start": 905, "end": 926}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "expression", "start": 18, "end": 28}]}, {"trigger": {"text": "uses", "start": 40, "end": 44}, "arguments": [{"role": "Theme", "text": "Induction", "start": 0, "end": 9}]}, {"trigger": {"text": "Stimulation", "start": 243, "end": 254}, "arguments": [{"role": "Theme", "text": "CD28", "start": 262, "end": 266}]}, {"trigger": {"text": "resulted", "start": 588, "end": 596}, "arguments": [{"role": "Theme", "text": "synergistic induction", "start": 602, "end": 623}]}, {"trigger": {"text": "synergistic induction", "start": 602, "end": 623}, "arguments": [{"role": "Theme", "text": "secretion", "start": 632, "end": 641}]}, {"trigger": {"text": "synergistic induction", "start": 905, "end": 926}, "arguments": [{"role": "Theme", "text": "expression", "start": 935, "end": 945}]}, {"trigger": {"text": "involvement", "start": 1002, "end": 1013}, "arguments": [{"role": "Theme", "text": "induction", "start": 1048, "end": 1057}]}, {"trigger": {"text": "induction", "start": 1048, "end": 1057}, "arguments": [{"role": "Theme", "text": "expression", "start": 1066, "end": 1076}]}, {"trigger": {"text": "increased", "start": 1198, "end": 1207}, "arguments": [{"role": "Theme", "text": "levels", "start": 1208, "end": 1214}]}], "regulation": [{"trigger": {"text": "response", "start": 828, "end": 836}, "arguments": [{"role": "Site", "text": "NF-kappa B-like sequence", "start": 749, "end": 773}, {"role": "Theme", "text": "IL-8", "start": 797, "end": 801}, {"role": "Cause", "text": "CD28", "start": 823, "end": 827}]}]}}, "schema": []}
{"input": "The severe phenotype of females with tiny ring X chromosomes is associated with inability of these chromosomes to undergo X inactivation. \nMental retardation and a constellation of congenital malformations not usually associated with Turner syndrome are seen in some females with a mosaic 45,X/46,X,r(X) karyotype. Studies of these females show that the XIST locus on their tiny ring X chromosomes is either not present or not expressed. As XIST transcription is well correlated with inactivation of the X chromosome in female somatic cells and spermatogonia, nonexpression of the locus even when it is present suggests that these chromosomes are transcriptionally active. We examined the transcriptional activity of ring X chromosomes lacking XIST expression (XISTE-), from three females with severe phenotypes. The two tiny ring X chromosomes studied with an antibody specific for the acetylated isoforms of histone H4 marking transcribed chromatin domains were labeled at a level consistent with their being active. We also examined tow of the XISTE- ring chromosomes to determine whether genes that are normally silent on an inactive X are expressed from these chromosomes. Analyses of hybrid cells show that TIMP, ZXDA, and ZXDB loci on the proximal short arm, and AR and PHKA1 loci on the long arm, are well expressed from the tiny ring X chromosome lacking XIST DNA. Studies of the ring chromosome that has XIST DNA but does not transcribe it show that its AR allele is transcribed along with the one on the normal X allele. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 427, "end": 436}, "arguments": [{"role": "Theme", "text": "XIST", "start": 354, "end": 358}]}, {"trigger": {"text": "nonexpression", "start": 560, "end": 573}, "arguments": [{"role": "Theme", "text": "XIST", "start": 441, "end": 445}]}, {"trigger": {"text": "expression", "start": 749, "end": 759}, "arguments": [{"role": "Theme", "text": "XIST", "start": 744, "end": 748}]}, {"trigger": {"text": "expressed", "start": 1314, "end": 1323}, "arguments": [{"role": "Theme", "text": "ZXDA", "start": 1219, "end": 1223}]}, {"trigger": {"text": "expressed", "start": 1314, "end": 1323}, "arguments": [{"role": "Theme", "text": "ZXDB", "start": 1229, "end": 1233}]}, {"trigger": {"text": "expressed", "start": 1314, "end": 1323}, "arguments": [{"role": "Theme", "text": "PHKA1", "start": 1277, "end": 1282}]}], "negative regulation": [{"trigger": {"text": "present", "start": 412, "end": 419}, "arguments": [{"role": "Theme", "text": "XIST", "start": 354, "end": 358}]}, {"trigger": {"text": "lacking", "start": 1356, "end": 1363}, "arguments": [{"role": "Theme", "text": "XIST", "start": 1364, "end": 1368}]}], "transcription": [{"trigger": {"text": "transcription", "start": 446, "end": 459}, "arguments": [{"role": "Theme", "text": "XIST", "start": 441, "end": 445}]}, {"trigger": {"text": "transcribe", "start": 1436, "end": 1446}, "arguments": [{"role": "Theme", "text": "XIST", "start": 1414, "end": 1418}]}]}}, "schema": []}
{"input": "Signals and nuclear factors that regulate the expression of interleukin-4 and interleukin-5 genes in helper T cells. \nMouse thymoma line EL-4 cells produce cytokines such as interleukin (IL)-2, IL-3, IL-4, IL-10, and granulocyte-macrophage colony-stimulating factor in response to phorbol 12-myristate 13-acetate (PMA). EL-4 cells also produce low levels of IL-5 when stimulated by PMA alone; however, cAMP greatly augments PMA-dependent IL-5 production. A transient transfection assay revealed that two signals, PMA and cAMP, are required for optimal activation of the IL-5 promoter. In contrast, cAMP almost completely inhibited the PMA-dependent activation of the endogenous IL-2 gene, as well as the transfected IL-2 promoter. These results indicate that the IL-5 gene is positively regulated by cAMP in a manner opposite to that for the IL-2 gene. One of the nuclear factors (NFs) that regulates the response of the IL-5 promoter to cAMP and PMA has properties similar to NF for activated t cell. The P sequence of the IL-4 gene, defined as a responsive element for PMA and calcium ionophore (A23187), shares sequence similarity with the NF kappa B and the NF-activated T cell binding sites. We attempted to determine whether NF(P), a nuclear factor specific for the P sequence, is related to NF-kappa B and nuclear factor for activated T cell (NF-AT). In electromobility shift assays both NF-kappa B (P65 or P65/P50 heterodimer) and NF-AT bound to the P sequence. However, sequence specificity of NF-AT was more similar to that of NF(P), and only a small amount of P65 was detected in NF(P). These results indicate that a component or components of NF-AT have the potential to reconstitute NF(P), whereas NF-kappa B alone does not account for NF(P) in Jurkat crude extract. Taken together, these results suggest that NF-AT-like factors are involved in the regulation of IL-4 and IL-5 genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 1445, "end": 1450}, "arguments": [{"role": "Theme", "text": "P65", "start": 1407, "end": 1410}]}, {"trigger": {"text": "bound", "start": 1445, "end": 1450}, "arguments": [{"role": "Theme", "text": "P65", "start": 1414, "end": 1417}]}, {"trigger": {"text": "bound", "start": 1445, "end": 1450}, "arguments": [{"role": "Theme", "text": "P50", "start": 1418, "end": 1421}]}], "gene expression": [{"trigger": {"text": "expression", "start": 46, "end": 56}, "arguments": [{"role": "Theme", "text": "interleukin-4", "start": 60, "end": 73}]}, {"trigger": {"text": "expression", "start": 46, "end": 56}, "arguments": [{"role": "Theme", "text": "interleukin-5", "start": 78, "end": 91}]}, {"trigger": {"text": "produce", "start": 148, "end": 155}, "arguments": [{"role": "Theme", "text": "interleukin (IL)-2", "start": 174, "end": 192}]}, {"trigger": {"text": "produce", "start": 148, "end": 155}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 194, "end": 198}]}, {"trigger": {"text": "produce", "start": 148, "end": 155}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 200, "end": 204}]}, {"trigger": {"text": "produce", "start": 148, "end": 155}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 206, "end": 211}]}, {"trigger": {"text": "produce", "start": 148, "end": 155}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 217, "end": 265}]}, {"trigger": {"text": "produce", "start": 336, "end": 343}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 358, "end": 362}]}, {"trigger": {"text": "production", "start": 443, "end": 453}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 438, "end": 442}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 621, "end": 630}, "arguments": [{"role": "Theme", "text": "activation", "start": 649, "end": 659}]}, {"trigger": {"text": "opposite", "start": 817, "end": 825}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 842, "end": 846}]}], "positive regulation": [{"trigger": {"text": "in response", "start": 266, "end": 277}, "arguments": [{"role": "Theme", "text": "produce", "start": 148, "end": 155}]}, {"trigger": {"text": "when", "start": 363, "end": 367}, "arguments": [{"role": "Theme", "text": "produce", "start": 336, "end": 343}]}, {"trigger": {"text": "augments", "start": 415, "end": 423}, "arguments": [{"role": "Theme", "text": "dependent", "start": 428, "end": 437}]}, {"trigger": {"text": "dependent", "start": 428, "end": 437}, "arguments": [{"role": "Theme", "text": "production", "start": 443, "end": 453}]}, {"trigger": {"text": "required", "start": 531, "end": 539}, "arguments": [{"role": "Theme", "text": "activation", "start": 552, "end": 562}]}, {"trigger": {"text": "activation", "start": 552, "end": 562}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 570, "end": 574}, {"role": "Site", "text": "promoter", "start": 575, "end": 583}]}, {"trigger": {"text": "activation", "start": 649, "end": 659}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 716, "end": 720}, {"role": "Site", "text": "promoter", "start": 721, "end": 729}]}, {"trigger": {"text": "activation", "start": 649, "end": 659}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 678, "end": 682}]}, {"trigger": {"text": "positively regulated", "start": 776, "end": 796}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 763, "end": 767}]}], "regulation": [{"trigger": {"text": "regulate", "start": 33, "end": 41}, "arguments": [{"role": "Theme", "text": "expression", "start": 46, "end": 56}]}, {"trigger": {"text": "regulates", "start": 891, "end": 900}, "arguments": [{"role": "Theme", "text": "response", "start": 905, "end": 913}]}, {"trigger": {"text": "response", "start": 905, "end": 913}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 921, "end": 925}, {"role": "Site", "text": "promoter", "start": 926, "end": 934}]}, {"trigger": {"text": "defined as a responsive element", "start": 1035, "end": 1066}, "arguments": [{"role": "Site", "text": "P sequence", "start": 1006, "end": 1016}, {"role": "Theme", "text": "IL-4", "start": 1024, "end": 1028}]}, {"trigger": {"text": "regulation", "start": 1862, "end": 1872}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1876, "end": 1880}]}, {"trigger": {"text": "regulation", "start": 1862, "end": 1872}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1885, "end": 1889}]}]}}, "schema": []}
{"input": "Structure and expression of the human GATA3 gene. \nGATA3, a member of the GATA family that is abundantly expressed in the T-lymphocyte lineage, is thought to participate in T-cell receptor gene activation through binding to enhancers. To understand GATA3 gene regulation, we cloned the human gene and the 5' end of the mouse GATA3 gene. We show that the human GATA3 gene contains six exons distributed over 17 kb of DNA. The two human GATA3 zinc fingers are encoded by two separate exons highly conserved with those of GATA1, but no other structural homologies between these two genes can be found. The human and mouse GATA3 transcription units start at a major initiation site. The promoter sequence analysis of these two genes revealed that they are embedded within a CpG island and share structural features often found in the promoters of housekeeping genes. Finally, we show that a DNA fragment containing the human GATA3 transcription unit, 3 kb upstream from the initiation site and 4 kb downstream from the polyadenylation site, displays T-cell specificity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 213, "end": 220}, "arguments": [{"role": "Theme", "text": "GATA3", "start": 51, "end": 56}]}], "gene expression": [{"trigger": {"text": "expression", "start": 14, "end": 24}, "arguments": [{"role": "Theme", "text": "GATA3", "start": 38, "end": 43}]}, {"trigger": {"text": "expressed", "start": 105, "end": 114}, "arguments": [{"role": "Theme", "text": "GATA3", "start": 51, "end": 56}]}], "regulation": [{"trigger": {"text": "regulation", "start": 260, "end": 270}, "arguments": [{"role": "Theme", "text": "GATA3", "start": 249, "end": 254}]}]}}, "schema": []}
{"input": "Characterization of NF(P), the nuclear factor that interacts with the regulatory P sequence (5'-CGAAAATTTCC-3') of the human interleukin-4 gene: relationship to NF-kappa B and NF-AT. \nThe P sequence of the human interleukin-4 (IL-4) gene, which was defined as a responsive element for phorbol 12-myristate 13-acetate and calcium ionophore (A23187) in Jurkat T cells, shares sequence similarity with the NF-kappa B and the NF-AT binding sites. We examined whether NF(P), a nuclear factor specific for the P sequence, is related to NF-kappa B and NF-AT. NF-kappa B (P65 or P65/P50 heterodimer) bound to the P sequence in electrophoretic mobility shift assays (EMSA) and activated transcription through the P sequence when expression plasmids were cotransfected with P sequence-driven reporter plasmids in Jurkat T cells. In EMSAs, NF(P) binding was inhibited by the unlabeled NF-AT binding site but not by the unlabeled AP1 binding site and purified NF-AT contained an activity that bound to the P sequence. Both mobility shift and sequence specificity of NF-AT were similar to those of NF(P) and only a small amount of P65 was detected in NF(P) in crude nuclear extracts. These results indicate that the component(s) of NF-AT has the potential to reconstitute NF(P) whereas NF-kappa B alone cannot account for NF(P) in crude extracts. Unlike NF-AT, NF(P) does not contain AP1 as its DNA binding component. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 51, "end": 60}, "arguments": [{"role": "Site", "text": "P sequence", "start": 81, "end": 91}, {"role": "Theme", "text": "interleukin-4", "start": 125, "end": 138}]}, {"trigger": {"text": "bound", "start": 592, "end": 597}, "arguments": [{"role": "Theme", "text": "P65", "start": 564, "end": 567}]}, {"trigger": {"text": "bound", "start": 592, "end": 597}, "arguments": [{"role": "Theme", "text": "P65", "start": 571, "end": 574}]}, {"trigger": {"text": "bound", "start": 592, "end": 597}, "arguments": [{"role": "Theme", "text": "P50", "start": 575, "end": 578}]}, {"trigger": {"text": "detected", "start": 1126, "end": 1134}, "arguments": [{"role": "Theme", "text": "P65", "start": 1118, "end": 1121}]}], "regulation": [{"trigger": {"text": "responsive element", "start": 262, "end": 280}, "arguments": [{"role": "Site", "text": "P sequence", "start": 188, "end": 198}, {"role": "Theme", "text": "interleukin-4", "start": 212, "end": 225}]}]}}, "schema": []}
{"input": "Hypoxia causes the activation of nuclear factor kappa B through the phosphorylation of I kappa B alpha on tyrosine residues. \nThe response of mammalian cells to stress is controlled by transcriptional regulatory proteins such as nuclear factor kappa B (NF-kappa B) to induce a wide variety of early response genes. In this report, we show that exposure of cells to hypoxia (0.02% O2) results in I kappa B alpha degradation, increased NF-kappa B DNA binding activity, and transactivation of a reporter gene construct containing two NF-kappa B DNA binding sites. Pretreatment of cells with protein tyrosine kinase inhibitors and the dominant negative allele of c-Raf-1 (Raf 301) inhibited I kappa B alpha degradation, NF-kappa B binding, and transactivation of kappa B reporter constructs by hypoxia. To demonstrate a direct link between changes in the phosphorylation pattern of I kappa B alpha with NF-kappa B activation, we immunoprecipitated I kappa B alpha after varying times of hypoxic exposure and found that its tyrosine phosphorylation status increased during hypoxic exposure. Inhibition of the transfer of tyrosine phosphoryl groups onto I kappa B alpha prevented I kappa B alpha degradation and NF-kappa B binding. In comparison to other activators of NF-kappa B such as phorbol myristate acetate or tumor necrosis factor, we did not detect changes in the tyrosine phosphorylation status of I kappa B alpha following treatment with either of these agents. These results suggest that tyrosine phosphorylation of I kappa B alpha during hypoxia is an important proximal step which precedes its dissociation and degradation from NF-kappa B. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibited", "start": 677, "end": 686}, "arguments": [{"role": "Theme", "text": "by", "start": 787, "end": 789}]}, {"trigger": {"text": "Inhibition", "start": 1086, "end": 1096}, "arguments": [{"role": "Theme", "text": "transfer of tyrosine phosphoryl groups", "start": 1104, "end": 1142}]}, {"trigger": {"text": "prevented", "start": 1164, "end": 1173}, "arguments": [{"role": "Cause", "text": "Inhibition", "start": 1086, "end": 1096}, {"role": "Theme", "text": "degradation", "start": 1190, "end": 1201}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 68, "end": 83}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 87, "end": 102}]}, {"trigger": {"text": "phosphorylation", "start": 851, "end": 866}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 878, "end": 893}]}, {"trigger": {"text": "phosphorylation", "start": 1028, "end": 1043}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 944, "end": 959}, {"role": "Site", "text": "tyrosine", "start": 1019, "end": 1027}]}, {"trigger": {"text": "transfer of tyrosine phosphoryl groups", "start": 1104, "end": 1142}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1148, "end": 1163}]}, {"trigger": {"text": "phosphorylation", "start": 1376, "end": 1391}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1367, "end": 1375}, {"role": "Theme", "text": "I kappa B alpha", "start": 1402, "end": 1417}]}, {"trigger": {"text": "phosphorylation", "start": 1503, "end": 1518}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1494, "end": 1502}, {"role": "Theme", "text": "I kappa B alpha", "start": 1522, "end": 1537}]}], "positive regulation": [{"trigger": {"text": "causes", "start": 8, "end": 14}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 68, "end": 83}]}, {"trigger": {"text": "results", "start": 384, "end": 391}, "arguments": [{"role": "Theme", "text": "degradation", "start": 411, "end": 422}]}, {"trigger": {"text": "by", "start": 787, "end": 789}, "arguments": [{"role": "Theme", "text": "degradation", "start": 703, "end": 714}]}, {"trigger": {"text": "increased", "start": 1051, "end": 1060}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1028, "end": 1043}]}, {"trigger": {"text": "during", "start": 1538, "end": 1544}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1503, "end": 1518}]}, {"trigger": {"text": "precedes", "start": 1589, "end": 1597}, "arguments": [{"role": "Cause", "text": "during", "start": 1538, "end": 1544}, {"role": "Theme", "text": "degradation", "start": 1619, "end": 1630}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 411, "end": 422}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 395, "end": 410}]}, {"trigger": {"text": "degradation", "start": 703, "end": 714}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 687, "end": 702}]}, {"trigger": {"text": "degradation", "start": 1190, "end": 1201}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1174, "end": 1189}]}, {"trigger": {"text": "degradation", "start": 1619, "end": 1630}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1522, "end": 1537}]}], "regulation": [{"trigger": {"text": "changes", "start": 1352, "end": 1359}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1376, "end": 1391}]}]}}, "schema": []}
{"input": "A transcriptional regulatory element is associated with a nuclease-hypersensitive site in the pol gene of human immunodeficiency virus type 1. \nAnalysis of the chromatin organization of the integrated human immunodeficiency virus type 1 (HIV-1) genome has previously revealed a major constitutive DNase I-hypersensitive site associated with the pol gene (E. Verdin, J. Virol. 65:6790-6799, 1991). In the present report, high-resolution mapping of this site with DNase I and micrococcal nuclease identified a nucleosome-free region centered around nucleotides (nt) 4490 to 4766. A 500-bp fragment encompassing this hypersensitive site (nt 4481 to 4982) exhibited transcription-enhancing activity (two- to threefold) when it was cloned in its natural position with respect to the HIV-1 promoter after transient transfection in U937 and CEM cells. Using in vitro footprinting and gel shift assays, we have identified four distinct binding sites for nuclear proteins within this positive regulatory element. Site B (nt 4519 to 4545) specifically bound four distinct nuclear protein complexes: a ubiquitous factor, a T-cell-specific factor, a B-cell-specific factor, and the monocyte/macrophage- and B-cell-specific transcription factor PU.1/Spi-1. In most HIV-1 isolates in which this PU box was not conserved, it was replaced by a binding site for the related factor Ets1. Factors binding to site C (nt 4681 to 4701) had a DNA-binding specificity similar to that of factors binding to site B, except for PU.1/Spi-1. A GC box containing a binding site for Sp1 was identified (nt 4623 to 4631). Site D (nt 4816 to 4851) specifically bound a ubiquitously expressed factor. These results identify a transcriptional regulatory element associated with a nuclease-hypersensitive site in the pol gene of HIV-1 and suggest that its activity may be controlled by a complex interplay of cis-regulatory elements. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 1042, "end": 1047}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1232, "end": 1236}]}, {"trigger": {"text": "binding", "start": 1328, "end": 1335}, "arguments": [{"role": "Theme", "text": "Ets1", "start": 1364, "end": 1368}]}, {"trigger": {"text": "containing a binding site", "start": 1522, "end": 1547}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1552, "end": 1555}]}]}}, "schema": []}
{"input": "Expression of v-src in T cells correlates with nuclear expression of NF-kappa B. \nNF-kappa B is a rapidly inducible transcriptional activator that responds to a variety of signals and influences the expression of many genes involved in the immune response. Protein tyrosine kinases transmit signals from cytokine and immune receptors. Very little information exists linking these two important classes of signaling molecules. We now demonstrate that v-src expression correlates with nuclear expression of a kappa B binding complex similar to that induced by phorbol ester and ionomycin, as detected by electrophoretic mobility shift assay using a variety of kappa B sites. This complex was blocked by the tyrosine kinase inhibitor, herbimycin A. The v-src-induced complex comprised the p50 and p65 components of NF-kappa B, as determined by supershift and immunoblot analysis. As a functional correlate of this finding, transient co-transfection of HIV-1 LTR reporter constructs in a different T cell line demonstrated that v-src activated this promoter in a kappa B-dependent manner. We found that transactivation of the HIV-1 LTR by v-src was more sensitive to mutations of the proximal, rather than the distal, kappa B element. The implications for T cell receptor signaling and HIV-1 gene expression are considered. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "induced complex", "start": 756, "end": 771}, "arguments": [{"role": "Theme", "text": "p50", "start": 786, "end": 789}, {"role": "Theme2", "text": "p65", "start": 794, "end": 797}]}], "gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "v-src", "start": 14, "end": 19}]}, {"trigger": {"text": "expression", "start": 456, "end": 466}, "arguments": [{"role": "Theme", "text": "v-src", "start": 450, "end": 455}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 756, "end": 763}, "arguments": [{"role": "Cause", "text": "v-src", "start": 750, "end": 755}, {"role": "Theme", "text": "induced complex", "start": 756, "end": 771}]}]}}, "schema": []}
{"input": "Human immunodeficiency virus type 1 Nef protein down-regulates transcription factors NF-kappa B and AP-1 in human T cells in vitro after T-cell receptor stimulation. \nHuman immunodeficiency virus type 1 (HIV-1) negative factor (Nef) has been shown to down-regulate the transcription factors NF-kappa B and AP-1 in vitro. To define the mechanism of action of the Nef protein, the signal transduction pathways which may be affected in T cells by constitutive expression of the nef gene were examined. Stimulation of T cells with tumor necrosis factor, interleukin-1, or lipopolysaccharide resulted in the recruitment of transcriptional factors to a similar level whether or not the cells expressed the nef gene. On the other hand, stimulation of T cells by mitogens or antibodies to the T-cell receptor (TCR)-CD3 complex resulted in the down-regulation of transcriptional factors NF-kappa B and AP-1 in cells expressing the nef gene compared with cells not expressing the nef gene. Because the Nef protein does not affect the surface expression of the CD3-TCR complex, we conclude that the Nef protein down-regulates the transcriptional factors NF-kappa B and AP-1 in T cells in vitro through an effect on the TCR-dependent signal transduction pathway. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 457, "end": 467}, "arguments": [{"role": "Theme", "text": "nef", "start": 475, "end": 478}]}, {"trigger": {"text": "expressing", "start": 907, "end": 917}, "arguments": [{"role": "Theme", "text": "nef", "start": 922, "end": 925}]}]}}, "schema": []}
{"input": "Activation of nuclear factor kappa B in human neuroblastoma cell lines. \nThe nuclear factor kappa B (NF-kappa B) is a eukaryotic transcription factor. In B cells and macrophages it is constitutively present in cell nuclei, whereas in many other cell types, NF-kappa B translocates from cytosol to nucleus as a result of transduction by tumor necrosis factor alpha (TNF alpha), phorbol ester, and other polyclonal signals. Using neuroblastoma cell lines as models, we have shown that in neural cells NF-kappa B was present in the cytosol and translocated into nuclei as a result of TNF alpha treatment. The TNF alpha-activated NF-kappa B was transcriptionally functional. NF-kappa B activation by TNF alpha was not correlated with cell differentiation or proliferation. However, reagents such as nerve growth factor (NGF) and the phorbol ester phorbol 12-myristate 13-acetate (PMA), which induce phenotypical differentiation of the SH-SY5Y neuroblastoma cell line, activated NF-kappa B, but only in that particular cell line. In a NGF-responsive rat pheochromocytoma cell line, PC12, PMA activated NF-kappa B, whereas NGF did not. In other neuroblastoma cell lines, such as SK-N-Be(2), the lack of PMA induction of differentiation was correlated with the lack of NF-kappa B activation. We found, moreover, that in SK-N-Be(2) cells protein kinase C (PKC) enzymatic activity was much lower compared with that in a control cell line and that the low PKC enzymatic activity was due to low PKC protein expression. NF-kappa B was not activated by retinoic acid, which induced morphological differentiation of all the neuroblastoma cell lines used in the present study. Thus, NF-kappa B activation was not required for neuroblastoma cell differentiation. Furthermore, the results obtained with TNF alpha proved that NF-kappa B activation was not sufficient for induction of neuroblastoma differentiation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Genes encoding general initiation factors for RNA polymerase II transcription are dispersed in the human genome. \nGeneral transcription factors are required for accurate initiation of transcription by RNA polymerase II. Human cDNAs encoding subunits of these factors have been cloned and sequenced. Using fluorescence in situ hybridization (FISH), we show here that the genes encoding the TATA-box binding protein (TBP), TFIIB, TFIIE alpha, TFIIE beta, RAP30, RAP74 and the 62 kDa subunit, of TFIIH are located at the human chromosomal bands 6q26-27, 1p21-22, 3q21-24, 8p12, 13q14, 19p13.3 and 11p14-15.1, respectively. This dispersed localization of a group of functionally related gene provides insights into the molecular mechanism of human genome evolution and their possible involvement in human diseases. ", "output": {"json_structures": {}}, "schema": []}
{"input": "A novel heterodimerization partner for thyroid hormone receptor. Peroxisome proliferator-activated receptor. \nRetinoid-like receptors play a central role in hormonal responses by forming heterodimers with other nuclear hormone receptors. In this study we have identified the peroxisome proliferator-activated receptor (PPAR) as a new thyroid hormone receptor (THR) auxiliary nuclear protein, heterodimerizing with THR in solution. Although these heterodimers do not recognize a classical thyroid hormone response element (TRE) characterized by direct repeat separated by four nucleotides (DR+4), PPAR behaves as a dominant negative regulator of thyroid hormone (TH) action. However, a TH-dependent positive effect is elicited by selective interaction of the THR beta-PPAR but not the THR alpha-PPAR heterodimer with a novel TRE (DR+2). The critical region of THR beta was mapped to 3 amino acids in the distal box of the DNA binding domain. Hence, PPAR can positively or negatively influence TH action depending on TRE structure and THR isotype. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Hypoxic induction of interleukin-8 gene expression in human endothelial cells. \nBecause leukocyte-mediated tissue damage is an important component of the pathologic picture in ischemia/reperfusion, we have sought mechanisms by which PMNs are directed into hypoxic tissue. Incubation of human endothelial cells (ECs) in hypoxia, PO2 approximately 14-18 Torr, led to time-dependent release of IL-8 antigen into the conditioned medium; this was accompanied by increased chemotactic activity for PMNs, blocked by antibody to IL-8. Production of IL-8 by hypoxic ECs occurred concomitantly with both increased levels of IL-8 mRNA, based on polymerase chain reaction analysis, and increased IL-8 transcription, based on nuclear run-on assays. Northern analysis of mRNA from hypoxic ECs also demonstrated increased levels of mRNA for macrophage chemotactic protein-1, another member of the chemokine superfamily of proinflammatory cytokines. IL-8 gene induction was associated with the presence of increased binding activity in nuclear extracts from hypoxic ECs for the NF-kB site. Studies with human umbilical vein segments exposed to hypoxia also demonstrated increased elaboration of IL-8 antigen compared with normoxic controls. In mice exposed to hypoxia (PO2 approximately 30-40 Torr), there was increased pulmonary leukostasis, as evidenced by increased myeloperoxidase activity in tissue homogenates. In parallel, increased levels of transcripts for IP-10, a murine homologue in the chemokine family related to IL-8, were observed in hypoxic lung tissue. Taken together, these data suggest that hypoxia constitutes a stimulus for leukocyte chemotaxis and tissue leukostasis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 40, "end": 50}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 21, "end": 34}]}], "localization": [{"trigger": {"text": "release", "start": 380, "end": 387}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 391, "end": 395}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 8, "end": 17}, "arguments": [{"role": "Theme", "text": "expression", "start": 40, "end": 50}]}, {"trigger": {"text": "led", "start": 358, "end": 361}, "arguments": [{"role": "Theme", "text": "release", "start": 380, "end": 387}]}, {"trigger": {"text": "Production", "start": 527, "end": 537}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 541, "end": 545}]}, {"trigger": {"text": "increased", "start": 594, "end": 603}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 614, "end": 618}]}, {"trigger": {"text": "increased", "start": 674, "end": 683}, "arguments": [{"role": "Theme", "text": "transcription", "start": 689, "end": 702}]}, {"trigger": {"text": "increased", "start": 797, "end": 806}, "arguments": [{"role": "Theme", "text": "macrophage chemotactic protein-1", "start": 826, "end": 858}]}, {"trigger": {"text": "induction", "start": 944, "end": 953}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 934, "end": 938}]}, {"trigger": {"text": "increased", "start": 1154, "end": 1163}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1179, "end": 1183}]}, {"trigger": {"text": "increased", "start": 1414, "end": 1423}, "arguments": [{"role": "Theme", "text": "IP-10", "start": 1450, "end": 1455}]}], "transcription": [{"trigger": {"text": "transcription", "start": 689, "end": 702}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 684, "end": 688}]}]}}, "schema": []}
{"input": "Function of NF-kappa B/Rel binding sites in the major histocompatibility complex class II invariant chain promoter is dependent on cell-specific binding of different NF-kappa B/Rel subunits. \nThe promoter of the human major histocompatibility complex class II-associated invariant-chain gene (Ii) contains two NF-kappa B/Rel binding sites located at -109 to -118 (Ii kappa B-1) and -163 to -172 (Ii kappa B-2) from the transcription start site. We report here that the differential function of each of these NF-kappa B/Rel sites in several distinct cell types depends on cell-specific binding of NF-kappa B/Rel transcription factors. Ii kappa B-1 is a positive regulatory element in B-cell lines and in the Ii-expressing T-cell line, H9, but acts as a negative regulatory element in myelomonocytic and glia cell lines. In vivo protein-DNA contacts are detectable at Ii kappa B-1 in cell lines in which this site is functional as either a positive or negative regulator. Electrophoretic mobility supershift assays determine that members of the NF-kappa B/Rel family of transcription factors can bind to this site in vitro and that DNA-binding complexes that contain p50, p52, p65, and cRel correlate with positive regulation whereas the presence of p50 correlates with negative regulation. Ii kappa B-2 is a site of positive regulation in B-cell lines and a site of negative regulation in H9 T cells, myelomonocytic, and glial cell lines. In vivo occupancy of this site is observed only in the H9 T-cell line. Again, in vitro supershift studies indicate that the presence of p50, p52, p65, and cRel correlates with positive function whereas the presence of only p50 and p52 correlates with negative function. This differential binding of specific NF-kappa B/Rel subunits is likely to mediate the disparate functions of these two NF-kappa B/Rel binding sites. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding complexes", "start": 1134, "end": 1151}, "arguments": [{"role": "Theme", "text": "p50", "start": 1165, "end": 1168}, {"role": "Theme2", "text": "p52", "start": 1170, "end": 1173}, {"role": "Theme3", "text": "p65", "start": 1175, "end": 1178}, {"role": "Theme4", "text": "cRel", "start": 1184, "end": 1188}]}, {"trigger": {"text": "presence", "start": 1236, "end": 1244}, "arguments": [{"role": "Theme", "text": "p50", "start": 1248, "end": 1251}]}, {"trigger": {"text": "presence", "start": 1562, "end": 1570}, "arguments": [{"role": "Theme", "text": "p50", "start": 1574, "end": 1577}, {"role": "Theme2", "text": "p52", "start": 1579, "end": 1582}, {"role": "Theme3", "text": "p65", "start": 1584, "end": 1587}, {"role": "Theme4", "text": "cRel", "start": 1593, "end": 1597}]}, {"trigger": {"text": "presence", "start": 1644, "end": 1652}, "arguments": [{"role": "Theme", "text": "p50", "start": 1661, "end": 1664}, {"role": "Theme2", "text": "p52", "start": 1669, "end": 1672}]}], "regulation": [{"trigger": {"text": "Function", "start": 0, "end": 8}, "arguments": [{"role": "Theme", "text": "major histocompatibility complex class II invariant chain", "start": 48, "end": 105}, {"role": "Site", "text": "promoter", "start": 106, "end": 114}]}, {"trigger": {"text": "dependent", "start": 118, "end": 127}, "arguments": [{"role": "Theme", "text": "Function", "start": 0, "end": 8}]}]}}, "schema": []}
{"input": "Positive regulators of the lineage-specific transcription factor GATA-1 in differentiating erythroid cells. \nThe zinc finger transcription factor GATA-1 is a major regulator of gene expression in erythroid, megakaryocyte, and mast cell lineages. GATA-1 binds to WGATAR consensus motifs in the regulatory regions of virtually all erythroid cell-specific genes. Analyses with cultured cells and cell-free systems have provided strong evidence that GATA-1 is involved in control of globin gene expression during erythroid differentiation. Targeted mutagenesis of the GATA-1 gene in embryonic stem cells has demonstrated its requirement in normal erythroid development. Efficient rescue of the defect requires an intact GATA element in the distal promoter, suggesting autoregulatory control of GATA-1 transcription. To examine whether GATA-1 expression involves additional regulatory factors or is maintained entirely by an autoregulatory loop, we have used a transient heterokaryon system to test the ability of erythroid factors to activate the GATA-1 gene in nonerythroid nuclei. We show here that proerythroblasts and mature erythroid cells contain a diffusible activity (TAG) capable of transcriptional activation of GATA-1 and that this activity decreases during the terminal differentiation of erythroid cells. Nuclei from GATA-1- mutant embryonic stem cells can still be reprogrammed to express their globin genes in erythroid heterokaryons, indicating that de novo induction of GATA-1 is not required for globin gene activation following cell fusion. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 253, "end": 258}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 246, "end": 252}]}], "gene expression": [{"trigger": {"text": "expression", "start": 838, "end": 848}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 831, "end": 837}]}], "negative regulation": [{"trigger": {"text": "decreases", "start": 1248, "end": 1257}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 1188, "end": 1214}]}], "positive regulation": [{"trigger": {"text": "Positive regulators", "start": 0, "end": 19}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 65, "end": 71}]}, {"trigger": {"text": "maintained", "start": 894, "end": 904}, "arguments": [{"role": "Theme", "text": "expression", "start": 838, "end": 848}]}, {"trigger": {"text": "activate", "start": 1030, "end": 1038}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1043, "end": 1049}]}, {"trigger": {"text": "transcriptional activation", "start": 1188, "end": 1214}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1218, "end": 1224}]}, {"trigger": {"text": "induction", "start": 1470, "end": 1479}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1483, "end": 1489}]}], "regulation": [{"trigger": {"text": "autoregulatory control", "start": 764, "end": 786}, "arguments": [{"role": "Theme", "text": "transcription", "start": 797, "end": 810}]}], "transcription": [{"trigger": {"text": "transcription", "start": 797, "end": 810}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 790, "end": 796}]}]}}, "schema": []}
{"input": "Patterns of Pan expression and role of Pan proteins in endocrine cell type-specific complex formation. \nThe Pan gene encodes at least two distinct transcripts, Pan-1 and Pan-2 (also known as E47 and E12, respectively), by the mechanism of alternative RNA splicing. Northern blot analyses performed on rat and mouse tissues have detected ubiquitously expressed Pan transcripts, but the abundance, distribution, and form of Pan proteins have not been clearly defined. Studies of cell lines representing endocrine, fibroblast, and lymphoid lineages using polyclonal antisera to detect E2A proteins have suggested that significant E2A protein expression is restricted to B-lymphocytes. We have developed a monoclonal antibody, Yae, which is specific for Pan/E2A proteins, and have used the Yae antibody to examine a variety of endocrine and nonendocrine cell lineages for differences in Pan/E2A protein expression, subcellular localization, and heteromeric complex formation. In contrast to previous results obtained using polyclonal antiseras to detect Pan/E2A proteins, we report comparable levels of Pan proteins in GH/PRL- and insulin-producing, B- and T-lymphocyte cells. IEF-1, a pancreatic beta-cell type-specific complex believed to regulate insulin expression, is demonstrated to consist of at least two distinct species, one of which does not contain Pan molecules. Although it has been postulated that pituitary endocrine cells and pancreatic endocrine beta-cells share identical Pan/E2A complexes, native-Western analyses of pituitary and endocrine beta-cells detect Pan proteins in distinct cell type-specific complexes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "heteromeric complex formation", "start": 941, "end": 970}, "arguments": [{"role": "Theme", "text": "Pan", "start": 883, "end": 886}]}], "gene expression": [{"trigger": {"text": "expression", "start": 639, "end": 649}, "arguments": [{"role": "Theme", "text": "E2A", "start": 627, "end": 630}]}, {"trigger": {"text": "expression", "start": 899, "end": 909}, "arguments": [{"role": "Theme", "text": "Pan", "start": 883, "end": 886}]}, {"trigger": {"text": "comparable levels", "start": 1078, "end": 1095}, "arguments": [{"role": "Theme", "text": "Pan", "start": 1099, "end": 1102}]}, {"trigger": {"text": "producing", "start": 1135, "end": 1144}, "arguments": [{"role": "Theme", "text": "GH", "start": 1115, "end": 1117}]}, {"trigger": {"text": "producing", "start": 1135, "end": 1144}, "arguments": [{"role": "Theme", "text": "insulin", "start": 1127, "end": 1134}]}, {"trigger": {"text": "expression", "start": 1254, "end": 1264}, "arguments": [{"role": "Theme", "text": "insulin", "start": 1246, "end": 1253}]}, {"trigger": {"text": "detect", "start": 1568, "end": 1574}, "arguments": [{"role": "Theme", "text": "Pan", "start": 1575, "end": 1578}]}], "regulation": [{"trigger": {"text": "regulate", "start": 1237, "end": 1245}, "arguments": [{"role": "Theme", "text": "expression", "start": 1254, "end": 1264}]}], "transcription": [{"trigger": {"text": "expressed", "start": 350, "end": 359}, "arguments": [{"role": "Theme", "text": "Pan", "start": 360, "end": 363}]}]}}, "schema": []}
{"input": "Functional block for 1 alpha,25-dihydroxyvitamin D3-mediated gene regulation in human B lymphocytes. \nElements necessary for the steroid hormone 1 alpha,25-dihydroxyvitamin D3 (1 alpha,25-(OH)2D3) to induce a biological response include the presence of specific intracellular receptors (vitamin D3 receptors (VDR)) and modulation of gene expression via hormone-activated receptor binding to regulatory regions of target genes. These parameters were examined in normal and Epstein-Barr virus-immortalized human B cells and compared with 1 alpha,25-(OH)2D3-responsive cells of the T and monocytic lineages. Although resting tonsillar B cells did not express VDR mRNA, activation of these cells with interleukin-4 induced VDR in the absence of exogenously supplemented 1 alpha,25-(OH)2D3. As indicators of hormone-mediated gene regulation we analyzed modulation of CD23, a common B cell/monocyte surface antigen, and 24-hydroxylase. 1 alpha,25-(OH)2D3 inhibited CD23 expression in U937 cells, yet failed to modulate CD23 expression in B cells. Furthermore, 1 alpha,25-(OH)2D3 induced 24-hydroxylase mRNA expression and metabolic activity in both U937 cells and lectin-activated T cells, yet failed to induce 24-hydroxylase mRNA or its metabolic activity in B cells. These findings suggest that although human B lymphocytes can express VDR mRNA and protein, they exhibit a functional block for vitamin D-dependent gene regulation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 964, "end": 974}, "arguments": [{"role": "Theme", "text": "CD23", "start": 959, "end": 963}]}, {"trigger": {"text": "expression", "start": 1018, "end": 1028}, "arguments": [{"role": "Theme", "text": "CD23", "start": 1013, "end": 1017}]}, {"trigger": {"text": "express", "start": 1324, "end": 1331}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1332, "end": 1335}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 949, "end": 958}, "arguments": [{"role": "Theme", "text": "expression", "start": 964, "end": 974}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 361, "end": 370}, "arguments": [{"role": "Theme", "text": "VDR", "start": 309, "end": 312}]}, {"trigger": {"text": "induced", "start": 711, "end": 718}, "arguments": [{"role": "Theme", "text": "VDR", "start": 719, "end": 722}]}, {"trigger": {"text": "induced", "start": 1073, "end": 1080}, "arguments": [{"role": "Theme", "text": "expression", "start": 1101, "end": 1111}]}, {"trigger": {"text": "induce", "start": 1198, "end": 1204}, "arguments": [{"role": "Theme", "text": "24-hydroxylase", "start": 1205, "end": 1219}]}], "regulation": [{"trigger": {"text": "modulation", "start": 848, "end": 858}, "arguments": [{"role": "Theme", "text": "CD23", "start": 862, "end": 866}]}, {"trigger": {"text": "modulation", "start": 848, "end": 858}, "arguments": [{"role": "Theme", "text": "24-hydroxylase", "start": 914, "end": 928}]}, {"trigger": {"text": "modulate", "start": 1004, "end": 1012}, "arguments": [{"role": "Theme", "text": "expression", "start": 1018, "end": 1028}]}], "transcription": [{"trigger": {"text": "express", "start": 648, "end": 655}, "arguments": [{"role": "Theme", "text": "VDR", "start": 656, "end": 659}]}, {"trigger": {"text": "expression", "start": 1101, "end": 1111}, "arguments": [{"role": "Theme", "text": "24-hydroxylase", "start": 1081, "end": 1095}]}, {"trigger": {"text": "express", "start": 1324, "end": 1331}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1332, "end": 1335}]}]}}, "schema": []}
{"input": "Effects of alpha-lipoic acid and dihydrolipoic acid on expression of proto-oncogene c-fos. \nThe transcription factor AP-1 is an important human mediator of the cellular response to serum, growth factors, and phorbol esters such as 12-O-tetradecanoyl-phorbol-13 acetate (TPA). The AP-1 complex consists of distinct protein heterodimers encoded by the proto-oncogene c-fos and c-jun mRNA whose gene expression can be induced by TPA, cyclic AMP and growth factors. Recent findings suggest an involvement of reactive oxygen species in the pathway of TPA and protein kinase C leading to expression of c-fos and c-jun mRNA. To investigate the role of reactive oxygen species we studied the effects of alpha-lipoic acid and dihydrolipoic acid (natural thiol antioxidants) on the expression of c-fos mRNA in human Jurkat T cells. When cells were preincubated with dihydrolipoic acid (0.2 mM) the expression of c-fos mRNA was suppressed at 30 min after stimulation of TPA (0.5 microM) whereas in the case of preincubation of alpha-lipoic acid (0.2 microM), the expression was enhanced at 30 min. These studies support the idea that superoxide anion radical plays a role in the expression of c-fos mRNA. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 55, "end": 65}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 84, "end": 89}]}], "negative regulation": [{"trigger": {"text": "suppressed", "start": 917, "end": 927}, "arguments": [{"role": "Theme", "text": "expression", "start": 888, "end": 898}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 415, "end": 422}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 392, "end": 407}]}, {"trigger": {"text": "leading", "start": 571, "end": 578}, "arguments": [{"role": "Theme", "text": "expression", "start": 582, "end": 592}]}, {"trigger": {"text": "When", "start": 822, "end": 826}, "arguments": [{"role": "Theme", "text": "suppressed", "start": 917, "end": 927}]}, {"trigger": {"text": "in the case of", "start": 984, "end": 998}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 1067, "end": 1075}]}, {"trigger": {"text": "enhanced", "start": 1067, "end": 1075}, "arguments": [{"role": "Theme", "text": "expression", "start": 888, "end": 898}]}], "regulation": [{"trigger": {"text": "Effects", "start": 0, "end": 7}, "arguments": [{"role": "Theme", "text": "expression", "start": 55, "end": 65}]}, {"trigger": {"text": "involvement", "start": 489, "end": 500}, "arguments": [{"role": "Theme", "text": "leading", "start": 571, "end": 578}]}, {"trigger": {"text": "role", "start": 637, "end": 641}, "arguments": [{"role": "Theme", "text": "expression", "start": 772, "end": 782}]}, {"trigger": {"text": "effects", "start": 684, "end": 691}, "arguments": [{"role": "Theme", "text": "expression", "start": 772, "end": 782}]}, {"trigger": {"text": "plays a role", "start": 1148, "end": 1160}, "arguments": [{"role": "Theme", "text": "expression", "start": 1168, "end": 1178}]}], "transcription": [{"trigger": {"text": "gene expression", "start": 392, "end": 407}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 365, "end": 370}]}, {"trigger": {"text": "gene expression", "start": 392, "end": 407}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 375, "end": 380}]}, {"trigger": {"text": "expression", "start": 582, "end": 592}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 596, "end": 601}]}, {"trigger": {"text": "expression", "start": 582, "end": 592}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 606, "end": 611}]}, {"trigger": {"text": "expression", "start": 772, "end": 782}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 786, "end": 791}]}, {"trigger": {"text": "expression", "start": 888, "end": 898}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 902, "end": 907}]}, {"trigger": {"text": "expression", "start": 1168, "end": 1178}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1182, "end": 1187}]}]}}, "schema": []}
{"input": "Alternative splicing of RNA transcripts encoded by the murine p105 NF-kappa B gene generates I kappa B gamma isoforms with different inhibitory activities. \nThe gene encoding the 105-kDa protein (p105) precursor of the p50 subunit of transcription factor NF-kappa B also encodes a p70 I kappa B protein, I kappa B gamma, which is identical to the C-terminal 607 amino acids of p105. Here we show that alternative RNA splicing generates I kappa B gamma isoforms with properties different from those of p70. One 63-kDa isoform, termed I kappa B gamma-1, which lacks 59 amino acids C-terminal to ankyrin repeat 7, has a novel 35-amino acid C terminus encoded by an alternative reading frame of the p105 gene. A 55-kDa isoform, I kappa B gamma-2, lacks the 190 C-terminal amino acids of p70I kappa B gamma. In contrast to p70I kappa B gamma, which is a cytoplasmic protein, I kappa B gamma-1 is found in both the cytoplasm and nucleus, whereas I kappa B gamma-2 is predominantly nuclear. The I kappa B gamma isoforms also display differences in specificity and affinity for Rel/NF-kappa B proteins. While p70I kappa B gamma inhibits p50-, p65-, and c-Rel-mediated transactivation and/or DNA binding, both I kappa B gamma-1 and I kappa B gamma-2 are specific for p50 and have different affinities for this subunit. The absence in I kappa B gamma-1 and I kappa B gamma-2 of a protein kinase A site whose phosphorylation modulates p70I kappa B gamma inhibitory activity suggests that alternative RNA splicing may be used to generate I kappa B gamma isoforms that respond differently to intracellular signals. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "specific", "start": 1245, "end": 1253}, "arguments": [{"role": "Theme", "text": "I kappa B gamma-1", "start": 1201, "end": 1218}, {"role": "Theme2", "text": "p50", "start": 1258, "end": 1261}]}, {"trigger": {"text": "specific", "start": 1245, "end": 1253}, "arguments": [{"role": "Theme", "text": "I kappa B gamma-2", "start": 1223, "end": 1240}, {"role": "Theme2", "text": "p50", "start": 1258, "end": 1261}]}], "gene expression": [{"trigger": {"text": "generates", "start": 83, "end": 92}, "arguments": [{"role": "Theme", "text": "I kappa B gamma", "start": 93, "end": 108}]}, {"trigger": {"text": "generates", "start": 426, "end": 435}, "arguments": [{"role": "Theme", "text": "I kappa B gamma", "start": 436, "end": 451}]}], "localization": [{"trigger": {"text": "found", "start": 891, "end": 896}, "arguments": [{"role": "Theme", "text": "I kappa B gamma-1", "start": 870, "end": 887}, {"role": "AtLoc", "text": "cytoplasm", "start": 909, "end": 918}]}, {"trigger": {"text": "found", "start": 891, "end": 896}, "arguments": [{"role": "Theme", "text": "I kappa B gamma-1", "start": 870, "end": 887}, {"role": "AtLoc", "text": "nucleus", "start": 923, "end": 930}]}, {"trigger": {"text": "found", "start": 891, "end": 896}, "arguments": [{"role": "Theme", "text": "I kappa B gamma-2", "start": 940, "end": 957}, {"role": "AtLoc", "text": "nuclear", "start": 975, "end": 982}]}], "positive regulation": [{"trigger": {"text": "generates", "start": 83, "end": 92}, "arguments": [{"role": "Theme", "text": "generates", "start": 83, "end": 92}]}, {"trigger": {"text": "generates", "start": 426, "end": 435}, "arguments": [{"role": "Theme", "text": "generates", "start": 426, "end": 435}]}, {"trigger": {"text": "generate", "start": 1517, "end": 1525}, "arguments": [{"role": "Theme", "text": "I kappa B gamma", "start": 1526, "end": 1541}]}], "regulation": [{"trigger": {"text": "respond", "start": 1556, "end": 1563}, "arguments": [{"role": "Theme", "text": "I kappa B gamma", "start": 1526, "end": 1541}]}]}}, "schema": []}
{"input": "Activation of nuclear factor kappa B in human lymphoblastoid cells by low-dose ionizing radiation. \nNuclear factor kappa B (NF-kappa B) is a pleiotropic transcription factor which is involved in the transcriptional regulation of several specific genes. Recent reports demonstrated that ionizing radiation in the dose range of 2-50 Gy results in expression of NF-kappa B in human KG-1 myeloid leukemia cells and human B-lymphocyte precursor cells; the precise mechanism involved and the significance are not yet known. The present report demonstrates that even lower doses of ionizing radiation, 0.25-2.0 Gy, are capable of inducing expression of NF-kappa B in EBV-transformed 244B human lymphoblastoid cells. These results are in a dose range where the viability of the cells remains very high. After exposure to 137Cs gamma rays at a dose rate of 1.17 Gy/min, a maximum in expression of NF-kappa B was seen at 8 h after a 0.5-Gy exposure. Time-course studies revealed a biphasic time-dependent expression after 0.5-, 1- and 2-Gy exposures. However, for each time examined, the expression of NF-kappa B was maximum after the 0.5-Gy exposure. The expression of the p50 and p65 NF-kappa B subunits was also shown to be regulated differentially after exposures to 1.0 and 2.0 Gy. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1146, "end": 1156}, "arguments": [{"role": "Theme", "text": "p50", "start": 1164, "end": 1167}]}, {"trigger": {"text": "expression", "start": 1146, "end": 1156}, "arguments": [{"role": "Theme", "text": "p65", "start": 1172, "end": 1175}]}], "regulation": [{"trigger": {"text": "regulated", "start": 1217, "end": 1226}, "arguments": [{"role": "Theme", "text": "expression", "start": 1146, "end": 1156}]}]}}, "schema": []}
{"input": "Some antioxidants inhibit, in a co-ordinate fashion, the production of tumor necrosis factor-alpha, IL-beta, and IL-6 by human peripheral blood mononuclear cells. \nSome antioxidants, including butylated hydroxyanisole (BHA), tetrahydropapaveroline (THP), nordihydroguiauretic acid, and 10,11-dihydroxyaporphine (DHA), were found to be potent inhibitors of the production of tumor necrosis factor (TNF)-alpha, IL-1 beta, and IL-6 by human peripheral blood mononuclear cells (PBMC) stimulated by lipopolysaccharide (LPS) (IC50s in the low micromolar range). Inhibition of cytokine production was gene selective and not due to general effects on protein synthesis. Inhibition of cytokine production by PBMC was observed also when other inducers were used (staphylococci, silica, zymosan). Much higher concentrations of other antioxidants--including ascorbic acid, trolox, alpha-tocopherol, butylated hydroxytoluene, and the 5-lipoxygenase inhibitor zileuton--did not affect the production of these cytokines. The active compounds did not inhibit IL-1-induced production of IL-6 in fibroblasts, showing the cell selectivity of the effect. Antioxidant-mediated inhibition of cytokine production was correlated with low levels of the corresponding messenger RNAs. Nuclear run-on experiments showed that THP inhibited transcription of the IL-1 beta gene. THP decreased the concentration of the transcription factors NF-kappa B and AP-1 detected in nuclear extracts of PBMC cultured in the presence or absence of LPS. THP and DHA markedly decreased the levels of TNF-alpha and IL-1 beta in the circulation of mice following LPS injection. Thus antioxidants vary widely in potency as inhibitors of the activation of transcription factors and of the transcription of genes for pro-inflammatory cytokines. Coordinate inhibition of the transcription of genes for inflammatory cytokines could provide a strategy for therapy of diseases with inflammatory pathogenesis and for septic shock. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 57, "end": 67}, "arguments": [{"role": "Theme", "text": "IL-beta", "start": 100, "end": 107}]}, {"trigger": {"text": "production", "start": 57, "end": 67}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 113, "end": 117}]}, {"trigger": {"text": "production", "start": 57, "end": 67}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 71, "end": 98}]}, {"trigger": {"text": "production", "start": 360, "end": 370}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor (TNF)-alpha", "start": 374, "end": 407}]}, {"trigger": {"text": "production", "start": 360, "end": 370}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 409, "end": 418}]}, {"trigger": {"text": "production", "start": 360, "end": 370}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 424, "end": 428}]}, {"trigger": {"text": "production", "start": 975, "end": 985}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor (TNF)-alpha", "start": 374, "end": 407}]}, {"trigger": {"text": "production", "start": 975, "end": 985}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 409, "end": 418}]}, {"trigger": {"text": "production", "start": 975, "end": 985}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 424, "end": 428}]}, {"trigger": {"text": "production", "start": 1056, "end": 1066}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1070, "end": 1074}]}, {"trigger": {"text": "levels", "start": 1545, "end": 1551}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1555, "end": 1564}]}, {"trigger": {"text": "levels", "start": 1545, "end": 1551}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1569, "end": 1578}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 18, "end": 25}, "arguments": [{"role": "Theme", "text": "production", "start": 57, "end": 67}]}, {"trigger": {"text": "inhibitors", "start": 342, "end": 352}, "arguments": [{"role": "Theme", "text": "production", "start": 360, "end": 370}]}, {"trigger": {"text": "inhibit", "start": 1035, "end": 1042}, "arguments": [{"role": "Theme", "text": "induced", "start": 1048, "end": 1055}]}, {"trigger": {"text": "inhibited", "start": 1301, "end": 1310}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1311, "end": 1324}]}, {"trigger": {"text": "decreased", "start": 1531, "end": 1540}, "arguments": [{"role": "Theme", "text": "levels", "start": 1545, "end": 1551}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1048, "end": 1055}, "arguments": [{"role": "Theme", "text": "production", "start": 1056, "end": 1066}]}], "regulation": [{"trigger": {"text": "affect", "start": 964, "end": 970}, "arguments": [{"role": "Theme", "text": "production", "start": 975, "end": 985}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1311, "end": 1324}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1332, "end": 1341}]}]}}, "schema": []}
{"input": "Calcineurin potentiates activation of the granulocyte-macrophage colony-stimulating factor gene in T cells: involvement of the conserved lymphokine element 0. \nGranulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-2 (IL-2) are produced by stimulation with phorbol-12-myristate acetate (PMA) and calcium ionophore (A23187) in human T cell leukemia Jurkat cells. The expression of GM-CSF and IL-2 is inhibited by immunosuppressive drugs such as cyclosporin A (CsA) and FK506. Earlier studies on the IL-2 gene expression showed that overexpression of calcineurin (CN), a Ca2+/calmodulin-dependent protein phosphatase, can stimulate transcription from the IL-2 promoter through the NF-AT-binding site. In this study, we obtained evidence that transfection of the cDNAs for CN A (catalytic) and CN B (regulatory) subunits also augments transcription from the GM-CSF promoter and recovers the transcription inhibited by CsA. The constitutively active type of the CN A subunit, which lacks the auto-inhibitory and calmodulin-binding domains, acts in synergy with PMA to activate transcription from the GM-CSF promoter. We also found that the active CN partially replaces calcium ionophore in synergy with PMA to induce expression of endogenous GM-CSF and IL-2. By multimerizing the regulatory elements of the GM-CSF promoter, we found that one of the target sites for the CN action is the conserved lymphokine element 0 (CLE0), located at positions between -54 and -40. Mobility shift assays showed that the CLE0 sequence has an AP1-binding site and is associated with an NF-AT-like factor, termed NF-CLE0 gamma. NF-CLE0 gamma binding is induced by PMA/A23187 and is inhibited by treatment with CsA. These results suggest that CN is involved in the coordinated induction of the GM-CSF and IL-2 genes and that the CLE0 sequence of the GM-CSF gene is a functional analogue of the NF-AT-binding site in the IL-2 promoter, which mediates signals downstream of T cell activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associated", "start": 1566, "end": 1576}, "arguments": [{"role": "Theme", "text": "NF-CLE0 gamma", "start": 1611, "end": 1624}]}, {"trigger": {"text": "binding", "start": 1640, "end": 1647}, "arguments": [{"role": "Theme", "text": "NF-CLE0 gamma", "start": 1626, "end": 1639}]}], "gene expression": [{"trigger": {"text": "produced", "start": 247, "end": 255}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 210, "end": 216}]}, {"trigger": {"text": "produced", "start": 247, "end": 255}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 237, "end": 241}]}, {"trigger": {"text": "expression", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 399, "end": 405}]}, {"trigger": {"text": "expression", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 410, "end": 414}]}, {"trigger": {"text": "expression", "start": 527, "end": 537}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 517, "end": 521}]}, {"trigger": {"text": "transfection", "start": 759, "end": 771}, "arguments": [{"role": "Theme", "text": "CN A", "start": 789, "end": 793}]}, {"trigger": {"text": "transfection", "start": 759, "end": 771}, "arguments": [{"role": "Theme", "text": "CN B", "start": 810, "end": 814}]}, {"trigger": {"text": "expression", "start": 1232, "end": 1242}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1257, "end": 1263}]}, {"trigger": {"text": "expression", "start": 1232, "end": 1242}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1268, "end": 1272}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 418, "end": 427}, "arguments": [{"role": "Theme", "text": "expression", "start": 385, "end": 395}]}, {"trigger": {"text": "recovers", "start": 894, "end": 902}, "arguments": [{"role": "Cause", "text": "transfection", "start": 759, "end": 771}, {"role": "Theme", "text": "inhibited", "start": 921, "end": 930}]}, {"trigger": {"text": "inhibited", "start": 921, "end": 930}, "arguments": [{"role": "Theme", "text": "transcription", "start": 851, "end": 864}]}, {"trigger": {"text": "inhibited", "start": 1680, "end": 1689}, "arguments": [{"role": "Theme", "text": "binding", "start": 1640, "end": 1647}]}], "positive regulation": [{"trigger": {"text": "potentiates", "start": 12, "end": 23}, "arguments": [{"role": "Theme", "text": "activation", "start": 24, "end": 34}]}, {"trigger": {"text": "activation", "start": 24, "end": 34}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 42, "end": 90}]}, {"trigger": {"text": "by stimulation with", "start": 256, "end": 275}, "arguments": [{"role": "Theme", "text": "produced", "start": 247, "end": 255}]}, {"trigger": {"text": "stimulate", "start": 639, "end": 648}, "arguments": [{"role": "Theme", "text": "transcription", "start": 649, "end": 662}]}, {"trigger": {"text": "transfection", "start": 759, "end": 771}, "arguments": [{"role": "Theme", "text": "transfection", "start": 759, "end": 771}]}, {"trigger": {"text": "augments", "start": 842, "end": 850}, "arguments": [{"role": "Cause", "text": "transfection", "start": 759, "end": 771}, {"role": "Theme", "text": "transcription", "start": 851, "end": 864}]}, {"trigger": {"text": "activate", "start": 1083, "end": 1091}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1092, "end": 1105}]}, {"trigger": {"text": "to induce", "start": 1222, "end": 1231}, "arguments": [{"role": "Theme", "text": "expression", "start": 1232, "end": 1242}]}, {"trigger": {"text": "induced", "start": 1651, "end": 1658}, "arguments": [{"role": "Theme", "text": "binding", "start": 1640, "end": 1647}]}, {"trigger": {"text": "induction", "start": 1774, "end": 1783}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1791, "end": 1797}]}, {"trigger": {"text": "induction", "start": 1774, "end": 1783}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1802, "end": 1806}]}], "transcription": [{"trigger": {"text": "transcription", "start": 649, "end": 662}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 672, "end": 676}]}, {"trigger": {"text": "transcription", "start": 851, "end": 864}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 874, "end": 880}]}, {"trigger": {"text": "transcription", "start": 1092, "end": 1105}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1115, "end": 1121}]}]}}, "schema": []}
{"input": "Central nervous system-derived cells express a kappa B-binding activity that enhances human immunodeficiency virus type 1 transcription in vitro and facilitates TAR-independent transactivation by Tat. \nThe Tat protein of human immunodeficiency virus type 1 (HIV-1) is a potent activator of long terminal repeat-directed transcription. While in most cell types, activation requires interaction of Tat with the unusual transcription element TAR, astrocytic glial cells support TAR-independent transactivation of HIV-1 transcription by Tat. This alternative pathway of Tat activation is mediated by the viral enhancer, a kappa B domain capable of binding the prototypical form of the transcription factor nuclear factor kappa B (NF-kappa B) present in many cell types, including T lymphocytes. Tat transactivation mediated by the kappa B domain is sufficient to allow replication of TAR-deleted mutant HIV-1 in astrocytes. The present study demonstrates the existence of kappa B-specific binding factors present in human glial astrocytes that differ from prototypical NF-kappa B. The novel astrocyte-derived kappa B-binding activity is retained on an HIV-1 Tat affinity column, while prototypical NF-kappa B from Jurkat T cells is not. In vitro transcription studies demonstrate that astrocyte-derived kappa B-binding factors activate transcription of the HIV-1 long terminal repeat and that this activation is dependent on the kappa B domain. Moreover, TAR-independent transactivation of HIV-1 transcription is reproduced in vitro in an astrocyte factor-dependent manner which correlates with kappa B-binding activity. The importance of the central nervous system-enriched kappa B transcription factor in the regulation of HIV-1 expression is discussed. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 381, "end": 392}, "arguments": [{"role": "Theme", "text": "Tat", "start": 396, "end": 399}]}]}}, "schema": []}
{"input": "An intricate arrangement of binding sites for the Ets family of transcription factors regulates activity of the alpha 4 integrin gene promoter. \nalpha 4 integrins mediate cell-cell and cell-extracellular matrix interactions that are critical for maturation and function of the immune system as well as differentiation of skeletal muscle. Here we examine molecular mechanisms controlling the pattern of alpha 4 expression. The activity of constructs containing 5' deletion mutants of the alpha 4 gene promoter was compared in transfection assays into cell lines that express alpha 4 and cell lines that do not. The sequence between position -42 and -76 base pairs (bp) was required for efficient transcription in cells that express alpha 4, but it showed no activity in HeLa cells, which do not express alpha 4. Three binding sites for the Ets family of transcription factors are found in this region: two adjacent sites at positions -50 and -54 bp and a more 5' site at position -67 bp. Using a series of constructs containing deletions and mutations in this region, we found that the 3'-most site alone was sufficient for binding GA-binding protein alpha (GABP alpha)/GABP beta and for a low level of transcriptional activation. When all three sites were present, a second complex \"a\" was detected, which contains an unknown member of the Ets family. Formation of complex a was cell-type specific and correlated with a high level of transcription. Deletion of the 5'-most Ets site had no effect on binding to GABP alpha/GABP beta, but it eliminated a. Concomitant with this loss of a, a new Ets-1-containing complex \"c\" appeared. Complex c substituted efficiently for complex a in transcriptional activation. We conclude that although neither of the two 5'-most Ets sites alone binds nuclear protein, they appear to act as modulators which control the pattern of Ets proteins that bind the alpha 4 gene promoter. This arrangement of Ets sites, coupled with the tissue- and developmental-specific expression of Ets members, likely play a key role in defining the pattern of alpha 4 integrin. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "sufficient for binding", "start": 1108, "end": 1130}, "arguments": [{"role": "Theme", "text": "GA-binding protein alpha", "start": 1131, "end": 1155}]}, {"trigger": {"text": "binding", "start": 1499, "end": 1506}, "arguments": [{"role": "Theme", "text": "GABP alpha", "start": 1510, "end": 1520}]}, {"trigger": {"text": "bind", "start": 1882, "end": 1886}, "arguments": [{"role": "Theme", "text": "alpha 4", "start": 1891, "end": 1898}, {"role": "Site", "text": "promoter", "start": 1904, "end": 1912}]}], "gene expression": [{"trigger": {"text": "expression", "start": 410, "end": 420}, "arguments": [{"role": "Theme", "text": "alpha 4 integrins", "start": 145, "end": 162}]}, {"trigger": {"text": "express", "start": 566, "end": 573}, "arguments": [{"role": "Theme", "text": "alpha 4 integrins", "start": 145, "end": 162}]}, {"trigger": {"text": "express", "start": 723, "end": 730}, "arguments": [{"role": "Theme", "text": "alpha 4 integrins", "start": 145, "end": 162}]}, {"trigger": {"text": "express", "start": 794, "end": 801}, "arguments": [{"role": "Theme", "text": "alpha 4 integrins", "start": 145, "end": 162}]}, {"trigger": {"text": "pattern", "start": 2063, "end": 2070}, "arguments": [{"role": "Theme", "text": "alpha 4 integrin", "start": 2074, "end": 2090}]}], "positive regulation": [{"trigger": {"text": "required", "start": 672, "end": 680}, "arguments": [{"role": "Theme", "text": "transcription", "start": 695, "end": 708}]}, {"trigger": {"text": "activity", "start": 757, "end": 765}, "arguments": [{"role": "Theme", "text": "transcription", "start": 695, "end": 708}]}, {"trigger": {"text": "sufficient", "start": 1108, "end": 1118}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 1202, "end": 1228}]}, {"trigger": {"text": "transcriptional activation", "start": 1202, "end": 1228}, "arguments": [{"role": "Theme", "text": "alpha 4", "start": 487, "end": 494}, {"role": "Site", "text": "promoter", "start": 500, "end": 508}]}, {"trigger": {"text": "high level", "start": 1420, "end": 1430}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1434, "end": 1447}]}, {"trigger": {"text": "in transcriptional activation", "start": 1679, "end": 1708}, "arguments": [{"role": "Theme", "text": "alpha 4 integrins", "start": 145, "end": 162}]}], "regulation": [{"trigger": {"text": "regulates", "start": 86, "end": 95}, "arguments": [{"role": "Theme", "text": "alpha 4 integrin", "start": 112, "end": 128}, {"role": "Site", "text": "promoter", "start": 134, "end": 142}]}, {"trigger": {"text": "controlling", "start": 375, "end": 386}, "arguments": [{"role": "Theme", "text": "expression", "start": 410, "end": 420}]}, {"trigger": {"text": "effect", "start": 1489, "end": 1495}, "arguments": [{"role": "Theme", "text": "binding", "start": 1499, "end": 1506}]}, {"trigger": {"text": "play a key role in defining", "start": 2031, "end": 2058}, "arguments": [{"role": "Theme", "text": "pattern", "start": 2063, "end": 2070}]}], "transcription": [{"trigger": {"text": "transcription", "start": 695, "end": 708}, "arguments": [{"role": "Theme", "text": "alpha 4 integrins", "start": 145, "end": 162}]}, {"trigger": {"text": "transcription", "start": 1434, "end": 1447}, "arguments": [{"role": "Theme", "text": "alpha 4 integrins", "start": 145, "end": 162}]}]}}, "schema": []}
{"input": "Lipopolysaccharide induction of tissue factor gene expression in monocytic cells is mediated by binding of c-Rel/p65 heterodimers to a kappa B-like site. \nExposure of monocytic cells to bacterial lipopolysaccharide (LPS) activates the NF-kappa B/Rel family of proteins and leads to the rapid induction of inflammatory gene products, including tissue factor (TF). TF is the primary cellular initiator of the coagulation protease cascades. Here we report the characterization of a nuclear complex from human monocytic cells that bound to a kappa B-like site, 5'-CGGAGTTTCC-3', in the 5'-flanking region of the human TF gene. This nuclear complex was activated by LPS with kinetics that preceded induction of the TF gene. In vitro binding studies demonstrated that the TF site bound translated c-Rel and p65 homodimers but not p50/p65 heterodimers or p50 homodimers. Base-pair substitutions in the TF site indicated that the presence of a cytosine at position 1 precluded binding of NF-kappa B. In fact, under low-ionic-strength conditions, the TF complex did not migrate with translated p50/p65 dimers but instead comigrated with c-Rel/p65 dimers. Antibodies against the NF-kappa B and Rel proteins and UV cross-linking studies revealed the presence of c-Rel and p65 and the absence of p50 in the TF complex and further showed that c-Rel/p65 heterodimers selectively bound to the TF kappa B-like site. Functional studies indicated that the TF site conferred LPS inducibility on a heterologous promoter and was transactivated by c-Rel or p65. Taken together, our results demonstrated that binding of c-Rel/p65 heterodimers to a novel kappa B-like site mediated LPS induction of TF gene expression in monocytic cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 96, "end": 103}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 107, "end": 112}]}, {"trigger": {"text": "binding", "start": 96, "end": 103}, "arguments": [{"role": "Theme", "text": "p65", "start": 113, "end": 116}]}, {"trigger": {"text": "bound", "start": 527, "end": 532}, "arguments": [{"role": "Site", "text": "kappa B-like site", "start": 538, "end": 555}, {"role": "Theme", "text": "TF", "start": 614, "end": 616}]}, {"trigger": {"text": "bound", "start": 774, "end": 779}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 791, "end": 796}]}, {"trigger": {"text": "bound", "start": 774, "end": 779}, "arguments": [{"role": "Theme", "text": "p65", "start": 801, "end": 804}]}, {"trigger": {"text": "bound", "start": 774, "end": 779}, "arguments": [{"role": "Theme", "text": "p50", "start": 824, "end": 827}]}, {"trigger": {"text": "bound", "start": 774, "end": 779}, "arguments": [{"role": "Theme", "text": "p65", "start": 828, "end": 831}]}, {"trigger": {"text": "bound", "start": 774, "end": 779}, "arguments": [{"role": "Theme", "text": "p50", "start": 848, "end": 851}]}, {"trigger": {"text": "migrate", "start": 1061, "end": 1068}, "arguments": [{"role": "Theme", "text": "TF", "start": 1042, "end": 1044}, {"role": "Theme2", "text": "p50", "start": 1085, "end": 1088}]}, {"trigger": {"text": "migrate", "start": 1061, "end": 1068}, "arguments": [{"role": "Theme", "text": "TF", "start": 1042, "end": 1044}, {"role": "Theme2", "text": "p65", "start": 1089, "end": 1092}]}, {"trigger": {"text": "comigrated", "start": 1112, "end": 1122}, "arguments": [{"role": "Theme", "text": "TF", "start": 1042, "end": 1044}, {"role": "Theme2", "text": "c-Rel", "start": 1128, "end": 1133}]}, {"trigger": {"text": "comigrated", "start": 1112, "end": 1122}, "arguments": [{"role": "Theme", "text": "TF", "start": 1042, "end": 1044}, {"role": "Theme2", "text": "p65", "start": 1134, "end": 1137}]}, {"trigger": {"text": "presence", "start": 1239, "end": 1247}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1251, "end": 1256}, {"role": "Theme2", "text": "TF", "start": 1295, "end": 1297}]}, {"trigger": {"text": "presence", "start": 1239, "end": 1247}, "arguments": [{"role": "Theme", "text": "p65", "start": 1261, "end": 1264}, {"role": "Theme2", "text": "TF", "start": 1295, "end": 1297}]}, {"trigger": {"text": "absence", "start": 1273, "end": 1280}, "arguments": [{"role": "Theme", "text": "p50", "start": 1284, "end": 1287}, {"role": "Theme2", "text": "TF", "start": 1295, "end": 1297}]}, {"trigger": {"text": "bound", "start": 1365, "end": 1370}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1330, "end": 1335}]}, {"trigger": {"text": "bound", "start": 1365, "end": 1370}, "arguments": [{"role": "Theme", "text": "p65", "start": 1336, "end": 1339}]}, {"trigger": {"text": "binding", "start": 1586, "end": 1593}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1597, "end": 1602}]}, {"trigger": {"text": "binding", "start": 1586, "end": 1593}, "arguments": [{"role": "Theme", "text": "p65", "start": 1603, "end": 1606}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1683, "end": 1693}, "arguments": [{"role": "Theme", "text": "TF", "start": 1675, "end": 1677}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 292, "end": 301}, "arguments": [{"role": "Theme", "text": "TF", "start": 358, "end": 360}]}, {"trigger": {"text": "induction", "start": 693, "end": 702}, "arguments": [{"role": "Theme", "text": "TF", "start": 710, "end": 712}]}, {"trigger": {"text": "mediated", "start": 1649, "end": 1657}, "arguments": [{"role": "Cause", "text": "binding", "start": 1586, "end": 1593}, {"role": "Theme", "text": "induction", "start": 1662, "end": 1671}]}, {"trigger": {"text": "induction", "start": 1662, "end": 1671}, "arguments": [{"role": "Theme", "text": "expression", "start": 1683, "end": 1693}]}]}}, "schema": []}
{"input": "Stimulation of HIV replication in mononuclear phagocytes by leukemia inhibitory factor. \nThis study examined the effects of leukemia inhibitory factor (LIF) on human immunodeficiency virus (HIV) replication in mononuclear phagocytes (MNP). LIF induced a dose-dependent increase in p24 antigen production in the chronically infected promonocytic cell line U1. The magnitude and time kinetics of the LIF effects were similar to interleukin 1 (IL-1), IL-6, and tumor necrosis factor (TNF), other cytokines known to induce HIV replication in this cell line. To characterize mechanisms responsible for these LIF effects, levels of HIV mRNA, activation of the DNA binding protein nuclear factor (NF)-kB, signal transduction pathways, and potential interactions with other cytokines were analyzed. LIF increased steady-state levels of HIV mRNA at 2.0, 4.3, and 9.2 kB. This was detectable by 24 h and persisted until 72 h. The DNA binding protein NF-kB is a central mediator in cytokine activation of HIV transcription. NF-kB levels were higher in unstimulated U1 cells as compared to the parent cell line U937. In both cell lines LIF increased NF-kB activity. Induction of NF-kB and HIV replication by cytokines are at least in part dependent on reactive oxygen intermediates. The oxygen radical scavenger N-acetyl-L-cysteine, but not an inhibitor of nitric oxide synthase, inhibited LIF-induced HIV replication. LIF induces the production of other cytokines in monocytes but its effects on HIV replication were not inhibited by antibodies to IL-1, TNF, or IL-6. These results identify LIF as a stimulus of HIV replication. (ABSTRACT TRUNCATED AT 250 WORDS) ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 293, "end": 303}, "arguments": [{"role": "Theme", "text": "p24 antigen", "start": 281, "end": 292}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 269, "end": 277}, "arguments": [{"role": "Cause", "text": "LIF", "start": 240, "end": 243}, {"role": "Theme", "text": "production", "start": 293, "end": 303}]}]}}, "schema": []}
{"input": "Human immunodeficiency virus type 1 Tat upregulates interleukin-2 secretion in activated T cells. \nDysregulation of cytokines secreted by T cells may play an important role in the pathogenesis of AIDS. To investigate the effects of human immunodeficiency virus type 1 (HIV-1) Tat on interleukin-2 (IL-2) expression, we used IL-2 promoter-chloramphenicol acetyltransferase constructs and IL-2-secreting Jurkat T cells as a model system. Transient expression of HIV-1 Tat induced a five- to eightfold increase in IL-2 promoter activity in Jurkat T cells stimulated with phytohemagglutinin and phorbol myristate acetate. IL-2 secretion was increased more than twofold in both Jurkat T cells and primary T cells stimulated by extracellular HIV-1 Tat protein. Analysis of mRNA suggested that Tat exerts its effect on IL-2 primarily at the transcriptional level. The NF-kappa B site at positions -206 to -195 of the IL-2 promoter was required but not sufficient for the Tat effect. The Tat-mediated increase in IL-2 promoter activity could selectively be blocked by antisense tat or-unlike the analogous effect of human T-cell lymphotropic virus type 1 Tax-by cyclosporin A. The observed increase in IL-2 levels might facilitate virus spread from or to T cells. Furthermore, it might contribute to the hypergammaglobulinemia or, together with other cytokines found to be dysregulated, the T-helper cell dysfunctions observed in AIDS patients. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 304, "end": 314}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 298, "end": 302}]}, {"trigger": {"text": "expression", "start": 446, "end": 456}, "arguments": [{"role": "Theme", "text": "Tat", "start": 466, "end": 469}]}], "localization": [{"trigger": {"text": "secretion", "start": 66, "end": 75}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 52, "end": 65}]}, {"trigger": {"text": "secreting", "start": 392, "end": 401}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 387, "end": 391}]}, {"trigger": {"text": "secretion", "start": 623, "end": 632}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 618, "end": 622}]}], "positive regulation": [{"trigger": {"text": "upregulates", "start": 40, "end": 51}, "arguments": [{"role": "Cause", "text": "Tat", "start": 36, "end": 39}, {"role": "Theme", "text": "secretion", "start": 66, "end": 75}]}, {"trigger": {"text": "increased", "start": 637, "end": 646}, "arguments": [{"role": "Theme", "text": "secretion", "start": 623, "end": 632}]}], "regulation": [{"trigger": {"text": "effects", "start": 221, "end": 228}, "arguments": [{"role": "Cause", "text": "Tat", "start": 276, "end": 279}, {"role": "Theme", "text": "expression", "start": 304, "end": 314}]}, {"trigger": {"text": "effect", "start": 802, "end": 808}, "arguments": [{"role": "Cause", "text": "Tat", "start": 787, "end": 790}, {"role": "Theme", "text": "transcriptional", "start": 834, "end": 849}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 834, "end": 849}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 812, "end": 816}]}]}}, "schema": []}
{"input": "The macrophage transcription factor PU.1 directs tissue-specific expression of the macrophage colony-stimulating factor receptor. \nThe macrophage colony-stimulating factor (M-CSF) receptor is expressed in a tissue-specific fashion from two distinct promoters in monocytes/macrophages and the placenta. In order to further understand the transcription factors which play a role in the commitment of multipotential progenitors to the monocyte/macrophage lineage, we have initiated an investigation of the factors which activate the M-CSF receptor very early during the monocyte differentiation process. Here we demonstrate that the human monocytic M-CSF receptor promoter directs reporter gene activity in a tissue-specific fashion. Since one of the few transcription factors which have been implicated in the regulation of monocyte genes is the macrophage- and B-cell-specific PU.1 transcription factor, we investigated whether PU.1 binds and activates the M-CSF receptor promoter. Here we demonstrate that both in vitro-translated PU.1 and PU.1 from nuclear extracts bind to a specific site in the M-CSF receptor promoter just upstream from the major transcription initiation site. Mutations in this site which eliminate PU.1 binding decrease M-CSF receptor promoter activity significantly in macrophage cell lines only. Furthermore, PU.1 transactivates the M-CSF receptor promoter in nonmacrophage cells. These results suggest that PU.1 plays a major role in macrophage gene regulation and development by directing the expression of a receptor for a key macrophage growth factor. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 932, "end": 937}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 927, "end": 931}, {"role": "Theme2", "text": "M-CSF receptor", "start": 956, "end": 970}, {"role": "Site2", "text": "promoter", "start": 971, "end": 979}]}, {"trigger": {"text": "bind", "start": 1067, "end": 1071}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1031, "end": 1035}, {"role": "Theme2", "text": "M-CSF receptor", "start": 1098, "end": 1112}, {"role": "Site2", "text": "promoter", "start": 1113, "end": 1121}]}, {"trigger": {"text": "bind", "start": 1067, "end": 1071}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1040, "end": 1044}, {"role": "Theme2", "text": "M-CSF receptor", "start": 1098, "end": 1112}, {"role": "Site2", "text": "promoter", "start": 1113, "end": 1121}]}, {"trigger": {"text": "binding", "start": 1226, "end": 1233}, "arguments": [{"role": "Site", "text": "specific site", "start": 1077, "end": 1090}, {"role": "Theme", "text": "M-CSF receptor", "start": 1098, "end": 1112}, {"role": "Theme2", "text": "PU.1", "start": 1221, "end": 1225}]}], "gene expression": [{"trigger": {"text": "expression", "start": 65, "end": 75}, "arguments": [{"role": "Theme", "text": "macrophage colony-stimulating factor receptor", "start": 83, "end": 128}]}, {"trigger": {"text": "expressed", "start": 192, "end": 201}, "arguments": [{"role": "Theme", "text": "macrophage colony-stimulating factor (M-CSF) receptor", "start": 135, "end": 188}]}], "negative regulation": [{"trigger": {"text": "eliminate", "start": 1211, "end": 1220}, "arguments": [{"role": "Theme", "text": "binding", "start": 1226, "end": 1233}]}, {"trigger": {"text": "decrease", "start": 1234, "end": 1242}, "arguments": [{"role": "Cause", "text": "eliminate", "start": 1211, "end": 1220}, {"role": "Theme", "text": "M-CSF receptor", "start": 1243, "end": 1257}, {"role": "Site", "text": "promoter", "start": 1258, "end": 1266}]}], "positive regulation": [{"trigger": {"text": "directs", "start": 41, "end": 48}, "arguments": [{"role": "Cause", "text": "PU.1", "start": 36, "end": 40}, {"role": "Theme", "text": "expression", "start": 65, "end": 75}]}, {"trigger": {"text": "activate", "start": 517, "end": 525}, "arguments": [{"role": "Theme", "text": "M-CSF receptor", "start": 530, "end": 544}]}, {"trigger": {"text": "activates", "start": 942, "end": 951}, "arguments": [{"role": "Cause", "text": "PU.1", "start": 927, "end": 931}, {"role": "Theme", "text": "M-CSF receptor", "start": 956, "end": 970}, {"role": "Site", "text": "promoter", "start": 971, "end": 979}]}, {"trigger": {"text": "transactivates", "start": 1339, "end": 1353}, "arguments": [{"role": "Cause", "text": "PU.1", "start": 1334, "end": 1338}, {"role": "Theme", "text": "M-CSF receptor", "start": 1358, "end": 1372}, {"role": "Site", "text": "promoter", "start": 1373, "end": 1381}]}], "regulation": [{"trigger": {"text": "from", "start": 231, "end": 235}, "arguments": [{"role": "Theme", "text": "expressed", "start": 192, "end": 201}]}]}}, "schema": []}
{"input": "Retinoic acid downmodulates erythroid differentiation and GATA1 expression in purified adult-progenitor culture. \nAll-trans retinoic acid (RA) is an important morphogen in vertebrate development, a normal constituent in human adult blood and is also involved in the control of cell growth and differentiation in acute promyelocytic leukemia. We have examined the effects of RA on normal hematopoiesis by using early hematopoietic progenitor cells (HPC) stringently purified from adult peripheral blood. In clonogenetic fetal calf serum-supplemented (FCS+) or -nonsupplemented (FCS-) culture treated with saturating levels of interleukin-3 (IL-3) granulocyte-macrophage colony-stimulating factor (GM-CSF) and erythropoietin (Ep) (combined with c-kit ligand in FCS(-)-culture conditions), RA induces a dramatic dose-dependent shift from erythroid to granulomonocytic colony formation, the latter colonies being essentially represented by granulocytic clones. This shift is apparently not caused by a recruitment phenomenon, because in FCS+ culture, the total number of colonies is not significantly modified by RA addition. In FCS- liquid-suspension culture supplemented with saturating Ep level and low-dose IL-3/GM-CSF, adult HPC undergo unilineage erythropoietic differentiation: Here again, treatment with high-dose RA induces a shift from the erythroid to granulocytic differentiation pathway. Studies on RA time-response or pulse treatment in semisolid or liquid culture show that early RA addition is most effective, thus indicating that early but not late HPC are sensitive to its action. We then analyzed the expression of the master GATA1 gene, which encodes a finger transcription factor required for normal erythroid development; addition of RA to HPC stimulated into unilineage erythropoietic differentiation in liquid culture caused a virtually complete inhibition of GATA1 mRNA induction. These results indicate that RA directly inhibits the erythroid differentiation program at the level of early adult HPC, and may lead to a shift from the erythroid to granulocytic differentiation pathway. This phenomenon is correlated with inhibition of GATA1 induction in the early stages of erythropoietic differentiation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 64, "end": 74}, "arguments": [{"role": "Theme", "text": "GATA1", "start": 58, "end": 63}]}, {"trigger": {"text": "expression", "start": 1616, "end": 1626}, "arguments": [{"role": "Theme", "text": "GATA1", "start": 1641, "end": 1646}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 1866, "end": 1876}, "arguments": [{"role": "Theme", "text": "induction", "start": 1891, "end": 1900}]}, {"trigger": {"text": "inhibition", "start": 2141, "end": 2151}, "arguments": [{"role": "Theme", "text": "induction", "start": 2161, "end": 2170}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 1891, "end": 1900}, "arguments": [{"role": "Theme", "text": "GATA1", "start": 1880, "end": 1885}]}, {"trigger": {"text": "induction", "start": 2161, "end": 2170}, "arguments": [{"role": "Theme", "text": "GATA1", "start": 2155, "end": 2160}]}]}}, "schema": []}
{"input": "Comparative analysis of NFAT (nuclear factor of activated T cells) complex in human T and B lymphocytes. \nNuclear factor of activated T cells (NFAT) is a transcriptional activator that binds to sequences in the interleukin-2 (IL-2) promoter and is thought to be largely responsible for the T cell-specific inducibility of IL-2 expression. Electrophoretic mobility shift assays (EMSA) showed that specific NFAT binding activity could also be induced in human B cells. The B cell NFAT complex, however, was not functional, since it failed to activate transcription from an NFAT-driven chloramphenicol acetyltransferase (CAT) construct. Competition with an AP-1 motif or with anti-Jun and anti-Fos antibodies abolished binding to the NFAT motif in both T and B cells, indicating that Jun and Fos are critical for NFAT complex formation in both cell types. Purified recombinant Jun and Fos proteins failed to bind directly to the NFAT motif. However, when combined with unstimulated B or T cell extracts, full-length, but not truncated, Jun/Fos heterodimers were able to form an NFAT complex, indicating the presence of a constitutively expressed nuclear factor(s) in B and T cells necessary for the formation of the NFAT complex in both cell types. An NFAT oligonucleotide carrying mutations in the 5' purine-rich part of the NFAT sequence failed to form a complex and to compete with the wild type motif for NFAT complex formation in both T and B cells. We therefore propose a model whereby a core NFAT complex consisting of Jun, Fos, and a constitutive nuclear factor is formed in both T and B cells, but an additional factor and/or post-translational modification of a factor, missing in B cells, might be required for transactivation by NFAT. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 185, "end": 190}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 211, "end": 224}, {"role": "Site", "text": "promoter", "start": 232, "end": 240}]}, {"trigger": {"text": "binding activity", "start": 410, "end": 426}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 211, "end": 224}, {"role": "Site", "text": "promoter", "start": 232, "end": 240}]}], "gene expression": [{"trigger": {"text": "expression", "start": 327, "end": 337}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 322, "end": 326}]}], "positive regulation": [{"trigger": {"text": "responsible", "start": 270, "end": 281}, "arguments": [{"role": "Theme", "text": "inducibility", "start": 306, "end": 318}]}, {"trigger": {"text": "inducibility", "start": 306, "end": 318}, "arguments": [{"role": "Theme", "text": "expression", "start": 327, "end": 337}]}, {"trigger": {"text": "induced", "start": 441, "end": 448}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 410, "end": 426}]}, {"trigger": {"text": "activate", "start": 540, "end": 548}, "arguments": [{"role": "Theme", "text": "transcription", "start": 549, "end": 562}]}], "transcription": [{"trigger": {"text": "transcription", "start": 549, "end": 562}, "arguments": [{"role": "Theme", "text": "chloramphenicol acetyltransferase", "start": 583, "end": 616}]}]}}, "schema": []}
{"input": "Differential autoregulation of glucocorticoid receptor expression in human T- and B-cell lines. \nRegulation of glucocorticoid receptor (GR) expression by its cognate ligand was examined in the glucocorticoid-sensitive human leukemic T-cell line 6TG1.1 and in the human B-cell line IM-9. In contrast to the decrease in GR mRNA seen in IM-9 cells after treatment with 1 microM dexamethasone for 16-18 h, treatment of 6TG1.1 cells resulted in an 8-fold increase in GR mRNA, as determined by Northern blot and RNase protection analysis, with a corresponding 3- to 4-fold increase in GR protein. Half-maximal induction of GR mRNA and protein in 6TG1.1 cells was observed between 10-100 nM dexamethasone, and inclusion of 1 microM RU 38486 completely blocked the effects of 100 nM dexamethasone, demonstrating that positive autoregulation of GR expression in 6TG1.1 cells is a receptor-mediated response. Positive autoregulation of GR expression was also observed in glucocorticoid-resistant CEM-C1 cells, which contain functional GR, but whose growth is unaffected by glucocorticoids. Thus, positive autoregulation is neither a consequence nor the sole cause of growth arrest. The degree of negative autoregulation in IM-9 cells and positive autoregulation in 6TG1.1 cells was unaffected by inhibition of protein synthesis with cycloheximide. Measurement of GR mRNA turnover in 6TG1.1 cells treated with actinomycin-D revealed a half-life of 2.5 h, which was unaffected by dexamethasone treatment. A similar half-life was determined in IM-9 cells and was also unaffected by steroid treatment. These results are consistent with the interpretation that glucocorticoid-mediated autoregulation of GR expression is a tissue-specific primary transcriptional response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 55, "end": 65}, "arguments": [{"role": "Theme", "text": "glucocorticoid receptor", "start": 31, "end": 54}]}, {"trigger": {"text": "expression", "start": 140, "end": 150}, "arguments": [{"role": "Theme", "text": "GR", "start": 136, "end": 138}]}, {"trigger": {"text": "expression", "start": 839, "end": 849}, "arguments": [{"role": "Theme", "text": "GR", "start": 836, "end": 838}]}, {"trigger": {"text": "expression", "start": 929, "end": 939}, "arguments": [{"role": "Theme", "text": "GR", "start": 926, "end": 928}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 306, "end": 314}, "arguments": [{"role": "Theme", "text": "GR", "start": 318, "end": 320}]}, {"trigger": {"text": "blocked", "start": 745, "end": 752}, "arguments": [{"role": "Theme", "text": "induction", "start": 604, "end": 613}]}, {"trigger": {"text": "negative autoregulation", "start": 1186, "end": 1209}, "arguments": [{"role": "Theme", "text": "expression", "start": 929, "end": 939}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 450, "end": 458}, "arguments": [{"role": "Theme", "text": "GR", "start": 462, "end": 464}]}, {"trigger": {"text": "increase", "start": 567, "end": 575}, "arguments": [{"role": "Theme", "text": "GR", "start": 579, "end": 581}]}, {"trigger": {"text": "positive autoregulation", "start": 809, "end": 832}, "arguments": [{"role": "Cause", "text": "GR", "start": 836, "end": 838}, {"role": "Theme", "text": "expression", "start": 839, "end": 849}]}, {"trigger": {"text": "consequence", "start": 1123, "end": 1134}, "arguments": [{"role": "Theme", "text": "Positive autoregulation", "start": 899, "end": 922}]}, {"trigger": {"text": "positive autoregulation", "start": 1228, "end": 1251}, "arguments": [{"role": "Theme", "text": "expression", "start": 929, "end": 939}]}], "regulation": [{"trigger": {"text": "autoregulation", "start": 13, "end": 27}, "arguments": [{"role": "Theme", "text": "expression", "start": 55, "end": 65}]}, {"trigger": {"text": "Regulation", "start": 97, "end": 107}, "arguments": [{"role": "Theme", "text": "expression", "start": 140, "end": 150}]}, {"trigger": {"text": "Positive autoregulation", "start": 899, "end": 922}, "arguments": [{"role": "Theme", "text": "expression", "start": 929, "end": 939}]}, {"trigger": {"text": "unaffected", "start": 1272, "end": 1282}, "arguments": [{"role": "Theme", "text": "negative autoregulation", "start": 1186, "end": 1209}]}, {"trigger": {"text": "unaffected", "start": 1272, "end": 1282}, "arguments": [{"role": "Theme", "text": "positive autoregulation", "start": 1228, "end": 1251}]}, {"trigger": {"text": "unaffected", "start": 1454, "end": 1464}, "arguments": [{"role": "Theme", "text": "GR", "start": 1353, "end": 1355}]}, {"trigger": {"text": "unaffected", "start": 1555, "end": 1565}, "arguments": [{"role": "Theme", "text": "GR", "start": 1353, "end": 1355}]}, {"trigger": {"text": "autoregulation", "start": 1670, "end": 1684}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 1731, "end": 1746}]}], "transcription": [{"trigger": {"text": "induction", "start": 604, "end": 613}, "arguments": [{"role": "Theme", "text": "GR", "start": 617, "end": 619}]}, {"trigger": {"text": "transcriptional", "start": 1731, "end": 1746}, "arguments": [{"role": "Theme", "text": "GR", "start": 1688, "end": 1690}]}]}}, "schema": []}
{"input": "Occurrence of a silencer of the interleukin-2 gene in naive but not in memory resting T helper lymphocytes. \nIn the immune system the first activation of a naive T cell by antigen is a key step in the shaping of the peripheral T cell specificity repertoire and maintenance of self-tolerance. In the present study, analysis of the interleukin-2 (IL-2) gene activation shows that naive human helper T cells (cord blood CD4+ T cells, adult CD4+CD45RO- T cells) regulate IL-2 transcription by a mechanism involving both a silencer and an activator acting on the purine-rich IL-2 promoter elements (NF-AT binding sites). By contrast, memory cells, either in vitro activated helper T cells reverting to a resting state, or CD4+ T (memory) clones, or CD4+CD45RO+ T cells isolated ex vivo, no longer have a silencer. Their IL-2 transcription seems to be controlled solely by the transition from inactive to active functional state of a positive transcription factor binding to these promoter elements as well as its cytoplasmic or nuclear location: in resting memory T cells the activator is located in the cytoplasm and is inactive, whereas in stimulated cells it is functional in promoting transcription and now resides in the nucleus. Thus, the regulation of the gene coding for the main T cell growth factor changes irreversibly after the first encounter of T cells with antigen. It is most likely that the presence of a silencer contributes to the more stringent activation requirements of naive CD4+ T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 958, "end": 965}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 570, "end": 574}, {"role": "Site", "text": "NF-AT binding sites", "start": 594, "end": 613}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 356, "end": 366}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 345, "end": 349}]}, {"trigger": {"text": "functional in promoting", "start": 1160, "end": 1183}, "arguments": [{"role": "Theme", "text": "transcription", "start": 820, "end": 833}]}], "regulation": [{"trigger": {"text": "regulate", "start": 458, "end": 466}, "arguments": [{"role": "Theme", "text": "transcription", "start": 472, "end": 485}, {"role": "Cause", "text": "acting", "start": 544, "end": 550}]}, {"trigger": {"text": "regulate", "start": 458, "end": 466}, "arguments": [{"role": "Theme", "text": "transcription", "start": 472, "end": 485}]}, {"trigger": {"text": "acting", "start": 544, "end": 550}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 570, "end": 574}, {"role": "Site", "text": "NF-AT binding sites", "start": 594, "end": 613}]}, {"trigger": {"text": "controlled", "start": 846, "end": 856}, "arguments": [{"role": "Theme", "text": "transcription", "start": 820, "end": 833}]}], "transcription": [{"trigger": {"text": "transcription", "start": 472, "end": 485}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 467, "end": 471}]}, {"trigger": {"text": "transcription", "start": 820, "end": 833}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 815, "end": 819}]}]}}, "schema": []}
{"input": "Stimulation of interleukin-1 alpha and interleukin-1 beta production in human monocytes by protein phosphatase 1 and 2A inhibitors. \nProtein phosphatases 1 and 2A are important in regulating cellular functions by controlling the phosphorylation state of their substrates. In human monocytes, the inhibitors of these phosphatases, okadaic acid and calyculin A, were found to increase the mRNA accumulation and cytokine production of interleukin-1 beta and interleukin-1 alpha. The increased mRNA accumulation was found to be primarily because of the increase in the transcription rate of the interleukin-1 genes. Stimulation of interleukin-1 gene transcription may be caused by the stimulation of transcription factor activities, including those of AP-1, by these protein phosphatase inhibitors. Okadaic acid increased the synthesis of the interleukin-1 beta precursor and mature forms and their secretion. This increased processing and secretion correlated with the stimulation of IL-1 beta convertase mRNA accumulation. The stimulation of interleukin-1 alpha production by okadaic acid was more modest than that of interleukin-1 beta. However, the phosphorylation of the precursor interleukin-1 alpha cytokine was increased. These results show that protein phosphatase 1 and 2A inhibitors exert multiple effects on cytokine production in human monocytes and suggest that these two phosphatases play important roles in regulating interleukin-1 production. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 58, "end": 68}, "arguments": [{"role": "Theme", "text": "interleukin-1 alpha", "start": 15, "end": 34}]}, {"trigger": {"text": "production", "start": 58, "end": 68}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 39, "end": 57}]}, {"trigger": {"text": "cytokine production", "start": 409, "end": 428}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 432, "end": 450}]}, {"trigger": {"text": "cytokine production", "start": 409, "end": 428}, "arguments": [{"role": "Theme", "text": "interleukin-1 alpha", "start": 455, "end": 474}]}, {"trigger": {"text": "production", "start": 1060, "end": 1070}, "arguments": [{"role": "Theme", "text": "interleukin-1 alpha", "start": 1040, "end": 1059}]}, {"trigger": {"text": "production", "start": 1060, "end": 1070}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 1116, "end": 1134}]}], "localization": [{"trigger": {"text": "secretion", "start": 895, "end": 904}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 839, "end": 857}]}], "negative regulation": [{"trigger": {"text": "Stimulation", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "production", "start": 58, "end": 68}, {"role": "Cause", "text": "2A", "start": 117, "end": 119}]}, {"trigger": {"text": "Stimulation", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "production", "start": 58, "end": 68}, {"role": "Cause", "text": "protein phosphatase 1", "start": 91, "end": 112}]}, {"trigger": {"text": "inhibitors", "start": 120, "end": 130}, "arguments": [{"role": "Theme", "text": "2A", "start": 117, "end": 119}]}, {"trigger": {"text": "inhibitors", "start": 120, "end": 130}, "arguments": [{"role": "Theme", "text": "protein phosphatase 1", "start": 91, "end": 112}]}, {"trigger": {"text": "inhibitors", "start": 296, "end": 306}, "arguments": [{"role": "Theme", "text": "Protein phosphatases 1", "start": 133, "end": 155}]}, {"trigger": {"text": "inhibitors", "start": 296, "end": 306}, "arguments": [{"role": "Theme", "text": "2A", "start": 160, "end": 162}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1149, "end": 1164}, "arguments": [{"role": "Theme", "text": "interleukin-1 alpha", "start": 1182, "end": 1201}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 374, "end": 382}, "arguments": [{"role": "Theme", "text": "mRNA accumulation", "start": 387, "end": 404}]}, {"trigger": {"text": "increase", "start": 374, "end": 382}, "arguments": [{"role": "Theme", "text": "cytokine production", "start": 409, "end": 428}]}, {"trigger": {"text": "mRNA accumulation", "start": 387, "end": 404}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 432, "end": 450}]}, {"trigger": {"text": "mRNA accumulation", "start": 387, "end": 404}, "arguments": [{"role": "Theme", "text": "interleukin-1 alpha", "start": 455, "end": 474}]}, {"trigger": {"text": "because of", "start": 534, "end": 544}, "arguments": [{"role": "Theme", "text": "increase", "start": 374, "end": 382}]}, {"trigger": {"text": "stimulation", "start": 681, "end": 692}, "arguments": [{"role": "Theme", "text": "AP-1", "start": 748, "end": 752}]}, {"trigger": {"text": "increased", "start": 808, "end": 817}, "arguments": [{"role": "Theme", "text": "secretion", "start": 895, "end": 904}]}, {"trigger": {"text": "stimulation", "start": 966, "end": 977}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1007, "end": 1019}]}, {"trigger": {"text": "accumulation", "start": 1007, "end": 1019}, "arguments": [{"role": "Theme", "text": "IL-1 beta convertase", "start": 981, "end": 1001}]}, {"trigger": {"text": "stimulation", "start": 1025, "end": 1036}, "arguments": [{"role": "Theme", "text": "production", "start": 1060, "end": 1070}]}, {"trigger": {"text": "increased", "start": 1215, "end": 1224}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1149, "end": 1164}]}]}}, "schema": []}
{"input": "Human CD3-CD16+ natural killer cells express the hGATA-3 T cell transcription factor and an unrearranged 2.3-kb TcR delta transcript. \nIn this study we analyzed the T cell receptor(TcR) delta transcripts expressed by CD3-CD16+ cells and we investigated whether these cells expressed the hGATA-3 T cell transcription factor and the recombination-activating gene (RAG)-1. Multiple TcR delta transcripts deriving from an unrearranged TcR delta gene were detected in both polyclonal and clonal CD3-CD16+ natural killer(NK) cell lines. Two unrearranged TcR delta transcripts had a size similar to that of the functional TcR delta mRNA (2.3 and 1.3 kb) found in TcR gamma/delta+ T lymphocytes. Sequence analysis of nine different 2.3-kb cDNA clones obtained from NK-derived polyA+ RNA confirmed that they corresponded to an unrearranged TcR delta gene. These cDNA were 2343 bp long and their transcription initiation site was located 814 bp upstream from the J delta 1 segment. The sequence located upstream of the J delta 1 segment corresponded to the previously reported germ-line sequence. The J delta 1 segment was correctly spliced to C delta; in addition the four C delta exons were found to be already assembled. Two polyadenylation sites were present in the fourth C delta exon. However, only that located at the 3' end appeared to be utilized in the 2.3-kb cDNA. The expression of hGATA-3, a T cell-specific factor known to be involved in the regulation of the transcription of TcR delta locus, was analyzed by Northern blot, in cultured NK cell population and clones (but not in freshly derived cell populations). All NK clones and cell lines studied were found to express hGATA-3-specific mRNA, suggesting that hGATA-3 may be involved in the regulation of the unrearranged TcR delta gene expression in NK cells. Finally, no transcription of the RAG-1 gene could be detected in all NK cell lines or clones analyzed. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "express", "start": 37, "end": 44}, "arguments": [{"role": "Theme", "text": "hGATA-3", "start": 49, "end": 56}]}, {"trigger": {"text": "expressed", "start": 273, "end": 282}, "arguments": [{"role": "Theme", "text": "hGATA-3", "start": 287, "end": 294}]}, {"trigger": {"text": "expressed", "start": 273, "end": 282}, "arguments": [{"role": "Theme", "text": "recombination-activating gene (RAG)-1", "start": 331, "end": 368}]}, {"trigger": {"text": "expression", "start": 1370, "end": 1380}, "arguments": [{"role": "Theme", "text": "hGATA-3", "start": 1384, "end": 1391}]}, {"trigger": {"text": "expression", "start": 1793, "end": 1803}, "arguments": [{"role": "Theme", "text": "TcR delta", "start": 1778, "end": 1787}]}], "regulation": [{"trigger": {"text": "involved in the regulation", "start": 1430, "end": 1456}, "arguments": [{"role": "Cause", "text": "hGATA-3", "start": 1384, "end": 1391}, {"role": "Theme", "text": "transcription", "start": 1464, "end": 1477}]}, {"trigger": {"text": "involved in the regulation", "start": 1731, "end": 1757}, "arguments": [{"role": "Cause", "text": "hGATA-3", "start": 1716, "end": 1723}, {"role": "Theme", "text": "expression", "start": 1793, "end": 1803}]}], "transcription": [{"trigger": {"text": "express", "start": 37, "end": 44}, "arguments": [{"role": "Theme", "text": "TcR delta", "start": 112, "end": 121}]}, {"trigger": {"text": "expressed", "start": 204, "end": 213}, "arguments": [{"role": "Theme", "text": "T cell receptor(TcR) delta", "start": 165, "end": 191}]}, {"trigger": {"text": "deriving", "start": 401, "end": 409}, "arguments": [{"role": "Theme", "text": "TcR delta", "start": 431, "end": 440}]}, {"trigger": {"text": "found", "start": 647, "end": 652}, "arguments": [{"role": "Theme", "text": "TcR delta", "start": 615, "end": 624}]}, {"trigger": {"text": "transcription", "start": 1464, "end": 1477}, "arguments": [{"role": "Theme", "text": "TcR delta", "start": 1481, "end": 1490}]}, {"trigger": {"text": "express", "start": 1669, "end": 1676}, "arguments": [{"role": "Theme", "text": "hGATA-3", "start": 1677, "end": 1684}]}, {"trigger": {"text": "transcription", "start": 1829, "end": 1842}, "arguments": [{"role": "Theme", "text": "RAG-1", "start": 1850, "end": 1855}]}]}}, "schema": []}
{"input": "Involvement of Alu sequences in the cell-specific regulation of transcription of the gamma chain of Fc and T cell receptors. \nThe Fc epsilon RI-gamma chains are expressed in a variety of hematopoietic cells where they play a critical role in signal transduction. They are part of the high affinity IgE receptor in mast cells, basophils, Langerhans cells, and possibly other cells; a component of the low affinity receptor for IgG (Fc gamma RIIIA or CD16) in natural killer cells and macrophages; and part of the T cell antigen receptor in subsets of T cells. Here we have investigated the transcriptional regulation of the gamma chain gene by analyzing the 2.5-kilobase sequence upstream of the transcription start site. This sequence contains a promoter specific to cells of hematopoietic lineage. However, the tissue specificity of this promoter is only partial because it is active in all of the hematopoietic cells tested here, regardless of whether they constitutively express Fc epsilon RI- gamma chain transcripts. We have identified two adjacent cis-acting regulatory elements, both of which are part of an Alu repeat. The first (-445/-366) is a positive element active in both basophils and T cells. The second (-365/-264) binds to nuclear factors, which appear to be different in basophils and T cells, and acts as a negative element in basophils and as a positive one in T cells. Thus, this Alu repeat (90% identical to Alu consensus sequences) has evolved to become both a positive and negative regulator. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 161, "end": 170}, "arguments": [{"role": "Theme", "text": "Fc epsilon RI-gamma chains", "start": 130, "end": 156}]}], "transcription": [{"trigger": {"text": "express", "start": 974, "end": 981}, "arguments": [{"role": "Theme", "text": "Fc epsilon RI- gamma chain", "start": 982, "end": 1008}]}]}}, "schema": []}
{"input": "Interleukin-3 expression by activated T cells involves an inducible, T-cell-specific factor and an octamer binding protein. \nInterleukin-3 (IL-3) is exclusively expressed by activated T and natural killer cells, a function that is tightly controlled both in a lineage-specific and in a stimulation-dependent manner. We have investigated the protein binding characteristics and functional importance of the ACT-1-activating region of the IL-3 promoter. This region binds an inducible, T-cell-specific factor over its 5' end, a site that is necessary for the expression of IL-3 in the absence of other upstream elements. Over its 3' end, it binds a factor that is ubiquitously and constitutively expressed. This factor is Oct-1 or an immunologically related octamer-binding protein, and it plays a role in coordinating the activity of several regulatory elements. These characteristics make the ACT-1 site analogous to the activating ARRE-1 site in the IL-2 promoter. Furthermore, and despite a lack of sequence homology, the promoters of IL-3 and IL-2 share an organizational pattern of regulatory elements that is likely to be important for the T-cell-specific expression of these genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 464, "end": 469}, "arguments": [{"role": "Site", "text": "ACT-1-activating region", "start": 406, "end": 429}, {"role": "Theme", "text": "IL-3", "start": 437, "end": 441}]}, {"trigger": {"text": "binds", "start": 639, "end": 644}, "arguments": [{"role": "Site", "text": "ACT-1-activating region", "start": 406, "end": 429}, {"role": "Theme", "text": "IL-3", "start": 437, "end": 441}]}], "gene expression": [{"trigger": {"text": "expression", "start": 14, "end": 24}, "arguments": [{"role": "Theme", "text": "Interleukin-3", "start": 0, "end": 13}]}, {"trigger": {"text": "expressed", "start": 161, "end": 170}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 140, "end": 144}]}, {"trigger": {"text": "expression", "start": 557, "end": 567}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 571, "end": 575}]}, {"trigger": {"text": "expression", "start": 1161, "end": 1171}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 1037, "end": 1041}]}, {"trigger": {"text": "expression", "start": 1161, "end": 1171}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1046, "end": 1050}]}], "positive regulation": [{"trigger": {"text": "necessary", "start": 539, "end": 548}, "arguments": [{"role": "Theme", "text": "expression", "start": 557, "end": 567}]}, {"trigger": {"text": "activating", "start": 921, "end": 931}, "arguments": [{"role": "Site", "text": "ARRE-1 site", "start": 932, "end": 943}, {"role": "Theme", "text": "IL-2", "start": 951, "end": 955}]}, {"trigger": {"text": "important", "start": 1127, "end": 1136}, "arguments": [{"role": "Theme", "text": "expression", "start": 1161, "end": 1171}]}], "regulation": [{"trigger": {"text": "controlled", "start": 239, "end": 249}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 140, "end": 144}]}]}}, "schema": []}
{"input": "ras protein activity is essential for T-cell antigen receptor signal transduction. \nIn a Jurkat cell model of T-cell activation an interleukin-2 promoter/reporter gene construct was activated by antigen receptor agonism in combination with the lymphokine interleukin-1. Antigen receptor signals could be mimicked by suboptimal activation of protein kinase C (PKC) with phorbol esters in combination with calcium mobilization by an ionophore. In cotransfection experiments, oncogenic rats obviated the need for PKC stimulation but did not replace either the calcium signal or interleukin-1. Activated ras expression also replaced the requirement for PKC stimulation in activation of the T-cell transcription factor NF-AT. A dominant inhibitory ras mutant specifically blocked antigen receptor agonism, indicating that ras activity is required for antigen receptor signaling. In addition, an inhibitor of PKC blocked both activated ras and phorbol ester stimulation, suggesting a role for ras upstream of PKC. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Characterization of the nuclear and cytoplasmic components of the lymphoid-specific nuclear factor of activated T cells (NF-AT) complex. \nThe lymphoid-specific transcription complex, NF-AT, is involved in early gene activation in T cells and is assembled from a pre-existing, T cell restricted cytoplasmic factor and an inducible ubiquitous nuclear component within 30 min after activation through the antigen receptor. Recent studies have implicated the family of AP1 factors as components of the murine NF-AT complex. Evidence is provided here that the nuclear component of human NF-AT contains the phorbol ester-inducible transcription factor AP1 (Jun/Fos). We further characterize which AP1 family members can assume this role. Antisera to Fos inhibits NF-AT DNA binding as does an oligonucleotide containing a binding site for AP1. Constitutive expression in vivo of Fos, and to a lesser extent Fra-1, eliminates the requirement for phorbol 12-myristate 13-acetate (PMA) stimulation, leaving NF-AT-directed transcription responsive to calcium ionophore alone. Overexpression of cJun or JunD, but not JunB, also eliminates the requirement for PMA, indicating that many but not all Jun- and Fos-related proteins functionally activate NF-AT-dependent transcription in the presence of the cytoplasmic component. NF-AT DNA binding can be reconstituted in vitro using semi-purified AP1 proteins mixed with cytosol from T lymphocytes. Fos proteins are not needed for this reconstitution, and although JunB is not functional, it can participate in the NF-AT DNA binding complex. Finally, we have partially purified the cytoplasmic component of NF-AT and show by elution and renaturation from SDS-polyacrylamide gel electrophoresis gels that it has a molecular mass between 94 and 116 kDa and may have multiple differentially modified forms. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 850, "end": 860}, "arguments": [{"role": "Theme", "text": "Fra-1", "start": 900, "end": 905}]}, {"trigger": {"text": "Overexpression", "start": 1065, "end": 1079}, "arguments": [{"role": "Theme", "text": "JunB", "start": 1105, "end": 1109}]}, {"trigger": {"text": "expression", "start": 1069, "end": 1079}, "arguments": [{"role": "Theme", "text": "cJun", "start": 1083, "end": 1087}]}, {"trigger": {"text": "expression", "start": 1069, "end": 1079}, "arguments": [{"role": "Theme", "text": "JunD", "start": 1091, "end": 1095}]}], "positive regulation": [{"trigger": {"text": "Overexpression", "start": 1065, "end": 1079}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 1065, "end": 1079}]}, {"trigger": {"text": "Overexpression", "start": 1065, "end": 1079}, "arguments": [{"role": "Theme", "text": "expression", "start": 1069, "end": 1079}]}]}}, "schema": []}
{"input": "Protease treatment of nuclear extracts distinguishes between class II MHC X1 box DNA-binding proteins in wild-type and class II-deficient B cells. \nThe X box region is critical for directing the expression of class II major histocompatibility complex genes in B lymphocytes. Although several class II promoter-specific DNA binding factors have been described, only the X box region factor, RFX, shows a genetic correlation with class II expression, being deficient in some B cell lines derived from patients with class II-deficient congenital immunodeficiency. To further evaluate the role of X box DNA-binding proteins in class II gene expression, the role of the X box region was examined in both class II-positive and -negative lymphoid cells. In addition to the wild-type B cell line Raji, two class II transcriptional mutant cell lines, SJO and RJ2.2.5, and Jurkat, a class II negative T cell line, were examined. In contrast to wild-type B cells, neither of the class II mutant cell lines could use the X box region to direct the expression of a transiently transfected reporter gene, indicating that the X box-dependent transcriptional pathway is defective in these cells. The binding activity of the X1 box DNA-binding protein RFX was examined and found to be present in wild-type B cells and the mutant RJ2.2.5 but was absent in SJO and Jurkat. However, other X1 box-specific activities were detected in all these cell lines. To determine whether these different X1 box activities represented distinct DNA binding proteins or multimeric forms of the same factor(s), protease treatment of the crude nuclear extracts followed by DNA-binding assays were carried out and demonstrated that B cell extracts contain at least two X1-specific factors. One of these cleaved products (band 1 pk) correlates with RFX activity. A similar comparison with protease-treated extracts prepared from Jurkat cells demonstrated the presence of the band 1pk activity despite an absence of the native RFX activity. In contrast, protease treatment and analysis of SJO extracts showed no detectable levels of the band 1pk activity. These results demonstrate that multiple X1 box-specific DNA-binding activities exist in all lymphoid cells, but the presence of an actively binding RFX species correlates with class II transcription. ", "output": {"json_structures": {}}, "schema": []}
{"input": "The human prointerleukin 1 beta gene requires DNA sequences both proximal and distal to the transcription start site for tissue-specific induction. \nIn these studies, we have identified DNA sequences and specific protein interactions necessary for transcriptional regulation of the human prointerleukin 1 beta (proIL-1 beta) gene. A cell-type-independent lipopolysaccharide (LPS)-responsive enhancer element located between -3757 and -2729 bp upstream from the transcription start site (cap site) consisted of at least six discrete subregions which were essential to the maximal induction by LPS in transfected monocytes. The enhancer also appeared to mediate phorbol myristate acetate induction in monocytes and IL-1 responsiveness in fibroblasts. Deletion and base substitution mutations along with DNA binding studies demonstrated that the enhancer contained a minimum of three functional protein binding sequences, two of which appeared to be important for gene induction. One of the essential proteins which bound to the enhancer was similar or identical to members of the C/EBP family of transcription factors required for both IL-1- and LPS-specific induction of the IL-6 gene (i.e., the NF-IL6 proteins). When ligated to the proIL-1 beta cap site-proximal region (located between -131 to +12), both the proIL-1 beta and the simian virus 40 enhancer elements functioned more efficiently in monocytes than in HeLa cells, which are not normally competent for IL-1 beta expression. When ligated to the murine c-fos promoter, however, the proIL-1 beta enhancer was inducible in phorbol myristate acetate-stimulated HeLa cells, suggesting the existence of a proIL-1 beta promoter-proximal requirement for tissue specificity. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "induction", "start": 966, "end": 975}, "arguments": [{"role": "Theme", "text": "proIL-1 beta", "start": 311, "end": 323}]}, {"trigger": {"text": "expression", "start": 1474, "end": 1484}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1464, "end": 1473}]}], "positive regulation": [{"trigger": {"text": "requires", "start": 37, "end": 45}, "arguments": [{"role": "Theme", "text": "induction", "start": 137, "end": 146}]}, {"trigger": {"text": "induction", "start": 137, "end": 146}, "arguments": [{"role": "Theme", "text": "human prointerleukin 1 beta", "start": 4, "end": 31}]}, {"trigger": {"text": "necessary", "start": 234, "end": 243}, "arguments": [{"role": "Theme", "text": "transcriptional regulation", "start": 248, "end": 274}]}, {"trigger": {"text": "important", "start": 947, "end": 956}, "arguments": [{"role": "Theme", "text": "induction", "start": 966, "end": 975}]}, {"trigger": {"text": "required", "start": 1116, "end": 1124}, "arguments": [{"role": "Theme", "text": "induction", "start": 1157, "end": 1166}, {"role": "Cause", "text": "NF-IL6", "start": 1195, "end": 1201}]}, {"trigger": {"text": "required", "start": 1116, "end": 1124}, "arguments": [{"role": "Theme", "text": "induction", "start": 1157, "end": 1166}]}, {"trigger": {"text": "induction", "start": 1157, "end": 1166}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1174, "end": 1178}]}, {"trigger": {"text": "When", "start": 1486, "end": 1490}, "arguments": [{"role": "Theme", "text": "inducible", "start": 1568, "end": 1577}]}, {"trigger": {"text": "inducible", "start": 1568, "end": 1577}, "arguments": [{"role": "Theme", "text": "proIL-1 beta", "start": 1542, "end": 1554}, {"role": "Site", "text": "enhancer", "start": 1555, "end": 1563}]}, {"trigger": {"text": "requirement", "start": 1691, "end": 1702}, "arguments": [{"role": "Cause", "text": "proIL-1 beta", "start": 1542, "end": 1554}, {"role": "CSite", "text": "enhancer", "start": 1555, "end": 1563}, {"role": "Theme", "text": "proIL-1 beta", "start": 1660, "end": 1672}, {"role": "Site", "text": "promoter", "start": 1673, "end": 1681}]}], "regulation": [{"trigger": {"text": "transcriptional regulation", "start": 248, "end": 274}, "arguments": [{"role": "Theme", "text": "proIL-1 beta", "start": 311, "end": 323}]}]}}, "schema": []}
{"input": "Expression of PILOT, a putative transcription factor, requires two signals and is cyclosporin A sensitive in T cells. \nFew known genes (IL-2, members of the IL-8 family, interferon-gamma) are induced in T cells only through the combined effect of phorbol myristic acetate (PMA) and a Ca(2+)-ionophore, and expression of only these genes can be fully suppressed by Cyclosporin A (CyA). We have identified a putative transcription factor, designated PILOT, with an identical dual signal requirement for expression. Induction of the PILOT gene is detectable in human T cells 20 min following activation in the presence of cycloheximide and is fully suppressed by CyA. The PILOT protein has a calculated M(r) of 42.6 kDa and contains three zinc fingers of the C2H2-type at the carboxyl-terminus which are highly homologous to the zinc finger regions of the transcription factors EGR1, EGR2, and pAT 133. In contrast to T cells, in fibroblasts PILOT gene expression requires only one signal (PMA) and is not affected by CyA. This observation directly demonstrates the existence of a Ca2+ signal-dependent regulatory element obligatory for expression of some genes in T cells but not in fibroblasts. This differential expression model will be valuable in the dissection of the dual signal pathway in T cells and the effects of CyA upon it. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "PILOT", "start": 14, "end": 19}]}, {"trigger": {"text": "expression", "start": 306, "end": 316}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 136, "end": 140}]}, {"trigger": {"text": "expression", "start": 306, "end": 316}, "arguments": [{"role": "Theme", "text": "interferon-gamma", "start": 170, "end": 186}]}, {"trigger": {"text": "expression", "start": 501, "end": 511}, "arguments": [{"role": "Theme", "text": "PILOT", "start": 448, "end": 453}]}, {"trigger": {"text": "expression", "start": 950, "end": 960}, "arguments": [{"role": "Theme", "text": "PILOT", "start": 939, "end": 944}]}], "negative regulation": [{"trigger": {"text": "suppressed", "start": 350, "end": 360}, "arguments": [{"role": "Theme", "text": "expression", "start": 306, "end": 316}]}, {"trigger": {"text": "suppressed", "start": 646, "end": 656}, "arguments": [{"role": "Theme", "text": "Induction", "start": 513, "end": 522}]}], "positive regulation": [{"trigger": {"text": "requires", "start": 54, "end": 62}, "arguments": [{"role": "Theme", "text": "Expression", "start": 0, "end": 10}]}, {"trigger": {"text": "induced", "start": 192, "end": 199}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 136, "end": 140}]}, {"trigger": {"text": "induced", "start": 192, "end": 199}, "arguments": [{"role": "Theme", "text": "interferon-gamma", "start": 170, "end": 186}]}, {"trigger": {"text": "requirement", "start": 485, "end": 496}, "arguments": [{"role": "Theme", "text": "expression", "start": 501, "end": 511}]}, {"trigger": {"text": "Induction", "start": 513, "end": 522}, "arguments": [{"role": "Theme", "text": "PILOT", "start": 530, "end": 535}]}, {"trigger": {"text": "requires", "start": 961, "end": 969}, "arguments": [{"role": "Theme", "text": "expression", "start": 950, "end": 960}]}], "regulation": [{"trigger": {"text": "affected", "start": 1003, "end": 1011}, "arguments": [{"role": "Theme", "text": "expression", "start": 950, "end": 960}]}]}}, "schema": []}
{"input": "Suppression of a cellular differentiation program by phorbol esters coincides with inhibition of binding of a cell-specific transcription factor (NF-E2) to an enhancer element required for expression of an erythroid-specific gene. \nInduction by hemin increases, while induction with 12-O-tetradecanoylphorbol-13-acetate (TPA) represses, erythroid-specific gene expression in the human cell line K562. We analyzed the effects of hemin or TPA induction on the binding and activity of transcription factors at a regulatory element found within the transcriptional regulatory sequences of many erythroid-specific genes. TPA induction increases the binding of ubiquitous AP-1 factors to this element. TPA induction inhibits the binding of the lineage limited transcription factor NF-E2 to this transcriptional control element. Hemin induction of K562 cells does not facilitate the binding of NF-E2 to its recognition site. Hemin induction appears to nonspecifically increase the expression of transiently transfected genes in K562 cells. Beyond this nonspecific increase in gene expression, hemin induction acts to increase the activity of the lineage limited transcription factor NF-E2. The divergent effects of hemin and TPA on gene expression in K562 cells are mediated, in part, by their contrasting effects on the transcription factor NF-E2. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Transcriptional regulation of the pyruvate kinase erythroid-specific promoter. \nMammal pyruvate kinases are encoded by two genes. The L gene produces the erythroid (R-PK) or the hepatic (L-PK) isozymes by the alternative use of two promoters. We report the characterization of the cis- and trans-acting elements involved in the tissue-specific activity of the L gene erythroid promoter. A R-PK DNA fragment extending from -870 to +54 relative to the cap site confers erythroid specificity to a reporter gene. Within this region, we define a minimal promoter (-62 to +54) that displays erythroid-specific activity and contains two DNA binding sites. One, located at -50, binds members of the CCACC/Sp1 family and the other, located at -20, binds the erythroid factor GATA-1. Although the -20 GATA binding site (AGATAA) is also a potential TFIID binding site, it does not bind TFIID. Furthermore, the substitution of this GATA binding site by a canonical TFIID binding site suppresses the promoter activity. Mutations and deletions of both sites indicate that only the association of CCACC/Sp1 and GATA binding sites can drive efficient and tissue-specific expression of this R-PK minimal promoter. Finally, by co-transfection experiments, we study the elements involved in the hGATA-1 transactivation of the R-PK promoter in HeLa cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 739, "end": 744}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 766, "end": 772}]}], "gene expression": [{"trigger": {"text": "produces", "start": 141, "end": 149}, "arguments": [{"role": "Theme", "text": "L-PK", "start": 187, "end": 191}]}, {"trigger": {"text": "expression", "start": 1155, "end": 1165}, "arguments": [{"role": "Theme", "text": "R-PK", "start": 1174, "end": 1178}]}], "positive regulation": [{"trigger": {"text": "by the alternative use of", "start": 202, "end": 227}, "arguments": [{"role": "Theme", "text": "produces", "start": 141, "end": 149}]}, {"trigger": {"text": "activity", "start": 344, "end": 352}, "arguments": [{"role": "Theme", "text": "L", "start": 360, "end": 361}, {"role": "Site", "text": "erythroid promoter", "start": 367, "end": 385}]}, {"trigger": {"text": "drive", "start": 1119, "end": 1124}, "arguments": [{"role": "Theme", "text": "expression", "start": 1155, "end": 1165}]}, {"trigger": {"text": "transactivation", "start": 1284, "end": 1299}, "arguments": [{"role": "Cause", "text": "hGATA-1", "start": 1276, "end": 1283}, {"role": "Theme", "text": "R-PK", "start": 1307, "end": 1311}, {"role": "Site", "text": "promoter", "start": 1312, "end": 1320}]}]}}, "schema": []}
{"input": "Transcriptional regulation of interleukin 3 (IL3) in primary human T lymphocytes. Role of AP-1- and octamer-binding proteins in control of IL3 gene expression. \nWe have investigated the molecular and biochemical basis for activation of interleukin 3 (IL3) gene expression in primary human T lymphocytes following CD3 and CD2 receptor stimulation or activation by phytohemagglutinin plus phorbol 12-myristate 13-acetate. Using transfection and reporter gene assays specifically designed for primary T lymphocytes in conjunction with gel retardation assays, Western blot analyses and UV cross-linking studies, we found that c-Jun, c-Fos, and octamer-binding proteins play a major role in transcriptional activation of the IL3 gene via their interaction with two specific regions contained within the IL3 5'-flanking sequence. Additionally, the region between bases -107 and -59 of the IL3 promoter containing putative AP-2 and Sp1 binding motifs appears necessary for basal level expression of the IL3 gene. The data also indicate that CD2 receptor activation and phytohemagglutinin plus phorbol 12-myristate 13-acetate stimulation augment T cell IL3 gene expression through the same cis- and trans-activating signals. These results should contribute to a better understanding of the regulation of IL3 gene expression in human T lymphocytes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 739, "end": 750}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 622, "end": 627}]}, {"trigger": {"text": "interaction", "start": 739, "end": 750}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 629, "end": 634}]}], "gene expression": [{"trigger": {"text": "expression", "start": 148, "end": 158}, "arguments": [{"role": "Theme", "text": "IL3", "start": 139, "end": 142}]}, {"trigger": {"text": "expression", "start": 261, "end": 271}, "arguments": [{"role": "Theme", "text": "IL3", "start": 251, "end": 254}]}, {"trigger": {"text": "expression", "start": 978, "end": 988}, "arguments": [{"role": "Theme", "text": "IL3", "start": 996, "end": 999}]}, {"trigger": {"text": "expression", "start": 1154, "end": 1164}, "arguments": [{"role": "Theme", "text": "IL3", "start": 1145, "end": 1148}]}, {"trigger": {"text": "expression", "start": 1305, "end": 1315}, "arguments": [{"role": "Theme", "text": "IL3", "start": 1296, "end": 1299}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 222, "end": 232}, "arguments": [{"role": "Theme", "text": "expression", "start": 261, "end": 271}, {"role": "Cause", "text": "stimulation", "start": 334, "end": 345}]}, {"trigger": {"text": "activation", "start": 222, "end": 232}, "arguments": [{"role": "Theme", "text": "expression", "start": 261, "end": 271}, {"role": "Cause", "text": "activation", "start": 349, "end": 359}]}, {"trigger": {"text": "activation", "start": 222, "end": 232}, "arguments": [{"role": "Theme", "text": "expression", "start": 261, "end": 271}]}, {"trigger": {"text": "stimulation", "start": 334, "end": 345}, "arguments": [{"role": "Theme", "text": "CD2", "start": 321, "end": 324}]}, {"trigger": {"text": "activation", "start": 349, "end": 359}, "arguments": [{"role": "Theme", "text": "phytohemagglutinin", "start": 363, "end": 381}]}, {"trigger": {"text": "play a major role", "start": 665, "end": 682}, "arguments": [{"role": "Theme", "text": "activation", "start": 702, "end": 712}, {"role": "Cause", "text": "interaction", "start": 739, "end": 750}]}, {"trigger": {"text": "play a major role", "start": 665, "end": 682}, "arguments": [{"role": "Theme", "text": "activation", "start": 702, "end": 712}]}, {"trigger": {"text": "activation", "start": 702, "end": 712}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 686, "end": 701}]}, {"trigger": {"text": "necessary", "start": 952, "end": 961}, "arguments": [{"role": "Theme", "text": "expression", "start": 978, "end": 988}]}, {"trigger": {"text": "activation", "start": 1047, "end": 1057}, "arguments": [{"role": "Theme", "text": "CD2", "start": 1034, "end": 1037}]}, {"trigger": {"text": "augment", "start": 1130, "end": 1137}, "arguments": [{"role": "Theme", "text": "expression", "start": 1154, "end": 1164}]}], "regulation": [{"trigger": {"text": "regulation", "start": 16, "end": 26}, "arguments": [{"role": "Theme", "text": "Transcriptional", "start": 0, "end": 15}]}, {"trigger": {"text": "Role", "start": 82, "end": 86}, "arguments": [{"role": "Theme", "text": "control", "start": 128, "end": 135}]}, {"trigger": {"text": "control", "start": 128, "end": 135}, "arguments": [{"role": "Theme", "text": "expression", "start": 148, "end": 158}]}, {"trigger": {"text": "regulation", "start": 1282, "end": 1292}, "arguments": [{"role": "Theme", "text": "expression", "start": 1305, "end": 1315}]}], "transcription": [{"trigger": {"text": "Transcriptional", "start": 0, "end": 15}, "arguments": [{"role": "Theme", "text": "IL3", "start": 45, "end": 48}]}, {"trigger": {"text": "transcriptional", "start": 686, "end": 701}, "arguments": [{"role": "Theme", "text": "IL3", "start": 720, "end": 723}]}]}}, "schema": []}
{"input": "Transcriptional activation of human zeta 2 globin promoter by the alpha globin regulatory element (HS-40): functional role of specific nuclear factor-DNA complexes. \nWe studied the functional interaction between human embryonic zeta 2 globin promoter and the alpha globin regulatory element (HS-40) located 40 kb upstream of the zeta 2 globin gene. It was shown by transient expression assay that HS-40 behaved as an authentic enhancer for high-level zeta 2 globin promoter activity in K562 cells, an erythroid cell line of embryonic and/or fetal origin. Although sequences located between -559 and -88 of the zeta 2 globin gene were dispensable for its expression on enhancerless plasmids, they were required for the HS-40 enhancer-mediated activity of the zeta 2 globin promoter. Site-directed mutagenesis demonstrated that this HS-40 enhancer-zeta 2 globin promoter interaction is mediated by the two GATA-1 factor binding motifs located at -230 and -104, respectively. The functional domains of HS-40 were also mapped. Bal 31 deletion mapping data suggested that one GATA-1 motif, one GT motif, and two NF-E2/AP1 motifs together formed the functional core of HS-40 in the erythroid-specific activation of the zeta 2 globin promoter. Site-directed mutagenesis further demonstrated that the enhancer function of one of the two NF-E2/AP1 motifs of HS-40 is mediated through its binding to NF-E2 but not AP1 transcription factor. Finally, we did genomic footprinting of the HS-40 enhancer region in K562 cells, adult nucleated erythroblasts, and different nonerythroid cells. All sequence motifs within the functional core of HS-40, as mapped by transient expression analysis, appeared to bind a nuclear factor(s) in living K562 cells but not in nonerythroid cells. On the other hand, only one of the apparently nonfunctional sequence motifs was bound with factors in vivo. In comparison to K562, nucleated erythroblasts from adult human bone marrow exhibited a similar but nonidentical pattern of nuclear factor binding in vivo at the HS-40 region. These data suggest that transcriptional activation of human embryonic zeta 2 globin gene and the fetal/adult alpha globin genes is mediated by erythroid cell-specific and developmental stage-specific nuclear factor-DNA complexes which form at the enhancer (HS-40) and the globin promoters. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 654, "end": 664}, "arguments": [{"role": "Theme", "text": "zeta 2 globin", "start": 610, "end": 623}]}], "positive regulation": [{"trigger": {"text": "Transcriptional activation", "start": 0, "end": 26}, "arguments": [{"role": "Theme", "text": "zeta 2 globin", "start": 36, "end": 49}, {"role": "Site", "text": "promoter", "start": 50, "end": 58}]}, {"trigger": {"text": "behaved as an authentic enhancer", "start": 403, "end": 435}, "arguments": [{"role": "Theme", "text": "zeta 2 globin", "start": 451, "end": 464}, {"role": "Site", "text": "promoter", "start": 465, "end": 473}]}, {"trigger": {"text": "dispensable", "start": 634, "end": 645}, "arguments": [{"role": "Theme", "text": "expression", "start": 654, "end": 664}]}, {"trigger": {"text": "required", "start": 701, "end": 709}, "arguments": [{"role": "Theme", "text": "mediated", "start": 733, "end": 741}]}, {"trigger": {"text": "mediated", "start": 733, "end": 741}, "arguments": [{"role": "Theme", "text": "activity", "start": 742, "end": 750}]}, {"trigger": {"text": "activation", "start": 1195, "end": 1205}, "arguments": [{"role": "Theme", "text": "zeta 2 globin", "start": 1213, "end": 1226}, {"role": "Site", "text": "promoter", "start": 1227, "end": 1235}]}, {"trigger": {"text": "activation", "start": 2090, "end": 2100}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 2074, "end": 2089}]}, {"trigger": {"text": "mediated", "start": 2181, "end": 2189}, "arguments": [{"role": "Theme", "text": "activation", "start": 2090, "end": 2100}]}], "regulation": [{"trigger": {"text": "activity", "start": 742, "end": 750}, "arguments": [{"role": "Theme", "text": "zeta 2 globin", "start": 758, "end": 771}, {"role": "Site", "text": "promoter", "start": 772, "end": 780}]}, {"trigger": {"text": "formed the functional core", "start": 1133, "end": 1159}, "arguments": [{"role": "Theme", "text": "activation", "start": 1195, "end": 1205}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 2074, "end": 2089}, "arguments": [{"role": "Theme", "text": "zeta 2 globin", "start": 2120, "end": 2133}]}, {"trigger": {"text": "transcriptional", "start": 2074, "end": 2089}, "arguments": [{"role": "Theme", "text": "alpha globin", "start": 2159, "end": 2171}]}]}}, "schema": []}
{"input": "Costimulation of peripheral blood T cell activation by human endothelial cells. Enhanced IL-2 transcription correlates with increased c-fos synthesis and increased Fos content of AP-1. \nEndothelial cells (EC) act as APC for resting PBL in vitro, and may have important roles in vivo in the pathogenesis of allograft rejection and delayed hypersensitivity. We previously reported that human umbilical vein EC provide costimulatory signals to PHA-stimulated PBL via CD2:lymphocyte function-associated Ag-3 and an unidentified ligand pair, resulting in a three- to eight-fold enhancement of IL-2 production. The physiologic relevance of this increase was demonstrated by the proliferative advantage provided by EC to PBL suboptimally stimulated with mAb OKT3. We now report that EC costimulation causes increased levels of IL-2 mRNA as a result of increased IL-2 transcription in PBL. We therefore examined the effects of EC on T cell nuclear factors known to regulate IL-2 transcription, including c-jun and c-fos-two components of the transcription factor AP-1, NFAT, and others. PBL constitutively express c-jun transcripts, and the level of c-jun mRNA is not altered by PHA activation in the absence or presence of EC. In contrast, c-fos mRNA is absent from resting T cells and is induced on PHA activation. EC alone do not induce c-fos mRNA but augment the level of c-fos mRNA in PHA-activated T cells by 3- to 10-fold. This effect is largely independent of the CD2:lymphocyte function-associated Ag-3 pathway. Gel-shift analysis reveals the constitutive presence of nuclear factors in resting PBL that bind to the proximal AP-1 site of the IL-2 promoter and that contain immunoreactive c-Jun but not c-Fos protein. In contrast, AP-1 from PHA-activated cells contains c-Jun and low levels of c-Fos. Strikingly, costimulation with EC results in a dramatic increase (up to 15-fold) in the c-Fos content of AP-1. Levels of other nuclear factors involved in IL-2 regulation were not altered by EC, although NFAT-DNA complexes migrated at a slightly different mobility. In summary, our data suggest that changes in the composition of transcription factor AP-1 is a key molecular mechanism for increasing IL-2 transcription and may underlie the phenomenon of costimulation by EC. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "content of AP-1", "start": 168, "end": 183}, "arguments": [{"role": "Theme", "text": "lymphocyte function-associated Ag-3", "start": 468, "end": 503}]}, {"trigger": {"text": ":", "start": 467, "end": 468}, "arguments": [{"role": "Theme", "text": "CD2", "start": 464, "end": 467}, {"role": "Theme2", "text": "lymphocyte function-associated Ag-3", "start": 468, "end": 503}]}, {"trigger": {"text": "pair", "start": 531, "end": 535}, "arguments": [{"role": "Theme", "text": "CD2", "start": 464, "end": 467}]}, {"trigger": {"text": "bind", "start": 1605, "end": 1609}, "arguments": [{"role": "Site", "text": "proximal AP-1 site", "start": 1617, "end": 1635}, {"role": "Theme", "text": "IL-2", "start": 1643, "end": 1647}]}], "gene expression": [{"trigger": {"text": "production", "start": 593, "end": 603}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 588, "end": 592}]}, {"trigger": {"text": "express", "start": 1098, "end": 1105}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1106, "end": 1111}]}], "positive regulation": [{"trigger": {"text": "Enhanced", "start": 80, "end": 88}, "arguments": [{"role": "Theme", "text": "transcription", "start": 94, "end": 107}]}, {"trigger": {"text": "provide costimulatory signals", "start": 408, "end": 437}, "arguments": [{"role": "Theme", "text": ":", "start": 467, "end": 468}]}, {"trigger": {"text": "provide costimulatory signals", "start": 408, "end": 437}, "arguments": [{"role": "Theme", "text": "pair", "start": 531, "end": 535}]}, {"trigger": {"text": "enhancement", "start": 573, "end": 584}, "arguments": [{"role": "Theme", "text": "production", "start": 593, "end": 603}]}, {"trigger": {"text": "causes", "start": 793, "end": 799}, "arguments": [{"role": "Theme", "text": "increased", "start": 800, "end": 809}, {"role": "Cause", "text": "increased", "start": 845, "end": 854}]}, {"trigger": {"text": "increased", "start": 800, "end": 809}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 820, "end": 824}]}, {"trigger": {"text": "increased", "start": 845, "end": 854}, "arguments": [{"role": "Theme", "text": "transcription", "start": 860, "end": 873}]}, {"trigger": {"text": "induced", "start": 1282, "end": 1289}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1233, "end": 1238}]}, {"trigger": {"text": "induce", "start": 1325, "end": 1331}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1332, "end": 1337}]}, {"trigger": {"text": "augment", "start": 1347, "end": 1354}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1368, "end": 1373}]}, {"trigger": {"text": "increasing", "start": 2190, "end": 2200}, "arguments": [{"role": "Theme", "text": "transcription", "start": 2206, "end": 2219}]}], "regulation": [{"trigger": {"text": "effects", "start": 908, "end": 915}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1006, "end": 1011}]}, {"trigger": {"text": "effects", "start": 908, "end": 915}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 996, "end": 1001}]}, {"trigger": {"text": "regulate", "start": 957, "end": 965}, "arguments": [{"role": "Theme", "text": "transcription", "start": 971, "end": 984}, {"role": "Cause", "text": "c-fos", "start": 1006, "end": 1011}]}, {"trigger": {"text": "regulate", "start": 957, "end": 965}, "arguments": [{"role": "Theme", "text": "transcription", "start": 971, "end": 984}, {"role": "Cause", "text": "c-jun", "start": 996, "end": 1001}]}, {"trigger": {"text": "altered", "start": 1160, "end": 1167}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1142, "end": 1147}]}, {"trigger": {"text": "involved", "start": 1944, "end": 1952}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1961, "end": 1971}]}, {"trigger": {"text": "regulation", "start": 1961, "end": 1971}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1956, "end": 1960}]}, {"trigger": {"text": "is a key molecular mechanism", "start": 2157, "end": 2185}, "arguments": [{"role": "Theme", "text": "increasing", "start": 2190, "end": 2200}, {"role": "Cause", "text": "transcription", "start": 2206, "end": 2219}]}], "transcription": [{"trigger": {"text": "transcription", "start": 94, "end": 107}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 89, "end": 93}]}, {"trigger": {"text": "transcription", "start": 860, "end": 873}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 855, "end": 859}]}, {"trigger": {"text": "transcription", "start": 971, "end": 984}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 966, "end": 970}]}, {"trigger": {"text": "absent", "start": 1247, "end": 1253}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1233, "end": 1238}]}, {"trigger": {"text": "transcription", "start": 2206, "end": 2219}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 2201, "end": 2205}]}]}}, "schema": []}
{"input": "Negative transcriptional regulation of human interleukin 2 (IL-2) gene by glucocorticoids through interference with nuclear transcription factors AP-1 and NF-AT. \nIL-2 gene transcription is affected by several nuclear proteins. We asked whether dexamethasone (Dex) and cyclosporin A (CsA) inhibit IL-2 gene transcription by interfering with the activity of nuclear proteins that bind to the IL-2 promoter. Nuclear extracts from primary human T lymphocytes were analyzed by electrophoretic DNA mobility shift assays. Both Dex and CsA inhibited the binding of transcription factors AP-1 and NF-AT, but not of NF-kB and OCT-1/OAF, to their corresponding sites on the IL-2 gene promoter. To correlate changes in nuclear factor binding in vitro with transcriptional activity in vivo and define the structural requirements for IL-2 promoter repression, we used transient DNA transfections. Jurkat cells were transfected with plasmids containing either the intact IL-2 promoter or its AP-1, NF-AT, and NF-kB motifs. Dex inhibited the IL-2 promoter and the AP-1, but not the NF-AT and NF-kB plasmids. In contrast, CsA inhibited the IL-2 promoter and the NF-AT, but not the AP-1 and NF-kB plasmids. These results suggest that in human T lymphocytes both Dex and CsA inhibited IL-2 gene transcription through interference with transcription factors AP-1 and NF-AT. We propose that, while maximum inhibition may involve interaction with both transcription factors, AP-1 is the primary target of Dex. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 379, "end": 383}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 391, "end": 395}, {"role": "Site", "text": "promoter", "start": 396, "end": 404}]}, {"trigger": {"text": "binding", "start": 547, "end": 554}, "arguments": [{"role": "Site", "text": "their corresponding sites", "start": 631, "end": 656}, {"role": "Theme", "text": "IL-2", "start": 664, "end": 668}]}], "negative regulation": [{"trigger": {"text": "Negative transcriptional regulation", "start": 0, "end": 35}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 60, "end": 64}]}, {"trigger": {"text": "inhibit", "start": 289, "end": 296}, "arguments": [{"role": "Theme", "text": "transcription", "start": 307, "end": 320}]}, {"trigger": {"text": "inhibited", "start": 533, "end": 542}, "arguments": [{"role": "Theme", "text": "binding", "start": 547, "end": 554}]}, {"trigger": {"text": "repression", "start": 835, "end": 845}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 821, "end": 825}, {"role": "Site", "text": "promoter", "start": 826, "end": 834}]}, {"trigger": {"text": "inhibited", "start": 1013, "end": 1022}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1027, "end": 1031}]}, {"trigger": {"text": "inhibited", "start": 1110, "end": 1119}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1124, "end": 1128}]}, {"trigger": {"text": "inhibited", "start": 1257, "end": 1266}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1277, "end": 1290}]}, {"trigger": {"text": "inhibition", "start": 1386, "end": 1396}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1277, "end": 1290}]}], "positive regulation": [{"trigger": {"text": "requirements", "start": 804, "end": 816}, "arguments": [{"role": "Theme", "text": "repression", "start": 835, "end": 845}]}, {"trigger": {"text": "involve", "start": 1401, "end": 1408}, "arguments": [{"role": "Theme", "text": "inhibition", "start": 1386, "end": 1396}]}], "regulation": [{"trigger": {"text": "affected", "start": 190, "end": 198}, "arguments": [{"role": "Theme", "text": "transcription", "start": 173, "end": 186}]}], "transcription": [{"trigger": {"text": "transcription", "start": 173, "end": 186}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 163, "end": 167}]}, {"trigger": {"text": "transcription", "start": 307, "end": 320}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 297, "end": 301}]}, {"trigger": {"text": "transcription", "start": 1277, "end": 1290}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1267, "end": 1271}]}]}}, "schema": []}
{"input": "Cell-specific expression of helix-loop-helix transcription factors encoded by the E2A gene. \nThe E2A gene encodes transcription factors of the helix-loop-helix family that are implicated in cell-specific gene expression as part of dimeric complexes that interact with E box enhancer elements. It has previously been shown that transcripts of the E2A gene can be detected in a wide range of cell types. We have now examined expression of the mouse E2A gene at the protein level using polyclonal antisera directed against distinct portions of the E2A protein to probe blots of cellular extracts. A 73 kDa protein was identified by this analysis: this protein is highly enriched in cell lines of B lymphoid origin as compared to pancreatic beta-cells and fibroblast cells. The detection of this protein selectively in extracts of lymphoid cells correlates with the presence of the E box-binding activity LEF1/BCF1 in these cells; this binding activity was previously shown to be efficiently recognized by antiserum directed against E2A gene products. Transfection of cells with full length E2A cDNA leads to appearance of protein co-migrating with the 73 kDa protein on SDS gel electrophoresis and co-migrating with LEF1/BCF1 on mobility shift analysis. Our results are consistent with the view that the DNA-binding activity LEF1/BCF1 is a homodimer of E2A proteins; the selective appearance of this putative cell-specific transcription factor in B lymphoid cells seems to be attributable, at least in part, to the elevated E2A protein concentrations in these cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 1305, "end": 1321}, "arguments": [{"role": "Theme", "text": "E2A", "start": 1350, "end": 1353}]}], "gene expression": [{"trigger": {"text": "expression", "start": 14, "end": 24}, "arguments": [{"role": "Theme", "text": "E2A", "start": 82, "end": 85}]}, {"trigger": {"text": "detected", "start": 362, "end": 370}, "arguments": [{"role": "Theme", "text": "E2A", "start": 346, "end": 349}]}, {"trigger": {"text": "expression", "start": 423, "end": 433}, "arguments": [{"role": "Theme", "text": "E2A", "start": 447, "end": 450}]}, {"trigger": {"text": "Transfection", "start": 1048, "end": 1060}, "arguments": [{"role": "Theme", "text": "E2A", "start": 1087, "end": 1090}]}, {"trigger": {"text": "appearance", "start": 1378, "end": 1388}, "arguments": [{"role": "Theme", "text": "E2A", "start": 1350, "end": 1353}]}], "positive regulation": [{"trigger": {"text": "Transfection", "start": 1048, "end": 1060}, "arguments": [{"role": "Theme", "text": "Transfection", "start": 1048, "end": 1060}]}, {"trigger": {"text": "attributable", "start": 1473, "end": 1485}, "arguments": [{"role": "Cause", "text": "appearance", "start": 1378, "end": 1388}, {"role": "Theme", "text": "elevated", "start": 1512, "end": 1520}]}, {"trigger": {"text": "elevated", "start": 1512, "end": 1520}, "arguments": [{"role": "Theme", "text": "E2A", "start": 1521, "end": 1524}]}]}}, "schema": []}
{"input": "HIV-1 Nef protein inhibits the recruitment of AP-1 DNA-binding activity in human T-cells. \nThe human immunodeficiency virus type 1 long terminal repeat, HIV-1-LTR, contains binding sites for several cellular transcription factors which contribute to HIV-1 gene expression. Our previous studies on the function of the HIV-1-encoded Nef protein suggested that Nef may be an inhibitor HIV-1 transcription. To determine whether Nef affects the binding of cellular factors implicated in HIV-1 regulation, 32P-labeled oligonucleotides corresponding to the binding sites were incubated with nuclear extracts prepared from Nef-expressing T-cell lines that were not stimulated or were stimulated with T-cell mitogens. We found that Nef inhibited the recruitment of AP-1 DNA-binding activity in mitogen-stimulated human T-cells. Additionally, Nef expressing cells were transiently transfected with a plasmid in which HIV-1 AP-1 DNA recognition sequences were cloned downstream of the chloramphenicol acetyltransferase (CAT) gene. Mitogen-mediated transcriptional activation of the CAT gene in this construct was inhibited in Nef-expressing cells but not in control cells. These studies suggest that, by inhibiting AP-1 activation, Nef may play a role in regulating HIV-1 gene expression in infected T-cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 619, "end": 629}, "arguments": [{"role": "Theme", "text": "Nef", "start": 615, "end": 618}]}, {"trigger": {"text": "expressing", "start": 837, "end": 847}, "arguments": [{"role": "Theme", "text": "Nef", "start": 833, "end": 836}]}, {"trigger": {"text": "expressing", "start": 1119, "end": 1129}, "arguments": [{"role": "Theme", "text": "Nef", "start": 1115, "end": 1118}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1102, "end": 1111}, "arguments": [{"role": "Theme", "text": "activation", "start": 1053, "end": 1063}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 1053, "end": 1063}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 1037, "end": 1052}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 1037, "end": 1052}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1071, "end": 1074}]}]}}, "schema": []}
{"input": "Cloning and functional characterization of early B-cell factor, a regulator of lymphocyte-specific gene expression. \nEarly B-cell factor (EBF) was identified previously as a tissue-specific and differentiation stage-specific DNA-binding protein that participates in the regulation of the pre-B and B lymphocyte-specific mb-1 gene. Partial amino acid sequences obtained from purified EBF were used to isolate cDNA clones, which by multiple criteria encode EBF. The recombinant polypeptide formed sequence-specific complexes with the EBF-binding site in the mb-1 promoter. The cDNA hybridized to multiple transcripts in pre-B and B-cell lines, but transcripts were not detected at significant levels in plasmacytoma, T-cell, and nonlymphoid cell lines. Expression of recombinant EBF in transfected nonlymphoid cells strongly activated transcription from reporter plasmids containing functional EBF-binding sites. Analysis of DNA binding by deletion mutants of EBF identified an amino-terminal cysteine-rich DNA-binding domain lacking obvious sequence similarity to known transcription factors. DNA-binding assays with cotranslated wild-type and truncated forms of EBF indicated that the protein interacts with its site as a homodimer. Deletions delineated a carboxy-terminal dimerization region containing two repeats of 15 amino acids that show similarity with the dimerization domains of basic-helix-loop-helix proteins. Together, these data suggest that EBF represents a novel regulator of B lymphocyte-specific gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding protein", "start": 229, "end": 244}, "arguments": [{"role": "Theme", "text": "EBF", "start": 138, "end": 141}]}, {"trigger": {"text": "interacts", "start": 1193, "end": 1202}, "arguments": [{"role": "Theme", "text": "EBF", "start": 1162, "end": 1165}]}, {"trigger": {"text": "homodimer", "start": 1222, "end": 1231}, "arguments": [{"role": "Theme", "text": "EBF", "start": 1162, "end": 1165}]}], "regulation": [{"trigger": {"text": "participates in the regulation", "start": 250, "end": 280}, "arguments": [{"role": "Cause", "text": "EBF", "start": 138, "end": 141}, {"role": "Theme", "text": "mb-1", "start": 320, "end": 324}]}], "transcription": [{"trigger": {"text": "The cDNA hybridized", "start": 571, "end": 590}, "arguments": [{"role": "Theme", "text": "EBF", "start": 455, "end": 458}]}, {"trigger": {"text": "detected", "start": 667, "end": 675}, "arguments": [{"role": "Theme", "text": "EBF", "start": 455, "end": 458}]}]}}, "schema": []}
{"input": "Regulation of the Ets-related transcription factor Elf-1 by binding to the retinoblastoma protein. \nThe retinoblastoma gene product (Rb) is a nuclear phosphoprotein that regulates cell cycle progression. Elf-1 is a lymphoid-specific Ets transcription factor that regulates inducible gene expression during T cell activation. In this report, it is demonstrated that Elf-1 contains a sequence motif that is highly related to the Rb binding sites of several viral oncoproteins and binds to the pocket region of Rb both in vitro and in vivo. Elf-1 binds exclusively to the underphosphorylated form of Rb and fails to bind to Rb mutants derived from patients with retinoblastoma. Co-immunoprecipitation experiments demonstrated an association between Elf-1 and Rb in resting normal human T cells. After T cell activation, the phosphorylation of Rb results in the release of Elf-1, which is correlated temporally with the activation of Elf-1-mediated transcription. Overexpression of a phosphorylation-defective form of Rb inhibited Elf-1-dependent transcription during T cell activation. These results demonstrate that Rb interacts specifically with a lineage-restricted Ets transcription factor. This regulated interaction may be important for the coordination of lineage-specific effector functions such as lymphokine production with cell cycle progression in activated T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 60, "end": 67}, "arguments": [{"role": "Theme", "text": "retinoblastoma protein", "start": 75, "end": 97}]}, {"trigger": {"text": "binds", "start": 478, "end": 483}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 365, "end": 370}, {"role": "Theme2", "text": "Rb", "start": 508, "end": 510}]}, {"trigger": {"text": "binds", "start": 544, "end": 549}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 538, "end": 543}, {"role": "Theme2", "text": "Rb", "start": 597, "end": 599}]}, {"trigger": {"text": "bind", "start": 613, "end": 617}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 538, "end": 543}, {"role": "Theme2", "text": "Rb", "start": 621, "end": 623}]}, {"trigger": {"text": "association", "start": 726, "end": 737}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 746, "end": 751}, {"role": "Theme2", "text": "Rb", "start": 756, "end": 758}]}, {"trigger": {"text": "interacts", "start": 1117, "end": 1126}, "arguments": [{"role": "Theme", "text": "Rb", "start": 1114, "end": 1116}]}], "gene expression": [{"trigger": {"text": "Overexpression", "start": 960, "end": 974}, "arguments": [{"role": "Theme", "text": "Rb", "start": 1014, "end": 1016}]}], "localization": [{"trigger": {"text": "release", "start": 858, "end": 865}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 869, "end": 874}]}], "negative regulation": [{"trigger": {"text": "underphosphorylated", "start": 569, "end": 588}, "arguments": [{"role": "Theme", "text": "underphosphorylated", "start": 569, "end": 588}]}], "phosphorylation": [{"trigger": {"text": "underphosphorylated", "start": 569, "end": 588}, "arguments": [{"role": "Theme", "text": "Rb", "start": 597, "end": 599}]}, {"trigger": {"text": "phosphorylation", "start": 821, "end": 836}, "arguments": [{"role": "Theme", "text": "Rb", "start": 840, "end": 842}]}, {"trigger": {"text": "phosphorylation-defective form", "start": 980, "end": 1010}, "arguments": [{"role": "Theme", "text": "Rb", "start": 1014, "end": 1016}]}], "positive regulation": [{"trigger": {"text": "results", "start": 843, "end": 850}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 821, "end": 836}, {"role": "Theme", "text": "release", "start": 858, "end": 865}]}, {"trigger": {"text": "Overexpression", "start": 960, "end": 974}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 960, "end": 974}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 51, "end": 56}, {"role": "Cause", "text": "binding", "start": 60, "end": 67}]}]}}, "schema": []}
{"input": "Expression levels of the thyrotropin receptor gene in autoimmune thyroid disease: coregulation with parameters of thyroid function and inverse relation to major histocompatibility complex classes I and II. \nUsing a human TSH receptor (TSH-R) cDNA probe, we investigated TSH-R transcript levels in 13 human thyroid fragments by Northern blot analysis; 7 Graves' disease, 2 Hashimoto's disease, 3 endemic goiter, and 1 healthy thyroid gland were studied. TSH-R expression levels were variable, but displayed a close correlation to the expression of thyroid peroxidase (r = 0.703; P < 0.05), thyroglobulin (r = 0.817; P < 0.01), and the nuclear oncogene c-fos (r = 0.935; P < 0.001), but not c-myc. Overall, TSH-R transcript levels were low or absent in those thyroids in which expression of the major histocompatibility complex class I or II (MHC I or II) was high, thus establishing an inverse relation (MHC I, r = -0.791; P < 0.01; MHC II, r = -0.784; P < 0.01). In situ hybridization showed that apart from lymphocytes, thyroid cells themselves were the source of MHC II transcripts. gamma-Interferon expression was only detectable in 1 Hashimoto's goiter. Our findings suggest that next to lymphocyte infiltration, active regulatory events in the thyrocyte are responsible for the inverse relation between functional parameters (TSH-R, thyroid peroxidase, thyroglobulin, and c-fos) and immunological markers (MHC I and II). ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "thyrotropin receptor", "start": 25, "end": 45}]}, {"trigger": {"text": "expression", "start": 459, "end": 469}, "arguments": [{"role": "Theme", "text": "TSH-R", "start": 453, "end": 458}]}, {"trigger": {"text": "expression", "start": 533, "end": 543}, "arguments": [{"role": "Theme", "text": "thyroid peroxidase", "start": 547, "end": 565}]}, {"trigger": {"text": "expression", "start": 533, "end": 543}, "arguments": [{"role": "Theme", "text": "thyroglobulin", "start": 589, "end": 602}]}, {"trigger": {"text": "expression", "start": 533, "end": 543}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 651, "end": 656}]}, {"trigger": {"text": "expression", "start": 533, "end": 543}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 689, "end": 694}]}, {"trigger": {"text": "expression", "start": 1102, "end": 1112}, "arguments": [{"role": "Theme", "text": "gamma-Interferon", "start": 1085, "end": 1101}]}], "regulation": [{"trigger": {"text": "coregulation", "start": 82, "end": 94}, "arguments": [{"role": "Theme", "text": "Expression", "start": 0, "end": 10}]}], "transcription": [{"trigger": {"text": "transcript levels", "start": 276, "end": 293}, "arguments": [{"role": "Theme", "text": "TSH-R", "start": 270, "end": 275}]}, {"trigger": {"text": "transcript levels", "start": 711, "end": 728}, "arguments": [{"role": "Theme", "text": "TSH-R", "start": 705, "end": 710}]}]}}, "schema": []}
{"input": "Regulation of the beta-globin locus. \nTranscription of the human beta-globin gene cluster depends upon upstream regulatory sequences, which are collectively termed the locus control region. Recent studies have provided new insights into how the individual genes of the cluster are regulated through development. The crux of transcriptional activation is how the locus control region communicates with the gene-proximal regulatory elements. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 18, "end": 29}]}, {"trigger": {"text": "depends", "start": 90, "end": 97}, "arguments": [{"role": "Theme", "text": "Transcription", "start": 38, "end": 51}]}, {"trigger": {"text": "regulated", "start": 281, "end": 290}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 65, "end": 76}]}], "transcription": [{"trigger": {"text": "Transcription", "start": 38, "end": 51}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 65, "end": 76}]}]}}, "schema": []}
{"input": "Ectopic expression of a conditional GATA-2/estrogen receptor chimera arrests erythroid differentiation in a hormone-dependent manner. \nThe GATA factors are a family of transcriptional regulatory proteins in eukaryotes that share extensive homology in their DNA-binding domains. One enigmatic aspect of GATA factor expression is that several GATA proteins, which ostensibly share the same DNA-binding site specificity, are coexpressed in erythroid cells. To elucidate the roles of individual GATA factors in erythropoiesis, conditional alleles of GATA-1, GATA-2, and GATA-3 were prepared by fusing each of the factors to the hormone-binding domain of the human estrogen receptor (ER). These GATA/ER chimeric factors were shown to be hormone-inducible trans-activating proteins in transient transfection assays. When stably introduced into primary erythroblasts or conditionally transformed erythroid progenitors cells, exogenous GATA-2/ER promoted proliferation and inhibited terminal differentiation in an estrogen-dependent manner. These phenotypic effects are specifically attributable to the action of ectopically expressed GATA-2/ER because erythroblasts expressing exogenous GATA-2 are constitutively arrested in differentiation and because erythroid progenitors expressing either Gal/ER or GATA-3/ER do not display a hormone-responsive block in differentiation. Thus, the GATA-2 transcription factor appears to play a role in regulating the self-renewal capacity of early erythroid progenitor cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 1159, "end": 1169}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 1180, "end": 1186}]}]}}, "schema": []}
{"input": "Molecular basis of a multiple lymphokine deficiency in a patient with severe combined immunodeficiency. \nWe have previously reported that the T lymphocytes of a child with severe combined immunodeficiency are defective in the transcription of several lymphokine genes that include IL2, IL3, IL4, and IL5, which encode interleukins 2, 3, 4, and 5 (IL-2, -3, -4, and -5). To determine whether the defect in the patient's T lymphocytes involved a trans-acting factor common to the affected lymphokine genes, we examined the ability of nuclear factors from the patient's T lymphocytes to bind response elements present in the regulatory region of IL2. Nuclear factor NF-kB, activation protein 1 (AP-1), OCT-1, and NF-IL-2B binding activity were normal. In contrast, the binding of the nuclear factor of activated T cells (NF-AT) to its response element in the IL2 enhancer and to an NF-AT-like response element present in the IL4 enhancer was abnormal. To ascertain whether the abnormal NF-AT binding activity was related to an impaired function, we transfected patient and control T lymphocytes with constructs containing the reporter gene encoding chloramphenicol acetyl transferase (CAT) under the control of the entire IL2 regulatory region or of multimers of individual enhancer sequences. CAT expression directed by the IL2 regulatory region or by a multimer of the NF-AT-binding site was markedly lower in the patient relative to controls. In contrast, CAT gene expression directed by a multimer of the OCT-1 proximal (OCT-1p)-binding site was equivalent in patient and controls. These results indicate that an abnormality of/or influencing NF-AT may underlie the multiple lymphokine deficiency in this patient. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 584, "end": 588}, "arguments": [{"role": "Site", "text": "response elements", "start": 589, "end": 606}, {"role": "Theme", "text": "IL2", "start": 643, "end": 646}]}, {"trigger": {"text": "binding", "start": 719, "end": 726}, "arguments": [{"role": "Site", "text": "response elements", "start": 589, "end": 606}, {"role": "Theme", "text": "IL2", "start": 643, "end": 646}, {"role": "Theme2", "text": "OCT-1", "start": 699, "end": 704}]}, {"trigger": {"text": "binding", "start": 719, "end": 726}, "arguments": [{"role": "Site", "text": "response elements", "start": 589, "end": 606}, {"role": "Theme", "text": "IL2", "start": 643, "end": 646}]}, {"trigger": {"text": "binding", "start": 766, "end": 773}, "arguments": [{"role": "Theme", "text": "IL2", "start": 856, "end": 859}, {"role": "Site", "text": "enhancer", "start": 860, "end": 868}]}, {"trigger": {"text": "binding", "start": 766, "end": 773}, "arguments": [{"role": "Theme", "text": "IL4", "start": 922, "end": 925}, {"role": "Site", "text": "enhancer", "start": 926, "end": 934}]}], "gene expression": [{"trigger": {"text": "transfected", "start": 1046, "end": 1057}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1182, "end": 1185}]}, {"trigger": {"text": "expression", "start": 1295, "end": 1305}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1291, "end": 1294}]}, {"trigger": {"text": "expression", "start": 1465, "end": 1475}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1456, "end": 1459}]}], "negative regulation": [{"trigger": {"text": "lower", "start": 1400, "end": 1405}, "arguments": [{"role": "Theme", "text": "expression", "start": 1295, "end": 1305}]}, {"trigger": {"text": "equivalent", "start": 1547, "end": 1557}, "arguments": [{"role": "Theme", "text": "expression", "start": 1465, "end": 1475}]}], "positive regulation": [{"trigger": {"text": "transfected", "start": 1046, "end": 1057}, "arguments": [{"role": "Theme", "text": "transfected", "start": 1046, "end": 1057}]}], "regulation": [{"trigger": {"text": "involved", "start": 433, "end": 441}, "arguments": [{"role": "Theme", "text": "transcription", "start": 226, "end": 239}]}, {"trigger": {"text": "under the control", "start": 1187, "end": 1204}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1182, "end": 1185}]}, {"trigger": {"text": "directed", "start": 1306, "end": 1314}, "arguments": [{"role": "Theme", "text": "expression", "start": 1295, "end": 1305}]}], "transcription": [{"trigger": {"text": "transcription", "start": 226, "end": 239}, "arguments": [{"role": "Theme", "text": "IL2", "start": 281, "end": 284}]}, {"trigger": {"text": "transcription", "start": 226, "end": 239}, "arguments": [{"role": "Theme", "text": "IL3", "start": 286, "end": 289}]}, {"trigger": {"text": "transcription", "start": 226, "end": 239}, "arguments": [{"role": "Theme", "text": "IL4", "start": 291, "end": 294}]}, {"trigger": {"text": "transcription", "start": 226, "end": 239}, "arguments": [{"role": "Theme", "text": "IL5", "start": 300, "end": 303}]}]}}, "schema": []}
{"input": "Expression of mRNA for the GATA-binding proteins in human eosinophils and basophils: potential role in gene transcription. \nThe expression of the hematopoietic transcription factors GATA-1, GATA-2, and GATA-3 was studied in eosinophils and basophils. Eosinophils express mRNA for GATA-1, GATA-2, and GATA-3. Basophils express GATA-2 and GATA-3. Treatment of HL-60 eosinophilic sublines with either interleukin-5 or butyric acid increased the expression of GATA-1 mRNA concomitant with the expression of eosinophil-specific genes, whereas levels of GATA-2 mRNA remained relatively constant. The presence of mRNA for these proteins in eosinophils and basophils suggests that gene transcription in these lineages may be regulated by GATA-binding proteins. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 128, "end": 138}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 182, "end": 188}]}, {"trigger": {"text": "expression", "start": 128, "end": 138}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 190, "end": 196}]}, {"trigger": {"text": "expression", "start": 128, "end": 138}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 202, "end": 208}]}, {"trigger": {"text": "express", "start": 318, "end": 325}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 326, "end": 332}]}, {"trigger": {"text": "express", "start": 318, "end": 325}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 337, "end": 343}]}], "localization": [{"trigger": {"text": "presence", "start": 594, "end": 602}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 280, "end": 286}]}, {"trigger": {"text": "presence", "start": 594, "end": 602}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 288, "end": 294}]}, {"trigger": {"text": "presence", "start": 594, "end": 602}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 300, "end": 306}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 428, "end": 437}, "arguments": [{"role": "Theme", "text": "expression", "start": 442, "end": 452}]}, {"trigger": {"text": "constant", "start": 580, "end": 588}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 548, "end": 554}]}], "transcription": [{"trigger": {"text": "express mRNA", "start": 263, "end": 275}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 280, "end": 286}]}, {"trigger": {"text": "express mRNA", "start": 263, "end": 275}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 288, "end": 294}]}, {"trigger": {"text": "express mRNA", "start": 263, "end": 275}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 300, "end": 306}]}, {"trigger": {"text": "expression", "start": 442, "end": 452}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 456, "end": 462}]}]}}, "schema": []}
{"input": "Dependence for the proliferative response to erythropoietin on an established erythroid differentiation program in a human hematopoietic cell line, UT-7. \nErythroid differentiation involves the activation of a number of erythroid-specific genes, most of which, including the globin genes and the erythropoietin receptor (Epo-R) gene, are, at least in part, regulated by the transcription factor GATA-1. In order to understand the relationship, if any, between expression of GATA-1, response to Epo and erythroid differentiation, we analyzed the expression of GATA-1, Epo-R and globin genes in an Epo-dependent human cell line, UT-7 Epo. The results were compared to those obtained with the parental granulocyte-macrophage colony-stimulating factor (GM-CSF)-dependent cell line, UT-7, which has a predominantly megakaryoblastic phenotype and is unable to proliferate continuously in the presence of Epo. UT-7 Epo and UT-7 expressed similar levels of GATA-1 mRNA and binding activity. The two lines also expressed comparable levels of Epo-R mRNA while the number of Epo-binding sites on UT-7 Epo cells was one-sixth the number of UT-7 cells (2400 +/- 3 vs. 13,800 +/- 300). This difference in the number of binding sites could be due to differences in cell surface (UT-7 cells are 20% smaller than the parental UT-7 cells) or in receptor turnover. By Northern analysis, UT-7 cells expressed detectable levels of beta- and gamma-globin but not alpha-globin. In comparison, UT-7 Epo cells expressed alpha-globin and higher levels of gamma-globin (5-fold) and beta-globin (from barely to clearly detectable). Globin chains (alpha, beta and gamma) were clearly detectable by affinity chromatography in UT-7 Epo but not in UT-7 cells. The frequency of the cells which expressed beta- and gamma- globin genes in the two cell populations was measured by immunofluorescence with beta- and gamma-specific antibodies. The number of gamma-positive cells and their fluorescence intensity were higher in UT-7 Epo than in UT-7 cells (0 to 17% barely positive cells and 23 to 40% clearly positive cells, respectively), indicating that the increase in globin mRNA observed in UT-7 Epo is due to both an increase of gene expression per cell and an increase in numbers of cells containing gamma-globin. The levels of GATA-1, Epo-R and globin mRNA expressed were not affected by a 24-hour incubation of either cell line with Epo, GM-CSF or interleukin-3 (IL-3). (ABSTRACT TRUNCATED AT 400 WORDS) ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 965, "end": 981}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 949, "end": 955}]}], "gene expression": [{"trigger": {"text": "expression", "start": 460, "end": 470}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 474, "end": 480}]}, {"trigger": {"text": "expression", "start": 545, "end": 555}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 559, "end": 565}]}, {"trigger": {"text": "expression", "start": 545, "end": 555}, "arguments": [{"role": "Theme", "text": "Epo-R", "start": 567, "end": 572}]}, {"trigger": {"text": "expressed", "start": 1379, "end": 1388}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 699, "end": 747}]}, {"trigger": {"text": "expressed", "start": 1485, "end": 1494}, "arguments": [{"role": "Theme", "text": "alpha-globin", "start": 1495, "end": 1507}]}, {"trigger": {"text": "expressed", "start": 1485, "end": 1494}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 1555, "end": 1566}]}, {"trigger": {"text": "detectable", "start": 1655, "end": 1665}, "arguments": [{"role": "Theme", "text": "Globin chains (alpha", "start": 1604, "end": 1624}]}, {"trigger": {"text": "detectable", "start": 1655, "end": 1665}, "arguments": [{"role": "Theme", "text": "beta", "start": 1626, "end": 1630}]}, {"trigger": {"text": "detectable", "start": 1655, "end": 1665}, "arguments": [{"role": "Theme", "text": "gamma", "start": 1635, "end": 1640}]}], "regulation": [{"trigger": {"text": "regulated", "start": 357, "end": 366}, "arguments": [{"role": "Theme", "text": "Epo-R", "start": 321, "end": 326}, {"role": "Cause", "text": "GATA-1", "start": 395, "end": 401}]}, {"trigger": {"text": "affected", "start": 2346, "end": 2354}, "arguments": [{"role": "Theme", "text": "expressed", "start": 2327, "end": 2336}]}], "transcription": [{"trigger": {"text": "expressed", "start": 921, "end": 930}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 949, "end": 955}]}, {"trigger": {"text": "expressed", "start": 1002, "end": 1011}, "arguments": [{"role": "Theme", "text": "Epo-R", "start": 1033, "end": 1038}]}, {"trigger": {"text": "expressed", "start": 2327, "end": 2336}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 2297, "end": 2303}]}, {"trigger": {"text": "expressed", "start": 2327, "end": 2336}, "arguments": [{"role": "Theme", "text": "Epo-R", "start": 2305, "end": 2310}]}]}}, "schema": []}
{"input": "Protein kinase C-zeta mediates NF-kappa B activation in human immunodeficiency virus-infected monocytes. \nThe molecular mechanisms regulating human immunodeficiency virus (HIV) persistence in a major cell reservoir such as the macrophage remain unknown. NF-kappa B is a transcription factor involved in the regulation of the HIV long terminal repeat and is selectively activated following HIV infection of human macrophages. Although little information as to what signal transduction pathways mediate NF-kappa B activation in monocytes-macrophages is available, our previous work indicated that classical protein kinase C (PKC) isoenzymes were not involved in the HIV-mediated NF-kappa B activation. In this study, we have focused on atypical PKC isoenzymes. PKC-zeta belongs to this family and is known to be an important step in NF-kappa B activation in other cell systems. Immunoblotting experiments with U937 cells demonstrate that PKC-zeta is present in these cells, and its expression can be downmodulated by antisense oligonucleotides (AO). The HIV-mediated NF-kappa B activation is selectively reduced by AO to PKC-zeta. In addition, cotransfection of a negative dominant molecule of PKC-zeta (PKC-zeta mut) with NF-kappa B-dependent reporter genes selectively inhibits the HIV- but not phorbol myristate acetate- or lipopolysaccharide-mediated activation of NF-kappa B. That PKC-zeta is specific in regulating NF-kappa B is concluded from the inability of PKC-zeta(mut) to interfere with the basal or phorbol myristate acetate-inducible CREB- or AP1-dependent transcriptional activity. Lastly, we demonstrate a selective inhibition of p24 production by HIV-infected human macrophages when treated with AO to PKC-zeta. Altogether, these results suggest that atypical PKC isoenzymes, including PKC-zeta, participate in the signal transduction pathways by which HIV infection results in the activation of NF-kappa B in human monocytic cells and macrophages. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "present", "start": 948, "end": 955}, "arguments": [{"role": "Theme", "text": "PKC-zeta", "start": 936, "end": 944}]}, {"trigger": {"text": "cotransfection", "start": 1142, "end": 1156}, "arguments": [{"role": "Theme", "text": "PKC-zeta", "start": 1192, "end": 1200}]}], "negative regulation": [{"trigger": {"text": "downmodulated", "start": 998, "end": 1011}, "arguments": [{"role": "Theme", "text": "present", "start": 948, "end": 955}]}]}}, "schema": []}
{"input": "Inhibition of NF-AT-dependent transcription by NF-kappa B: implications for differential gene expression in T helper cell subsets. \nActivation of individual CD4+ T cells results in differential lymphokine expression: interleukin 2 (IL-2) is preferentially produced by T helper type 1 (TH1) cells, which are involved in cell-mediated immune responses, whereas IL-4 is synthesized by TH2 cells, which are essential for humoral immunity. The Ca(2+)-dependent factor NF-ATp plays a key role in the inducible transcription of both these lymphokine genes. However, while IL2 expression requires the contribution of Ca(2+)- and protein kinase C-dependent signals, we report that activation of human IL4 transcription through the Ca(2+)-dependent pathway is diminished by protein kinase C stimulation in Jurkat T cells. This phenomenon is due to mutually exclusive binding of NF-ATp and NF-kappa B to the P sequence, an element located 69 bp upstream of the IL4 transcription initiation site. Human IL4 promoter-mediated transcription is downregulated in Jurkat cells stimulated with the NF-kappa B-activating cytokine tumor necrosis factor alpha and suppressed in RelA-overexpressing cells. In contrast, protein kinase C stimulation or RelA overexpression does not affect the activity of a human IL4 promoter containing a mouse P sequence, which is a higher-affinity site for NF-ATp and a lower-affinity site for RelA. Thus, competition between two general transcriptional activators, RelA and NF-ATp, mediates the inhibitory effect of protein kinase C stimulation on IL4 expression and may contribute to differential gene expression in TH cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 857, "end": 864}, "arguments": [{"role": "Theme", "text": "NF-ATp", "start": 868, "end": 874}]}, {"trigger": {"text": "higher-affinity site", "start": 1344, "end": 1364}, "arguments": [{"role": "Theme", "text": "NF-ATp", "start": 1369, "end": 1375}]}, {"trigger": {"text": "lower-affinity site", "start": 1382, "end": 1401}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1406, "end": 1410}]}, {"trigger": {"text": "competition", "start": 1418, "end": 1429}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1478, "end": 1482}]}, {"trigger": {"text": "competition", "start": 1418, "end": 1429}, "arguments": [{"role": "Theme", "text": "NF-ATp", "start": 1487, "end": 1493}]}], "gene expression": [{"trigger": {"text": "produced", "start": 256, "end": 264}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 232, "end": 236}]}, {"trigger": {"text": "synthesized", "start": 367, "end": 378}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 359, "end": 363}]}, {"trigger": {"text": "expression", "start": 569, "end": 579}, "arguments": [{"role": "Theme", "text": "IL2", "start": 565, "end": 568}]}, {"trigger": {"text": "overexpressing", "start": 1162, "end": 1176}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1157, "end": 1161}]}, {"trigger": {"text": "overexpression", "start": 1234, "end": 1248}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1229, "end": 1233}]}, {"trigger": {"text": "expression", "start": 1565, "end": 1575}, "arguments": [{"role": "Theme", "text": "IL4", "start": 1561, "end": 1564}]}], "negative regulation": [{"trigger": {"text": "diminished", "start": 750, "end": 760}, "arguments": [{"role": "Theme", "text": "activation", "start": 672, "end": 682}]}, {"trigger": {"text": "competition", "start": 1418, "end": 1429}, "arguments": [{"role": "Theme", "text": "competition", "start": 1418, "end": 1429}, {"role": "Cause", "text": "RelA", "start": 1478, "end": 1482}]}, {"trigger": {"text": "competition", "start": 1418, "end": 1429}, "arguments": [{"role": "Theme", "text": "competition", "start": 1418, "end": 1429}, {"role": "Cause", "text": "NF-ATp", "start": 1487, "end": 1493}]}, {"trigger": {"text": "inhibitory", "start": 1508, "end": 1518}, "arguments": [{"role": "Theme", "text": "expression", "start": 1565, "end": 1575}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 446, "end": 455}, "arguments": [{"role": "Theme", "text": "NF-ATp", "start": 463, "end": 469}]}, {"trigger": {"text": "key role", "start": 478, "end": 486}, "arguments": [{"role": "Cause", "text": "NF-ATp", "start": 463, "end": 469}, {"role": "Theme", "text": "inducible", "start": 494, "end": 503}]}, {"trigger": {"text": "inducible", "start": 494, "end": 503}, "arguments": [{"role": "Theme", "text": "transcription", "start": 504, "end": 517}]}, {"trigger": {"text": "requires", "start": 580, "end": 588}, "arguments": [{"role": "Theme", "text": "expression", "start": 569, "end": 579}]}, {"trigger": {"text": "activation", "start": 672, "end": 682}, "arguments": [{"role": "Theme", "text": "transcription", "start": 696, "end": 709}]}, {"trigger": {"text": "due to", "start": 831, "end": 837}, "arguments": [{"role": "Theme", "text": "diminished", "start": 750, "end": 760}, {"role": "Cause", "text": "binding", "start": 857, "end": 864}]}, {"trigger": {"text": "due to", "start": 831, "end": 837}, "arguments": [{"role": "Theme", "text": "diminished", "start": 750, "end": 760}]}, {"trigger": {"text": "overexpressing", "start": 1162, "end": 1176}, "arguments": [{"role": "Theme", "text": "overexpressing", "start": 1162, "end": 1176}]}, {"trigger": {"text": "overexpression", "start": 1234, "end": 1248}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1234, "end": 1248}]}, {"trigger": {"text": "mediates", "start": 1495, "end": 1503}, "arguments": [{"role": "Cause", "text": "competition", "start": 1418, "end": 1429}, {"role": "Theme", "text": "inhibitory", "start": 1508, "end": 1518}]}], "regulation": [{"trigger": {"text": "affect", "start": 1258, "end": 1264}, "arguments": [{"role": "Cause", "text": "overexpression", "start": 1234, "end": 1248}, {"role": "Theme", "text": "IL4", "start": 1289, "end": 1292}, {"role": "Site", "text": "promoter", "start": 1293, "end": 1301}]}, {"trigger": {"text": "affect", "start": 1258, "end": 1264}, "arguments": [{"role": "Theme", "text": "IL4", "start": 1289, "end": 1292}, {"role": "Site", "text": "promoter", "start": 1293, "end": 1301}]}], "transcription": [{"trigger": {"text": "transcription", "start": 504, "end": 517}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 232, "end": 236}]}, {"trigger": {"text": "transcription", "start": 504, "end": 517}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 359, "end": 363}]}, {"trigger": {"text": "transcription", "start": 696, "end": 709}, "arguments": [{"role": "Theme", "text": "IL4", "start": 692, "end": 695}]}]}}, "schema": []}
{"input": "Functional characterization of the murine homolog of the B cell-specific coactivator BOB.1/OBF.1. \nB cell-specific transcriptional promoter activity mediated by the octamer motif requires the Oct1 or Oct2 protein and additional B cell-restricted cofactors. One such cofactor, BOB.1/OBF.1, was recently isolated from human B cells. Here, we describe the isolation and detailed characterization of the murine homolog. Full-length cDNAs and genomic clones were isolated, and the gene structure was determined. Comparison of the deduced amino acids shows 88% sequence identity between mouse and human BOB.1/OBF.1. The NH2-terminal 126 amino acids of BOB.1/OBF.1 are both essential and sufficient for interaction with the POU domains of either Oct1 or Oct2. This protein-protein interaction does not require the simultaneous binding of Oct proteins to DNA, and high resolution footprinting of the Oct-DNA interaction reveals that binding of BOB.1/OBF.1 to Oct1 or Oct2 does not alter the interaction with DNA. BOB.1/OBF.1 can efficiently activate octamer-dependent promoters in fibroblasts; however, it fails to stimulate octamer-dependent enhancer activity. Fusion of subdomains of BOB.1/OBF.1 with the GAL4 DNA binding domain reveals that both NH2- and COOH-terminal domains of BOB.1/OBF.1 contribute to full transactivation function, the COOH-terminal domain is more efficient in this transactivation assay. Consistent with the failure of full-length BOB.1/OBF.1 to stimulate octamer-dependent enhancer elements in non B cells, the GAL4 fusions likewise only stimulate from a promoter-proximal position. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 696, "end": 707}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 646, "end": 651}, {"role": "Site2", "text": "POU domains", "start": 717, "end": 728}, {"role": "Theme2", "text": "Oct1", "start": 739, "end": 743}]}, {"trigger": {"text": "interaction", "start": 696, "end": 707}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 646, "end": 651}, {"role": "Site2", "text": "POU domains", "start": 717, "end": 728}, {"role": "Theme2", "text": "Oct2", "start": 747, "end": 751}]}, {"trigger": {"text": "binding", "start": 925, "end": 932}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 936, "end": 941}, {"role": "Theme2", "text": "Oct1", "start": 951, "end": 955}]}, {"trigger": {"text": "binding", "start": 925, "end": 932}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 936, "end": 941}, {"role": "Theme2", "text": "Oct2", "start": 959, "end": 963}]}], "positive regulation": [{"trigger": {"text": "essential and sufficient", "start": 667, "end": 691}, "arguments": [{"role": "CSite", "text": "NH2-terminal 126 amino acids", "start": 614, "end": 642}, {"role": "Cause", "text": "BOB.1", "start": 646, "end": 651}, {"role": "Theme", "text": "interaction", "start": 696, "end": 707}]}, {"trigger": {"text": "require", "start": 795, "end": 802}, "arguments": [{"role": "Theme", "text": "interaction", "start": 696, "end": 707}]}]}}, "schema": []}
{"input": "Polymorphic nucleotides within the human IL-4 promoter that mediate overexpression of the gene. \nAtopy, which predisposes individuals to develop asthma, severe systemic anaphylaxis, and atopic dermatitis, is usually associated with dramatically elevated total serum IgE levels and is thought to be controlled by a major susceptibility gene and multiple minor susceptibility genes. A recent sib-pair analysis revealed a tight linkage between markers on 5q31.1 and a major susceptibility gene controlling total serum IgE levels. Due to its location within this cluster and its biologic role in Ig class switching and Th2 cell differentiation, the IL-4 gene has emerged as one major candidate for the atopy gene. In one model, polymorphisms within IL-4 regulatory elements might result in overexpression of the gene, amplifying Th2 cell differentiation and class switching to IgE. In support of this model, we report that the human IL-4 promoter exists in multiple allelic forms that exhibit distinct transcriptional activities in IL-4-positive T cells. A particular allele has an unusually high transcriptional activity. A nucleotide substitution within a recently described OAP40 element located just upstream of an NF-AT site (P sequence) appears to be largely responsible for the increased promotor strength of this particular allelic form of the IL-4 promoter. In EMSAs, this substitution results in a markedly enhanced affinity for sequence-specific complexes exhibiting an AP-1 specificity. The identification of allelic nucleotides, which results in overexpression of the IL-4 gene, provides specific targets for a comprehensive screening of atopic and nonatopic individuals and may provide a clue for genetic predisposition for atopy. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "overexpression", "start": 68, "end": 82}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 41, "end": 45}]}, {"trigger": {"text": "overexpression", "start": 786, "end": 800}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 745, "end": 749}]}, {"trigger": {"text": "positive", "start": 1033, "end": 1041}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1028, "end": 1032}]}, {"trigger": {"text": "overexpression", "start": 1555, "end": 1569}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1577, "end": 1581}]}], "positive regulation": [{"trigger": {"text": "mediate", "start": 60, "end": 67}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 41, "end": 45}, {"role": "CSite", "text": "promoter", "start": 46, "end": 54}, {"role": "Theme", "text": "overexpression", "start": 68, "end": 82}]}, {"trigger": {"text": "overexpression", "start": 68, "end": 82}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 68, "end": 82}]}, {"trigger": {"text": "result", "start": 776, "end": 782}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 786, "end": 800}]}, {"trigger": {"text": "overexpression", "start": 786, "end": 800}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 786, "end": 800}]}, {"trigger": {"text": "high", "start": 1088, "end": 1092}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 1093, "end": 1117}]}, {"trigger": {"text": "results", "start": 1544, "end": 1551}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1555, "end": 1569}]}, {"trigger": {"text": "overexpression", "start": 1555, "end": 1569}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1555, "end": 1569}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 998, "end": 1013}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 929, "end": 933}]}, {"trigger": {"text": "transcriptional activity", "start": 1093, "end": 1117}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 929, "end": 933}]}]}}, "schema": []}
{"input": "IL-10 cooperates with TNF-alpha to activate HIV-1 from latently and acutely infected cells of monocyte/macrophage lineage. \nIL-10 is elevated in HIV-1-infected individuals and has been implicated in disease progression. In this study, we investigated the effects of IL-10 on the activation of HIV-1 from infected monocytes and macrophages. Although IL-10 alone did not induce HIV-1 replication, in the presence of TNF-alpha, IL-10 markedly enhanced virion production from a chronically infected promonocytic cell line (U1) and in acutely infected monocyte-derived macrophages. Neutralizing mAbs to IL-10 and TNF-alpha indicated that both cytokines were essential for the induction and were required to generate a synergistic increase in virus expression. The effects of the two cytokines were distinguishable functionally since pretreatment with TNF-alpha attenuated the cytokine cooperativity, while pretreatment with IL-10 potentiated their cooperativity, suggesting that IL-10 and TNF-alpha play different roles in the activation of virus. Northern blot analysis as well as Ab blocking and cytokine secretion studies indicated that the induction of either endogenous TNF-alpha or IL-10 was not involved in the cooperativity, nor was an up-regulation of TNF-alpha receptors. In combination with TNF-alpha, IL-10 stimulated activating protein-1 (AP-1) and nuclear factor (NF)-kappa B binding activities and cooperated to increase HIV-1 steady-state mRNA levels and enhance long terminal repeat-directed transcription through activation of the NF-kappa B binding sites, suggesting the IL-10 effect occurs at least in part at the transcriptional level. These results indicate that IL-10, in addition to down-regulating the cellular immune response to HIV-1, may also play a role in TNF-alpha-mediated activation of HIV-1 replication in the monocyte/macrophage lineage. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "elevated", "start": 133, "end": 141}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 124, "end": 129}]}, {"trigger": {"text": "induction", "start": 1139, "end": 1148}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1170, "end": 1179}]}, {"trigger": {"text": "induction", "start": 1139, "end": 1148}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 1183, "end": 1188}]}]}}, "schema": []}
{"input": "The promoter and 5' flanking sequences controlling human B29 gene expression. \nThe product of the B-cell-specific B29 gene (B29, Ig beta, CD79b) is essential for Ig-mediated B-cell activation via the B-cell antigen receptor complex (BCR) on human and murine B lymphocytes. To better understand the regulation of this pivotal gene, we have analyzed the human genomic DNA sequence upstream of the B29 ATG start codon for transcriptional control activity. The human B29 gene lacks either a TATA or a CAAT box and transcription is initiated at multiple sites. The minimal promoter of the human B29 gene is contained within a 193-bp region 5' of these multiple start sites. This minimal promoter exhibits B-cell-specific activity and contains SP1, ETS, OCT, and IKAROS/LYF-1 transcription factor motifs. All these motifs are strikingly conserved in sequence and placement relative to the previously characterized murine B29 promoter. Additional upstream gene segments dramatically affected B29 minimal promoter activity. A newly identified motif called the B29 conserved sequence (BCS), found upstream of both human and murine B29 promoters, appears to stimulate B29 transcription through a novel mechanism. A single BCS had little effect either on the minimal B29 promoter or on a heterologous promoter. Instead, the BCS stimulated transcription by counteracting 5' negative regulatory DNA sequences that block the activity of the B29 minimal promoter in its absence. These findings indicate that B29 gene expression is controlled by the complex interplay of positive and negative regulatory elements. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 66, "end": 76}, "arguments": [{"role": "Theme", "text": "B29", "start": 57, "end": 60}]}, {"trigger": {"text": "expression", "start": 1502, "end": 1512}, "arguments": [{"role": "Theme", "text": "B29", "start": 1493, "end": 1496}]}], "negative regulation": [{"trigger": {"text": "block", "start": 1401, "end": 1406}, "arguments": [{"role": "Theme", "text": "B29", "start": 1427, "end": 1430}, {"role": "Site", "text": "minimal promoter", "start": 1431, "end": 1447}]}], "positive regulation": [{"trigger": {"text": "stimulated", "start": 1317, "end": 1327}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1162, "end": 1175}]}], "regulation": [{"trigger": {"text": "controlling", "start": 39, "end": 50}, "arguments": [{"role": "Theme", "text": "expression", "start": 66, "end": 76}]}, {"trigger": {"text": "regulation", "start": 298, "end": 308}, "arguments": [{"role": "Theme", "text": "B29", "start": 395, "end": 398}]}, {"trigger": {"text": "affected", "start": 976, "end": 984}, "arguments": [{"role": "Theme", "text": "B29", "start": 985, "end": 988}, {"role": "Site", "text": "minimal promoter", "start": 989, "end": 1005}]}, {"trigger": {"text": "stimulate", "start": 1148, "end": 1157}, "arguments": [{"role": "Cause", "text": "B29", "start": 1052, "end": 1055}, {"role": "Theme", "text": "transcription", "start": 1162, "end": 1175}]}, {"trigger": {"text": "effect", "start": 1227, "end": 1233}, "arguments": [{"role": "Theme", "text": "B29", "start": 1256, "end": 1259}, {"role": "Site", "text": "promoter", "start": 1260, "end": 1268}]}, {"trigger": {"text": "controlled", "start": 1516, "end": 1526}, "arguments": [{"role": "Theme", "text": "expression", "start": 1502, "end": 1512}]}], "transcription": [{"trigger": {"text": "initiated", "start": 527, "end": 536}, "arguments": [{"role": "Theme", "text": "B29", "start": 463, "end": 466}]}, {"trigger": {"text": "transcription", "start": 1162, "end": 1175}, "arguments": [{"role": "Theme", "text": "B29", "start": 1158, "end": 1161}]}]}}, "schema": []}
{"input": "MEK1 and the extracellular signal-regulated kinases are required for the stimulation of IL-2 gene transcription in T cells. \nTCR engagement stimulates the activation of the protein kinase Raf-1. Active Raf-1 phosphorylates and activates the mitogen-activated protein (MAP) kinase/extracellular signal-regulated kinase kinase 1 (MEK1), which in turn phosphorylates and activates the MAP kinases/extracellular signal regulated kinases, ERK1 and ERK2. Raf-1 activity promotes IL-2 production in activated T lymphocytes. Therefore, we sought to determine whether MEK1 and ERK activities also stimulate IL-2 gene transcription. Expression of constitutively active Raf-1 or MEK1 in Jurkat T cells enhanced the stimulation of IL-2 promoter-driven transcription stimulated by a calcium ionophore and PMA, and together with a calcium ionophore the expression of each protein was sufficient to stimulate NF-AT activity. Expression of MEK1-interfering mutants inhibited the stimulation of IL-2 promoter-driven transcription and blocked the ability of constitutively active Ras and Raf-1 to costimulate NF-AT activity with a calcium ionophore. Expression of the MAP kinase-specific phosphatase, MKP-1, which blocks ERK activation, inhibited IL-2 promoter and NF-AT-driven transcription stimulated by a calcium ionophore and PMA, and in addition, MKP-1 neutralized the transcriptional enhancement caused by active Raf-1 and MEK1 expression. We conclude that the MAP kinase signal transduction pathway consisting of Raf-1, MEK1, and ERK1 and ERK2 functions in the stimulation IL-2 gene transcription in activated T lymphocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 478, "end": 488}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 473, "end": 477}]}, {"trigger": {"text": "expression", "start": 839, "end": 849}, "arguments": [{"role": "Theme", "text": "Raf-1", "start": 659, "end": 664}]}, {"trigger": {"text": "expression", "start": 839, "end": 849}, "arguments": [{"role": "Theme", "text": "MEK1", "start": 668, "end": 672}]}, {"trigger": {"text": "Expression", "start": 1132, "end": 1142}, "arguments": [{"role": "Theme", "text": "MKP-1", "start": 1183, "end": 1188}]}], "phosphorylation": [{"trigger": {"text": "phosphorylates", "start": 208, "end": 222}, "arguments": [{"role": "Theme", "text": "MEK1", "start": 328, "end": 332}]}, {"trigger": {"text": "phosphorylates", "start": 349, "end": 363}, "arguments": [{"role": "Theme", "text": "ERK1", "start": 434, "end": 438}]}, {"trigger": {"text": "phosphorylates", "start": 349, "end": 363}, "arguments": [{"role": "Theme", "text": "ERK2", "start": 443, "end": 447}]}], "positive regulation": [{"trigger": {"text": "required", "start": 56, "end": 64}, "arguments": [{"role": "Cause", "text": "MEK1", "start": 0, "end": 4}, {"role": "Theme", "text": "stimulation", "start": 73, "end": 84}]}, {"trigger": {"text": "required", "start": 56, "end": 64}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 73, "end": 84}]}, {"trigger": {"text": "stimulation", "start": 73, "end": 84}, "arguments": [{"role": "Theme", "text": "transcription", "start": 98, "end": 111}]}, {"trigger": {"text": "stimulates the activation", "start": 140, "end": 165}, "arguments": [{"role": "Theme", "text": "Raf-1", "start": 188, "end": 193}]}, {"trigger": {"text": "phosphorylates", "start": 208, "end": 222}, "arguments": [{"role": "Cause", "text": "Raf-1", "start": 202, "end": 207}, {"role": "Theme", "text": "phosphorylates", "start": 208, "end": 222}]}, {"trigger": {"text": "activates", "start": 227, "end": 236}, "arguments": [{"role": "Cause", "text": "Raf-1", "start": 202, "end": 207}, {"role": "Theme", "text": "MEK1", "start": 328, "end": 332}]}, {"trigger": {"text": "phosphorylates", "start": 349, "end": 363}, "arguments": [{"role": "Cause", "text": "MEK1", "start": 328, "end": 332}, {"role": "Theme", "text": "phosphorylates", "start": 349, "end": 363}]}, {"trigger": {"text": "activates", "start": 368, "end": 377}, "arguments": [{"role": "Cause", "text": "MEK1", "start": 328, "end": 332}, {"role": "Theme", "text": "ERK1", "start": 434, "end": 438}]}, {"trigger": {"text": "activates", "start": 368, "end": 377}, "arguments": [{"role": "Cause", "text": "MEK1", "start": 328, "end": 332}, {"role": "Theme", "text": "ERK2", "start": 443, "end": 447}]}, {"trigger": {"text": "promotes", "start": 464, "end": 472}, "arguments": [{"role": "Cause", "text": "Raf-1", "start": 449, "end": 454}, {"role": "Theme", "text": "production", "start": 478, "end": 488}]}, {"trigger": {"text": "stimulate", "start": 588, "end": 597}, "arguments": [{"role": "Cause", "text": "MEK1", "start": 559, "end": 563}, {"role": "Theme", "text": "transcription", "start": 608, "end": 621}]}, {"trigger": {"text": "stimulate", "start": 588, "end": 597}, "arguments": [{"role": "Theme", "text": "transcription", "start": 608, "end": 621}]}, {"trigger": {"text": "Expression", "start": 623, "end": 633}, "arguments": [{"role": "Theme", "text": "Raf-1", "start": 659, "end": 664}]}, {"trigger": {"text": "Expression", "start": 623, "end": 633}, "arguments": [{"role": "Theme", "text": "MEK1", "start": 668, "end": 672}]}, {"trigger": {"text": "expression", "start": 1416, "end": 1426}, "arguments": [{"role": "Theme", "text": "Raf-1", "start": 1401, "end": 1406}]}, {"trigger": {"text": "expression", "start": 1416, "end": 1426}, "arguments": [{"role": "Theme", "text": "MEK1", "start": 1411, "end": 1415}]}, {"trigger": {"text": "stimulation", "start": 1550, "end": 1561}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1572, "end": 1585}]}], "regulation": [{"trigger": {"text": "functions", "start": 1533, "end": 1542}, "arguments": [{"role": "Cause", "text": "Raf-1", "start": 1502, "end": 1507}, {"role": "Theme", "text": "stimulation", "start": 1550, "end": 1561}]}, {"trigger": {"text": "functions", "start": 1533, "end": 1542}, "arguments": [{"role": "Cause", "text": "MEK1", "start": 1509, "end": 1513}, {"role": "Theme", "text": "stimulation", "start": 1550, "end": 1561}]}, {"trigger": {"text": "functions", "start": 1533, "end": 1542}, "arguments": [{"role": "Cause", "text": "ERK1", "start": 1519, "end": 1523}, {"role": "Theme", "text": "stimulation", "start": 1550, "end": 1561}]}, {"trigger": {"text": "functions", "start": 1533, "end": 1542}, "arguments": [{"role": "Cause", "text": "ERK2", "start": 1528, "end": 1532}, {"role": "Theme", "text": "stimulation", "start": 1550, "end": 1561}]}, {"trigger": {"text": "functions", "start": 1533, "end": 1542}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 1550, "end": 1561}]}], "transcription": [{"trigger": {"text": "transcription", "start": 98, "end": 111}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 88, "end": 92}]}, {"trigger": {"text": "transcription", "start": 608, "end": 621}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 598, "end": 602}]}, {"trigger": {"text": "transcription", "start": 1572, "end": 1585}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1562, "end": 1566}]}]}}, "schema": []}
{"input": "Cross-linking of Fc gamma receptors activates HIV-1 long terminal repeat-driven transcription in human monocytes. \nElevation of the levels of circulating immune complexes frequently accompanies HIV-1 infection and is a prognostic indicator of clinical progression from asymptomatic infection to AIDS. Here we report that cross-linking of Fc gamma RI or Fc gamma RII by adherent human IgG or by specific anti-Fc gamma R mAb activates HIV-1 gene expression in the human monocytic cell line BF24 and increased HIV RNA expression in monocytes from HIV infected patients as assayed by reverse transcription-PCR. In THP-1 cells, Fc gamma R cross-linking induced NF-kappa B, which is known to bind to the regulatory region of the long terminal repeat (LTR) of HIV-1 and to activate HIV-1 transcription. Anti-TNF-alpha antibody but not anti-IL-1 beta antibody strongly inhibited both the induction of HIV-1-LTR-driven transcription and the induction of NF-kappa B by Fc gamma R cross-linking. These results indicate that Fc gamma R can mediate a TNF-alpha-dependent induction of HIV-1 gene transcription and suggest that immune complexes may contribute to the pathophysiology of HIV-1 infection by augmenting viral replication in monocytes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 321, "end": 334}, "arguments": [{"role": "Theme", "text": "Fc gamma RI", "start": 338, "end": 349}]}, {"trigger": {"text": "cross-linking", "start": 321, "end": 334}, "arguments": [{"role": "Theme", "text": "Fc gamma RII", "start": 353, "end": 365}]}]}}, "schema": []}
{"input": "The effect of Toremifene on the expression of some genes in human mononuclear cells. \nToremifene exerts multiple and varied effects on the gene expression of human peripheral mononuclear cells. After short-term, in vitro exposure to therapeutical levels, distinct changes in P-glycoprotein, steroid receptors, p53 and Bcl-2 expression take place. In view of the increasing use of antiestrogens in cancer therapy and prevention, there is obvious merit in long-term in vivo studies to be conducted. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "p53", "start": 310, "end": 313}]}, {"trigger": {"text": "expression", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 318, "end": 323}]}], "regulation": [{"trigger": {"text": "changes", "start": 264, "end": 271}, "arguments": [{"role": "Theme", "text": "expression", "start": 324, "end": 334}]}]}}, "schema": []}
{"input": "Identification of an ionomycin/cyclosporin A-responsive element within the human T cell receptor gamma enhancer. \nActivation through the Ca2+/calcineurin pathway is essential to the transcription of many cytokine genes. The conserved cis-acting sequence, GGAAAA, and transcription factors binding to this sequence are involved in the response to increased intracellular Ca2+ concentrations. Here we report the identification and importance of the same sequence in a non-cytokine gene, the human T cell receptor gamma (TCRG) enhancer. Results from site-directed mutations and electrophoretic mobility shift assays strongly suggest that this sequence mediates the ionomycin-induced activation of the TCRG enhancer. Our studies provide an explanation for a previous observation that TCRG mRNA levels, but not mRNA levels for T cell receptor alpha and -beta, are increased by ionomycin treatment. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "mediates", "start": 649, "end": 657}, "arguments": [{"role": "Theme", "text": "activation", "start": 680, "end": 690}]}, {"trigger": {"text": "activation", "start": 680, "end": 690}, "arguments": [{"role": "Theme", "text": "TCRG", "start": 698, "end": 702}, {"role": "Site", "text": "enhancer", "start": 703, "end": 711}]}, {"trigger": {"text": "increased", "start": 859, "end": 868}, "arguments": [{"role": "Theme", "text": "TCRG", "start": 780, "end": 784}]}]}}, "schema": []}
{"input": "Inhibition of NF-kappa B activation in human T-cell lines by anetholdithiolthione. \nNuclear factor (NF)-kappa B is a redox sensitive cytosolic transcription factor. Redox regulation of NF-kappa B has been implicated in the activation of the human immuno-deficiency virus (HIV). Therefore, inhibition of NF-kappa B activation may be an effective strategy for acquired immunodeficiency syndrome therapy. Anetholdithiolthione (ADT, 5-[p-methoxyphenyl]-3H-1,2-dithiol-3-thione) is an antioxidant which has been used to protect against acetaminophen- and CCl4-induced hepatotoxicity, lipid peroxidation, radiation injury, and also has been used clinically as an anti-choleretic agent. The present study examined the effect of ADT pretreatment on NF-kappa B activation in response to a variety of stimuli such as H2O2, phorbol myristate acetate (PMA) or tumor necrosis factor alpha (TNF alpha). PMA and TNF alpha induced activation of (NF)-kappa B in human Jurkat T-cells was partially inhibited by ADT (0.1 mM) pretreatment. ADT (0.1 mM) also inhibited H2O2 induced activation of the transcription factor in the peroxide sensitive human Wurzburg T-cells. Furthermore, ADT treated Wurzburg cells had significantly higher glutathione levels as compared with untreated cells. H2O2 induced lipid peroxidation in Wurzburg cells was remarkably inhibited by ADT pretreatment. ADT, a pro-glutathione antioxidant, was observed to be capable of modulating NF-kappa B activation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "In vivo anergized CD4+ T cells express perturbed AP-1 and NF-kappa B transcription factors. \nAnergy is a major mechanism to ensure antigen-specific tolerance in T lymphocytes in the adult. In vivo, anergy has mainly been studied at the cellular level. In this study, we used the T-cell-activating superantigen staphylococcal enterotoxin A (SEA) to investigate molecular mechanisms of T-lymphocyte anergy in vivo. Injection of SEA to adult mice activates CD4+ T cells expressing certain T-cell receptor (TCR) variable region beta-chain families and induces strong and rapid production of interleukin 2 (IL-2). In contrast, repeated injections of SEA cause CD4+ T-cell deletion and anergy in the remaining CD4+ T cells, characterized by reduced expression of IL-2 at mRNA and protein levels. We analyzed expression of AP-1, NF-kappa B, NF-AT, and octamer binding transcription factors, which are known to be involved in the regulation of IL-2 gene promoter activity. Large amounts of AP-1 and NF-kappa B and significant quantities of NF-AT were induced in SEA-activated CD4+ spleen T cells, whereas Oct-1 and Oct-2 DNA binding activity was similar in both resting and activated T cells. In contrast, anergic CD4+ T cells contained severely reduced levels of AP-1 and Fos/Jun-containing NF-AT complexes but expressed significant amounts of NF-kappa B and Oct binding proteins after SEA stimulation. Resolution of the NF-kappa B complex demonstrated predominant expression of p50-p65 heterodimers in activated CD4+ T cells, while anergic cells mainly expressed the transcriptionally inactive p50 homodimer. These alterations of transcription factors are likely to be responsible for repression of IL-2 in anergic T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 1117, "end": 1133}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 1097, "end": 1102}]}, {"trigger": {"text": "binding activity", "start": 1117, "end": 1133}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 1107, "end": 1112}]}], "gene expression": [{"trigger": {"text": "production", "start": 573, "end": 583}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 602, "end": 606}]}, {"trigger": {"text": "protein", "start": 774, "end": 781}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 757, "end": 761}]}, {"trigger": {"text": "expression", "start": 1458, "end": 1468}, "arguments": [{"role": "Theme", "text": "p50", "start": 1472, "end": 1475}]}, {"trigger": {"text": "expression", "start": 1458, "end": 1468}, "arguments": [{"role": "Theme", "text": "p65", "start": 1476, "end": 1479}]}, {"trigger": {"text": "expressed", "start": 1547, "end": 1556}, "arguments": [{"role": "Theme", "text": "p50", "start": 1588, "end": 1591}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "mRNA", "start": 765, "end": 769}]}, {"trigger": {"text": "reduced", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "protein", "start": 774, "end": 781}]}, {"trigger": {"text": "reduced", "start": 1238, "end": 1245}, "arguments": [{"role": "Theme", "text": "Fos", "start": 1265, "end": 1268}]}, {"trigger": {"text": "reduced", "start": 1238, "end": 1245}, "arguments": [{"role": "Theme", "text": "Jun", "start": 1269, "end": 1272}]}, {"trigger": {"text": "repression", "start": 1679, "end": 1689}, "arguments": [{"role": "Cause", "text": "expressed", "start": 1547, "end": 1556}, {"role": "Theme", "text": "IL-2", "start": 1693, "end": 1697}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 548, "end": 555}, "arguments": [{"role": "Theme", "text": "production", "start": 573, "end": 583}]}], "transcription": [{"trigger": {"text": "mRNA", "start": 765, "end": 769}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 757, "end": 761}]}]}}, "schema": []}
{"input": "Surfactant suppresses NF-kappa B activation in human monocytic cells. \nIn addition to biophysical properties, pulmonary surfactant has immunomodulatory activity. We previously demonstrated that both synthetic (Exosurf) and modified natural surfactant (Survanta) downregulated endotoxin-stimulated inflammatory cytokine mRNA levels and protein products (tumor necrosis factor-alpha [TNF], interleukin-1-beta [IL-1], interleukin-6 [IL-6]) in human alveolar macrophages. In this study, we report that both Exosurf and Survanta suppress TNF mRNA and secretion (85 +/- 4% mean percent inhibition +/- SEM by Exosurf; 71 +/- 6% by Survanta) by endotoxin-stimulated THP-1, a human monocytic cell line. Because surfactant downregulated inflammatory cytokine production similarly in both normal human alveolar macrophages and the THP-1 cell line, we used this cell line to investigate whether surfactant affected transcriptional mechanisms. Specifically, we examined nuclear factor-kappa B (NF-kappa B) activation because it is crucial in transcriptional regulation of many inflammatory cytokine genes including TNF, IL-1, and IL-6. Electrophoretic mobility shift assays showed that both surfactants decreased activation of NF-kappa B. The presence of both p65 and p50 NF-kappa B components in LPS-activated THP-1 cells was confirmed by specific antibody induction of supershifts in mobility assays. These results are the first to suggest that surfactant's suppressive effects on inflammatory cytokine production may involve transcriptional regulation through inhibition of NF-kappa B activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "presence", "start": 1230, "end": 1238}, "arguments": [{"role": "Theme", "text": "p65", "start": 1247, "end": 1250}]}, {"trigger": {"text": "presence", "start": 1230, "end": 1238}, "arguments": [{"role": "Theme", "text": "p50", "start": 1255, "end": 1258}]}], "localization": [{"trigger": {"text": "secretion", "start": 546, "end": 555}, "arguments": [{"role": "Theme", "text": "TNF", "start": 533, "end": 536}]}], "negative regulation": [{"trigger": {"text": "downregulated", "start": 262, "end": 275}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 286, "end": 296}]}, {"trigger": {"text": "suppress", "start": 524, "end": 532}, "arguments": [{"role": "Theme", "text": "TNF", "start": 533, "end": 536}]}, {"trigger": {"text": "suppress", "start": 524, "end": 532}, "arguments": [{"role": "Theme", "text": "secretion", "start": 546, "end": 555}]}], "positive regulation": [{"trigger": {"text": "stimulated", "start": 286, "end": 296}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 353, "end": 380}]}, {"trigger": {"text": "stimulated", "start": 286, "end": 296}, "arguments": [{"role": "Theme", "text": "interleukin-1-beta", "start": 388, "end": 406}]}, {"trigger": {"text": "stimulated", "start": 286, "end": 296}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 430, "end": 434}]}], "regulation": [{"trigger": {"text": "transcriptional regulation", "start": 1029, "end": 1055}, "arguments": [{"role": "Theme", "text": "TNF", "start": 1102, "end": 1105}]}, {"trigger": {"text": "transcriptional regulation", "start": 1029, "end": 1055}, "arguments": [{"role": "Theme", "text": "IL-1", "start": 1107, "end": 1111}]}, {"trigger": {"text": "transcriptional regulation", "start": 1029, "end": 1055}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1117, "end": 1121}]}]}}, "schema": []}
{"input": "A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p [see comments] \nTrapoxin is a microbially derived cyclotetrapeptide that inhibits histone deacetylation in vivo and causes mammalian cells to arrest in the cell cycle. A trapoxin affinity matrix was used to isolate two nuclear proteins that copurified with histone deacetylase activity. Both proteins were identified by peptide microsequencing, and a complementary DNA encoding the histone deacetylase catalytic subunit (HD1) was cloned from a human Jurkat T cell library. As the predicted protein is very similar to the yeast transcriptional regulator Rpd3p, these results support a role for histone deacetylase as a key regulator of eukaryotic transcription. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Coexpression of the interleukin-13 and interleukin-4 genes correlates with their physical linkage in the cytokine gene cluster on human chromosome 5q23-31. \nInterleukin-13 (IL-13) and IL-4 are cytokines produced by T cells that are encoded by the q23-31 region of human chromosome 5. To investigate the regulation of IL-13 gene expression by T cells, we isolated and sequenced the human IL-13 gene, analyzed its 5'-flanking region for potential transcriptional activation elements, and examined its expression in nontransformed T-lineage cell populations. The human IL-13 gene was located 12.5-kb upstream of the IL-4 gene and 2-kb downstream of a CpG island. The IL-13 gene 5' flank region included a segment with sequence homology to P elements of the IL-4 promoter involved in transcriptional activation in T cells. Mutation of the IL-13 P element site significantly reduced IL-13 promoter activity in response to T-cell activation. Oligonucleotides containing the IL-13 or IL-4 P element sites specifically bound the transcriptional activator protein, nuclear factor-activated T cells, preformed (NF-ATp), when incubated with nuclear protein extracts from activated T cells. Similar to IL-4, IL-13 mRNA expression was highest in T-cell populations enriched for cells that had previously been primed in vivo or in vitro, indicating that priming increases the expression of the IL-13 and IL-4 genes in a coordinate manner. Because the primed T cells contain higher levels of nuclear NF-ATp, capable of binding to P elements of the IL-4 and IL-13 promoters, than do freshly-isolated T cells, the NF-AT-binding P elements are attractive candidates to mediate the coordinate expression of these two cytokine genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "linkage", "start": 90, "end": 97}, "arguments": [{"role": "Theme", "text": "interleukin-13", "start": 20, "end": 34}, {"role": "Theme2", "text": "interleukin-4", "start": 39, "end": 52}]}, {"trigger": {"text": "bound", "start": 1011, "end": 1016}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 968, "end": 973}, {"role": "Site", "text": "P element sites", "start": 982, "end": 997}, {"role": "Theme2", "text": "NF-ATp", "start": 1101, "end": 1107}]}, {"trigger": {"text": "bound", "start": 1011, "end": 1016}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 977, "end": 981}, {"role": "Site", "text": "P element sites", "start": 982, "end": 997}, {"role": "Theme2", "text": "NF-ATp", "start": 1101, "end": 1107}]}, {"trigger": {"text": "binding", "start": 1504, "end": 1511}, "arguments": [{"role": "Theme", "text": "NF-ATp", "start": 1485, "end": 1491}, {"role": "Site2", "text": "P elements", "start": 1515, "end": 1525}, {"role": "Theme2", "text": "IL-4", "start": 1533, "end": 1537}]}, {"trigger": {"text": "binding", "start": 1504, "end": 1511}, "arguments": [{"role": "Theme", "text": "NF-ATp", "start": 1485, "end": 1491}, {"role": "Site2", "text": "P elements", "start": 1515, "end": 1525}, {"role": "Theme2", "text": "IL-13", "start": 1542, "end": 1547}]}], "gene expression": [{"trigger": {"text": "Coexpression", "start": 0, "end": 12}, "arguments": [{"role": "Theme", "text": "interleukin-13", "start": 20, "end": 34}]}, {"trigger": {"text": "Coexpression", "start": 0, "end": 12}, "arguments": [{"role": "Theme", "text": "interleukin-4", "start": 39, "end": 52}]}, {"trigger": {"text": "produced", "start": 203, "end": 211}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 173, "end": 178}]}, {"trigger": {"text": "produced", "start": 203, "end": 211}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 184, "end": 188}]}, {"trigger": {"text": "expression", "start": 328, "end": 338}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 317, "end": 322}]}, {"trigger": {"text": "expression", "start": 499, "end": 509}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 387, "end": 392}]}, {"trigger": {"text": "expression", "start": 1362, "end": 1372}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 1380, "end": 1385}]}, {"trigger": {"text": "expression", "start": 1362, "end": 1372}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1390, "end": 1394}]}, {"trigger": {"text": "expression", "start": 1674, "end": 1684}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1533, "end": 1537}]}, {"trigger": {"text": "expression", "start": 1674, "end": 1684}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 1542, "end": 1547}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 870, "end": 877}, "arguments": [{"role": "Theme", "text": "in response to", "start": 902, "end": 916}]}], "positive regulation": [{"trigger": {"text": "transcriptional activation", "start": 780, "end": 806}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 754, "end": 758}]}, {"trigger": {"text": "increases", "start": 1348, "end": 1357}, "arguments": [{"role": "Theme", "text": "expression", "start": 1362, "end": 1372}]}, {"trigger": {"text": "higher levels", "start": 1460, "end": 1473}, "arguments": [{"role": "Theme", "text": "NF-ATp", "start": 1485, "end": 1491}]}, {"trigger": {"text": "mediate", "start": 1651, "end": 1658}, "arguments": [{"role": "Theme", "text": "expression", "start": 1674, "end": 1684}]}], "regulation": [{"trigger": {"text": "regulation", "start": 303, "end": 313}, "arguments": [{"role": "Theme", "text": "expression", "start": 328, "end": 338}]}, {"trigger": {"text": "involved", "start": 768, "end": 776}, "arguments": [{"role": "CSite", "text": "P elements", "start": 736, "end": 746}, {"role": "Cause", "text": "IL-4", "start": 754, "end": 758}, {"role": "Theme", "text": "transcriptional activation", "start": 780, "end": 806}]}, {"trigger": {"text": "in response to", "start": 902, "end": 916}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 878, "end": 883}, {"role": "Site", "text": "promoter", "start": 884, "end": 892}]}], "transcription": [{"trigger": {"text": "expression", "start": 1207, "end": 1217}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1190, "end": 1194}]}, {"trigger": {"text": "expression", "start": 1207, "end": 1217}, "arguments": [{"role": "Theme", "text": "IL-13", "start": 1196, "end": 1201}]}]}}, "schema": []}
{"input": "Transactivation of the interleukin-1alpha promoter by human T-cell leukemia virus type I and type II Tax proteins. \nHuman T-cell leukemia virus type I (HTLV-I)-infected T-cell lines constitutively produce high levels of interleukin-1alpha (IL-1alpha). To analyze the mechanisms that lead to the expression of IL-1alpha in HTLV-I-infected cell lines, we studied regulatory regions of the human IL-1alpha promoter involved in activation of the IL-1alpha gene. IL-1alpha promoter constructs drive transcription of the chloramphenicol acetyltransferase (CAT) reporter gene in HTLV-I-positive MT-2 cells, which constitutively produce IL-1alpha. In a cotransfection assay, the Tax protein of both HTLV-I and HTLV-II specifically activated transcription from the IL-1alpha promoter in an uninfected Jurkat cell line. A mutant Tax protein deficient in transactivation of genes by the nuclear factor (NF)-kappaB pathway was unable to induce transcriptional activity of IL-1alpha promoter-CAT constructs, but was rescued by exogenous provision of p65/p50 NF-kappaB. We found that two IL-1alpha kappaB-like sites (positions -1,065 to -1,056 and +646 to +655) specifically formed a complex with NF-kappaB-containing nuclear extract from MT-2 cells and that NF-kappaB bound with higher affinity to the 3' NF-kappaB binding site than to the 5' NF-kappaB site. Moreover, deletion of either 5' or 3' NF-kappaB sites reduced IL-1alpha promoter activity in MT-2 cells and transactivation of the IL-1alpha promoter by exogenous NF-kappaB and Tax in Jurkat cells. These data suggest a general role for Tax induction of IL-1alpha gene transcription by the NF-kappaB pathway. Expression of IL-1alpha by HTLV-I productively infected cells may be important in the hypercalcemia, osteolytic bone lesions, neutrophilia, elevation of C-reactive protein, and fever frequently seen in patients with HTLV-I-induced adult T-cell leukemia/lymphoma. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "produce", "start": 197, "end": 204}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 240, "end": 249}]}, {"trigger": {"text": "expression", "start": 295, "end": 305}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 309, "end": 318}]}, {"trigger": {"text": "produce", "start": 621, "end": 628}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 629, "end": 638}]}, {"trigger": {"text": "Expression", "start": 1654, "end": 1664}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 1668, "end": 1677}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 1400, "end": 1407}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 1454, "end": 1469}]}], "positive regulation": [{"trigger": {"text": "Transactivation", "start": 0, "end": 15}, "arguments": [{"role": "Theme", "text": "interleukin-1alpha", "start": 23, "end": 41}, {"role": "Site", "text": "promoter", "start": 42, "end": 50}, {"role": "Cause", "text": "Tax", "start": 101, "end": 104}]}, {"trigger": {"text": "high levels", "start": 205, "end": 216}, "arguments": [{"role": "Theme", "text": "produce", "start": 197, "end": 204}]}, {"trigger": {"text": "activation", "start": 424, "end": 434}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 442, "end": 451}]}, {"trigger": {"text": "transactivation", "start": 1454, "end": 1469}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 1477, "end": 1486}, {"role": "Site", "text": "promoter", "start": 1487, "end": 1495}, {"role": "Cause", "text": "Tax", "start": 1523, "end": 1526}]}, {"trigger": {"text": "transactivation", "start": 1454, "end": 1469}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 1477, "end": 1486}, {"role": "Site", "text": "promoter", "start": 1487, "end": 1495}]}, {"trigger": {"text": "induction", "start": 1586, "end": 1595}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1582, "end": 1585}]}, {"trigger": {"text": "by", "start": 1628, "end": 1630}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1614, "end": 1627}]}], "regulation": [{"trigger": {"text": "general role", "start": 1565, "end": 1577}, "arguments": [{"role": "Cause", "text": "induction", "start": 1586, "end": 1595}, {"role": "Theme", "text": "by", "start": 1628, "end": 1630}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1614, "end": 1627}, "arguments": [{"role": "Theme", "text": "IL-1alpha", "start": 1599, "end": 1608}]}]}}, "schema": []}
{"input": "Soluble tumor necrosis factor receptors inhibit phorbol myristate acetate and cytokine-induced HIV-1 expression chronically infected U1 cells. \nRecombinant human tumor necrosis factor (TNF) binding protein-1 (r-h TBP-1) and recombinant human soluble dimeric TNF receptor (rhu TNFR:Fc) were used to determine the relative contributions of TNF to phorbol myristate acetate (PMA) and cytokine-induced human immunodeficiency virus type 1 (HIV-1) replication in chronically infected cell lines. Treatment of HIV-1-infected promonocytic U1 cells with r-h-TBP-1 or rhu TNFR:Fc reduced PMA-induced HIV-1 p24 antigen production in a concentration-dependent manner, with a maximal inhibition of approximately 90%. Maximal inhibition of p24 antigen production in T-lymphocytic ACH-2 cells was 47% with r-hTBP-1 and 42% with rhu TNFR:Fc. r-hTBP-1 and rhu TNFR:Fc also decreased p24 antigen synthesized by U1 cells in response to other stimuli, including phytohemagglutinin (PHA)-induced supernatant, granulocyte-macrophage colony-stimulating factor, interleukin-6, and TNF. Addition of r-hTBP-1 to U1 cells during the last 4 h of a 24 h incubation with PMA still inhibited p24 antigen production by 15%. U1 cells stimulated with 10(-7) M PMA released approximately 1 ng/ml endogenous TBP-1 with an initial peak observed at 1 h and a second peak at 24 h after PMA stimulation. r-hTBP-1 also partially reversed inhibition of U1 cellular proliferation caused by PMA. Both r-hTBP-1 and rhu TNFR:Fc blocked PMA induction of nuclear factor (NK)- kappa B DNA-binding activity in U1 cells in association with decreases in HIV-1 replication. We conclude that soluble TNF receptors can inhibit stimuli-induced HIV-1 expression and NK- kappa B DNA-binding activity in chronically infected U1 cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 608, "end": 618}, "arguments": [{"role": "Theme", "text": "p24", "start": 596, "end": 599}]}, {"trigger": {"text": "production", "start": 738, "end": 748}, "arguments": [{"role": "Theme", "text": "p24", "start": 726, "end": 729}]}, {"trigger": {"text": "synthesized", "start": 878, "end": 889}, "arguments": [{"role": "Theme", "text": "p24", "start": 866, "end": 869}]}, {"trigger": {"text": "production", "start": 1173, "end": 1183}, "arguments": [{"role": "Theme", "text": "p24", "start": 1161, "end": 1164}]}], "localization": [{"trigger": {"text": "released", "start": 1230, "end": 1238}, "arguments": [{"role": "Theme", "text": "TBP-1", "start": 1272, "end": 1277}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 570, "end": 577}, "arguments": [{"role": "Theme", "text": "induced", "start": 582, "end": 589}]}, {"trigger": {"text": "inhibition", "start": 712, "end": 722}, "arguments": [{"role": "Theme", "text": "production", "start": 738, "end": 748}]}, {"trigger": {"text": "decreased", "start": 856, "end": 865}, "arguments": [{"role": "Theme", "text": "in response to", "start": 902, "end": 916}]}, {"trigger": {"text": "inhibited", "start": 1151, "end": 1160}, "arguments": [{"role": "Theme", "text": "production", "start": 1173, "end": 1183}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 582, "end": 589}, "arguments": [{"role": "Theme", "text": "production", "start": 608, "end": 618}]}, {"trigger": {"text": "in response to", "start": 902, "end": 916}, "arguments": [{"role": "Theme", "text": "synthesized", "start": 878, "end": 889}, {"role": "Cause", "text": "interleukin-6", "start": 1038, "end": 1051}]}, {"trigger": {"text": "in response to", "start": 902, "end": 916}, "arguments": [{"role": "Theme", "text": "synthesized", "start": 878, "end": 889}, {"role": "Cause", "text": "granulocyte-macrophage colony-stimulating factor", "start": 988, "end": 1036}]}, {"trigger": {"text": "in response to", "start": 902, "end": 916}, "arguments": [{"role": "Theme", "text": "synthesized", "start": 878, "end": 889}]}, {"trigger": {"text": "after", "start": 1341, "end": 1346}, "arguments": [{"role": "Theme", "text": "released", "start": 1230, "end": 1238}]}]}}, "schema": []}
{"input": "AM580, a stable benzoic derivative of retinoic acid, has powerful and selective cyto-differentiating effects on acute promyelocytic leukemia cells. \nAll-trans retinoic acid (ATRA) is successfully used in the cyto-differentiating treatment of acute promyelocytic leukemia (APL). Paradoxically, APL cells express PML-RAR, an aberrant form of the retinoic acid receptor type alpha (RAR alpha) derived from the leukemia-specific t(15;17) chromosomal translocation. We show here that AM580, a stable retinobenzoic derivative originally synthesized as a RAR alpha agonist, is a powerful inducer of granulocytic maturation in NB4, an APL-derived cell line, and in freshly isolated APL blasts. After treatment of APL cells with AM580 either alone or in combination with granulocyte colony-stimulating factor (G-CSF), the compound induces granulocytic maturation, as assessed by determination of the levels of leukocyte alkaline phosphatase, CD11b, CD33, and G-CSF receptor mRNA, at concentrations that are 10- to 100-fold lower than those of ATRA necessary to produce similar effects. By contrast, AM580 is not effective as ATRA in modulating the expression of these differentiation markers in the HL-60 cell line and in freshly isolated granulocytes obtained from the peripheral blood of chronic myelogenous leukemia patients during the stable phase of the disease. In NB4 cells, two other synthetic nonselective RAR ligands are capable of inducing LAP as much as AM580, whereas RAR beta- or RAR gamma-specific ligands are totally ineffective. These results show that AM580 is more powerful than ATRA in modulating the expression of differentiation antigens only in cells in which PML-RAR is present. Binding experiments, using COS-7 cells transiently transfected with PML-RAR and the normal RAR alpha, show that AM580 has a lower affinity than ATRA for both receptors. However, in the presence of PML-RAR, the synthetic retinoid is a much better transactivator of retinoic acid-responsive element-containing promoters than the natural retinoid, whereas, in the presence of RAR alpha, AM580 and ATRA have similar activity. This may explain the strong cyto-differentiating potential of AM580 in PML-RAR-containing leukemic cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "affinity", "start": 1824, "end": 1832}, "arguments": [{"role": "Theme", "text": "PML-RAR", "start": 1762, "end": 1769}]}, {"trigger": {"text": "affinity", "start": 1824, "end": 1832}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 1785, "end": 1794}]}], "gene expression": [{"trigger": {"text": "express", "start": 303, "end": 310}, "arguments": [{"role": "Theme", "text": "PML-RAR", "start": 311, "end": 318}]}, {"trigger": {"text": "expression", "start": 1139, "end": 1149}, "arguments": [{"role": "Theme", "text": "leukocyte alkaline phosphatase", "start": 901, "end": 931}]}, {"trigger": {"text": "expression", "start": 1139, "end": 1149}, "arguments": [{"role": "Theme", "text": "CD11b", "start": 933, "end": 938}]}, {"trigger": {"text": "expression", "start": 1139, "end": 1149}, "arguments": [{"role": "Theme", "text": "CD33", "start": 940, "end": 944}]}, {"trigger": {"text": "expression", "start": 1139, "end": 1149}, "arguments": [{"role": "Theme", "text": "G-CSF receptor", "start": 950, "end": 964}]}, {"trigger": {"text": "present", "start": 1685, "end": 1692}, "arguments": [{"role": "Theme", "text": "PML-RAR", "start": 1674, "end": 1681}]}, {"trigger": {"text": "containing", "start": 2195, "end": 2205}, "arguments": [{"role": "Theme", "text": "PML-RAR", "start": 2187, "end": 2194}]}], "positive regulation": [{"trigger": {"text": "derived", "start": 390, "end": 397}, "arguments": [{"role": "Theme", "text": "PML-RAR", "start": 311, "end": 318}]}, {"trigger": {"text": "inducing", "start": 1433, "end": 1441}, "arguments": [{"role": "Theme", "text": "LAP", "start": 1442, "end": 1445}]}], "regulation": [{"trigger": {"text": "modulating", "start": 1124, "end": 1134}, "arguments": [{"role": "Theme", "text": "expression", "start": 1139, "end": 1149}]}]}}, "schema": []}
{"input": "Transcriptional basis for hyporesponsiveness of the human inducible nitric oxide synthase gene to lipopolysaccharide/interferon-gamma. \nThe work reported here resolves, at the level of gene regulation, the controversy as to whether or not human monocytes/macrophages can produce nitric oxide (NO) when stimulated with lipopolysaccharide (LPS), with or without co-stimulation by interferon-gamma (IFN-gamma). Studies included structural comparison of the promoters for human and mouse inducible NO synthase (iNOS) genes, transfection and assay of human and mouse iNOS promoter regions in response to LPS +/- IFN-gamma, and electrophoretic mobility shift assays of kappa B response elements. Two explanations for hyporesponsiveness of the human iNOS promoter to LPS +/- IFN-gamma were found: (1) multiple inactivating nucleotide substitutions in the human counterpart of the enhancer element that has been shown to regulate LPS/IFN-gamma induced expression of the mouse iNOS gene; and (2) and absence of one or more nuclear factors in human macrophages (e.g., an LPS-inducible nuclear factor-kappa B/Rel complex), that is (are) required for maximal expression of the gene. The importance of resolution of this controversy is that future research in this area should be directed toward the understanding of alternative mechanisms that can result in the successful production of NO. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 944, "end": 954}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 968, "end": 972}]}, {"trigger": {"text": "expression", "start": 1147, "end": 1157}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 968, "end": 972}]}], "negative regulation": [{"trigger": {"text": "hyporesponsiveness", "start": 26, "end": 44}, "arguments": [{"role": "Theme", "text": "hyporesponsiveness", "start": 26, "end": 44}]}, {"trigger": {"text": "hyporesponsiveness", "start": 711, "end": 729}, "arguments": [{"role": "Theme", "text": "hyporesponsiveness", "start": 711, "end": 729}]}, {"trigger": {"text": "regulate", "start": 913, "end": 921}, "arguments": [{"role": "Theme", "text": "induced", "start": 936, "end": 943}]}], "positive regulation": [{"trigger": {"text": "explanations", "start": 694, "end": 706}, "arguments": [{"role": "Theme", "text": "hyporesponsiveness", "start": 711, "end": 729}, {"role": "Cause", "text": "regulate", "start": 913, "end": 921}]}, {"trigger": {"text": "explanations", "start": 694, "end": 706}, "arguments": [{"role": "Theme", "text": "hyporesponsiveness", "start": 711, "end": 729}]}, {"trigger": {"text": "induced", "start": 936, "end": 943}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 926, "end": 935}, {"role": "Theme", "text": "expression", "start": 944, "end": 954}]}, {"trigger": {"text": "induced", "start": 936, "end": 943}, "arguments": [{"role": "Theme", "text": "expression", "start": 944, "end": 954}]}, {"trigger": {"text": "required", "start": 1126, "end": 1134}, "arguments": [{"role": "Theme", "text": "expression", "start": 1147, "end": 1157}]}], "regulation": [{"trigger": {"text": "hyporesponsiveness", "start": 26, "end": 44}, "arguments": [{"role": "Theme", "text": "inducible nitric oxide synthase", "start": 58, "end": 89}, {"role": "Cause", "text": "interferon-gamma", "start": 117, "end": 133}]}, {"trigger": {"text": "hyporesponsiveness", "start": 26, "end": 44}, "arguments": [{"role": "Theme", "text": "inducible nitric oxide synthase", "start": 58, "end": 89}]}, {"trigger": {"text": "response", "start": 587, "end": 595}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 562, "end": 566}, {"role": "Site", "text": "promoter regions", "start": 567, "end": 583}, {"role": "Cause", "text": "IFN-gamma", "start": 607, "end": 616}]}, {"trigger": {"text": "response", "start": 587, "end": 595}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 562, "end": 566}, {"role": "Site", "text": "promoter regions", "start": 567, "end": 583}]}, {"trigger": {"text": "hyporesponsiveness", "start": 711, "end": 729}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 743, "end": 747}, {"role": "Site", "text": "promoter", "start": 748, "end": 756}, {"role": "Cause", "text": "IFN-gamma", "start": 768, "end": 777}]}, {"trigger": {"text": "hyporesponsiveness", "start": 711, "end": 729}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 743, "end": 747}, {"role": "Site", "text": "promoter", "start": 748, "end": 756}]}]}}, "schema": []}
{"input": "GATA transcription factors associate with a novel class of nuclear bodies in erythroblasts and megakaryocytes. \nThe nuclear distribution of GATA transcription factors in murine haemopoietic cells was examined by indirect immunofluorescence. Specific bright foci of GATA-1 fluorescence were observed in erythroleukaemia cells and primary murine erythroblasts and megakaryocytes, in addition to diffuse nucleoplasmic localization. These foci, which were preferentially found adjacent to nucleoli or at the nuclear periphery, did not represent sites of active transcription or binding of GATA-1 to consensus sites in the beta-globin loci. Immunoelectron microscopy demonstrated the presence of intensely labelled structures likely to represent the GATA-1 foci seen by immunofluorescence. The GATA-1 nuclear bodies differed from previously described nuclear structures and there was no co-localization with nuclear antigens involved in RNA processing or other ubiquitous (Spl, c-Jun and TBP) or haemopoietic (NF-E2) transcription factors. Interestingly, GATA-2 and GATA-3 proteins also localized to the same nuclear bodies in cell lines co-expressing GATA-1 and -2 or GATA-1 and -3 gene products. This pattern of distribution is, thus far, unique to the GATA transcription factors and suggests a protein-protein interaction with other components of the nuclear bodies via the GATA zinc finger domain. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 574, "end": 581}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 585, "end": 591}, {"role": "Site2", "text": "consensus sites", "start": 595, "end": 610}, {"role": "Theme2", "text": "beta-globin", "start": 618, "end": 629}]}], "gene expression": [{"trigger": {"text": "bright foci", "start": 250, "end": 261}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 265, "end": 271}]}, {"trigger": {"text": "co-expressing", "start": 1133, "end": 1146}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1147, "end": 1153}]}, {"trigger": {"text": "co-expressing", "start": 1133, "end": 1146}, "arguments": [{"role": "Theme", "text": "-2", "start": 1158, "end": 1160}]}, {"trigger": {"text": "co-expressing", "start": 1133, "end": 1146}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1164, "end": 1170}]}, {"trigger": {"text": "co-expressing", "start": 1133, "end": 1146}, "arguments": [{"role": "Theme", "text": "-3", "start": 1175, "end": 1177}]}], "localization": [{"trigger": {"text": "localization", "start": 415, "end": 427}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 265, "end": 271}, {"role": "ToLoc", "text": "nucleoplasmic", "start": 401, "end": 414}]}, {"trigger": {"text": "found", "start": 467, "end": 472}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 265, "end": 271}, {"role": "AtLoc", "text": "nucleoli", "start": 485, "end": 493}]}, {"trigger": {"text": "found", "start": 467, "end": 472}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 265, "end": 271}, {"role": "AtLoc", "text": "nuclear periphery", "start": 504, "end": 521}]}, {"trigger": {"text": "co-localization", "start": 882, "end": 897}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 973, "end": 978}]}, {"trigger": {"text": "co-localization", "start": 882, "end": 897}, "arguments": [{"role": "Theme", "text": "TBP", "start": 983, "end": 986}]}, {"trigger": {"text": "localized", "start": 1082, "end": 1091}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 1050, "end": 1056}, {"role": "AtLoc", "text": "nuclear bodies", "start": 1104, "end": 1118}]}, {"trigger": {"text": "localized", "start": 1082, "end": 1091}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 1061, "end": 1067}, {"role": "AtLoc", "text": "nuclear bodies", "start": 1104, "end": 1118}]}]}}, "schema": []}
{"input": "Permanent occupancy of the human immunodeficiency virus type 1 enhancer by NF-kappa B is needed for persistent viral replication in monocytes. \nThis work aimed to ascertain the role of kappaB-responsive elements of the human immunodeficiency virus type 1 (HIV-1) enhancer not only in early initiation but also in long-term maintenance of proviral transcription in cells of the monocytic lineage. For this purpose, we used three main approaches. The first was to abruptly terminate tumor necrosis factor-induced NF-kappaB binding to the enhancer sequences in U1 monocytic cells, using a short pulse of exogenous tumor necrosis factor. This resulted in concomitant decrease in nuclear NF-kappaB DNA-binding activity and endogenous long terminal repeat transcriptional activity. The second was to suppress the permanent NF-kappaB translocation induced by HIV-1 replication itself in chronically infected U937 cells, using a specific proteasome inhibitor (Z-LLL-H). As early as 2 h after addition of the inhibitor to the culture medium, there was an inhibition of both constitutive activation of NF-kappaB and HIV-1 genome expression. The third approach was to monitor the replication competence in U937 cells of an infectious HIV-1 provirus carrying point mutations in the kappaB-responsive elements of both long terminal repeats. Compared with its wild-type counterpart, this mutated provirus showed a profoundly decreased, Z-LLL-H-insensitive transcriptional and replicative activity in U937 monocytes. Together, our results indicate that occupancy of the viral enhancer by NF-kappaB (p50/p65) heterodimers is required for ongoing transcription of integrated HIV provirus in monocytes, even in cells chronically infected and permanently producing functional HIV Tat protein. Thus, the ability of HIV-1 replication to activate NF-kappaB is crucial to the intense self-perpetuated viral transcription observed in cells of the monocytic lineage. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "occupancy", "start": 1538, "end": 1547}, "arguments": [{"role": "Theme", "text": "p50", "start": 1584, "end": 1587}]}, {"trigger": {"text": "occupancy", "start": 1538, "end": 1547}, "arguments": [{"role": "Theme", "text": "p65", "start": 1588, "end": 1591}]}], "gene expression": [{"trigger": {"text": "producing", "start": 1736, "end": 1745}, "arguments": [{"role": "Theme", "text": "Tat", "start": 1761, "end": 1764}]}]}}, "schema": []}
{"input": "Efficient transcription and replication of simian immunodeficiency virus in the absence of NF-kappaB and Sp1 binding elements. \nTen mutants of the simian immunodeficiency virus (SIV) SIVmac239 bearing deletions (delta) or substitutions (subst) in the NF-kappaB and/or Sp1 binding elements were created, and the replicative capacities of the mutants were analyzed. All mutants, including one extensively mutagenized strain entirely missing the NF-kappaB and four Spl binding elements, replicated with wild-type kinetics and to a wild-type level in peripheral blood mononuclear cell cultures in 50 to 100% of the experiments. One group of mutants replicated very similarly to SIVmac239 in kinetics and yield in CEMxl74 cells (2xNFKappaB > or = SlVmac239 approximately deltaNFkappaB approximately deltaSpl234 approximately substNFkappaB approximately substSpl2 approximately substSp23), while a second group replicated with delayed or slightly delayed kinetics in CEMxl74 cells (SIVmac239 > substSp34 > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSp1 > substSpl234). Reversions or additional mutations were not detected in the U3 and R regions of proviral DNA from CEMxl74 cells infected with the SIVmac239 mutants. Similar results were obtained when mutants of SIVmacMER (a macrophage-competent derivative of SIVmac239) were tested in peripheral blood mononuclear cell and CEMx174 cultures. However, the growth of most mutated viruses was suppressed in primary rhesus monkey alveolar macrophages (SIVmacMER approximately 2xNFkappaB approximately substNFkappaB > deltaNFkappaB > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSpl > deltaSpl234 approximately substSpl2 > substSp23 approximately substSp34 approximately substSpl234 > or = SIVmac239). Thus, changes in the Sp1 binding sites had the most dramatic effects on SIVmac replication in primary macrophage cultures. Analysis of long terminal repeat-driven secreted alkaline phosphatase activity in transient assays showed that, unlike human immunodeficiency virus type 1, the SIV long terminal repeat possesses an enhancer region just upstream of the NF-kappaB element which maintains significant levels of basal transcription in the absence of NF-kappaB and Sp1 sites. This region is responsive to transactivation by Tat. In addition, the SIV TATA box was shown to be stronger than that of human immunodeficiency virus type 1. Therefore, the surprisingly high replicative capacity of NF-kappaB and Sp1 binding site mutants of SIVmac is due to unique features or the enhancer/promoter region. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Inactivation of IkappaBbeta by the tax protein of human T-cell leukemia virus type 1: a potential mechanism for constitutive induction of NF-kappaB. \nIn resting T lymphocytes, the transcription factor NF-kappaB is sequestered in the cytoplasm via interactions with members of the I kappa B family of inhibitors, including IkappaBalpha and IkappaBbeta. During normal T-cell activation, IkappaBalpha is rapidly phosphorylated, ubiquitinated, and degraded by the 26S proteasome, thus permitting the release of functional NF-kappaB. In contrast to its transient pattern of nuclear induction during an immune response, NF-kappaB is constitutively activated in cells expressing the Tax transforming protein of human T-cell leukemia virus type I (HTLV-1). Recent studies indicate that HTLV-1 Tax targets IkappaBalpha to the ubiquitin-proteasome pathway. However, it remains unclear how this viral protein induces a persistent rather than transient NF-kappaB response. In this report, we provide evidence that in addition to acting on IkappaBalpha, Tax stimulates the turnover Of IkappaBbeta via a related targeting mechanism. Like IkappaBalpha, Tax-mediated breakdown of IkappaBbeta in transfected T lymphocytes is blocked either by cell-permeable proteasome inhibitors or by mutation Of IkappaBbeta at two serine residues present within its N-terminal region. Despite the dual specificity of HTLV-1 Tax for IkappaBalpha and IkappaBbeta at the protein level, Tax selectively stimulates NF-kappaB-directed transcription of the IkappaBalpha gene. Consequently, IkappaBbeta protein expression is chronically downregulated in HTLV-1-infected T lymphocytes. These findings with IkappaBbeta provide a potential mechanism for the constitutive activation of NF-kappaB in Tax-expressing cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interactions", "start": 247, "end": 259}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 322, "end": 334}]}, {"trigger": {"text": "interactions", "start": 247, "end": 259}, "arguments": [{"role": "Theme", "text": "IkappaBbeta", "start": 339, "end": 350}]}], "gene expression": [{"trigger": {"text": "expressing", "start": 661, "end": 671}, "arguments": [{"role": "Theme", "text": "Tax", "start": 676, "end": 679}]}, {"trigger": {"text": "transfected", "start": 1179, "end": 1190}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1138, "end": 1141}]}, {"trigger": {"text": "expression", "start": 1572, "end": 1582}, "arguments": [{"role": "Theme", "text": "IkappaBbeta", "start": 1552, "end": 1563}]}, {"trigger": {"text": "expressing", "start": 1760, "end": 1770}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1756, "end": 1759}]}], "negative regulation": [{"trigger": {"text": "Inactivation", "start": 0, "end": 12}, "arguments": [{"role": "Theme", "text": "IkappaBbeta", "start": 16, "end": 27}, {"role": "Cause", "text": "tax", "start": 35, "end": 38}]}, {"trigger": {"text": "blocked", "start": 1208, "end": 1215}, "arguments": [{"role": "Theme", "text": "transfected", "start": 1179, "end": 1190}]}, {"trigger": {"text": "downregulated", "start": 1598, "end": 1611}, "arguments": [{"role": "Theme", "text": "expression", "start": 1572, "end": 1582}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 409, "end": 423}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 385, "end": 397}]}], "positive regulation": [{"trigger": {"text": "by", "start": 453, "end": 455}, "arguments": [{"role": "Theme", "text": "degraded", "start": 444, "end": 452}]}, {"trigger": {"text": "targets", "start": 789, "end": 796}, "arguments": [{"role": "Cause", "text": "Tax", "start": 785, "end": 788}, {"role": "Theme", "text": "ubiquitin-proteasome pathway", "start": 817, "end": 845}]}, {"trigger": {"text": "mediated", "start": 1142, "end": 1150}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1138, "end": 1141}, {"role": "Theme", "text": "breakdown", "start": 1151, "end": 1160}]}, {"trigger": {"text": "transfected", "start": 1179, "end": 1190}, "arguments": [{"role": "Theme", "text": "transfected", "start": 1179, "end": 1190}]}, {"trigger": {"text": "stimulates", "start": 1468, "end": 1478}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1452, "end": 1455}, {"role": "Theme", "text": "directed", "start": 1489, "end": 1497}]}, {"trigger": {"text": "directed", "start": 1489, "end": 1497}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1498, "end": 1511}]}], "protein catabolism": [{"trigger": {"text": "degraded", "start": 444, "end": 452}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 385, "end": 397}]}, {"trigger": {"text": "ubiquitin-proteasome pathway", "start": 817, "end": 845}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 797, "end": 809}]}, {"trigger": {"text": "breakdown", "start": 1151, "end": 1160}, "arguments": [{"role": "Theme", "text": "IkappaBbeta", "start": 1164, "end": 1175}]}], "regulation": [{"trigger": {"text": "acting", "start": 1017, "end": 1023}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1027, "end": 1039}, {"role": "Cause", "text": "Tax", "start": 1041, "end": 1044}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1498, "end": 1511}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1519, "end": 1531}]}]}}, "schema": []}
{"input": "Role of EGR1 in regulation of stimulus-dependent CD44 transcription in B lymphocytes. \nThe immediate-early gene egr-1 encodes a transcription factor (EGR1) that links B-cell antigen receptor (BCR) signals to downstream activation events through the regulation of previously unidentified target genes. Here we identify the gene encoding the lymphocyte homing and migration protein CD44 as a target of EGR1 regulation in B cells. BCR-induced increases in CD44 mRNA expression and transcription levels are shown to occur in EGR1-expressing but not in nonexpressing subclones of the B-cell line WEHI-231. Kinetics of egr-1 transcription and the appearance of nuclear EGR1 protein precede CD44 induction and occur within 30 min after stimulation in the EGR1-expressing subclone. A single EGR1 binding motif is demonstrated at bp -301 of the human CD44 promoter. Cotransfection of a CD44 promoter-chloramphenicol acetyltransferase reporter construct with an egr-1 expression vector resulted in a 6.5- to 8.5-fold induction of transcriptional activity relative to an empty expression vector. The EGR1 binding motif was shown to be necessary for stimulus-induced expression of a CD44 promoter-chloramphenicol acetyltransferase reporter construct in nontransformed B lymphocytes and was required for transactivation by an EGR1 expression vector in a B-cell line. These studies identify EGR1 as an intermediary linking BCR-derived signals to the induction of CD44. The relevance of these molecular events to BCR signal transduction and antigen-stimulated B-cell-mediated immune responses is discussed. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 526, "end": 536}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 521, "end": 525}]}, {"trigger": {"text": "nonexpressing", "start": 548, "end": 561}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 521, "end": 525}]}, {"trigger": {"text": "expressing", "start": 753, "end": 763}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 748, "end": 752}]}, {"trigger": {"text": "expression", "start": 958, "end": 968}, "arguments": [{"role": "Theme", "text": "egr-1", "start": 952, "end": 957}]}], "localization": [{"trigger": {"text": "appearance", "start": 641, "end": 651}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 655, "end": 662}, {"role": "Theme", "text": "EGR1", "start": 663, "end": 667}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 39, "end": 48}, "arguments": [{"role": "Theme", "text": "transcription", "start": 54, "end": 67}]}, {"trigger": {"text": "increases", "start": 440, "end": 449}, "arguments": [{"role": "Theme", "text": "expression and transcription", "start": 463, "end": 491}]}, {"trigger": {"text": "induction", "start": 689, "end": 698}, "arguments": [{"role": "Theme", "text": "CD44", "start": 684, "end": 688}]}, {"trigger": {"text": "occur", "start": 703, "end": 708}, "arguments": [{"role": "Theme", "text": "transcription", "start": 619, "end": 632}]}, {"trigger": {"text": "occur", "start": 703, "end": 708}, "arguments": [{"role": "Theme", "text": "appearance", "start": 641, "end": 651}]}, {"trigger": {"text": "Cotransfection", "start": 857, "end": 871}, "arguments": [{"role": "Theme", "text": "expression", "start": 958, "end": 968}]}, {"trigger": {"text": "induction", "start": 1007, "end": 1016}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 1020, "end": 1044}]}, {"trigger": {"text": "intermediary linking", "start": 1388, "end": 1408}, "arguments": [{"role": "Cause", "text": "intermediary linking", "start": 1388, "end": 1408}, {"role": "Theme", "text": "induction", "start": 1436, "end": 1445}]}, {"trigger": {"text": "intermediary linking", "start": 1388, "end": 1408}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 1377, "end": 1381}]}, {"trigger": {"text": "induction", "start": 1436, "end": 1445}, "arguments": [{"role": "Theme", "text": "CD44", "start": 1449, "end": 1453}]}], "regulation": [{"trigger": {"text": "Role", "start": 0, "end": 4}, "arguments": [{"role": "Cause", "text": "EGR1", "start": 8, "end": 12}, {"role": "Theme", "text": "regulation", "start": 16, "end": 26}]}, {"trigger": {"text": "regulation", "start": 16, "end": 26}, "arguments": [{"role": "Theme", "text": "dependent", "start": 39, "end": 48}]}, {"trigger": {"text": "regulation", "start": 405, "end": 415}, "arguments": [{"role": "Theme", "text": "CD44", "start": 380, "end": 384}, {"role": "Cause", "text": "EGR1", "start": 400, "end": 404}]}], "transcription": [{"trigger": {"text": "transcription", "start": 54, "end": 67}, "arguments": [{"role": "Theme", "text": "CD44", "start": 49, "end": 53}]}, {"trigger": {"text": "expression and transcription", "start": 463, "end": 491}, "arguments": [{"role": "Theme", "text": "EGR1", "start": 400, "end": 404}]}, {"trigger": {"text": "transcription", "start": 619, "end": 632}, "arguments": [{"role": "Theme", "text": "egr-1", "start": 613, "end": 618}]}, {"trigger": {"text": "transcriptional activity", "start": 1020, "end": 1044}, "arguments": [{"role": "Theme", "text": "CD44", "start": 877, "end": 881}]}]}}, "schema": []}
{"input": "Identification of an inducible regulator of c-myb expression during T-cell activation. \nResting T cells express very low levels of c-Myb protein. During T-cell activation, c-myb expression is induced and much of the increase in expression occurs at the transcriptional level. We identified a region of the c-myb 5' flanking sequence that increased c-myb expression during T-cell activation. In vivo footprinting by ligation-mediated PCR was performed to correlate in vivo protein binding with functional activity. A protein footprint was visible over this region of the c-myb 5' flanking sequence in activated T cells but not in unactivated T cells. An electrophoretic mobility shift assay (EMSA) with nuclear extract from activated T cells and an oligonucleotide of this binding site demonstrated a new protein-DNA complex, referred to as CMAT for c-myb in activated T cells; this complex was not present in unactivated T cells. Because the binding site showed some sequence similarity with the nuclear factor of activated T cells (NFAT) binding site, we compared the kinetics of induction of the two binding complexes and the molecular masses of the two proteins. Studies of the kinetics of induction showed that the NFAT EMSA binding complex appeared earlier than the CMAT complex. The NFAT protein migrated more slowly in a sodium dodecyl sulfate-polyacrylamide gel than the CMAT protein did. In addition, an antibody against NFAT did not cross-react with the CMAT protein. The appearance of the CMAT binding complex was inhibited by both cyclosporin A and rapamycin. The CMAT protein appears to be a novel inducible protein involved in the regulation of c-myb expression during T-cell activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 50, "end": 60}, "arguments": [{"role": "Theme", "text": "c-myb", "start": 44, "end": 49}]}, {"trigger": {"text": "express", "start": 104, "end": 111}, "arguments": [{"role": "Theme", "text": "c-Myb", "start": 131, "end": 136}]}, {"trigger": {"text": "expression", "start": 178, "end": 188}, "arguments": [{"role": "Theme", "text": "c-myb", "start": 172, "end": 177}]}, {"trigger": {"text": "expression", "start": 354, "end": 364}, "arguments": [{"role": "Theme", "text": "c-myb", "start": 348, "end": 353}]}, {"trigger": {"text": "expression", "start": 1665, "end": 1675}, "arguments": [{"role": "Theme", "text": "c-myb", "start": 1659, "end": 1664}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 192, "end": 199}, "arguments": [{"role": "Theme", "text": "expression", "start": 178, "end": 188}]}, {"trigger": {"text": "increased", "start": 338, "end": 347}, "arguments": [{"role": "Theme", "text": "expression", "start": 354, "end": 364}]}], "regulation": [{"trigger": {"text": "regulator", "start": 31, "end": 40}, "arguments": [{"role": "Theme", "text": "expression", "start": 50, "end": 60}]}, {"trigger": {"text": "regulation", "start": 1645, "end": 1655}, "arguments": [{"role": "Theme", "text": "expression", "start": 1665, "end": 1675}]}]}}, "schema": []}
{"input": "Structural and functional characterization of the human CD36 gene promoter: identification of a proximal PEBP2/CBF site. \nCD36 is a cell surface glycoprotein composed of a single polypeptide chain, which interacts with thrombospondin, collagens type I and IV, oxidized low density lipoprotein, fatty acids, anionic phospholipids, and erythrocytes parasitized with Plasmodium falciparum. Its expression is restricted to a few cell types, including monocyte/macrophages. In these cells, CD36 is involved in phagocytosis of apoptotic cells, and foam cell formation by uptake of oxidized low density lipoprotein. To study the molecular mechanisms that control the transcription of the CD36 gene in monocytic cells we have isolated and analyzed the CD36 promoter. Transient expression experiments of 5'-deletion fragments of the CD36 promoter coupled to luciferase demonstrated that as few as 158 base pairs upstream from the transcription initiation site were sufficient to direct the monocyte-specific transcription of the reporter gene. Within the above region, the fragment spanning nucleotides -158 to -90 was required for optimal transcription in monocytic cells. Biochemical analysis of the region -158/-90 revealed a binding site for transcription factors of the polyomavirus enhancer-binding protein 2/core-binding factor (PEBP2/CBF) family at position -103. Disruption of the PEBP2/CBF site markedly diminished the role of the PEBP2/CBF factors in the constitutive transcription of the CD36 gene. The involvement of members of the PEBP2/CBF family in chromosome translocations associated with acute myeloid leukemia, and in the transcriptional regulation of the myeloid-specific genes encoding for myeloperoxidase, elastase, and the colony-stimulating factor receptor, highlights the relevance of the regulation of the CD36 gene promoter in monocytic cells by members of the PEBP2/CBF family. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 204, "end": 213}, "arguments": [{"role": "Theme", "text": "CD36", "start": 122, "end": 126}]}], "gene expression": [{"trigger": {"text": "expression", "start": 391, "end": 401}, "arguments": [{"role": "Theme", "text": "CD36", "start": 122, "end": 126}]}], "negative regulation": [{"trigger": {"text": "diminished", "start": 1405, "end": 1415}, "arguments": [{"role": "Theme", "text": "role", "start": 1420, "end": 1424}]}], "regulation": [{"trigger": {"text": "control", "start": 648, "end": 655}, "arguments": [{"role": "Theme", "text": "transcription", "start": 660, "end": 673}]}, {"trigger": {"text": "role", "start": 1420, "end": 1424}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1470, "end": 1483}]}, {"trigger": {"text": "transcriptional regulation", "start": 1633, "end": 1659}, "arguments": [{"role": "Theme", "text": "myeloperoxidase", "start": 1703, "end": 1718}]}, {"trigger": {"text": "regulation", "start": 1806, "end": 1816}, "arguments": [{"role": "Theme", "text": "CD36", "start": 1824, "end": 1828}, {"role": "Site", "text": "promoter", "start": 1834, "end": 1842}]}], "transcription": [{"trigger": {"text": "transcription", "start": 660, "end": 673}, "arguments": [{"role": "Theme", "text": "CD36", "start": 681, "end": 685}]}, {"trigger": {"text": "transcription", "start": 1470, "end": 1483}, "arguments": [{"role": "Theme", "text": "CD36", "start": 1491, "end": 1495}]}]}}, "schema": []}
{"input": "CNI-1493 inhibits monocyte/macrophage tumor necrosis factor by suppression of translation efficiency. \nTumor necrosis factor (TNF) mediates a wide variety of disease states including septic shock, acute and chronic inflammation, and cachexia. Recently, a multivalent guanylhydrazone (CNI-1493) developed as an inhibitor of macrophage activation was shown to suppress TNF production and protect against tissue inflammation and endotoxin lethality [Bianchi, M., Ulrich, P., Bloom, O., Meistrell, M., Zimmerman, G.A., Schmidtmayerova, H., Bukrinsky, M., Donnelley, T., Bucala, R., Sherry, B., Manogue, K.R., Tortolani, A.J., Cerami, A.& Tracey, K.J.(1995) Mol.Med.1, 254-266, and Bianchi, M., Bloom, O., Raabe, T., Cohen, P. S., Chesney, J., Sherry, B., Schmidtmayerova, H., Zhang, X., Bukrinsky, M., Ulrich, P., Cerami, A.& Tracey, J.(1996) J.Exp.Med., in press]. We have now elucidated the mechanism by which CNI-1493 inhibits macrophage TNF synthesis and show here that it acts through suppression of TNF translation efficiency. CNI-1493 blocked neither the lipopolysaccharide (LPS)-induced increases in the expression of TNF mRNA nor the translocation of nuclear factor NF-kappa B to the nucleus in macrophages activated by 15 min of LPS stimulation, indicating that CNI-1493 does not interfere with early NF-kappa B-mediated transcriptional regulation of TNF. However, synthesis of the 26-kDa membrane form of TNF was effectively blocked by CNI-1493. Further evidence for the translational suppression of TNF is given by experiments using chloram-phenicol acetyltransferase (CAT) constructs containing elements of the TNF gene that are involved in TNF translational regulation. Both the 5' and 3' untranslated regions of the TNF gene were required to elicit maximal translational suppression by CNI-1493. Identification of the molecular target through which CNI- 1493 inhibits TNF translation should provide insight into the regulation of macrophage activation and mechanisms of inflammation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "STAT-related transcription factors are constitutively activated in peripheral blood cells from acute leukemia patients. \nA signal transduction pathway activated by many cytokines has recently been elaborated. The JAK kinases and the signal transducers and activators of transcription (STAT) factors have been found to be essential components. In this report, we describe the presence of constitutively activated STAT factors in peripheral blood cells from patients with acute leukemia. We used oligonucleotide probes from the beta-casein and IRF-1 gene promoters and the ISRE probe to detect STAT proteins in nuclear extracts from acute leukemia cells in bandshift assays. Specific DNA protein complex formation was observed with the probes from the beta-casein and IRF-1 gene promoters, but not with the ISRE oligonucleotide probe, when cell extracts from acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) were investigated. We used nonradioactive oligonucleotides as competitors to show the specificity of the complex formation. Specific antibodies directed against the individual STAT proteins were used in supershift experiments. STAT5- and STAT1-related factors were detected in ALL and STAT1-, STAT3-, and STAT5-related proteins were present in nuclear cell extracts from AML. Since the cells were not treated with cytokines before the nuclear proteins were extracted, we conclude that these factors are constitutively activated in vivo. It is likely that the constitutive activation of STAT proteins is a part of the events of leukemogenesis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complex formation", "start": 694, "end": 711}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 750, "end": 761}, {"role": "Site", "text": "promoters", "start": 777, "end": 786}]}, {"trigger": {"text": "complex formation", "start": 694, "end": 711}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 766, "end": 771}, {"role": "Site", "text": "promoters", "start": 777, "end": 786}]}]}}, "schema": []}
{"input": "Reversible differentiation of human monoblastic leukemia U937 cells by ML-9, an inhibitor of myosin light chain kinase. \nHuman monoblastic leukemia U937 cells are induced to differentiate into monocytes and macrophages by various agents. We have shown that 1-(5-chloronaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine hydrochloride (ML-9), an inhibitor of myosin light chain kinase, induces differentiation of monocytoid leukemia cell lines U937 and THP-1 but not of myeloblastic leukemic ML-1 cell or erythroleukemia K562 cells. In the present study, we further analyzed the effect of ML-9 in comparison with that of 1 alpha, 25-dihydroxyvitamin D3 (VD3) a typical inducer of monocytic differentiation. ML-9 induced nitroblue tetrazolium (NBT)-reducing activity of U937 cell more rapidly than VD3: This differentiation marker was induced significantly after incubation with ML-9 and VD3 for 4 hours and 1 day, respectively. ML-9 also induced alpha-naphthyl acetate esterase (ANAE) activity, another monocytic differentiation marker, more rapidly than VD3. The maximum levels of these markers induced by ML-9 were comparable to those induced by VD3, but after removal of ML-9 from the medium by washing the cells, the expressions of theses markers decreased within 4 hours and reached basal levels in 1 day, indicating that ML-9's induction of expression of differentiation-associated phenotypes was reversible. The growth inhibition of U937 cells by ML-9 was also reversible. Similar effects were observed in another line of human monoblastic cells, THP-1. ML-9 had little or no effect on the morphology of U937 cells but increased the expression of monocyte-macrophage lineage-associated surface antigen, CD14, to some extent. Irreversible terminal differentiation induced by VD3 is associated with down regulation of the expression of c-myc and upregulation of the expression of c-fos and c-jun, but ML-9 did not affect the expression of these oncogenes appreciably. ML-9-induced differentiation was also reversible when the cells were cultured with cultured with ML-9 plus an anti-cancer drug such as 1-beta-D-arabino-furanosylcytosine or daunomycin. it became irreversible, however, upon simultaneous treatment with dexamethasone and transforming growth factor-beta 1 (TGF-beta 1), which did not induce differentiation of U937 cells but caused growth arrest of the cells in the G0/G1 phase of the cell cycle. These results suggest that ML-9 should be useful for studying the mechanisms of monocytic differentiation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1638, "end": 1648}, "arguments": [{"role": "Theme", "text": "CD14", "start": 1708, "end": 1712}]}, {"trigger": {"text": "expression", "start": 1825, "end": 1835}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 1839, "end": 1844}]}, {"trigger": {"text": "expression", "start": 1869, "end": 1879}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1883, "end": 1888}]}, {"trigger": {"text": "expression", "start": 1869, "end": 1879}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1893, "end": 1898}]}, {"trigger": {"text": "expression", "start": 1928, "end": 1938}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 1839, "end": 1844}]}, {"trigger": {"text": "expression", "start": 1928, "end": 1938}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1883, "end": 1888}]}, {"trigger": {"text": "expression", "start": 1928, "end": 1938}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1893, "end": 1898}]}], "negative regulation": [{"trigger": {"text": "down regulation", "start": 1802, "end": 1817}, "arguments": [{"role": "Theme", "text": "expression", "start": 1825, "end": 1835}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 1624, "end": 1633}, "arguments": [{"role": "Theme", "text": "expression", "start": 1638, "end": 1648}]}, {"trigger": {"text": "upregulation", "start": 1849, "end": 1861}, "arguments": [{"role": "Theme", "text": "expression", "start": 1869, "end": 1879}]}], "regulation": [{"trigger": {"text": "affect", "start": 1917, "end": 1923}, "arguments": [{"role": "Theme", "text": "expression", "start": 1928, "end": 1938}]}]}}, "schema": []}
{"input": "Interferon-gamma modulates the lipopolysaccharide-induced expression of AP-1 and NF-kappa B at the mRNA and protein level in human monocytes. \nInterferon-gamma (IFN-gamma) modulates the expression of several cytokines by human monocytes at the transcriptional level. In view of these findings, we analyzed the effects of IFN-gamma on the expression of different transcription factors in activated human monocytes. Priming of human monocytes with IFN-gamma resulted in the down regulation of c-fos and c-jun mRNA in response to stimulation with lipopolysaccharide (LPS) compared to the effects of LPS alone. Not only was this effect observed at the mRNA level, but activator protein-1 (AP-1) DNA binding capacity was affected as well, A strong reduction was observed in the LPS-induced DNA-binding activity of AP-1 in the presence of IFN-gamma. LPS-stimulated monocytes showed an increased expression of p105 mRNA, the precursor of the p50 subunit of the transcription factor nuclear factor-kappa B (NF-kappa B), while no effect was noticed on the expression of p65 mRNA. In contrast, IFN-gamma priming did not affect the expression of p105 transcripts but enhanced the expression of p65 mRNA (two-fold). Priming with IFN-gamma followed by LPS stimulation resulted in a further increase in the expression of p65 mRNA. This was due to an increase in the half-life of p65 mRNA (75 vs 150 minutes). Electrophoretic mobility shift assays (EMSAs) demonstrated that unstimulated monocytes predominantly expressed p50 NF-kappa B. Stimulation with LPS or IFN-gamma resulted in the expression of p50 and p65 subunits, while the combination of IFN-gamma plus LPS caused a further increase in the expression of NF-kappa B. With Western blotting, it was shown that nuclear extracts from monocytes contained p50 and p65 protein in response to LPS and IFN-gamma stimulation. However, the combined stimulation did not result in enhanced p50 and p65 protein expression. The effects of IFN-gamma on the transcription factors were specific, since no change was observed in the expression of NF-IL-6 or I kappa B alpha, the inhibitor of NF-kappa B. We conclude that the effects of IFN-gamma on the expression of the transcription factors AP-1 and NF-kappa B may be important for the modulatory effects of IFN-gamma on the cytokine expression in activated human monocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 1496, "end": 1505}, "arguments": [{"role": "Theme", "text": "p50", "start": 1506, "end": 1509}]}, {"trigger": {"text": "expression", "start": 1572, "end": 1582}, "arguments": [{"role": "Theme", "text": "p50", "start": 1586, "end": 1589}]}, {"trigger": {"text": "expression", "start": 1572, "end": 1582}, "arguments": [{"role": "Theme", "text": "p65", "start": 1594, "end": 1597}]}, {"trigger": {"text": "contained", "start": 1784, "end": 1793}, "arguments": [{"role": "Theme", "text": "p50", "start": 1794, "end": 1797}]}, {"trigger": {"text": "contained", "start": 1784, "end": 1793}, "arguments": [{"role": "Theme", "text": "p65", "start": 1802, "end": 1805}]}, {"trigger": {"text": "expression", "start": 1941, "end": 1951}, "arguments": [{"role": "Theme", "text": "p50", "start": 1921, "end": 1924}]}, {"trigger": {"text": "expression", "start": 1941, "end": 1951}, "arguments": [{"role": "Theme", "text": "p65", "start": 1929, "end": 1932}]}, {"trigger": {"text": "expression", "start": 2058, "end": 2068}, "arguments": [{"role": "Theme", "text": "NF-IL-6", "start": 2072, "end": 2079}]}, {"trigger": {"text": "expression", "start": 2058, "end": 2068}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 2083, "end": 2098}]}], "negative regulation": [{"trigger": {"text": "down regulation", "start": 472, "end": 487}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 491, "end": 496}]}, {"trigger": {"text": "down regulation", "start": 472, "end": 487}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 501, "end": 506}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 879, "end": 888}, "arguments": [{"role": "Theme", "text": "expression", "start": 889, "end": 899}]}, {"trigger": {"text": "enhanced", "start": 1156, "end": 1164}, "arguments": [{"role": "Theme", "text": "expression", "start": 1169, "end": 1179}]}, {"trigger": {"text": "increase", "start": 1277, "end": 1285}, "arguments": [{"role": "Theme", "text": "expression", "start": 1293, "end": 1303}]}, {"trigger": {"text": "due to", "start": 1326, "end": 1332}, "arguments": [{"role": "Theme", "text": "increase", "start": 1277, "end": 1285}, {"role": "Cause", "text": "increase", "start": 1336, "end": 1344}]}, {"trigger": {"text": "increase", "start": 1336, "end": 1344}, "arguments": [{"role": "Theme", "text": "p65", "start": 1365, "end": 1368}]}, {"trigger": {"text": "resulted", "start": 1556, "end": 1564}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 1546, "end": 1555}, {"role": "Theme", "text": "expression", "start": 1572, "end": 1582}]}, {"trigger": {"text": "resulted", "start": 1556, "end": 1564}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1546, "end": 1555}]}, {"trigger": {"text": "resulted", "start": 1556, "end": 1564}, "arguments": [{"role": "Theme", "text": "expression", "start": 1572, "end": 1582}]}, {"trigger": {"text": "in response to", "start": 1814, "end": 1828}, "arguments": [{"role": "Theme", "text": "contained", "start": 1784, "end": 1793}, {"role": "Cause", "text": "IFN-gamma", "start": 1837, "end": 1846}]}, {"trigger": {"text": "in response to", "start": 1814, "end": 1828}, "arguments": [{"role": "Theme", "text": "contained", "start": 1784, "end": 1793}]}, {"trigger": {"text": "enhanced", "start": 1912, "end": 1920}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 1837, "end": 1846}, {"role": "Theme", "text": "expression", "start": 1941, "end": 1951}]}], "regulation": [{"trigger": {"text": "effect", "start": 1021, "end": 1027}, "arguments": [{"role": "Theme", "text": "expression", "start": 1047, "end": 1057}]}, {"trigger": {"text": "affect", "start": 1110, "end": 1116}, "arguments": [{"role": "Theme", "text": "expression", "start": 1121, "end": 1131}]}, {"trigger": {"text": "change", "start": 2031, "end": 2037}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 1968, "end": 1977}, {"role": "Theme", "text": "expression", "start": 2058, "end": 2068}]}], "transcription": [{"trigger": {"text": "expression", "start": 889, "end": 899}, "arguments": [{"role": "Theme", "text": "p105", "start": 903, "end": 907}]}, {"trigger": {"text": "expression", "start": 1047, "end": 1057}, "arguments": [{"role": "Theme", "text": "p65", "start": 1061, "end": 1064}]}, {"trigger": {"text": "expression", "start": 1121, "end": 1131}, "arguments": [{"role": "Theme", "text": "p105", "start": 1135, "end": 1139}]}, {"trigger": {"text": "expression", "start": 1169, "end": 1179}, "arguments": [{"role": "Theme", "text": "p65", "start": 1183, "end": 1186}]}, {"trigger": {"text": "expression", "start": 1293, "end": 1303}, "arguments": [{"role": "Theme", "text": "p65", "start": 1307, "end": 1310}]}]}}, "schema": []}
{"input": "Expression of c-fos and c-jun proteins and AP-1 binding activity during cell cycle progression of HL60 cells and phytohemagglutinin-stimulated lymphocytes. \nThe protein products of the c-fos (p62c-fos) and c-jun (p39c-jun) genes are members of the AP-1 transcription factor family and are thought to play important roles in the regulation of gene expression during the cell cycle. Most studies on the expression of these proteins in relation to the cell cycle have been performed at the mRNA level, and therefore do not give direct information about the presence of the proteins during the cell cycle. We have used Western blotting to investigate the presence of these proteins during the cell cycles of two different cellular systems: a continuously growing myeloid leukemic cell line, HL60, and normal cells stimulated into cycle, phyto- hemagglutinin (PHA)-stimulated normal human peripheral blood lymphocytes (PBL). The binding activity of transcription factor AP-1, which consists of dimers of Fos and Jun family proteins, was also studied using a gel shift assay. We found nuclear p62c-fos, p39c-jun, and AP-1 binding activity throughout the cell cycle both in HL60 cells and in PHA-stimulated PBL, and we postulate that these proteins are required throughout the cell cycle and not transiently in the G0 to G1 transition as previous mRNA studies have indicated. We demonstrated an uncoupling of AP-1 binding activity from p62c-fos, and p39c-jun AP-1 activity was expressed more strongly in the G1- and G2/M-phase enriched samples than in the S-phase enriched samples of HL60 cells, while levels of nuclear p62c-fos and p39c-jun were constant. Nuclei of unstimulated PBL from different donors expressed p62c-fos and p39c-jun, but AP-1 was not detected in the majority of samples. Following PHA stimulation of PBL, the increase in AP-1 activity was delayed with respect to the augmentation of p39c-jun expression. We also observed that cytoplasmic p62c-fos and p39c-jun were present in HL60 cells and PHA-stimulated PBL. However, no cytoplasmic p62c-fos was detected in unstimulated PBL, although in some cases cytoplasmic p39c-jun was detected, suggesting that subcellular compartmentalization of these proteinsmay occur under certain circumstances. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 14, "end": 19}]}, {"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 24, "end": 29}]}, {"trigger": {"text": "presence", "start": 554, "end": 562}, "arguments": [{"role": "Theme", "text": "p62c-fos", "start": 192, "end": 200}]}, {"trigger": {"text": "presence", "start": 554, "end": 562}, "arguments": [{"role": "Theme", "text": "p39c-jun", "start": 213, "end": 221}]}, {"trigger": {"text": "presence", "start": 651, "end": 659}, "arguments": [{"role": "Theme", "text": "p62c-fos", "start": 192, "end": 200}]}, {"trigger": {"text": "presence", "start": 651, "end": 659}, "arguments": [{"role": "Theme", "text": "p39c-jun", "start": 213, "end": 221}]}, {"trigger": {"text": "expression", "start": 1907, "end": 1917}, "arguments": [{"role": "Theme", "text": "p39c-jun", "start": 1898, "end": 1906}]}, {"trigger": {"text": "present", "start": 1980, "end": 1987}, "arguments": [{"role": "Theme", "text": "p62c-fos", "start": 1953, "end": 1961}]}, {"trigger": {"text": "present", "start": 1980, "end": 1987}, "arguments": [{"role": "Theme", "text": "p39c-jun", "start": 1966, "end": 1974}]}, {"trigger": {"text": "detected", "start": 2063, "end": 2071}, "arguments": [{"role": "Theme", "text": "p62c-fos", "start": 2050, "end": 2058}]}, {"trigger": {"text": "detected", "start": 2141, "end": 2149}, "arguments": [{"role": "Theme", "text": "p39c-jun", "start": 2128, "end": 2136}]}], "localization": [{"trigger": {"text": "found", "start": 1073, "end": 1078}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 1079, "end": 1086}, {"role": "Theme", "text": "p62c-fos", "start": 1087, "end": 1095}]}, {"trigger": {"text": "found", "start": 1073, "end": 1078}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 1079, "end": 1086}, {"role": "Theme", "text": "p39c-jun", "start": 1097, "end": 1105}]}, {"trigger": {"text": "expressed", "start": 1699, "end": 1708}, "arguments": [{"role": "AtLoc", "text": "Nuclei", "start": 1650, "end": 1656}, {"role": "Theme", "text": "p62c-fos", "start": 1709, "end": 1717}]}, {"trigger": {"text": "expressed", "start": 1699, "end": 1708}, "arguments": [{"role": "AtLoc", "text": "Nuclei", "start": 1650, "end": 1656}, {"role": "Theme", "text": "p39c-jun", "start": 1722, "end": 1730}]}], "positive regulation": [{"trigger": {"text": "constant", "start": 1640, "end": 1648}, "arguments": [{"role": "Theme", "text": "p62c-fos", "start": 1613, "end": 1621}]}, {"trigger": {"text": "constant", "start": 1640, "end": 1648}, "arguments": [{"role": "Theme", "text": "p39c-jun", "start": 1626, "end": 1634}]}, {"trigger": {"text": "augmentation", "start": 1882, "end": 1894}, "arguments": [{"role": "Theme", "text": "expression", "start": 1907, "end": 1917}]}], "transcription": [{"trigger": {"text": "at the mRNA level", "start": 480, "end": 497}, "arguments": [{"role": "Theme", "text": "p62c-fos", "start": 192, "end": 200}]}, {"trigger": {"text": "at the mRNA level", "start": 480, "end": 497}, "arguments": [{"role": "Theme", "text": "p39c-jun", "start": 213, "end": 221}]}]}}, "schema": []}
{"input": "Involvement of intracellular Ca2+ in oxidant-induced NF-kappa B activation. \nIn human Jurkat T cells and its subclone Wurzburg cells oxidant challenge elevated [Ca2+]i by mobilizing Ca2+ from intracellular stores. In Jurkat cells this effect was rapid and transient, but in Wurzburg cells the response was slow and sustained. H2O2-induced NF-kappaB activation in Wurzburg cells was not influenced by the presence of extracellular EGTA but was totally inhibited in cells that were loaded with esterified EGTA. In Jurkat cells that are not sensitive to H2O2-induced NF-kappaB activation, H2O2 potentiated NF-kappaB activation in the presence of sustained high [Ca2+]i following thapsigargin treatment. NF-kappaB regulatory effect of alpha-lipoate and N-acetylcysteine appeared to be, at least in part, due to their ability to stabilize elevation of [Ca2+]i following oxidant challenge. Results of this study indicate that a sustained elevated [Ca2+]i is a significant factor in oxidant-induced NF-kappaB activation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "A cell type-specific enhancer in the human B7.1 gene regulated by NF-kappaB. \nThe costimulatory molecule B7.1 provides a second signal critical for T cell activation. The distribution of this integral membrane protein is restricted to certain tissues where its level of expression is modulated by multiple exogenous stimuli. To identify the molecular basis for specificity and inducibility, the chromatin configuration of the human B7.1 gene was examined in intact nuclei from various cell types. The identification of a tissue-specific deoxyribonuclease I hypersensitive site approximately 3kb upstream of the transcription start site led to the characterization of a cell type-specific enhancer region. This 183-bp region was both cell type specific and responsive to two distinct stimuli, lipopolysaccharide and dibutyryl cAMP, known to regulate B7.1 expression. Deletional and site-directed mutagenesis revealed the presence of multiple functionally critical cis elements within this region, one of which was a nuclear factor (NF)-kappaB consensus sequence. In B7.1-positive B cells, this element bound several members of the NF-kappaB family, transcription factors already implicated in signal transduction pathways relevant to B7.1 expression. This is the first description, to our knowledge, of regulatory elements that control expression of a gene encoding a B7 costimulatory molecule. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "distribution", "start": 171, "end": 183}, "arguments": [{"role": "Theme", "text": "B7.1", "start": 105, "end": 109}]}, {"trigger": {"text": "expression", "start": 270, "end": 280}, "arguments": [{"role": "Theme", "text": "B7.1", "start": 105, "end": 109}]}, {"trigger": {"text": "expression", "start": 854, "end": 864}, "arguments": [{"role": "Theme", "text": "B7.1", "start": 849, "end": 853}]}, {"trigger": {"text": "positive", "start": 1070, "end": 1078}, "arguments": [{"role": "Theme", "text": "B7.1", "start": 1065, "end": 1069}]}, {"trigger": {"text": "expression", "start": 1238, "end": 1248}, "arguments": [{"role": "Theme", "text": "B7.1", "start": 1233, "end": 1237}]}], "regulation": [{"trigger": {"text": "regulated", "start": 53, "end": 62}, "arguments": [{"role": "Theme", "text": "B7.1", "start": 43, "end": 47}]}, {"trigger": {"text": "modulated", "start": 284, "end": 293}, "arguments": [{"role": "Theme", "text": "expression", "start": 270, "end": 280}]}, {"trigger": {"text": "regulate", "start": 840, "end": 848}, "arguments": [{"role": "Theme", "text": "expression", "start": 854, "end": 864}]}]}}, "schema": []}
{"input": "Heat shock induces HIV-1 replication in chronically infected promyelocyte cell line OM10.1. \nA long period of clinical latency before development of symptoms is characteristic of human immunodeficiency virus type 1 (HIV-1) infection. OM10.1, a promyelocyte cell line latently infected with HIV-1, has been developed as a model for studying the mechanism of viral latency and the activation of virus expression. We found that this latently infected cell line with heat shock at 42 degrees C for 2 h resulted in a high level of HIV-1 production without addition of any cytokines. The mechanism of activation was analyzed by using anti-TNF-alpha antibody and various inhibitors. Although the TNF-alpha level in culture supernatants was below the sensitivity of an ELISA assay system, addition of anti-TNF-alpha antibody in culture medium could partially suppress the heat shock induced HIV-1 production. Staurosporine (PKC inhibitor), pentoxifylline (NF-kappa B inhibitor), and Ro5-3335 (HIV-1 Tat inhibitor) also inhibited significantly the heat shock induced virus activation. In particular, staurosporine achieved approximately 90% inhibition of the HIV-1 antigen expression in heat shock-treated OM10.1 at a non-toxic concentration. Although the mechanism of HIV-1 activation with heat shock has not been fully elucidated yet, it is presumed PKC plays an important role in HIV-1 activation. Thus, the present observations will provide a further insight into the pathogenesis of HIV-1 infections. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitor", "start": 995, "end": 1004}, "arguments": [{"role": "Theme", "text": "Tat", "start": 991, "end": 994}]}]}}, "schema": []}
{"input": "Abundant expression of erythroid transcription factor P45 NF-E2 mRNA in human peripheral granurocytes. \nTranscription factor NF-E2 is crucial for regulation of erythroid-specific gene expression. p45 subunit of NF-E2 contains a basic-leucine zipper domain and dimerizes with the small Maf family protein to form functional NF-E2 complex. While p45 expression was shown to be restricted to erythroid cells, megakaryocytes and mast cells in hematopoietic lineage, we found in this study that p45 mRNA is abundantly transcribed in the granulocyte fraction of human peripheral blood cells. As neutrophils occupy approximately 92% of the cells in granulocyte fraction of human peripheral blood cells. As neutrophils occupy approximately 92% of the cells in this fraction, the cells expressing p45 is most likely to be neutrophils. p45 mRNA is also expressed in HL-60 promyelocytes, albeit the expression level is much lower than that of the granulocyte fraction. HL-60 cells were found to express mafK mRNA, indicating the presence of genuine NF-E2 complex in the cells. Although p45 mRNA is transcribed from two different promoters, aNF-E2 promoter and fNF-E2 promoter, in erythroid and megakaryocytic lineage cells, p45 mRNA is transcribed only from aNF-E2 promoter. The expression of p45 megakaryocytic lineage cells, p45 mRNA is transcribed only from aNF-E2 promoter. The expression of p45 mRNA in the neutrophils declined rapidly after transfer of the cells to in vitro culture and G-CSF could not sustain the expression from the down-regulation, suggesting the E2 may also participate in the regulation of neutrophil-specific gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "dimerizes", "start": 260, "end": 269}, "arguments": [{"role": "Theme", "text": "p45", "start": 196, "end": 199}]}], "gene expression": [{"trigger": {"text": "expression", "start": 348, "end": 358}, "arguments": [{"role": "Theme", "text": "p45", "start": 344, "end": 347}]}, {"trigger": {"text": "expressing", "start": 777, "end": 787}, "arguments": [{"role": "Theme", "text": "p45", "start": 788, "end": 791}]}, {"trigger": {"text": "expression", "start": 1268, "end": 1278}, "arguments": [{"role": "Theme", "text": "p45", "start": 1282, "end": 1285}]}], "negative regulation": [{"trigger": {"text": "declined", "start": 1413, "end": 1421}, "arguments": [{"role": "Theme", "text": "expression", "start": 1371, "end": 1381}]}, {"trigger": {"text": "sustain", "start": 1498, "end": 1505}, "arguments": [{"role": "Theme", "text": "declined", "start": 1413, "end": 1421}, {"role": "Cause", "text": "G-CSF", "start": 1482, "end": 1487}]}], "positive regulation": [{"trigger": {"text": "from", "start": 1099, "end": 1103}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 1087, "end": 1098}]}, {"trigger": {"text": "from", "start": 1242, "end": 1246}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 1225, "end": 1236}]}, {"trigger": {"text": "from", "start": 1345, "end": 1349}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 1328, "end": 1339}]}], "transcription": [{"trigger": {"text": "expression", "start": 9, "end": 19}, "arguments": [{"role": "Theme", "text": "erythroid transcription factor P45 NF-E2", "start": 23, "end": 63}]}, {"trigger": {"text": "transcribed", "start": 513, "end": 524}, "arguments": [{"role": "Theme", "text": "p45", "start": 490, "end": 493}]}, {"trigger": {"text": "expressed", "start": 843, "end": 852}, "arguments": [{"role": "Theme", "text": "p45", "start": 826, "end": 829}]}, {"trigger": {"text": "expression", "start": 888, "end": 898}, "arguments": [{"role": "Theme", "text": "p45", "start": 826, "end": 829}]}, {"trigger": {"text": "express", "start": 984, "end": 991}, "arguments": [{"role": "Theme", "text": "mafK", "start": 992, "end": 996}]}, {"trigger": {"text": "transcribed", "start": 1087, "end": 1098}, "arguments": [{"role": "Theme", "text": "p45", "start": 1075, "end": 1078}]}, {"trigger": {"text": "transcribed", "start": 1225, "end": 1236}, "arguments": [{"role": "Theme", "text": "p45", "start": 1213, "end": 1216}]}, {"trigger": {"text": "transcribed", "start": 1328, "end": 1339}, "arguments": [{"role": "Theme", "text": "p45", "start": 1316, "end": 1319}]}, {"trigger": {"text": "expression", "start": 1371, "end": 1381}, "arguments": [{"role": "Theme", "text": "p45", "start": 1385, "end": 1388}]}]}}, "schema": []}
{"input": "Identification of a human LIM-Hox gene, hLH-2, aberrantly expressed in chronic myelogenous leukaemia and located on 9q33-34.1. \nWe describe the isolation of human LH-2, a putative transcription factor containing two cysteine-rich regions (LIM domains) and a homeobox (Hox) DNA-binding domain. High levels of hLH-2 expression were observed in all cases of chronic myelogenous leukaemia (CML) tested, regardless of disease status. hLH-2 was mapped to chromosome 9Q33-34.1, in the same region as the reciprocal translocation that creates the BCR-ABL chimera of the Philadelphia chromosome (Ph'), the hallmark of CML; hLH-2 was retained on the derivative 9 chromosome and is therefore centromeric of c-ABL. The proximity of hLH-2 to the breakpoint on chromosome 9 raises the possibility of cis-activation by the t(9;22)(q34;q11) translocation. In addition to finding hLH-2 expression in all cases of CML, expression was observed in lymphoid malignancies and myeloid cell lines, but not in primary cases of acute myelogenous leukaemia. The role of hLH-2 in the development or progression of leukaemia is not known. However, hLH-2 may prove useful as a marker of CML for monitoring residual disease. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 58, "end": 67}, "arguments": [{"role": "Theme", "text": "hLH-2", "start": 40, "end": 45}]}, {"trigger": {"text": "expression", "start": 314, "end": 324}, "arguments": [{"role": "Theme", "text": "hLH-2", "start": 308, "end": 313}]}, {"trigger": {"text": "expression", "start": 869, "end": 879}, "arguments": [{"role": "Theme", "text": "hLH-2", "start": 863, "end": 868}]}, {"trigger": {"text": "expression", "start": 901, "end": 911}, "arguments": [{"role": "Theme", "text": "hLH-2", "start": 863, "end": 868}]}], "positive regulation": [{"trigger": {"text": "High levels", "start": 293, "end": 304}, "arguments": [{"role": "Theme", "text": "expression", "start": 314, "end": 324}]}, {"trigger": {"text": "cis-activation", "start": 786, "end": 800}, "arguments": [{"role": "Theme", "text": "hLH-2", "start": 720, "end": 725}]}]}}, "schema": []}
{"input": "BCL-6 expression during B-cell activation. \nTranslocations involving the BCL-6 gene are common in the diffuse large cell subtype of non-Hodgkin's lymphoma. Invariably, the BCL-6 coding region is intact, but its 5' untranslated region is replaced with sequences from the translocation partner. The present study shows that BCL-6 expression is regulated in lymphocytes during mitogenic stimulation. Resting B and T lymphocytes contain high levels of BCL-6 mRNA. Stimulation of mouse B cells with anti-IgM or IgD antibodies, bacterial lipopolysaccharide, phorbol 12-myristate 13-acetate plus ionomycin, or CD40 ligand led to a five-fold to 35-fold decrease in BCL-6 mRNA levels. Similar downregulation of BCL-6 mRNA was seen in human B cells stimulated with Staphylococcus aureus plus interleukin-2 or anti-IgM antibodies and in human T lymphocytes stimulated with phytohemagglutinin. BCL-6 mRNA levels began to decrease 8 to 16 hours after stimulation, before cells entered S phase. Although polyclonal activation of B cells in vitro invariably decreased BCL-6 MRNA expression, activated B cells from human germinal centers expressed BCL-6 mRNA at levels comparable to the levels in resting B cells. Despite these similar mRNA levels, BCL-6 protein expression was threefold to 34-fold higher in germinal center B cells than in resting B cells, suggesting that BCL-6 protein levels are controlled by translational or posttranslational mechanisms. These observations suggest that the germinal center reaction provides unique activation signals to B cells that allow for continued, high-level BCL-6 expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 6, "end": 16}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 0, "end": 5}]}, {"trigger": {"text": "expression", "start": 328, "end": 338}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 322, "end": 327}]}, {"trigger": {"text": "expression", "start": 1247, "end": 1257}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 1233, "end": 1238}]}, {"trigger": {"text": "expression", "start": 1594, "end": 1604}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 1588, "end": 1593}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 645, "end": 653}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 657, "end": 662}]}, {"trigger": {"text": "downregulation", "start": 684, "end": 698}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 702, "end": 707}]}, {"trigger": {"text": "decrease", "start": 909, "end": 917}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 882, "end": 887}]}, {"trigger": {"text": "decreased", "start": 1043, "end": 1052}, "arguments": [{"role": "Theme", "text": "expression", "start": 1064, "end": 1074}]}], "positive regulation": [{"trigger": {"text": "allow", "start": 1556, "end": 1561}, "arguments": [{"role": "Theme", "text": "high-level", "start": 1577, "end": 1587}]}, {"trigger": {"text": "allow", "start": 1556, "end": 1561}, "arguments": [{"role": "Theme", "text": "expression", "start": 1594, "end": 1604}]}, {"trigger": {"text": "high-level", "start": 1577, "end": 1587}, "arguments": [{"role": "Theme", "text": "expression", "start": 1594, "end": 1604}]}], "regulation": [{"trigger": {"text": "regulated", "start": 342, "end": 351}, "arguments": [{"role": "Theme", "text": "expression", "start": 328, "end": 338}]}, {"trigger": {"text": "controlled", "start": 1383, "end": 1393}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 1358, "end": 1363}]}], "transcription": [{"trigger": {"text": "expression", "start": 1064, "end": 1074}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 1053, "end": 1058}]}, {"trigger": {"text": "expressed", "start": 1122, "end": 1131}, "arguments": [{"role": "Theme", "text": "BCL-6", "start": 1132, "end": 1137}]}]}}, "schema": []}
{"input": "A novel interferon regulatory factor family transcription factor, ICSAT/Pip/LSIRF, that negatively regulates the activity of interferon-regulated genes. \nWe have isolated a novel cDNA clone encoding interferon (IFN) consensus sequence-binding protein in adult T-cell leukemia cell line or activated T cells (ICSAT); this protein is the human homolog of the recently cloned Pip/LSIRF. ICSAT is structurally most closely related to the previously cloned ICSBP, a member of the IFN regulatory factor (IRF) family of proteins that binds to interferon consensus sequences (ICSs) found in many promoters of the IFN-regulated genes. Among T-cell lines investigated, ICSAT was abundantly expressed in human T-cell leukemia virus type 1 (HTLV-1)-infected T cells. When the HTLV-1 tax gene was expressed or phorbol myristake acetate-A23187 stimulation was used, ICSAT expression was induced in Jurkat cells which otherwise do not express ICSAT. When the binding of ICSAT to four different ICSs was tested, the relative differences in binding affinities for those ICSs were determined. To study the functional role of ICSAT, we performed cotransfection experiments with the human embryonal carcinoma cell line N-Tera2. ICSAT was demonstrated to possess repressive function over the gene activation induced by IFN stimulation or by IRF-1 cotransfection. Such repressive function is similar to that seen in IRF-2 or ICSBP. However, we have found that ICSAT has a different repressive effect from that of IRF-2 or ICSBP in some IFN-responsive reporter constructs. These results suggest that a novel mechanism of gene regulation by \"differential repression\" is used by multiple members of repressor proteins with different repressive effects on the IFN-responsive genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 527, "end": 532}, "arguments": [{"role": "Theme", "text": "ICSBP", "start": 452, "end": 457}]}, {"trigger": {"text": "binding", "start": 944, "end": 951}, "arguments": [{"role": "Theme", "text": "ICSAT", "start": 955, "end": 960}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 680, "end": 689}, "arguments": [{"role": "Theme", "text": "ICSAT", "start": 659, "end": 664}]}, {"trigger": {"text": "expressed", "start": 784, "end": 793}, "arguments": [{"role": "Theme", "text": "tax", "start": 771, "end": 774}]}, {"trigger": {"text": "expression", "start": 858, "end": 868}, "arguments": [{"role": "Theme", "text": "ICSAT", "start": 852, "end": 857}]}, {"trigger": {"text": "express", "start": 920, "end": 927}, "arguments": [{"role": "Theme", "text": "ICSAT", "start": 928, "end": 933}]}, {"trigger": {"text": "cotransfection", "start": 1326, "end": 1340}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1320, "end": 1325}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 873, "end": 880}, "arguments": [{"role": "Cause", "text": "expressed", "start": 784, "end": 793}, {"role": "Theme", "text": "expression", "start": 858, "end": 868}]}, {"trigger": {"text": "induced", "start": 873, "end": 880}, "arguments": [{"role": "Theme", "text": "expression", "start": 858, "end": 868}]}, {"trigger": {"text": "cotransfection", "start": 1326, "end": 1340}, "arguments": [{"role": "Theme", "text": "cotransfection", "start": 1326, "end": 1340}]}]}}, "schema": []}
{"input": "Transcription factors of T and B lymphocytes--basic research and clinical perspectives for gastroenterology. \nTissue specific regulation of gene expression by transcription factors is a fascinating new field in molecular immunology. This review summarizes data on specific regulation of promoters and enhancers by nuclear trans-acting factors in lymphocytes. The structural classes of transcription factors are described and basic methods for detection and analysis of transcription factors are detailed. Furthermore, the most important trans-acting factors of T and B lymphocytes (e.g. NF-kB, NF-AT and STAT families) and their functional importance are described. Several methods for specific down-regulation of transcription factors are shown that may be relevant to treatment of human disease. The data are discussed with regard to their potential clinical relevance for gastroenterology. ", "output": {"json_structures": {}}, "schema": []}
{"input": "DNA triplex formation selectively inhibits granulocyte-macrophage colony-stimulating factor gene expression in human T cells. \nGranulocyte-macrophage colony-stimulating factor (GM-CSF) is a hemopoietic growth factor that is expressed in activated T cells, fibroblasts, macrophages, and endothelial cells. Although GM-CSF does not appear to be essential for normal hemopoiesis, overexpression of GM-CSF has been implicated in the pathogenesis of some diseases such as myeloid leukemia and chronic inflammation. An NF-kappaB/Rel binding site within the GM-CSF promoter, termed the kappaB element appears to be important for controlling expression in reporter gene assays in response to a number of stimuli in T cells. We investigated oligonucleotide-directed triple helix formation across this regulatory sequence as a potential tool to inhibit GM-CSF gene transcription. A 15-base oligonucleotide, GM3, was targeted to a purine-rich region in the GM-CSF proximal promoter, which overlaps the kappaB element. Gel mobility shift assays and DNase I footprinting demonstrated that GM3 formed a sequence-specific collinear triplex with its double-stranded DNA target. Triplex formation by GM3 blocked recombinant and nuclear NF-kappaB proteins binding to the GM-CSF element. GM3 also caused selective inhibition of the human T-cell lymphotrophic virus-1 Tax transactivator-induced luciferase activity from a reporter construct driven by the GM-CSF promoter in Jurkat T cells. Finally, GM3 greatly reduced the concentration of endogenous GM-CSF mRNA induced by different stimuli in Jurkat T cells but did not affect interleukin 3 mRNA levels in the same cells. We conclude that the kappaB element in the GM-CSF promoter plays a central role in the transcriptional activation of the endogenous GM-CSF gene. Colinear triplex formation acts as a selective transcriptional repressor of the GM-CSF gene and may have potential therapeutic application in cases of undesirable overexpression of this protein. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "targeted", "start": 906, "end": 914}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 946, "end": 952}, {"role": "Site", "text": "proximal promoter", "start": 953, "end": 970}]}], "gene expression": [{"trigger": {"text": "expression", "start": 97, "end": 107}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 43, "end": 91}]}, {"trigger": {"text": "expressed", "start": 224, "end": 233}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 177, "end": 183}]}, {"trigger": {"text": "overexpression", "start": 377, "end": 391}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 395, "end": 401}]}, {"trigger": {"text": "overexpression", "start": 1962, "end": 1976}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1879, "end": 1885}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 34, "end": 42}, "arguments": [{"role": "Theme", "text": "expression", "start": 97, "end": 107}]}, {"trigger": {"text": "inhibit", "start": 835, "end": 842}, "arguments": [{"role": "Theme", "text": "transcription", "start": 855, "end": 868}]}, {"trigger": {"text": "reduced", "start": 1491, "end": 1498}, "arguments": [{"role": "Theme", "text": "induced", "start": 1543, "end": 1550}]}, {"trigger": {"text": "transcriptional repressor", "start": 1846, "end": 1871}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1879, "end": 1885}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 377, "end": 391}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 377, "end": 391}]}, {"trigger": {"text": "induced", "start": 1543, "end": 1550}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1531, "end": 1537}]}, {"trigger": {"text": "central role", "start": 1721, "end": 1733}, "arguments": [{"role": "CSite", "text": "kappaB element", "start": 1675, "end": 1689}, {"role": "Cause", "text": "GM-CSF", "start": 1697, "end": 1703}, {"role": "Theme", "text": "transcriptional activation", "start": 1741, "end": 1767}]}, {"trigger": {"text": "transcriptional activation", "start": 1741, "end": 1767}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1786, "end": 1792}]}, {"trigger": {"text": "overexpression", "start": 1962, "end": 1976}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1962, "end": 1976}]}], "regulation": [{"trigger": {"text": "affect", "start": 1602, "end": 1608}, "arguments": [{"role": "Theme", "text": "interleukin 3", "start": 1609, "end": 1622}]}], "transcription": [{"trigger": {"text": "transcription", "start": 855, "end": 868}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 843, "end": 849}]}]}}, "schema": []}
{"input": "Cooperation between core binding factor and adjacent promoter elements contributes to the tissue-specific expression of interleukin-3. \nTissue-specific expression of interleukin-3 (IL-3) is mediated via cis-acting elements located within 315 base pairs of the transcription start. This is achieved in part through the positive activities of the AP-1 and Elf-1 sites in the IL-3 promoter. The contribution to T cell-specific expression by other promoter sites was assessed in a transient expression assay with IL-3 promoter constructs linked to a luciferase gene, focusing initially on the core binding factor (CBF) site, which is footprinted in vivo upon T cell activation. Activity of the CBF site is shown to be critically dependent on the adjacent activator site Act-1. Together the Act-1 and CBF sites form a functional unit (AC unit) with dual activity. The AC unit is demonstrated to enhance basal activity of promoters both in fibroblasts and T cells. This activity is further inducible in activated T cells, but not in fibroblasts. In addition to the already identified NIP repressor site, evidence is presented for a second repressor region that restricts promoter activity in fibroblasts. Finally, a novel positive regulatory element has been mapped in the IL-3 promoter between nucleotide -180 and -210 that leads to increased expression in T cells. Together these results demonstrate that T cell expression of IL-3 is not specified by the activity of a single tissue-specific element, but instead involves multiple interacting elements that provide both specific positive regulation in T cells and specific negative regulation in fibroblasts. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 106, "end": 116}, "arguments": [{"role": "Theme", "text": "interleukin-3", "start": 120, "end": 133}]}, {"trigger": {"text": "expression", "start": 152, "end": 162}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 181, "end": 185}]}, {"trigger": {"text": "expression", "start": 1408, "end": 1418}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 1422, "end": 1426}]}], "positive regulation": [{"trigger": {"text": "contributes", "start": 71, "end": 82}, "arguments": [{"role": "Theme", "text": "expression", "start": 106, "end": 116}]}, {"trigger": {"text": "mediated", "start": 190, "end": 198}, "arguments": [{"role": "Theme", "text": "expression", "start": 152, "end": 162}]}, {"trigger": {"text": "specified", "start": 1434, "end": 1443}, "arguments": [{"role": "Theme", "text": "expression", "start": 1408, "end": 1418}]}]}}, "schema": []}
{"input": "Octamer binding factors and their coactivator can activate the murine PU.1 (spi-1) promoter. \nPU.1 (spi-1), a member of the Ets transcription factor family, is predominantly expressed in myeloid and B cells, activates many B cell and myeloid genes, and is critical for development of both of these lineages. Our previous studies (Chen, H.M., Ray-Gallet, D., Zhang, P., Hetherington, C.J., Gonzalez, D.A., Zhang, D.-E., Moreau-Gachelin, F., and Tenen, D.G.(1995) Oncogene 11, 1549-1560) demonstrate that the PU.1 promoter directs cell type-specific reporter gene expression in myeloid cell lines, and that PU.1 activates its own promoter in an autoregulatory loop. Here we show that the murine PU.1 promoter is also specifically and highly functional in B cell lines as well. Oct-1 and Oct-2 can bind specifically to a site at base pair -55 in vitro, and this site is specifically protected in B cells in vivo. We also demonstrate that two other sites contribute to promoter activity in B cells; an Sp1 binding site adjacent to the octamer site, and the PU.1 autoregulatory site. Finally, we show that the B cell coactivator OBF-1/Bob1/OCA-B is only expressed in B cells and not in myeloid cells, and that OBF-1/Bob1/OCA-B can transactivate the PU.1 promoter in HeLa and myeloid cells. This B cell restricted coactivator may be responsible for the B cell specific expression of PU.1 mediated by the octamer site. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 795, "end": 799}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 775, "end": 780}]}, {"trigger": {"text": "bind", "start": 795, "end": 799}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 785, "end": 790}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 174, "end": 183}, "arguments": [{"role": "Theme", "text": "spi-1", "start": 100, "end": 105}]}, {"trigger": {"text": "expressed", "start": 1149, "end": 1158}, "arguments": [{"role": "Theme", "text": "OBF-1", "start": 1124, "end": 1129}]}, {"trigger": {"text": "expression", "start": 1363, "end": 1373}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 1377, "end": 1381}]}], "positive regulation": [{"trigger": {"text": "activate", "start": 50, "end": 58}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 70, "end": 74}, {"role": "Site", "text": "promoter", "start": 83, "end": 91}]}, {"trigger": {"text": "activates", "start": 610, "end": 619}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 507, "end": 511}, {"role": "Site", "text": "promoter", "start": 512, "end": 520}, {"role": "Cause", "text": "PU.1", "start": 605, "end": 609}]}, {"trigger": {"text": "transactivate", "start": 1226, "end": 1239}, "arguments": [{"role": "Cause", "text": "OBF-1", "start": 1205, "end": 1210}, {"role": "Theme", "text": "PU.1", "start": 1244, "end": 1248}, {"role": "Site", "text": "promoter", "start": 1249, "end": 1257}]}, {"trigger": {"text": "responsible", "start": 1327, "end": 1338}, "arguments": [{"role": "Cause", "text": "OBF-1", "start": 1205, "end": 1210}, {"role": "Theme", "text": "mediated", "start": 1382, "end": 1390}]}, {"trigger": {"text": "mediated", "start": 1382, "end": 1390}, "arguments": [{"role": "Theme", "text": "expression", "start": 1363, "end": 1373}]}]}}, "schema": []}
{"input": "Tissue-specific activity of the gammac chain gene promoter depends upon an Ets binding site and is regulated by GA-binding protein. \nThe gammac chain is a subunit of multiple cytokine receptors (interleukin (IL)-2, IL-4, IL-7, IL-9, and IL-15), the expression of which is restricted to hematopoietic lineages. A defect in gammac leads to the X-linked severe combined immunodeficiency characterized by a block in T cell differentiation. In order to better characterize the human gammac promoter and define the minimal tissue-specific promoter region, progressive 5'-deletion constructs of a segment extending 1053 base pairs upstream of the major transcription start site were generated and tested for promoter activity in various hematopoietic and nonhematopoietic cell types. The -1053/+34 construct allowed promoter activity only in cells of hematopoietic origin, and tissue specificity was conserved in all other constructs tested. The region downstream of -90 appeared critical for basal promoter activity. It contains two potential Ets binding sites conserved in the murine gammac promoter gene, one of which was found essential for functional promoter activity as determined by mutational analysis. The functional Ets binding site was found to bind Ets family proteins, principally GA-binding protein and Elf-1 and could be transactivated by GABPalpha and -beta synergistically. These results indicate that, as already reported for the IL2Rbeta promoter, GA-binding protein is an essential component of gammac basal promoter activity. Although GABP expression is not restricted to the hematopoietic lineage, its interaction with other specific factors may contribute to the tissue-specific expression of the gammac gene. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 1250, "end": 1254}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 1311, "end": 1316}]}, {"trigger": {"text": "interaction", "start": 1618, "end": 1629}, "arguments": [{"role": "Theme", "text": "GABP", "start": 1550, "end": 1554}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1555, "end": 1565}, "arguments": [{"role": "Theme", "text": "GABP", "start": 1550, "end": 1554}]}, {"trigger": {"text": "expression", "start": 1696, "end": 1706}, "arguments": [{"role": "Theme", "text": "gammac", "start": 1714, "end": 1720}]}], "negative regulation": [{"trigger": {"text": "defect", "start": 312, "end": 318}, "arguments": [{"role": "Theme", "text": "gammac", "start": 322, "end": 328}]}], "positive regulation": [{"trigger": {"text": "contribute", "start": 1662, "end": 1672}, "arguments": [{"role": "Cause", "text": "interaction", "start": 1618, "end": 1629}, {"role": "Theme", "text": "expression", "start": 1696, "end": 1706}]}]}}, "schema": []}
{"input": "Multiple transcription factors are required for activation of human interleukin 9 gene in T cells. \nThe genetic elements and regulatory mechanisms responsible for human interleukin 9 (IL-9) gene expression in a human T cell leukemia virus type I-transformed human T cell line, C5MJ2, were investigated. We demonstrated that IL-9 gene expression is controlled, at least in part, by transcriptional activation. Transient expression of the luciferase reporter gene linked to serially deleted sequences of the 5'-flanking region of the IL-9 gene has revealed several positive and negative regulatory elements involved in the basal and inducible expression of the IL-9 gene in C5MJ2 cells. An AP-1 site at -146 to -140 was shown to be involved in the expression of the IL-9 gene. A proximal region between -46 and -80 was identified as the minimum sequence for the basal and inducible expression of the IL-9 gene in C5MJ2 cells. Within this region, an NF-kappaB site at -59 to -50 and its adjacent 20-base pair upstream sequence were demonstrated to play a critical role for the IL-9 promoter activity. DNA-protein binding studies indicated that NF-kappaB, c-Jun, and potentially novel proteins (around 35 kDa) can bind to this important sequence. Mutations at different sites within this proximal promoter region abolished the promoter activity as well as the DNA binding. Taken together, these results suggest that the cooperation of different transcription factors is essential for IL-9 gene expression in T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 1210, "end": 1214}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 1152, "end": 1157}]}], "gene expression": [{"trigger": {"text": "expression", "start": 195, "end": 205}, "arguments": [{"role": "Theme", "text": "interleukin 9", "start": 169, "end": 182}]}, {"trigger": {"text": "expression", "start": 334, "end": 344}, "arguments": [{"role": "Theme", "text": "IL-9", "start": 324, "end": 328}]}, {"trigger": {"text": "expression", "start": 641, "end": 651}, "arguments": [{"role": "Theme", "text": "IL-9", "start": 659, "end": 663}]}, {"trigger": {"text": "expression", "start": 746, "end": 756}, "arguments": [{"role": "Theme", "text": "IL-9", "start": 764, "end": 768}]}, {"trigger": {"text": "expression", "start": 880, "end": 890}, "arguments": [{"role": "Theme", "text": "IL-9", "start": 898, "end": 902}]}, {"trigger": {"text": "expression", "start": 1490, "end": 1500}, "arguments": [{"role": "Theme", "text": "IL-9", "start": 1480, "end": 1484}]}], "negative regulation": [{"trigger": {"text": "abolished", "start": 1309, "end": 1318}, "arguments": [{"role": "Theme", "text": "bind", "start": 1210, "end": 1214}]}], "positive regulation": [{"trigger": {"text": "required", "start": 35, "end": 43}, "arguments": [{"role": "Theme", "text": "activation", "start": 48, "end": 58}]}, {"trigger": {"text": "activation", "start": 48, "end": 58}, "arguments": [{"role": "Theme", "text": "interleukin 9", "start": 68, "end": 81}]}, {"trigger": {"text": "responsible", "start": 147, "end": 158}, "arguments": [{"role": "Theme", "text": "expression", "start": 195, "end": 205}]}, {"trigger": {"text": "as the minimum sequence", "start": 828, "end": 851}, "arguments": [{"role": "Theme", "text": "expression", "start": 880, "end": 890}]}, {"trigger": {"text": "play a critical role", "start": 1045, "end": 1065}, "arguments": [{"role": "Theme", "text": "IL-9", "start": 1074, "end": 1078}, {"role": "Site", "text": "promoter", "start": 1079, "end": 1087}]}, {"trigger": {"text": "essential", "start": 1466, "end": 1475}, "arguments": [{"role": "Cause", "text": "c-Jun", "start": 1152, "end": 1157}, {"role": "Theme", "text": "expression", "start": 1490, "end": 1500}]}], "regulation": [{"trigger": {"text": "controlled", "start": 348, "end": 358}, "arguments": [{"role": "Theme", "text": "expression", "start": 334, "end": 344}]}]}}, "schema": []}
{"input": "Mapping of the transcriptional repression domain of the lymphoid-specific transcription factor oct-2A. \nThe lymphoid-specific transcription factor Oct-2a is implicated in B cell-specific transcriptional activity via the octamer motif. Structure/function analysis of various Oct-2a effector regions in the context of the GAL4 DNA-binding domain revealed that Oct-2a contains two functionally different activation domains at the N and the C termini. The transcriptional activity of both domains is strongly potentiated by interactions with distinct B cell-specific coactivators. Recently, we have identified a repression domain located within the N terminus of Oct-2a (amino acids 2-99). When this domain was transferred to a potent activator, transcription was strongly inhibited. In this study we present a deletion analysis of the N-terminal region of Oct-2a to determine the minimal repression domain. We identified a stretch of 23 amino acids, rich in serine and threonine residues, which was responsible for most of the repression activity. We show that repression is strongly dependent on the type of enhancer present in the reporter plasmid as well as on the cell line tested. The possibility that Oct-2a can act as an activator and/or a repressor may have important consequences for the function of Oct-2a in B cell differentiation and other developmental processes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interactions", "start": 520, "end": 532}, "arguments": [{"role": "Theme", "text": "Oct-2a", "start": 358, "end": 364}, {"role": "Site", "text": "N", "start": 427, "end": 428}]}, {"trigger": {"text": "interactions", "start": 520, "end": 532}, "arguments": [{"role": "Theme", "text": "Oct-2a", "start": 358, "end": 364}, {"role": "Site", "text": "termini", "start": 439, "end": 446}]}], "positive regulation": [{"trigger": {"text": "potentiated", "start": 505, "end": 516}, "arguments": [{"role": "Theme", "text": "Oct-2a", "start": 358, "end": 364}, {"role": "Site", "text": "N", "start": 427, "end": 428}, {"role": "Cause", "text": "interactions", "start": 520, "end": 532}]}, {"trigger": {"text": "potentiated", "start": 505, "end": 516}, "arguments": [{"role": "Theme", "text": "Oct-2a", "start": 358, "end": 364}, {"role": "Site", "text": "termini", "start": 439, "end": 446}, {"role": "Cause", "text": "interactions", "start": 520, "end": 532}]}]}}, "schema": []}
{"input": "The role of BSAP (Pax-5) in B-cell development. \nThe hierarchy of transcriptional control in B-cell development has recently been analyzed by targeted gene inactivation in the mouse. In this manner, the paired box containing gene Pax-5, encoding the B cell specific transcription factor BSAP, has been shown to play a key role in early B lymphopoiesis. Other experimental strategies have implicated BSAP in the control of cell proliferation, isotype switching and transcription of the immunoglobulin heavy-chain gene at late stages of B-cell differentiation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Modulation of the expression of the IFN-gamma receptor beta-chain controls responsiveness to IFN-gamma in human peripheral blood T cells. \nIFN-gamma has potent antiproliferative and apoptotic effects in T cells that are important in determining T cell development and polarized differentiation. Therefore, any event that enables T cells to become less responsive to IFN- gamma may potentially alter immune responsiveness to Ag. In this work, we show that human peripheral blood T cells that are stimulated through the TCR and expanded with IL-2 are unresponsive to IFN-gamma, as determined by a lack of activation of jak kinases and the transcription factor, STAT1(alpha), a signal transducer and activator of transcription. This nonresponsiveness occurs because of a lack of expression of the beta- chain (accessory factor) of the IFN-gamma receptor, while at the same time maintaining IFN-gamma receptor alpha-chain expression. Expression of the beta-chain can be restored by secondary TCR ligation or PMA treatment. T cell blasts treated with PMA are now responsive to IFN-gamma. When freshly isolated, highly enriched (>98%) T cells are examined for IFN-gamma responsiveness; these cells can respond to IFN-gamma and express beta-chain. Therefore, as T cells progress from primary TCR activation through IL-2-dependent proliferation, followed by secondary TCR stimulation, their responsiveness to IFN-gamma varies, and this may affect their ability to participate in an ongoing immune response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 18, "end": 28}, "arguments": [{"role": "Theme", "text": "IFN-gamma receptor beta-chain", "start": 36, "end": 65}]}, {"trigger": {"text": "expression", "start": 918, "end": 928}, "arguments": [{"role": "Theme", "text": "IFN-gamma receptor alpha-chain", "start": 887, "end": 917}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 603, "end": 613}, "arguments": [{"role": "Theme", "text": "STAT1(alpha)", "start": 659, "end": 671}]}], "regulation": [{"trigger": {"text": "Modulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 18, "end": 28}]}]}}, "schema": []}
{"input": "Induction of CIITA and modification of in vivo HLA-DR promoter occupancy in normal thymic epithelial cells treated with IFN-gamma: similarities and distinctions with respect to HLA-DR-constitutive B cells. \nIn this study, the IFN-gamma induction of MHC class II gene expression in primary cultures of thymic epithelial cells (TEC) was analyzed. This cellular system offers the advantage that MHC class II induction is studied in a \"physiologic\" cell lineage that, as a result of this expression within the thymus, is thought to participate to the selection and maturation of the T cells. It was found that the MHC class II gene expression was associated with the de novo transcription of the gene encoding the CIITA trans-activator, a crucial MHC class II gene regulatory factor. Furthermore, the anatomy of interaction between the MHC class II DRA promoter and corresponding binding factors was analyzed by in vivo DNAse I footprint. It was found that treatment with IFN-gamma induces changes in the occupancy of the DRA gene regulatory sequences by nuclear factors. The resulting occupancy displays strong similarities with the one observed in the MHC class II-constitutive B cells, represented by both the Burkitt lymphoma line Raji and normal tonsil- derived B cells. However, some peculiar differences were observed between the TEC, either IFN-gamma-induced or not, and the constitutive B cells. These results suggest that both common mechanisms, such as the one mediated by the CIITA trans-activator, and distinct tissue-specific constraints contribute to the transcriptional control of constitutive and IFN-gamma-induced MHC class II gene expression. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 13, "end": 18}]}], "transcription": [{"trigger": {"text": "transcription", "start": 671, "end": 684}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 710, "end": 715}]}]}}, "schema": []}
{"input": "Recombinant NFAT1 (NFATp) is regulated by calcineurin in T cells and mediates transcription of several cytokine genes. \nTranscription factors of the NFAT family play a key role in the transcription of cytokine genes and other genes during the immune response. We have identified two new isoforms of the transcription factor NFAT1 (previously termed NFATp) that are the predominant isoforms expressed in murine and human T cells. When expressed in Jurkat T cells, recombinant NFAT1 is regulated, as expected, by the calmodulin-dependent phosphatase calcineurin, and its function is inhibited by the immunosuppressive agent cyclosporin A (CsA). Transactivation by recombinant NFAT1 in Jurkat T cells requires dual stimulation with ionomycin and phorbol 12-myristate 13-acetate; this activity is potentiated by coexpression of constitutively active calcineurin and is inhibited by CsA. Immunocytochemical analysis indicates that recombinant NFAT1 localizes in the cytoplasm of transiently transfected T cells and translocates into the nucleus in a CsA-sensitive manner following ionomycin stimulation. When expressed in COS cells, however, NFAT1 is capable of transactivation, but it is not regulated correctly: its subcellular localization and transcriptional function are not affected by stimulation of the COS cells with ionomycin and phorbol 12-myristate 13-acetate. Recombinant NFAT1 can mediate transcription of the interleukin-2, interleukin-4, tumor necrosis factor alpha, and granulocyte-macrophage colony-stimulating factor promoters in T cells, suggesting that NFAT1 contributes to the CsA-sensitive transcription of these genes during the immune response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 1104, "end": 1113}, "arguments": [{"role": "Theme", "text": "NFAT1", "start": 1137, "end": 1142}]}], "positive regulation": [{"trigger": {"text": "mediate", "start": 1390, "end": 1397}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1398, "end": 1411}]}, {"trigger": {"text": "contributes", "start": 1575, "end": 1586}, "arguments": [{"role": "Cause", "text": "NFAT1", "start": 1569, "end": 1574}, {"role": "Theme", "text": "transcription", "start": 1608, "end": 1621}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1398, "end": 1411}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 1419, "end": 1432}]}, {"trigger": {"text": "transcription", "start": 1398, "end": 1411}, "arguments": [{"role": "Theme", "text": "interleukin-4", "start": 1434, "end": 1447}]}, {"trigger": {"text": "transcription", "start": 1398, "end": 1411}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 1449, "end": 1476}]}, {"trigger": {"text": "transcription", "start": 1398, "end": 1411}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 1482, "end": 1530}]}, {"trigger": {"text": "transcription", "start": 1608, "end": 1621}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 1419, "end": 1432}]}, {"trigger": {"text": "transcription", "start": 1608, "end": 1621}, "arguments": [{"role": "Theme", "text": "interleukin-4", "start": 1434, "end": 1447}]}, {"trigger": {"text": "transcription", "start": 1608, "end": 1621}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 1449, "end": 1476}]}, {"trigger": {"text": "transcription", "start": 1608, "end": 1621}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 1482, "end": 1530}]}]}}, "schema": []}
{"input": "An alternatively spliced isoform of the Spi-B transcription factor. \nSpi-B is an Ets transcription factor related to the oncoprotein Spi-1/PU.1 and highly expressed in B lymphoid cells. The Ets proteins share a conserved Ets domain that mediates specific DNA binding. Spi-B binds DNA sequences containing a core 5'-GGAA-3' and activates transcription through this motif. Up to date, the biological function of Spi-B remains unknown. Here, we describe the characterization of an alternatively spliced variant of Spi-B, named deltaSpi-B, which has lost the Ets domain. In B lymphoid cells, deltaspi-B and spi-B mRNAs were present simultaneously in a ratio of around 10%. DeltaSpi-B product was not able to bind DNA and was recovered in cytoplasmic cellular extracts. We raise the hypothesis that delta Spi-B might affect Spi-B function by recruiting factors involved in Spi-B activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 274, "end": 279}, "arguments": [{"role": "Theme", "text": "Spi-B", "start": 268, "end": 273}]}, {"trigger": {"text": "bind", "start": 704, "end": 708}, "arguments": [{"role": "Theme", "text": "DeltaSpi-B", "start": 669, "end": 679}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 155, "end": 164}, "arguments": [{"role": "Theme", "text": "Spi-B", "start": 69, "end": 74}]}], "localization": [{"trigger": {"text": "recovered", "start": 721, "end": 730}, "arguments": [{"role": "Theme", "text": "DeltaSpi-B", "start": 669, "end": 679}, {"role": "AtLoc", "text": "cytoplasmic cellular extracts", "start": 734, "end": 763}]}], "regulation": [{"trigger": {"text": "affect", "start": 812, "end": 818}, "arguments": [{"role": "Theme", "text": "Spi-B", "start": 819, "end": 824}]}], "transcription": [{"trigger": {"text": "present", "start": 620, "end": 627}, "arguments": [{"role": "Theme", "text": "deltaspi-B", "start": 588, "end": 598}]}, {"trigger": {"text": "present", "start": 620, "end": 627}, "arguments": [{"role": "Theme", "text": "spi-B", "start": 603, "end": 608}]}]}}, "schema": []}
{"input": "Activation protein 1-dependent transcriptional activation of interleukin 2 gene by Ca2+/calmodulin kinase type IV/Gr. \nThe Ca2+/calmodulin-dependent protein kinase (CaMK) type IV/Gr is selectively expressed in T lymphocytes and is activated after signaling via the T cell antigen receptor (TCR), indicating that it mediates some of the Ca(2+)-dependent transcriptional events that follow TCR engagement. Here we show that CaMKIV/Gr induces the transcription factor activation protein 1 (AP-1) alone or in synergy with T cell mitogens and with the p21ras oncoprotein. CaMKIV/ Gr signaling is associated with transcriptional activation of c-fos but is independent of p21ras or calcineurin. AP-1 is an integral component of the nuclear factor of activated T cells (NFAT) transcriptional complex, which is required for interleukin 2 gene expression in T cells. We demonstrate that CaMKIV/Gr reconstitutes the capacity of the cytosolic component of NFAT to direct transcription from NFAT sites in non-T cells. These results reveal a central role for CaMKIV/Gr as a Ca(2+)-regulated activator of gene transcription in T lymphocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 197, "end": 206}, "arguments": [{"role": "Theme", "text": "Ca2+/calmodulin-dependent protein kinase (CaMK) type IV/Gr", "start": 123, "end": 181}]}, {"trigger": {"text": "expression", "start": 834, "end": 844}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 815, "end": 828}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 21, "end": 30}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 31, "end": 57}]}, {"trigger": {"text": "transcriptional activation", "start": 31, "end": 57}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 61, "end": 74}, {"role": "Cause", "text": "Ca2+/calmodulin kinase type IV/Gr", "start": 83, "end": 116}]}, {"trigger": {"text": "activated", "start": 231, "end": 240}, "arguments": [{"role": "Theme", "text": "expressed", "start": 197, "end": 206}]}, {"trigger": {"text": "transcriptional activation", "start": 607, "end": 633}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 637, "end": 642}]}, {"trigger": {"text": "required", "start": 802, "end": 810}, "arguments": [{"role": "Theme", "text": "expression", "start": 834, "end": 844}]}]}}, "schema": []}
{"input": "Mechanisms of transactivation by nuclear factor of activated T cells-1. \nNuclear factor of activated T cells-family proteins (NFAT1/NFATp, NFATc, NFAT3, and NFAT4/NFATx/NFATc3) play a key role in the transcription of cytokine genes and other genes during the immune response. We have defined the mechanisms of transactivation by NFAT1. NFAT1 possesses two transactivation domains whose sequences are not conserved in the other NFAT-family proteins, and a conserved DNA-binding domain that mediates the recruitment of cooperating nuclear transcription factors even when it is expressed in the absence of other regions of the protein. The activity of the NH2-terminal transactivation domain is modulated by an adjacent regulatory region that contains several conserved sequence motifs represented only in the NFAT family. Our results emphasize the multiple levels at which NFAT-dependent transactivation is regulated, and predict significant differences in the architecture of cooperative transcription complexes containing different NFAT-family proteins. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 575, "end": 584}, "arguments": [{"role": "Theme", "text": "NFAT1", "start": 336, "end": 341}]}]}}, "schema": []}
{"input": "BCL-6, a POZ/zinc-finger protein, is a sequence-specific transcriptional repressor. \nApproximately 40% of diffuse large cell lymphoma are associated with chromosomal translocations that deregulate the expression of the BCL6 gene by juxtaposing heterologous promoters to the BCL-6 coding domain. The BCL6 gene encodes a 95-kDa protein containing six C-terminal zinc-finger motifs and an N-terminal POZ domain, suggesting that it may function as a transcription factor. By using a DNA sequence selected for its ability to bind recombinant BCL-6 in vitro, we show here that BCL-6 is present in DNA-binding complexes in nuclear extracts from various B-cell lines. In transient transfectin experiments, BCL6 can repress transcription from promoters linked to its DNA target sequence and this activity is dependent upon specific DNA-binding and the presence of an intact N-terminal half of the protein. We demonstrate that this part of the BCL6 molecule contains an autonomous transrepressor domain and that two noncontiguous regions, including the POZ motif, mediate maximum transrepressive activity. These results indicate that the BCL-6 protein can function as a sequence-specific transcriptional repressor and have implications for the role of BCL6 in normal lymphoid development and lymphomagenesis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 201, "end": 211}, "arguments": [{"role": "Theme", "text": "BCL6", "start": 219, "end": 223}]}], "regulation": [{"trigger": {"text": "deregulate", "start": 186, "end": 196}, "arguments": [{"role": "Theme", "text": "expression", "start": 201, "end": 211}]}]}}, "schema": []}
{"input": "Constitutive expression of specific interferon isotypes in peripheral blood leukocytes from normal individuals and in promonocytic U937 cells. \nConstitutive expression of IFN-alpha5 and IFN-beta was detected in different lymphoid cells including peripheral blood mononuclear cells from normal individuals following amplification of IFN mRNA by reverse transcriptase-polymerase chain reaction and direct sequencing of the amplified product. The activated form of the interferon-induced transcription factor complex ISGF3 was also detected in nuclear extracts from uninduced cells. Culture supernatants from uninduced U937 cells were also found to activate an ISRE cloned upstream of the luciferase reporter gene, indicating the presence of endogenous IFN activity equivalent to approximately 0.3 to 0.5 IU/mL. This endogenous IFN was also shown to play a role in maintaining the basal level of expression of the major histocompatibility class I genes in lymphoid cells. These results suggest that IFN-alpha5 and IFN-beta are produced at low levels in normal tissues and play an important role in the regulation of cell function and in the maintenance of homeostasis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 157, "end": 167}, "arguments": [{"role": "Theme", "text": "IFN-alpha5", "start": 171, "end": 181}]}, {"trigger": {"text": "expression", "start": 157, "end": 167}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 186, "end": 194}]}, {"trigger": {"text": "produced", "start": 1024, "end": 1032}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 1011, "end": 1019}]}, {"trigger": {"text": "produced", "start": 1024, "end": 1032}, "arguments": [{"role": "Theme", "text": "IFN-alpha5", "start": 996, "end": 1006}]}]}}, "schema": []}
{"input": "Characterization of a new isoform of the NFAT (nuclear factor of activated T cells) gene family member NFATc [published erratum appears in J Biol Chem 1996 Dec 27;271(52):33705] \nThe cyclosporin A (CsA)/FK506-sensitive nuclear factor of activated T cells (NFAT) plays a key role in the inducible expression of cytokine genes in T cells. Although NFAT has been recently shown to be inducible in several non-T immune cells, the NFAT gene family members characterized to date have been isolated only from T cells. To further characterize NFAT function in human B cells and to demonstrate cytokine gene specificity of NFAT proteins, we report here the isolation and characterization of a cDNA clone from the Raji B cell line. The cDNA clone encodes a new isoform, NFATc.beta, of the NFAT gene family member NFATc (designated here NFATc.alpha). The amino acid sequence of NFATc.beta differs from that of NFATc.alpha in the first NH2-terminal 29 residues and contains an additional region of 142 residues at the COOH terminus. Northern analysis using a probe encompassing a common region of both isoforms showed two mRNA species of 2.7 and 4.5 kilobase pairs, while an NFATc.beta-specific probe detected only the 4.5-kilobase pair mRNA which was preferentially expressed in the spleen. Transient expression of NFATc.beta was capable of activating an interleukin-2 NFAT-driven reporter gene in stimulated Jurkat cells in a CsA-sensitive manner. However, NFATc.beta neither bound to the kappa3 element ( an NFAT-binding site ) in the tumor necrosis factor-alpha promoter nor activated the tumor necrosis factor-alpha promoter in cotransfection assays. These data suggest that different members or isoforms of NFAT gene family may regulate inducible expression of different cytokine genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 1466, "end": 1471}, "arguments": [{"role": "Theme", "text": "NFATc.beta", "start": 1447, "end": 1457}, {"role": "Site2", "text": "kappa3 element", "start": 1479, "end": 1493}, {"role": "Theme2", "text": "tumor necrosis factor-alpha", "start": 1526, "end": 1553}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1290, "end": 1300}, "arguments": [{"role": "Theme", "text": "NFATc.beta", "start": 1304, "end": 1314}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 1567, "end": 1576}, "arguments": [{"role": "Cause", "text": "NFATc.beta", "start": 1447, "end": 1457}, {"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 1581, "end": 1608}, {"role": "Site", "text": "promoter", "start": 1609, "end": 1617}]}]}}, "schema": []}
{"input": "Cytokine-modulating activity of tepoxalin, a new potential antirheumatic. \nTepoxalin is a new dual cyclooxygenase/5-lipoxygenase anti-inflammatory compound currently under clinical investigation. It has been shown to possess anti-inflammatory activity in a variety of animal models and more recently to inhibit IL-2 induced signal transduction. The current study was conducted to evaluate the cytokine modulating activity of tepoxalin and the role of iron in these effects. In human peripheral blood mononuclear cells (PBMC) stimulated with OKT3/PMA, tepoxalin inhibited lymphocyte proliferation with an IC50 of 6 microM. Additionally, it inhibited the production of LTB4 (IC50 = 0.5 microM) and the cytokines IL-2, IL-6 and TNF alpha (IC50 = 10-12 microM). Cytotoxicity was not demonstrated at these concentrations. Add-back experiments with either cytokines (IL-2 or IL-6), LTB4 or conditioned media failed to restore the proliferative response in the presence of tepoxalin. However, the concurrent addition of iron (in the form of ferrous or ferric chloride and other iron salts) reversed the inhibition of proliferation caused by tepoxalin. Tepoxalin also inhibits the activation of NF kappa B, a transcription factor which acts on several cytokine genes. Tepoxalin's effect on NF kappa B is also reversed by the addition of iron salts. These data suggest that the action of tepoxalin to inhibit proliferation in PBMC may be at least in part due to its ability to reduce the amount of available iron resulting in decreased activation of NF kappa B and subsequent inhibition of cytokine production. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 653, "end": 663}, "arguments": [{"role": "Theme", "text": "LTB4", "start": 667, "end": 671}]}, {"trigger": {"text": "production", "start": 653, "end": 663}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 710, "end": 714}]}, {"trigger": {"text": "production", "start": 653, "end": 663}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 716, "end": 720}]}, {"trigger": {"text": "production", "start": 653, "end": 663}, "arguments": [{"role": "Theme", "text": "TNF alpha", "start": 725, "end": 734}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 639, "end": 648}, "arguments": [{"role": "Theme", "text": "production", "start": 653, "end": 663}]}]}}, "schema": []}
{"input": "oriP is essential for EBNA gene promoter activity in Epstein-Barr virus-immortalized lymphoblastoid cell lines. \nDuring Epstein-Barr virus latent infection of B lymphocytes in vitro, six viral nuclear antigens (EBNAs) are expressed from one of two promoters, Cp or Wp, whose activities are mutually exclusive. Upon infection, Wp is initially active, followed by a switch to Cp for the duration of latency. In this study, the region upstream of Cp was analyzed for the presence of cis elements involved in regulating the activities of the EBNA gene promoters in established in vitro immortalized lymphoblastoid cell lines (LCLs). It was determined that oriP, the origin for episomal maintenance during latency, is essential for efficient transcription initiation from either Cp or Wp in LCLs, as well as in some Burkitt's lymphoma cell lines. Deletion of the EBNA2-dependent enhancer located upstream of Cp resulted in a ca. two- to fivefold reduction in Cp activity in the LCLs assayed. More extensive deletion of sequences upstream of Cp, including the EBNA2-dependent enhancer, resulted in nearly complete loss of Cp activity. This loss of activity was shown to correlate with deletion of two CCAAT boxes, a proximal CCAAT box located at bp -61 to -65 and a distal CCAAT box located at bp -253 to -257, upstream of Cp. Site-directed mutagenesis of these cis elements demonstrated that Cp activity is highly dependent on the presence of a properly positioned CCAAT box, with the dependence on the distal CCAAT box apparent only when the proximal CCAAT box was deleted or mutated. Deletion of the glucocorticoid response elements located at ca. bp -850 upstream of Cp did not result in a significant loss in activity. In general, deletions which diminished Cp activity resulted in induction of Wp activity, consistent with suppression of Wp activity by transcriptional interference from Cp. The identification of oriP and the EBNA2-dependent enhancer as the major positive cis elements involved in regulating Cp activity in LCL suggests that EBNA gene transcription is largely autoregulated by EBNA 1 and EBNA 2. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "switch", "start": 364, "end": 370}, "arguments": [{"role": "Theme", "text": "active", "start": 342, "end": 348}]}, {"trigger": {"text": "reduction", "start": 941, "end": 950}, "arguments": [{"role": "Theme", "text": "Cp", "start": 954, "end": 956}]}, {"trigger": {"text": "loss", "start": 1108, "end": 1112}, "arguments": [{"role": "Theme", "text": "Cp", "start": 1116, "end": 1118}]}, {"trigger": {"text": "loss", "start": 1700, "end": 1704}, "arguments": [{"role": "Theme", "text": "Cp", "start": 1387, "end": 1389}]}, {"trigger": {"text": "diminished", "start": 1746, "end": 1756}, "arguments": [{"role": "Theme", "text": "Cp", "start": 1757, "end": 1759}]}, {"trigger": {"text": "suppression", "start": 1823, "end": 1834}, "arguments": [{"role": "Theme", "text": "Wp", "start": 1838, "end": 1840}]}], "positive regulation": [{"trigger": {"text": "active", "start": 342, "end": 348}, "arguments": [{"role": "Theme", "text": "Wp", "start": 326, "end": 328}]}, {"trigger": {"text": "switch", "start": 364, "end": 370}, "arguments": [{"role": "Theme", "text": "Cp", "start": 374, "end": 376}]}, {"trigger": {"text": "dependent", "start": 1409, "end": 1418}, "arguments": [{"role": "Theme", "text": "Cp", "start": 1387, "end": 1389}]}, {"trigger": {"text": "dependence", "start": 1480, "end": 1490}, "arguments": [{"role": "Theme", "text": "Cp", "start": 1387, "end": 1389}]}, {"trigger": {"text": "induction", "start": 1781, "end": 1790}, "arguments": [{"role": "Cause", "text": "diminished", "start": 1746, "end": 1756}, {"role": "Theme", "text": "Wp", "start": 1794, "end": 1796}]}], "regulation": [{"trigger": {"text": "regulating", "start": 1998, "end": 2008}, "arguments": [{"role": "Cause", "text": "oriP", "start": 1913, "end": 1917}, {"role": "Theme", "text": "Cp", "start": 2009, "end": 2011}]}, {"trigger": {"text": "regulating", "start": 1998, "end": 2008}, "arguments": [{"role": "Theme", "text": "Cp", "start": 2009, "end": 2011}]}]}}, "schema": []}
{"input": "Various modes of basic helix-loop-helix protein-mediated regulation of murine leukemia virus transcription in lymphoid cell lines. \nThe transcriptionally regulatory regions of the lymphomagenic Akv and SL3-3 murine leukemia retroviruses (MLVs) contain two types of E-box consensus motifs, CAGATG. One type, EA/S, is located in the upstream promoter region, and the other, E(gre), is located in a tandem repeat with enhancer properties. We have examined the requirements of the individual E-boxes in MLV transcriptional regulation. In lymphoid cell lines only, the E(gre)-binding protein complexes included ALF1 or HEB and E2A basic helix-loop-helix proteins. Ectopic ALF1 and E2A proteins required intact E(gre) motifs for mediating transcriptional activation. ALF1 transactivated transcription of Akv MLV through the two E(gre) motifs equally, whereas E2A protein required the promoter-proximal E(gre) motif. In T- and B-cell lines, the E(gre) motifs were of major importance for Akv MLV transcriptional activity, while the EA/S motif had some effect. In contrast, neither E(gre) nor EA/S motifs contributed pronouncedly to Akv MLV transcription in NIH 3T3 cells lacking DNA-binding ALF1 or HEB and E2A proteins. The Id1 protein was found to repress ALF1 activity in vitro and in vivo. Moreover, ectopic Id1 repressed E(gre)-directed but not EA/S-directed MLV transcription in lymphoid cell lines. In conclusion, E(gre) motifs and interacting basic helix-loop-helix proteins are important determinants for MLV transcriptional activity in lymphocytic cell lines. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 571, "end": 578}, "arguments": [{"role": "Theme", "text": "ALF1", "start": 606, "end": 610}]}, {"trigger": {"text": "binding", "start": 571, "end": 578}, "arguments": [{"role": "Theme", "text": "HEB", "start": 614, "end": 617}]}, {"trigger": {"text": "binding", "start": 1176, "end": 1183}, "arguments": [{"role": "Theme", "text": "ALF1", "start": 1184, "end": 1188}]}, {"trigger": {"text": "binding", "start": 1176, "end": 1183}, "arguments": [{"role": "Theme", "text": "HEB", "start": 1192, "end": 1195}]}, {"trigger": {"text": "interacting", "start": 1432, "end": 1443}, "arguments": [{"role": "Theme", "text": "ALF1", "start": 606, "end": 610}]}, {"trigger": {"text": "interacting", "start": 1432, "end": 1443}, "arguments": [{"role": "Theme", "text": "HEB", "start": 614, "end": 617}]}], "negative regulation": [{"trigger": {"text": "lacking", "start": 1164, "end": 1171}, "arguments": [{"role": "Theme", "text": "binding", "start": 1176, "end": 1183}]}]}}, "schema": []}
{"input": "Gene transcription through activation of G-protein-coupled chemoattractant receptors. \nReceptors for leukocyte chemoattractants, including chemokines, are traditionally considered to be responsible for the activation of special leukocyte functions such as chemotaxis, degranulation, and the release of superoxide anions. Recently, these G-protein-coupled serpentine receptors have been found to transduce signals leading to gene transcription and translation in leukocytes. Transcription factors, such as NF kappa B and AP-1, are activated upon stimulation of the cells with several chemoattractants at physiologically relevant concentrations. Activation of transcription factors through these receptors involves G-protein coupling and the activation of protein kinases. The underlying signaling pathways appear to be different from those utilized by TNF-alpha, a better characterized cytokine that induces the transcription of immediate-early genes. Chemoattractants stimulate the expression of several inflammatory cytokines and chemokines, which in turn may activate their respective receptors and initiate an autocrine regulatory mechanism for persistent cytokine and chemokine gene expression. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Regulation of gene expression at early stages of B-cell and T-cell differentiation. \nThe expression of distinct sets of genes at different stages of B-lymphocyte and T-lymphocyte differentiation is controlled at the level of transcription. A number of recent studies have described interactions between transcription factors in lymphocytes that provide new insights into mechanisms regulating gene expression. These mechanisms include the assembly of higher order nucleoprotein complexes and other protein-protein interactions that enhance the functional specificity of transcriptional regulators in lymphocytes. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Involvement of tyrosine phosphorylation in endothelial adhesion molecule induction. \nInduction of endothelial adhesion molecules by the cytokine tumor necrosis factor-alpha (TNF) can occur independently of protein kinase C and activation of a protein tyrosine kinase (PTK) has recently been implicated in the upregulation of vascular cell adhesion molecule 1 (VCAM-1) by interleukin-4 (IL-4) on endothelial cells. We demonstrate that the PTK inhibitors herbimycin A or genistein suppress induction of endothelial VCAM-1 and E-selectin, as well as subsequent monocytic cell adhesion to endothelial cells stimulated by TNF. Inhibition studies indicate that specific tyrosine phosphorylation following PTK activation is involved in the mobilization of the transcription factor, nuclear factor kappa B, and VCAM-1 mRNA expression. This may have implications for pathophysiological conditions that involve the upregulation of these molecules (e.g. inflammation and atherosclerosis). ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "suppress", "start": 479, "end": 487}, "arguments": [{"role": "Theme", "text": "induction", "start": 488, "end": 497}]}], "positive regulation": [{"trigger": {"text": "upregulation", "start": 309, "end": 321}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 360, "end": 366}, {"role": "Cause", "text": "IL-4", "start": 386, "end": 390}]}, {"trigger": {"text": "induction", "start": 488, "end": 497}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 513, "end": 519}, {"role": "Cause", "text": "TNF", "start": 617, "end": 620}]}, {"trigger": {"text": "induction", "start": 488, "end": 497}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 524, "end": 534}, {"role": "Cause", "text": "TNF", "start": 617, "end": 620}]}], "transcription": [{"trigger": {"text": "expression", "start": 815, "end": 825}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 803, "end": 809}]}]}}, "schema": []}
{"input": "Transcription specific differences visualized by fluorescence in situ hybridization pattern on interphase nuclei of different cell types. \nApplication of a \"formamide free\" and thus \"material preserving\" in situ hybridization technique using the cDNA of the myf3 gene revealed the following results: Human rhabdomyosarcoma cells, characterized by a high expression of myf3 show intensive hybridization signals in their interphase. RNase treatment prior to hybridization considerably reduces the size of this signals. In comparison, isolated nuclei of human lymphocytes in which no need for the expression of this gene exists, show barely hybridization signals. Correspondingly, RNase treatment had no effect on hybridization pattern at all. In conclusion an increased transcription efficiency of a cell type specific gene is accompanied by a higher hybridization accessibility in the corresponding cell nuclei. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 354, "end": 364}, "arguments": [{"role": "Theme", "text": "myf3", "start": 368, "end": 372}]}, {"trigger": {"text": "hybridization signals", "start": 388, "end": 409}, "arguments": [{"role": "Theme", "text": "myf3", "start": 368, "end": 372}]}, {"trigger": {"text": "expression", "start": 594, "end": 604}, "arguments": [{"role": "Theme", "text": "myf3", "start": 368, "end": 372}]}], "positive regulation": [{"trigger": {"text": "intensive", "start": 378, "end": 387}, "arguments": [{"role": "Theme", "text": "hybridization signals", "start": 388, "end": 409}]}]}}, "schema": []}
{"input": "Precise alignment of sites required for mu enhancer activation in B cells. \nThe lymphocyte-specific immunoglobulin mu heavy-chain gene intronic enhancer is regulated by multiple nuclear factors. The previously defined minimal enhancer containing the muA, muE3, and muB sites is transactivated by a combination of the ETS-domain proteins PU.1 and Ets-1 in nonlymphoid cells. The core GGAAs of the muA and muB sites are separated by 30 nucleotides, suggesting that ETS proteins bind to these sites from these same side of the DNA helix. We tested the necessity for appropriate spatial alignment of these elements by using mutated enhancers with altered spacings. A 4- or 10-bp insertion between muE3 and muB inactivated the mu enhancer in S194 plasma cells but did not affect in vitro binding of Ets-1, PU.1, or the muE3-binding protein TFE3, alone or in pairwise combinations. Circular permutation and phasing analyses demonstrated that PU.1 binding but not TFE3 or Ets-1 bends mu enhancer DNA toward the major groove. We propose that the requirement for precise spacing of the muA and muB elements is due in part to a directed DNA bend induced by PU.1. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "combination", "start": 298, "end": 309}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 337, "end": 341}, {"role": "Theme2", "text": "Ets-1", "start": 346, "end": 351}]}, {"trigger": {"text": "binding", "start": 783, "end": 790}, "arguments": [{"role": "Theme", "text": "Ets-1", "start": 794, "end": 799}]}, {"trigger": {"text": "binding", "start": 783, "end": 790}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 801, "end": 805}]}, {"trigger": {"text": "binding", "start": 783, "end": 790}, "arguments": [{"role": "Theme", "text": "TFE3", "start": 835, "end": 839}]}, {"trigger": {"text": "binding", "start": 941, "end": 948}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 936, "end": 940}]}, {"trigger": {"text": "binding", "start": 941, "end": 948}, "arguments": [{"role": "Theme", "text": "TFE3", "start": 957, "end": 961}]}, {"trigger": {"text": "binding", "start": 941, "end": 948}, "arguments": [{"role": "Theme", "text": "Ets-1", "start": 965, "end": 970}]}], "regulation": [{"trigger": {"text": "affect", "start": 767, "end": 773}, "arguments": [{"role": "Theme", "text": "binding", "start": 783, "end": 790}]}]}}, "schema": []}
{"input": "Alpha 4 beta 1 (CD49d/CD29) integrin costimulation of human T cells enhances transcription factor and cytokine induction in the absence of altered sensitivity to anti-CD3 stimulation. \nThe integrin alpha 4 beta 1 can provide a costimulus to induce IL-2 secretion and IL-2R expression leading to enhanced proliferation of purified, peripheral blood T cells. Similar to expression of IL-2, we demonstrated that recombinant vascular-cell adhesion molecule-1, when co-immobilized with anti-CD3 mAb, significantly enhanced the induction of transcription factors NF-AT, AP-1, and NF-kappa B as determined by electromobility shift assays. alpha 4 beta 1 ligation alone had no effect on transcription factor binding. The requirements for induction of transcription factors reflected the requirements for the secretion of multiple cytokines, including IL-2, TNF-alpha, IFN-gamma, and granulocyte macrophage-CSF. In contrast to freshly isolated T cells, in vitro-cultured T cells did not require costimulation for cytokine secretion in response to anti-CD3 alone. Comparison of the dose response to anti-CD3 stimulation demonstrated that half-maximal induction of IL-2 was achieved using the same dose of anti-CD3 for both freshly isolated and cultured T cells. Furthermore, the dose of OKT3 required to achieve half-maximal activation was the same using PMA or different concentrations of alpha 4 beta 1 ligands. Therefore, costimulation by alpha 4 beta 1 ligands was not due to stabilization of the interaction of the cells with its substrate. We conclude, rather, that alpha 4 beta 1 in freshly isolated T cells delivers a distinct signal that synergizes early with signals initiated by TCR/CD3 ligation to induce DNA binding of multiple transcription factors required for cytokine gene induction. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 647, "end": 655}, "arguments": [{"role": "Theme", "text": "alpha 4 beta 1", "start": 632, "end": 646}]}], "gene expression": [{"trigger": {"text": "expression", "start": 273, "end": 283}, "arguments": [{"role": "Theme", "text": "IL-2R", "start": 267, "end": 272}]}, {"trigger": {"text": "expression", "start": 368, "end": 378}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 382, "end": 386}]}], "localization": [{"trigger": {"text": "secretion", "start": 253, "end": 262}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 248, "end": 252}]}, {"trigger": {"text": "secretion", "start": 800, "end": 809}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 843, "end": 847}]}, {"trigger": {"text": "secretion", "start": 800, "end": 809}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 849, "end": 858}]}, {"trigger": {"text": "secretion", "start": 800, "end": 809}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 860, "end": 869}]}, {"trigger": {"text": "secretion", "start": 800, "end": 809}, "arguments": [{"role": "Theme", "text": "granulocyte macrophage-CSF", "start": 875, "end": 901}]}], "positive regulation": [{"trigger": {"text": "induce", "start": 241, "end": 247}, "arguments": [{"role": "Cause", "text": "integrin alpha 4 beta 1", "start": 189, "end": 212}, {"role": "Theme", "text": "secretion", "start": 253, "end": 262}]}, {"trigger": {"text": "induce", "start": 241, "end": 247}, "arguments": [{"role": "Cause", "text": "integrin alpha 4 beta 1", "start": 189, "end": 212}, {"role": "Theme", "text": "expression", "start": 273, "end": 283}]}, {"trigger": {"text": "induction", "start": 1141, "end": 1150}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1154, "end": 1158}]}]}}, "schema": []}
{"input": "Defective transcription of the IL-2 gene is associated with impaired expression of c-Fos, FosB, and JunB in anergic T helper 1 cells. \nAnergic CD4+ Th cells do not produce IL-2 when challenged with Ag-pulsed accessory cells because of a transcriptional defect. In this work, we report that these anergic T cells are defective in their ability to up-regulate protein binding and transactivation at two critical IL-2 DNA enhancer elements: NF-AT (nuclear factor of activated T cells; a sequence that binds a heterotrimeric NFATp, Fos, and Jun protein complex) and Activator Protein-1 (AP-1) (that binds Fos and Jun heterodimers). Western blot analysis of nuclear extracts showed that the impaired DNA-protein interactions in anergic T cells were associated with poor expression of the inducible AP-1 family members c-Fos, FosB, and JunB. However, the reduced expression of these proteins was not the result of a global TCR/CD3-signaling defect because CD3 cross-linking induced an equivalent increase in intracellular-free calcium ions, as well as NFATp dephosphorylation, translocation to the nucleus, and DNA binding in both normal and anergic T cells. Thus, defective IL-2 gene transcription appears to be due, at least in part, to a selective block in the expression of the AP-1 Fos and Jun family members in anergic T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 498, "end": 503}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 521, "end": 526}]}, {"trigger": {"text": "binds", "start": 498, "end": 503}, "arguments": [{"role": "Theme", "text": "Fos", "start": 528, "end": 531}]}, {"trigger": {"text": "binds", "start": 498, "end": 503}, "arguments": [{"role": "Theme", "text": "Jun", "start": 537, "end": 540}]}, {"trigger": {"text": "binds", "start": 595, "end": 600}, "arguments": [{"role": "Theme", "text": "Fos", "start": 601, "end": 604}]}, {"trigger": {"text": "binds", "start": 595, "end": 600}, "arguments": [{"role": "Theme", "text": "Jun", "start": 609, "end": 612}]}, {"trigger": {"text": "binding", "start": 1109, "end": 1116}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1046, "end": 1051}]}], "gene expression": [{"trigger": {"text": "expression", "start": 69, "end": 79}, "arguments": [{"role": "Theme", "text": "JunB", "start": 100, "end": 104}]}, {"trigger": {"text": "expression", "start": 69, "end": 79}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 83, "end": 88}]}, {"trigger": {"text": "expression", "start": 69, "end": 79}, "arguments": [{"role": "Theme", "text": "FosB", "start": 90, "end": 94}]}, {"trigger": {"text": "produce", "start": 164, "end": 171}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 172, "end": 176}]}, {"trigger": {"text": "expression", "start": 765, "end": 775}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 813, "end": 818}]}, {"trigger": {"text": "expression", "start": 765, "end": 775}, "arguments": [{"role": "Theme", "text": "FosB", "start": 820, "end": 824}]}, {"trigger": {"text": "expression", "start": 765, "end": 775}, "arguments": [{"role": "Theme", "text": "JunB", "start": 830, "end": 834}]}, {"trigger": {"text": "expression", "start": 857, "end": 867}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 813, "end": 818}]}, {"trigger": {"text": "expression", "start": 857, "end": 867}, "arguments": [{"role": "Theme", "text": "FosB", "start": 820, "end": 824}]}, {"trigger": {"text": "expression", "start": 857, "end": 867}, "arguments": [{"role": "Theme", "text": "JunB", "start": 830, "end": 834}]}, {"trigger": {"text": "expression", "start": 1258, "end": 1268}, "arguments": [{"role": "Theme", "text": "Fos", "start": 1281, "end": 1284}]}, {"trigger": {"text": "expression", "start": 1258, "end": 1268}, "arguments": [{"role": "Theme", "text": "Jun", "start": 1289, "end": 1292}]}], "localization": [{"trigger": {"text": "translocation", "start": 1071, "end": 1084}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1046, "end": 1051}, {"role": "ToLoc", "text": "nucleus", "start": 1092, "end": 1099}]}], "negative regulation": [{"trigger": {"text": "Defective", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "transcription", "start": 10, "end": 23}]}, {"trigger": {"text": "impaired", "start": 60, "end": 68}, "arguments": [{"role": "Theme", "text": "expression", "start": 69, "end": 79}]}, {"trigger": {"text": "poor", "start": 760, "end": 764}, "arguments": [{"role": "Theme", "text": "expression", "start": 765, "end": 775}]}, {"trigger": {"text": "reduced", "start": 849, "end": 856}, "arguments": [{"role": "Theme", "text": "expression", "start": 857, "end": 867}]}, {"trigger": {"text": "defective", "start": 1159, "end": 1168}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1179, "end": 1192}]}, {"trigger": {"text": "block", "start": 1245, "end": 1250}, "arguments": [{"role": "Theme", "text": "expression", "start": 1258, "end": 1268}]}], "positive regulation": [{"trigger": {"text": "when", "start": 177, "end": 181}, "arguments": [{"role": "Theme", "text": "produce", "start": 164, "end": 171}]}, {"trigger": {"text": "because of", "start": 224, "end": 234}, "arguments": [{"role": "Theme", "text": "when", "start": 177, "end": 181}]}, {"trigger": {"text": "induced", "start": 968, "end": 975}, "arguments": [{"role": "Cause", "text": "induced", "start": 968, "end": 975}, {"role": "Theme", "text": "binding", "start": 1109, "end": 1116}]}, {"trigger": {"text": "induced", "start": 968, "end": 975}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1071, "end": 1084}]}, {"trigger": {"text": "induced", "start": 968, "end": 975}, "arguments": [{"role": "Theme", "text": "binding", "start": 1109, "end": 1116}]}, {"trigger": {"text": "due", "start": 1207, "end": 1210}, "arguments": [{"role": "Theme", "text": "defective", "start": 1159, "end": 1168}, {"role": "Cause", "text": "block", "start": 1245, "end": 1250}]}], "transcription": [{"trigger": {"text": "transcription", "start": 10, "end": 23}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 31, "end": 35}]}, {"trigger": {"text": "transcription", "start": 1179, "end": 1192}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1169, "end": 1173}]}]}}, "schema": []}
{"input": "C/EBP activators are required for HIV-1 replication and proviral induction in monocytic cell lines. \nPrevious work has shown that C/EBP sites and C/EBP transcriptional activators are necessary for HIV-1 LTR activity in monocytes/macrophages. We have investigated the role that C/EBP proteins play in induction and replication of HIV-1. Ectopic expression of the dominant negative C/EBP protein LIP inhibited HIV-1 mRNA and virus production in activated U1 cells, demonstrating that C/EBP proteins are required for provirus induction. U1 lines overexpressing C/EBP activator NF-IL-6 produced more viral mRNA and virus particles following cellular activation than control lines, demonstrating that C/EBP proteins are limiting for virus transcription. HIV-1 harboring mutations within two C/EBP sites were crippled in their ability to replicate in U937 promonocytic cells, indicating that these sites are required for replication. These data identify C/EBP proteins as regulators of HIV-1 expression in monocytes/macrophages. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "overexpressing", "start": 543, "end": 557}, "arguments": [{"role": "Theme", "text": "NF-IL-6", "start": 574, "end": 581}]}], "positive regulation": [{"trigger": {"text": "overexpressing", "start": 543, "end": 557}, "arguments": [{"role": "Theme", "text": "overexpressing", "start": 543, "end": 557}]}]}}, "schema": []}
{"input": "Inhibition of transcription factor Stat1 activity in mononuclear cell cultures and T cells by the cyclic AMP signaling pathway. \nActivation of T cells results in a cascade of gene activation and subsequent proliferation and differentiation into effector phenotypes. The regulation of transcription factors belonging to the signal transducer and activator of transcription (STAT) family was analyzed in PHA-activated mononuclear cells and in purified T cells activated by cross-linking cell surface CD3. Cell activation resulted in a delayed induction of STAT DNA-binding activity, which was sustained for several days, was composed predominantly of Stat1 and Stat3, and was blocked by cycloheximide and actinomycin D. Increased Stat1 and Stat3 mRNA and protein levels were detected, respectively 4 and 24 h after activation. Stimulation of the cAMP signal transduction pathway, which skews cytokine production toward a Th2 pattern, resulted in the preferential suppression of Stat1 activity. cAMP inhibited the induction of expression of IL-2 receptor components, but did not inhibit IL-4 receptor alpha-chain and CD69 expression or the induction of activator protein 1 transcription factors. cAMP signaling inhibited Stat1 at several different levels, including suppression of DNA binding and down-regulation of Stat1 protein and mRNA levels. Our results demonstrate the regulation of STAT activity by a signaling pathway that regulates the T cell functional phenotype and is distinct from the cytokine-activated Janus kinase-STAT signaling pathway. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1282, "end": 1289}, "arguments": [{"role": "Theme", "text": "Stat1", "start": 1218, "end": 1223}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1119, "end": 1129}, "arguments": [{"role": "Theme", "text": "IL-4 receptor alpha-chain", "start": 1084, "end": 1109}]}, {"trigger": {"text": "expression", "start": 1119, "end": 1129}, "arguments": [{"role": "Theme", "text": "CD69", "start": 1114, "end": 1118}]}], "negative regulation": [{"trigger": {"text": "Inhibition", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "Stat1", "start": 35, "end": 40}]}, {"trigger": {"text": "suppression", "start": 961, "end": 972}, "arguments": [{"role": "Theme", "text": "Stat1", "start": 976, "end": 981}]}, {"trigger": {"text": "inhibit", "start": 1076, "end": 1083}, "arguments": [{"role": "Theme", "text": "expression", "start": 1119, "end": 1129}]}, {"trigger": {"text": "inhibited", "start": 1208, "end": 1217}, "arguments": [{"role": "Theme", "text": "Stat1", "start": 1218, "end": 1223}]}, {"trigger": {"text": "suppression", "start": 1263, "end": 1274}, "arguments": [{"role": "Theme", "text": "binding", "start": 1282, "end": 1289}]}, {"trigger": {"text": "down-regulation", "start": 1294, "end": 1309}, "arguments": [{"role": "Theme", "text": "levels", "start": 1336, "end": 1342}]}], "positive regulation": [{"trigger": {"text": "resulted", "start": 932, "end": 940}, "arguments": [{"role": "Theme", "text": "suppression", "start": 961, "end": 972}]}], "regulation": [{"trigger": {"text": "resulted", "start": 932, "end": 940}, "arguments": [{"role": "Theme", "text": "suppression", "start": 961, "end": 972}]}], "transcription": [{"trigger": {"text": "levels", "start": 1336, "end": 1342}, "arguments": [{"role": "Theme", "text": "Stat1", "start": 1313, "end": 1318}]}]}}, "schema": []}
{"input": "Transcriptional analysis of Epstein-Barr virus gene expression in EBV-positive gastric carcinoma: unique viral latency in the tumour cells. \nAlthough case-oriented evidence for an association of Epstein-Barr virus (EBV) with gastric carcinoma has been accumulating recently, the interaction(s) between EBV and gastric epithelial cells is/are largely unknown. In this study, we examined seven EBV-positive gastric carcinoma tissues for viral gene expression at the mRNA level, from which studies on the EBV oncogenicity in human epithelial cells will benefit. Reverse transcription-PCR analysis showed that all seven EBV-positive tumour tissues constitutively expressed EBV nuclear antigen (EBNA) 1 mRNA, but not EBNA2 mRNA. The EBNA transcription was initiated from one of three EBNA promoters, Qp: by contrast, both Cp and Wp were silent, thus resulting in the lack of EBNA2 mRNA. Latent membrane protein (LMP) 2A mRNA was detected in three of seven cases; however, neither LMP1 nor LMP2B mRNA was detected in any of the tumours tested. Transcripts from the BamHI-A region of the viral genome were detectable in all cases. BZLF1 mRNA and the product, an immediate-early gene for EBV replication, was not expressed in any of them, thereby suggesting that the tumour cells carried EBV genomes in a tightly latent form. These findings further extended our previous data regarding EBV latency in gastric carcinoma cells at the protein level, and have affirmed that the programme of viral gene expression in the tumour more closely resembles 'latency I' represented by Burkitt's lymphoma than 'latency II' represented by the majority of nasopharyngeal carcinomas. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "resulting", "start": 845, "end": 854}, "arguments": [{"role": "Theme", "text": "lack", "start": 862, "end": 866}]}], "transcription": [{"trigger": {"text": "expressed", "start": 659, "end": 668}, "arguments": [{"role": "Theme", "text": "EBV nuclear antigen (EBNA) 1", "start": 669, "end": 697}]}, {"trigger": {"text": "expressed", "start": 659, "end": 668}, "arguments": [{"role": "Theme", "text": "EBNA2", "start": 712, "end": 717}]}, {"trigger": {"text": "lack", "start": 862, "end": 866}, "arguments": [{"role": "Theme", "text": "EBNA2", "start": 870, "end": 875}]}, {"trigger": {"text": "detected", "start": 924, "end": 932}, "arguments": [{"role": "Theme", "text": "Latent membrane protein (LMP) 2A", "start": 882, "end": 914}]}, {"trigger": {"text": "detected", "start": 999, "end": 1007}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 975, "end": 979}]}, {"trigger": {"text": "detected", "start": 999, "end": 1007}, "arguments": [{"role": "Theme", "text": "LMP2B", "start": 984, "end": 989}]}, {"trigger": {"text": "expressed", "start": 1205, "end": 1214}, "arguments": [{"role": "Theme", "text": "BZLF1", "start": 1124, "end": 1129}]}]}}, "schema": []}
{"input": "The role of early growth response gene 1 (egr-1) in regulation of the immune response. \nThe induction of immediate early genes in cells of the immune system is critical to determining the ultimate outcome of exposure to antigen. The importance of many of these genes relates to the role their transcription factor products play in dictating patterns of expression of downstream, function-related genes. Evidence from several systems indicates that the immediate early gene, egr-1 may be of particular importance in the immune system. Recently, the egr-1 promoter has been shown to be highly responsive to the diverse biochemical signals generated by antigen and cytokines in cells of the immune system. Furthermore, an important role for egr-1 in determining the differentiation pathway of myeloid cell precursors has been recently elaborated. Finally, potential targets of regulation by the zinc-finger transcription factor encoded by egr-1 include the interleukin-2, CD44, ICAM-1, and tumor necrosis factor genes. The role of egr-1 in regulation of the immune response will be discussed in the context of these recent studies. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "regulation", "start": 874, "end": 884}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 954, "end": 967}]}, {"trigger": {"text": "regulation", "start": 874, "end": 884}, "arguments": [{"role": "Theme", "text": "CD44", "start": 969, "end": 973}]}, {"trigger": {"text": "regulation", "start": 874, "end": 884}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 975, "end": 981}]}, {"trigger": {"text": "regulation", "start": 874, "end": 884}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor", "start": 987, "end": 1008}]}]}}, "schema": []}
{"input": "Apoptosis mediated by HIV protease is preceded by cleavage of Bcl-2. \nExpression of the human immunodeficiency virus type 1 (HIV) protease in cultured cells leads to apoptosis, preceded by cleavage of bcl-2, a key negative regulator of cell death. In contrast, a high level of bcl-2 protects cells in vitro and in vivo from the viral protease and prevents cell death following HIV infection of human lymphocytes, while reducing the yields of viral structural proteins, infectivity, and tumor necrosis factor alpha. We present a model for HIV replication in which the viral protease depletes the infected cells of bcl-2, leading to oxidative stress-dependent activation of NF kappa B, a cellular factor required for HIV transcription, and ultimately to cell death. Purified bcl-2 is cleaved by HIV protease between phenylalanine 112 and alanine 113. The results suggest a new option for HIV gene therapy; bcl-2 muteins that have noncleavable alterations surrounding the HIV protease cleavage site. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 70, "end": 80}, "arguments": [{"role": "Theme", "text": "human immunodeficiency virus type 1 (HIV) protease", "start": 88, "end": 138}]}], "negative regulation": [{"trigger": {"text": "reducing", "start": 419, "end": 427}, "arguments": [{"role": "Cause", "text": "bcl-2", "start": 277, "end": 282}, {"role": "Theme", "text": "tumor necrosis factor alpha", "start": 486, "end": 513}]}, {"trigger": {"text": "depletes", "start": 582, "end": 590}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 613, "end": 618}]}], "protein catabolism": [{"trigger": {"text": "cleavage", "start": 50, "end": 58}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 62, "end": 67}]}, {"trigger": {"text": "cleavage", "start": 189, "end": 197}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 201, "end": 206}]}, {"trigger": {"text": "cleaved", "start": 782, "end": 789}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 773, "end": 778}]}]}}, "schema": []}
{"input": "Activation of Stat 5b in erythroid progenitors correlates with the ability of ErbB to induce sustained cell proliferation. \nSelf renewal of normal erythroid progenitors is induced by the receptor tyrosine kinase c-ErbB, whereas other receptors (c-Kit/Epo-R) regulate erythroid differentiation. To address possible mechanisms that could explain this selective activity of c-ErbB, we analyzed the ability of these receptors to activate the different members of the Stat transcription factor family. Ligand activation of c-ErbB induced the tyrosine phosphorylation, DNA-binding, and reporter gene transcription of Stat 5b in erythroblasts. In contrast, ligand activation of c-Kit was unable to induce any of these effects in the same cells. Activation of the erythropoietin receptor caused specific DNA-binding of Stat 5b, but failed to induce reporter gene transcription. These biochemical findings correlate perfectly with the selective ability of c-ErbB to cause sustained self renewal in erythroid progenitors. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 567, "end": 574}, "arguments": [{"role": "Theme", "text": "Stat 5b", "start": 611, "end": 618}]}, {"trigger": {"text": "binding", "start": 800, "end": 807}, "arguments": [{"role": "Theme", "text": "Stat 5b", "start": 811, "end": 818}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 546, "end": 561}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 537, "end": 545}, {"role": "Theme", "text": "Stat 5b", "start": 611, "end": 618}]}], "positive regulation": [{"trigger": {"text": "Activation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "Stat 5b", "start": 14, "end": 21}]}, {"trigger": {"text": "induced", "start": 525, "end": 532}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 546, "end": 561}]}, {"trigger": {"text": "induced", "start": 525, "end": 532}, "arguments": [{"role": "Theme", "text": "binding", "start": 567, "end": 574}]}, {"trigger": {"text": "activation", "start": 657, "end": 667}, "arguments": [{"role": "Theme", "text": "c-Kit", "start": 671, "end": 676}]}, {"trigger": {"text": "induce", "start": 691, "end": 697}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 546, "end": 561}, {"role": "Cause", "text": "activation", "start": 657, "end": 667}]}, {"trigger": {"text": "induce", "start": 691, "end": 697}, "arguments": [{"role": "Theme", "text": "binding", "start": 567, "end": 574}, {"role": "Cause", "text": "activation", "start": 657, "end": 667}]}, {"trigger": {"text": "Activation", "start": 738, "end": 748}, "arguments": [{"role": "Theme", "text": "erythropoietin receptor", "start": 756, "end": 779}]}, {"trigger": {"text": "caused", "start": 780, "end": 786}, "arguments": [{"role": "Cause", "text": "Activation", "start": 738, "end": 748}, {"role": "Theme", "text": "binding", "start": 800, "end": 807}]}]}}, "schema": []}
{"input": "Evidence for lowered induction of nuclear factor kappa B in activated human T lymphocytes during aging. \nTranscription factor NF kappa B (nuclear factor kappa B) is induced in T lymphocytes from young individuals following activation with a variety of stimuli including anti-CD3, phorbol myristate acetate (PMA), and tumor necrosis factor-alpha (TNF-alpha). In contrast, activated T lymphocytes from older individuals show a significant reduction in the induction of NF kappa B in response to the same stimuli. The age-related decline in induction of NF kappa B could not be attributed to alteration in the composition of subunits, p50 and p65 were found to be the predominant subunits of induced NF kappa B in T cells from young as well as elderly donors. Furthermore, similar levels of NF kappa B were found in the cytosols of unactivated T cells from both young and elderly donors suggesting that precursor levels of NF kappa B remain unaltered during aging. These results suggest that an age-associated decline in the induction of NF kappa B in activated T cells from elderly individuals may be attributable to altered regulation of the inhibitor, I kappa B, and may play an important role in immune dysregulation accompanying aging. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "be the predominant subunits", "start": 658, "end": 685}, "arguments": [{"role": "Theme", "text": "p50", "start": 632, "end": 635}]}], "positive regulation": [{"trigger": {"text": "be the predominant subunits", "start": 658, "end": 685}, "arguments": [{"role": "Theme", "text": "p65", "start": 640, "end": 643}]}, {"trigger": {"text": "induced", "start": 689, "end": 696}, "arguments": [{"role": "Theme", "text": "p50", "start": 632, "end": 635}]}, {"trigger": {"text": "induced", "start": 689, "end": 696}, "arguments": [{"role": "Theme", "text": "p65", "start": 640, "end": 643}]}]}}, "schema": []}
{"input": "Interaction of HTLV-I Tax with the human proteasome: implications for NF-kappa B induction. \nThe human T-cell leukemia virus type I (HTLV-I) has been etiologically associated with the development of the adult T-cell leukemia (ATL) as well as degenerative neurologic syndrome termed tropical spastic paraparesis (TSP). HTLV-I encodes a potent transactivator protein termed Tax that appears to play an important role in the process of T-cell immortalization. Even though the mechanisms by which Tax induces transformation are still unknown, it seems likely that the ability of Tax to alter the expression of many cellular genes plays an important part in this process. Tax does not bind directly to DNA but rather deregulates the activity of cellular transcription factors. One family of host transcription factors whose activity is altered by Tax includes NF-kappa B/Rel. These transcription factors are post-transcriptionally regulated by their assembly with a second family of inhibitory proteins termed I kappa B that serve to sequester the NF-kappa B/Rel complexes in the cytoplasm. Upon cellular activation, I kappa B alpha is phosphorylated, polyubiquitinated, and degraded in the proteasome. This proteolytic event liberates NF-kappa B, permitting its rapid translocation into the nucleus where it binds to its cognate enhancer elements. Similarly, the p105 precursor of the NF-kappa B p50 subunit is also post-translationally processed in the proteasome. The mechanisms by which Tax activates NF-kappa B remain unclear, and findings presented in the literature are often controversial. We identified a physical interaction between Tax and the HsN3 subunit of the human proteasome. This raises the intriguing possibility that physical association of the HsN3 proteasome subunit with HTLV-I Tax coupled with the independent interaction of Tax with either p100 or p65-I kappa B alpha targets these cytoplasmic NF-kappa B/Rel complexes to the proteasome for processing. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Interaction", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "Tax", "start": 22, "end": 25}]}, {"trigger": {"text": "bind", "start": 680, "end": 684}, "arguments": [{"role": "Theme", "text": "Tax", "start": 667, "end": 670}]}, {"trigger": {"text": "physical interaction", "start": 1609, "end": 1629}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1638, "end": 1641}, {"role": "Theme2", "text": "HsN3", "start": 1650, "end": 1654}]}, {"trigger": {"text": "physical association", "start": 1732, "end": 1752}, "arguments": [{"role": "Theme", "text": "HsN3", "start": 1760, "end": 1764}, {"role": "Theme2", "text": "Tax", "start": 1796, "end": 1799}]}, {"trigger": {"text": "interaction", "start": 1829, "end": 1840}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1844, "end": 1847}, {"role": "Theme2", "text": "p100", "start": 1860, "end": 1864}, {"role": "Theme3", "text": "I kappa B alpha", "start": 1872, "end": 1887}]}, {"trigger": {"text": "interaction", "start": 1829, "end": 1840}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1844, "end": 1847}, {"role": "Theme2", "text": "p65", "start": 1868, "end": 1871}, {"role": "Theme3", "text": "I kappa B alpha", "start": 1872, "end": 1887}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 1131, "end": 1145}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1112, "end": 1127}]}], "positive regulation": [{"trigger": {"text": "Upon", "start": 1086, "end": 1090}, "arguments": [{"role": "Theme", "text": "phosphorylated", "start": 1131, "end": 1145}]}, {"trigger": {"text": "Upon", "start": 1086, "end": 1090}, "arguments": [{"role": "Theme", "text": "degraded", "start": 1170, "end": 1178}]}], "protein catabolism": [{"trigger": {"text": "degraded", "start": 1170, "end": 1178}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1112, "end": 1127}]}]}}, "schema": []}
{"input": "Epstein-Barr viral latency is disrupted by the immediate-early BRLF1 protein through a cell-specific mechanism. \nEpstein-Barr virus (EBV), the causative agent of infectious mononucleosis, is a human herpesvirus associated with epithelial cell malignancies (nasopharyngeal carcinoma) as well as B-cell malignancies. Understanding how viral latency is disrupted is a central issue in herpesvirus biology. Epithelial cells are the major site of lytic EBV replication within the human host, and viral reactivation occurs in EBV-associated nasopharyngeal carcinomas. It is known that expression of a single viral immediate-early protein, BZLF1, is sufficient to initiate the switch from latent to lytic infection in B cells. Cellular regulation of BZLF1 transcription is therefore thought to play a key role in regulating the stringency of viral latency. Here we show that, unexpectedly, expression of another viral immediate-early protein, BRLF1, can disrupt viral latency in an epithelial cell-specific fashion. Therefore, the mechanisms leading to disruption of EBV latency appear to be cell-type specific. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 579, "end": 589}, "arguments": [{"role": "Theme", "text": "BZLF1", "start": 633, "end": 638}]}, {"trigger": {"text": "expression", "start": 883, "end": 893}, "arguments": [{"role": "Theme", "text": "BRLF1", "start": 936, "end": 941}]}], "regulation": [{"trigger": {"text": "regulation", "start": 729, "end": 739}, "arguments": [{"role": "Theme", "text": "transcription", "start": 749, "end": 762}]}], "transcription": [{"trigger": {"text": "transcription", "start": 749, "end": 762}, "arguments": [{"role": "Theme", "text": "BZLF1", "start": 743, "end": 748}]}]}}, "schema": []}
{"input": "Attenuated function of a variant form of the helix-loop-helix protein, Id-3, generated by an alternative splicing mechanism. \nThe Id family of helix-loop-helix proteins function as negative regulators of DNA binding, basic helix-loop-helix proteins in the regulation of cell growth and differentiation. We report here on the identification of a 17 kDa variant of the 14 kDa Id-3 protein termed Id-3L (long version) which possesses a unique 60 amino acid carboxy-terminus generated by read through of a 'coding intron' and alternative splicing. Northern analysis revealed expression of a minor 1.1 kb Id-3L transcript together with the predominant 0.95 kb Id-3 transcript in the majority of adult human tissues analysed. The variant Id-3L protein is functionally distinguishable from conventional Id-3 since in in vitro DNA mobility shift assays, it was greatly impaired in its ability to abrogate binding of the basic helix-loop-helix protein, E47, to an E box recognition sequence. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 897, "end": 904}, "arguments": [{"role": "Theme", "text": "E47", "start": 944, "end": 947}]}], "negative regulation": [{"trigger": {"text": "Attenuated function", "start": 0, "end": 19}, "arguments": [{"role": "Theme", "text": "Id-3", "start": 71, "end": 75}]}, {"trigger": {"text": "abrogate", "start": 888, "end": 896}, "arguments": [{"role": "Theme", "text": "binding", "start": 897, "end": 904}]}], "positive regulation": [{"trigger": {"text": "generated by", "start": 77, "end": 89}, "arguments": [{"role": "Theme", "text": "Id-3", "start": 71, "end": 75}]}], "transcription": [{"trigger": {"text": "read through", "start": 484, "end": 496}, "arguments": [{"role": "Theme", "text": "Id-3", "start": 374, "end": 378}]}, {"trigger": {"text": "expression", "start": 571, "end": 581}, "arguments": [{"role": "Theme", "text": "Id-3", "start": 655, "end": 659}]}]}}, "schema": []}
{"input": "Multifactor cis-dominant negative regulation of IL-2 gene expression in anergized T cells. \nThe molecular mechanism underlying IL-2 transcriptional blockade in anergic T cell clones is not fully understood. To examine whether an active negative regulatory process occurs, we created a reporter construct containing as an enhancer four copies of the NF-AT site and one copy of the octamer site (4X NF-AT-Oct). This construct was only slightly reduced (1.3-fold) in its expression when stimulated under anergic conditions, while a whole mouse IL-2 enhancer construct showed a reduction of 4.3-fold. Addition of the -176 to -96 sequence to the 4X NF-AT-Oct construct did not impart the ability to be affected by anergy, but addition of the -236 to -96 sequence did, demonstrating that anergy is an active inhibitory process and that more than the presence of the -150 AP-1 binding site (-152 to -147) is required to mediate the effect. Mutational studies of the -236 to -96 sequence indicated that the presence of both the -130 AP-1-like site (-187 to -181) and the -150 proximal AP-1 site were necessary to observe anergy. Because the -180 site is not required for trans-activation, it was possible to confirm by mutation in the normal mouse IL-2 enhancer that this site is absolutely essential for anergy induction. The simplest model to explain these results is that anergy is mediated by a complex of multiple transcription factors that exert a cis-acting dominant negative regulatory effect on the trans-activation of the IL-2 gene. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 58, "end": 68}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 48, "end": 52}]}], "negative regulation": [{"trigger": {"text": "dominant negative regulation", "start": 16, "end": 44}, "arguments": [{"role": "Theme", "text": "expression", "start": 58, "end": 68}]}, {"trigger": {"text": "transcriptional blockade", "start": 132, "end": 156}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 127, "end": 131}]}, {"trigger": {"text": "dominant negative regulatory effect", "start": 1457, "end": 1492}, "arguments": [{"role": "Theme", "text": "trans-activation", "start": 1500, "end": 1516}]}], "positive regulation": [{"trigger": {"text": "exert", "start": 1438, "end": 1443}, "arguments": [{"role": "Theme", "text": "dominant negative regulatory effect", "start": 1457, "end": 1492}]}, {"trigger": {"text": "trans-activation", "start": 1500, "end": 1516}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1524, "end": 1528}]}]}}, "schema": []}
{"input": "Characterization of the human myeloid cell nuclear differentiation antigen gene promoter. \nMNDA (myeloid cell nuclear differentiation antigen) is an interferon alpha regulated nuclear protein expressed only in cells of the human myelomonocytic lineage. To identify mechanisms responsible for this lineage-specific and interferon-regulated expression, the 5' flanking sequence of the gene has been characterized. Two interferon-stimulated response elements (ISRE) flank a multiple transcription start site region identifying MNDA as a TATA-less interferon-regulated gene. Other DNA elements present include a cluster of Myb sites, several Ets, an Ets related PU.1 site and an Sp1 site located within 600 bp of the transcription start sites. In addition, DNA methylation was revealed as one of the possible factors in establishing MNDA expression. The 5' flanking sequence has promoter activity which is elevated by interferon alpha. The findings indicate that MNDA expression is regulated by mechanisms similar to other myelomonocytic cell specific genes and genes up-regulated by interferon alpha. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 192, "end": 201}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 91, "end": 95}]}, {"trigger": {"text": "expression", "start": 339, "end": 349}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 91, "end": 95}]}, {"trigger": {"text": "expression", "start": 834, "end": 844}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 829, "end": 833}]}, {"trigger": {"text": "expression", "start": 964, "end": 974}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 959, "end": 963}]}], "positive regulation": [{"trigger": {"text": "responsible", "start": 276, "end": 287}, "arguments": [{"role": "Theme", "text": "regulated", "start": 329, "end": 338}]}, {"trigger": {"text": "establishing", "start": 816, "end": 828}, "arguments": [{"role": "Theme", "text": "expression", "start": 834, "end": 844}]}], "regulation": [{"trigger": {"text": "regulated", "start": 166, "end": 175}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 91, "end": 95}]}, {"trigger": {"text": "regulated", "start": 329, "end": 338}, "arguments": [{"role": "Theme", "text": "expression", "start": 339, "end": 349}]}, {"trigger": {"text": "regulated", "start": 555, "end": 564}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 524, "end": 528}]}, {"trigger": {"text": "regulated", "start": 978, "end": 987}, "arguments": [{"role": "Theme", "text": "expression", "start": 964, "end": 974}]}]}}, "schema": []}
{"input": "Regulation of GM-CSF gene transcription by core-binding factor. \nGM-CSF gene activation in T cells is known to involve the transcription factors nuclear factor-kappa B, AP-1, NFAT, and Sp1. Here we demonstrate that the human GM-CSF promoter and enhancer also encompass binding sites for core-binding factor (CBF). Significantly, the CBF sites are in each case contained within the minimum essential core regions required for inducible activation of transcription. Furthermore, these core regions of the enhancer and promoter each encompass closely linked binding sites for CBF, AP-1, and NFATp. The GM-CSF promoter CBF site TGTGGTCA is located 51 bp upstream of the transcription start site and also overlaps a YY-1 binding site. A 2-bp mutation within the CBF site resulted in a 2-3-fold decrease in the activities of both a 69-bp proximal promoter fragment and a 627-bp full-length promoter fragment. Stepwise deletions into the proximal promoter also revealed that the CBF site, but not the YY-1 site, was required for efficient induction of transcriptional activation. The AML1 and CBF beta genes that encode CBF each have the ability to influence cell growth and differentiation and have been implicated as proto-oncogenes in acute myeloid leukemia. This study adds GM-CSF to a growing list of cytokines and receptors that are regulated by CBF and which control the growth, differentiation, and activation of hemopoietic cells. The GM-CSF locus may represent one of several target genes that are dysregulated in acute myeloid leukemia. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 269, "end": 276}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 225, "end": 231}, {"role": "Site", "text": "promoter", "start": 232, "end": 240}]}, {"trigger": {"text": "binding", "start": 269, "end": 276}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 225, "end": 231}, {"role": "Site", "text": "enhancer", "start": 245, "end": 253}]}, {"trigger": {"text": "binding", "start": 555, "end": 562}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 588, "end": 593}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 77, "end": 87}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 65, "end": 71}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "transcription", "start": 26, "end": 39}]}, {"trigger": {"text": "dysregulated", "start": 1501, "end": 1513}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 1437, "end": 1443}]}], "transcription": [{"trigger": {"text": "transcription", "start": 26, "end": 39}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 14, "end": 20}]}]}}, "schema": []}
{"input": "Requirements for induction of vitamin D-mediated gene regulation in normal human B lymphocytes. \nMature human lymphocytes are unique targets of 1 alpha,25-dihydroxyvitamin D3 (1 alpha,25(OH)2D3) in that vitamin D receptors (VDR) are not constitutively expressed, and specific cellular activation signals are required for both the up-regulation of VDR and establishment of reactivity to the lipophilic ligand. Treatment of B lymphocytes with the cytokine IL-4 (IL-4), in the absence of prior activation, induces a weak up-regulation of VDR expression but fails to generate vitamin D-responsive element (VDRE)-reactive nuclear protein complexes or to initiate the genomic transcription of 25-hydroxyvitamin D3 24-hydroxylase. Stimulation of B lymphocytes by either ligation of CD40 Ag or cross-linking the Ig receptor is also insufficient to render B lymphocytes responsive to 1 alpha,25(OH)2D3. However, this apparent lack of response to the secosterol can be overcome by stimulation of B lymphocytes with a combination of these cellular activation signals, which are sufficient to lead to G1 cell cycle progression. In the presence of 1 alpha,25(OH)2D3, cellular activation associated with stimulation of such a progression appears to be sufficient for the up-regulation of VDR message and protein and necessary for the establishment of VDRE binding complexes and the induction of 24-hydroxylase message. Furthermore, biologic functions are modulated, in that the hormone inhibits proliferation in a subset of the activated B cells. These observations suggest that reactivity to 1 alpha,25(OH)2D3 is tightly regulated in B lymphocytes, requiring specific signals for its initiation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "reactivity", "start": 372, "end": 382}, "arguments": [{"role": "Theme", "text": "VDR", "start": 347, "end": 350}]}, {"trigger": {"text": "ligation", "start": 763, "end": 771}, "arguments": [{"role": "Theme", "text": "CD40 Ag", "start": 775, "end": 782}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 252, "end": 261}, "arguments": [{"role": "Theme", "text": "VDR", "start": 224, "end": 227}]}, {"trigger": {"text": "expression", "start": 539, "end": 549}, "arguments": [{"role": "Theme", "text": "VDR", "start": 535, "end": 538}]}], "positive regulation": [{"trigger": {"text": "required", "start": 308, "end": 316}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 330, "end": 343}]}, {"trigger": {"text": "required", "start": 308, "end": 316}, "arguments": [{"role": "Theme", "text": "reactivity", "start": 372, "end": 382}]}, {"trigger": {"text": "up-regulation", "start": 330, "end": 343}, "arguments": [{"role": "Theme", "text": "VDR", "start": 347, "end": 350}]}, {"trigger": {"text": "induces", "start": 503, "end": 510}, "arguments": [{"role": "Theme", "text": "up-regulation", "start": 518, "end": 531}]}, {"trigger": {"text": "up-regulation", "start": 518, "end": 531}, "arguments": [{"role": "Theme", "text": "expression", "start": 539, "end": 549}]}, {"trigger": {"text": "initiate", "start": 649, "end": 657}, "arguments": [{"role": "Theme", "text": "transcription", "start": 670, "end": 683}]}, {"trigger": {"text": "In the presence of", "start": 1116, "end": 1134}, "arguments": [{"role": "Theme", "text": "sufficient for the up-regulation", "start": 1238, "end": 1270}]}, {"trigger": {"text": "In the presence of", "start": 1116, "end": 1134}, "arguments": [{"role": "Theme", "text": "necessary", "start": 1302, "end": 1311}]}, {"trigger": {"text": "sufficient for the up-regulation", "start": 1238, "end": 1270}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1274, "end": 1277}]}, {"trigger": {"text": "necessary", "start": 1302, "end": 1311}, "arguments": [{"role": "Theme", "text": "induction", "start": 1368, "end": 1377}]}, {"trigger": {"text": "induction", "start": 1368, "end": 1377}, "arguments": [{"role": "Theme", "text": "24-hydroxylase", "start": 1381, "end": 1395}]}], "transcription": [{"trigger": {"text": "transcription", "start": 670, "end": 683}, "arguments": [{"role": "Theme", "text": "25-hydroxyvitamin D3 24-hydroxylase", "start": 687, "end": 722}]}]}}, "schema": []}
{"input": "Regulation of sialoadhesin expression on rat macrophages. Induction by glucocorticoids and enhancement by IFN-beta, IFN-gamma, IL-4, and lipopolysaccharide. \nSialoadhesin is a macrophage-restricted member of the Ig superfamily that mediates adhesion with lymphoid and myeloid cells. It is expressed on a subpopulation of macrophages in lymphoid tissues and in chronic inflammation (e.g., during autoimmune diseases). We have studied the regulation of sialoadhesin expression in vitro and show that glucocorticoids (GC) induce sialoadhesin expression on freshly isolated rat macrophages and the rat macrophage cell line R2. The cytokines IFN-beta, IFN-gamma, IL-4, and LPS, although unable to induce sialoadhesin expression by themselves, were able to enhance GC-mediated induction of sialoadhesin. Sialoadhesin expression was functional as shown by cell adhesion assays with human RBCs. Northern blotting experiments indicated that regulation predominantly occurred at the mRNA level. Comparison of the different combinations of GC and cytokines/LPS revealed differences in the level of GC-dependent enhancement of sialoadhesin expression, with IFN-beta and IL-4 being more potent than IFN-gamma and LPS. Moreover, the effects of IFN-gamma and LPS could be reproduced by priming, whereas IFN-beta and IL-4 were required simultaneously with GC. The regulation of sialoadhesin expression was mediated by the GC receptor, and not by mineralocorticoid receptor, as shown by inhibition experiments with specific antagonists. Finally, it is demonstrated that macrophages in the adrenal gland, the major site of endogenous GC production, express sialoadhesin. This study demonstrates that GC act as a primary inducer of sialoadhesin expression on rat macrophages, and that the response can be enhanced by IFN-beta, T cell-derived cytokines, or LPS. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "potent", "start": 1174, "end": 1180}, "arguments": [{"role": "Theme", "text": "IFN-beta", "start": 1145, "end": 1153}]}, {"trigger": {"text": "potent", "start": 1174, "end": 1180}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1158, "end": 1162}]}, {"trigger": {"text": "potent", "start": 1174, "end": 1180}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1186, "end": 1195}]}], "gene expression": [{"trigger": {"text": "expression", "start": 27, "end": 37}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 14, "end": 26}]}, {"trigger": {"text": "expressed", "start": 289, "end": 298}, "arguments": [{"role": "Theme", "text": "Sialoadhesin", "start": 158, "end": 170}]}, {"trigger": {"text": "expression", "start": 464, "end": 474}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 451, "end": 463}]}, {"trigger": {"text": "expression", "start": 539, "end": 549}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 526, "end": 538}]}, {"trigger": {"text": "expression", "start": 712, "end": 722}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 699, "end": 711}]}, {"trigger": {"text": "expression", "start": 811, "end": 821}, "arguments": [{"role": "Theme", "text": "Sialoadhesin", "start": 798, "end": 810}]}, {"trigger": {"text": "expression", "start": 1128, "end": 1138}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 1115, "end": 1127}]}, {"trigger": {"text": "expression", "start": 1375, "end": 1385}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 1362, "end": 1374}]}, {"trigger": {"text": "express", "start": 1631, "end": 1638}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 1639, "end": 1651}]}, {"trigger": {"text": "expression", "start": 1726, "end": 1736}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 1713, "end": 1725}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 58, "end": 67}, "arguments": [{"role": "Theme", "text": "Regulation", "start": 0, "end": 10}]}, {"trigger": {"text": "enhancement", "start": 91, "end": 102}, "arguments": [{"role": "Theme", "text": "Regulation", "start": 0, "end": 10}, {"role": "Cause", "text": "IFN-beta", "start": 106, "end": 114}]}, {"trigger": {"text": "enhancement", "start": 91, "end": 102}, "arguments": [{"role": "Theme", "text": "Regulation", "start": 0, "end": 10}, {"role": "Cause", "text": "IFN-gamma", "start": 116, "end": 125}]}, {"trigger": {"text": "enhancement", "start": 91, "end": 102}, "arguments": [{"role": "Theme", "text": "Regulation", "start": 0, "end": 10}, {"role": "Cause", "text": "IL-4", "start": 127, "end": 131}]}, {"trigger": {"text": "enhancement", "start": 91, "end": 102}, "arguments": [{"role": "Theme", "text": "Regulation", "start": 0, "end": 10}]}, {"trigger": {"text": "induce", "start": 519, "end": 525}, "arguments": [{"role": "Theme", "text": "expression", "start": 539, "end": 549}]}, {"trigger": {"text": "induce", "start": 692, "end": 698}, "arguments": [{"role": "Cause", "text": "IFN-beta", "start": 637, "end": 645}, {"role": "Theme", "text": "expression", "start": 712, "end": 722}]}, {"trigger": {"text": "induce", "start": 692, "end": 698}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 647, "end": 656}, {"role": "Theme", "text": "expression", "start": 712, "end": 722}]}, {"trigger": {"text": "induce", "start": 692, "end": 698}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 658, "end": 662}, {"role": "Theme", "text": "expression", "start": 712, "end": 722}]}, {"trigger": {"text": "induce", "start": 692, "end": 698}, "arguments": [{"role": "Theme", "text": "expression", "start": 712, "end": 722}]}, {"trigger": {"text": "enhance", "start": 751, "end": 758}, "arguments": [{"role": "Cause", "text": "IFN-beta", "start": 637, "end": 645}, {"role": "Theme", "text": "induction", "start": 771, "end": 780}]}, {"trigger": {"text": "enhance", "start": 751, "end": 758}, "arguments": [{"role": "Cause", "text": "IFN-gamma", "start": 647, "end": 656}, {"role": "Theme", "text": "induction", "start": 771, "end": 780}]}, {"trigger": {"text": "enhance", "start": 751, "end": 758}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 658, "end": 662}, {"role": "Theme", "text": "induction", "start": 771, "end": 780}]}, {"trigger": {"text": "enhance", "start": 751, "end": 758}, "arguments": [{"role": "Theme", "text": "induction", "start": 771, "end": 780}]}, {"trigger": {"text": "induction", "start": 771, "end": 780}, "arguments": [{"role": "Theme", "text": "sialoadhesin", "start": 784, "end": 796}]}, {"trigger": {"text": "functional", "start": 826, "end": 836}, "arguments": [{"role": "Theme", "text": "expression", "start": 811, "end": 821}]}, {"trigger": {"text": "regulation", "start": 932, "end": 942}, "arguments": [{"role": "Theme", "text": "mRNA level", "start": 973, "end": 983}]}, {"trigger": {"text": "level", "start": 1078, "end": 1083}, "arguments": [{"role": "Theme", "text": "enhancement", "start": 1100, "end": 1111}]}, {"trigger": {"text": "enhancement", "start": 1100, "end": 1111}, "arguments": [{"role": "Theme", "text": "expression", "start": 1128, "end": 1138}]}, {"trigger": {"text": "mediated", "start": 1390, "end": 1398}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1348, "end": 1358}, {"role": "Cause", "text": "GC receptor", "start": 1406, "end": 1417}]}, {"trigger": {"text": "mediated", "start": 1390, "end": 1398}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1348, "end": 1358}, {"role": "Cause", "text": "mineralocorticoid receptor", "start": 1430, "end": 1456}]}, {"trigger": {"text": "inducer", "start": 1702, "end": 1709}, "arguments": [{"role": "Theme", "text": "expression", "start": 1726, "end": 1736}]}, {"trigger": {"text": "enhanced", "start": 1786, "end": 1794}, "arguments": [{"role": "Theme", "text": "inducer", "start": 1702, "end": 1709}, {"role": "Cause", "text": "IFN-beta", "start": 1798, "end": 1806}]}, {"trigger": {"text": "enhanced", "start": 1786, "end": 1794}, "arguments": [{"role": "Theme", "text": "inducer", "start": 1702, "end": 1709}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 27, "end": 37}]}, {"trigger": {"text": "regulation", "start": 437, "end": 447}, "arguments": [{"role": "Theme", "text": "expression", "start": 464, "end": 474}]}, {"trigger": {"text": "regulation", "start": 1348, "end": 1358}, "arguments": [{"role": "Theme", "text": "expression", "start": 1375, "end": 1385}]}], "transcription": [{"trigger": {"text": "mRNA level", "start": 973, "end": 983}, "arguments": [{"role": "Theme", "text": "Sialoadhesin", "start": 798, "end": 810}]}]}}, "schema": []}
{"input": "Cell-type-specific regulation of the human tumor necrosis factor alpha gene in B cells and T cells by NFATp and ATF-2/JUN. \nThe human tumor necrosis factor alpha (TNF-alpha) gene is one of the earliest genes transcribed after the stimulation of a B cell through its antigen receptor or via the CD-40 pathway. In both cases, induction of TNF-alpha gene transcription can be blocked by the immunosuppressants cyclosporin A and FK506, which suggested a role for the NFAT family of proteins in the regulation of the gene in B cells. Furthermore, in T cells, two molecules of NFATp bind to the TNF-alpha promoter element kappa 3 in association with ATF-2 and Jun proteins bound to an immediately adjacent cyclic AMP response element (CRE) site. Here, using the murine B-cell lymphoma cell line A20, we show that the TNF-alpha gene is regulated in a cell-type-specific manner. In A20 B cells, the TNF-alpha gene is not regulated by NFATp bound to the kappa 3 element. Instead, ATF-2 and Jun proteins bind to the composite kappa 3/CRE site and NFATp binds to a newly identified second NFAT site centered at -76 nucleotides relative to the TNF-alpha transcription start site. This new site plays a critical role in the calcium-mediated, cyclosporin A-sensitive induction of TNF-alpha in both A20 B cells and Ar-5 cells. Consistent with these results, quantitative DNase footprinting of the TNF-alpha promoter using increasing amounts of recombinant NFATp demonstrated that the -76 site binds to NFATp with a higher affinity than the kappa 3 site. Two other previously unrecognized NFATp-binding sites in the proximal TNF-alpha promoter were also identified by this analysis. Thus, through the differential use of the same promoter element, the composite kappa 3/CRE site, the TNF-alpha gene is regulated in a cell-type-specific manner in response to the same extracellular signal. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 577, "end": 581}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 571, "end": 576}]}, {"trigger": {"text": "bound", "start": 667, "end": 672}, "arguments": [{"role": "Theme", "text": "ATF-2", "start": 644, "end": 649}]}, {"trigger": {"text": "bound", "start": 932, "end": 937}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 926, "end": 931}]}, {"trigger": {"text": "bind", "start": 994, "end": 998}, "arguments": [{"role": "Theme", "text": "ATF-2", "start": 971, "end": 976}]}, {"trigger": {"text": "binds", "start": 1043, "end": 1048}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1037, "end": 1042}]}, {"trigger": {"text": "binds", "start": 1478, "end": 1483}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1487, "end": 1492}]}, {"trigger": {"text": "binding", "start": 1579, "end": 1586}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1573, "end": 1578}, {"role": "Theme2", "text": "TNF-alpha", "start": 1609, "end": 1618}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 373, "end": 380}, "arguments": [{"role": "Theme", "text": "induction", "start": 324, "end": 333}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 324, "end": 333}, "arguments": [{"role": "Theme", "text": "transcription", "start": 352, "end": 365}]}, {"trigger": {"text": "induction", "start": 1253, "end": 1262}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1266, "end": 1275}]}], "regulation": [{"trigger": {"text": "regulation", "start": 19, "end": 29}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 43, "end": 70}, {"role": "Cause", "text": "NFATp", "start": 102, "end": 107}]}, {"trigger": {"text": "regulation", "start": 19, "end": 29}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor alpha", "start": 43, "end": 70}, {"role": "Cause", "text": "ATF-2", "start": 112, "end": 117}]}, {"trigger": {"text": "through", "start": 254, "end": 261}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 208, "end": 219}]}, {"trigger": {"text": "via", "start": 286, "end": 289}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 208, "end": 219}, {"role": "Cause", "text": "CD-40", "start": 294, "end": 299}]}, {"trigger": {"text": "role", "start": 450, "end": 454}, "arguments": [{"role": "Theme", "text": "regulation", "start": 494, "end": 504}]}, {"trigger": {"text": "regulation", "start": 494, "end": 504}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 337, "end": 346}]}, {"trigger": {"text": "regulated", "start": 829, "end": 838}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 811, "end": 820}]}, {"trigger": {"text": "regulated", "start": 913, "end": 922}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 891, "end": 900}, {"role": "Cause", "text": "NFATp", "start": 926, "end": 931}]}, {"trigger": {"text": "role", "start": 1199, "end": 1203}, "arguments": [{"role": "Theme", "text": "induction", "start": 1253, "end": 1262}]}, {"trigger": {"text": "through", "start": 1673, "end": 1680}, "arguments": [{"role": "Theme", "text": "regulated", "start": 1786, "end": 1795}]}, {"trigger": {"text": "regulated", "start": 1786, "end": 1795}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1768, "end": 1777}]}], "transcription": [{"trigger": {"text": "transcribed", "start": 208, "end": 219}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 163, "end": 172}]}, {"trigger": {"text": "transcription", "start": 352, "end": 365}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 337, "end": 346}]}]}}, "schema": []}
{"input": "Analysis of the ligand-binding domain of human retinoic acid receptor alpha by site-directed mutagenesis. \nThree subtypes of retinoic acid receptors (RAR), termed RAR alpha, RAR beta, and RAR gamma, have been described. They are composed of different structural domains, including distinct domains for DNA and ligand binding. RARs specifically bind all-trans-retinoic acid (RA), 9-cis-RA, and retinoid analogs. In this study, we examined the functional role of cysteine and arginine residues in the ligand-binding domain of hRAR alpha (hRAR alpha-LBD, amino acids 154 to 462). All conserved cysteine and arginine residues in this domain were mutated by site-directed mutagenesis, and the mutant proteins were characterized by blocking reactions, ligand-binding experiments, transactivation assays, and protease mapping. Changes of any cysteine residue of the hRAR alpha-LBD had no significant influence on the binding of all-trans RA or 9-cis RA. Interestingly, residue C-235 is specifically important in antagonist binding. With respect to arginine residues, only the two single mutations of R-276 and R-394 to alanine showed a dramatic decrease of agonist and antagonist binding whereas the R272A mutation showed only a slight effect. For all other arginine mutations, no differences in affinity were detectable. The two mutations R217A and R294A caused an increased binding efficiency for antagonists but no change in agonist binding. From these results, we can conclude that electrostatic interactions of retinoids with the RAR alpha-LBD play a significant role in ligand binding. In addition, antagonists show distinctly different requirements for efficient binding, which may contribute to their interference in the ligand-inducible transactivation function of RAR alpha. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 23, "end": 30}, "arguments": [{"role": "Theme", "text": "human retinoic acid receptor alpha", "start": 41, "end": 75}]}, {"trigger": {"text": "binding", "start": 1576, "end": 1583}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 1528, "end": 1537}]}], "negative regulation": [{"trigger": {"text": "interference", "start": 1702, "end": 1714}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 1739, "end": 1754}]}], "positive regulation": [{"trigger": {"text": "significant role", "start": 1549, "end": 1565}, "arguments": [{"role": "Theme", "text": "binding", "start": 1576, "end": 1583}]}, {"trigger": {"text": "transactivation", "start": 1739, "end": 1754}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 1767, "end": 1776}]}]}}, "schema": []}
{"input": "Cloning and characterization of the beta subunit of human proximal sequence element-binding transcription factor and its involvement in transcription of small nuclear RNA genes by RNA polymerases II and III. \nThe proximal sequence element (PSE)-binding transcription factor (PTF), which binds the PSE of both RNA polymerase II- and RNA polymerase III-transcribed mammalian small nuclear RNA (snRNA) genes, is essential for their transcription. We previously reported the purification of human PTF, a complex of four subunits, and the molecular cloning and characterization of PTF gamma and delta subunits. Here we describe the isolation and expression of a cDNA encoding PTF beta, as well as functional studies using anti-PTF beta antibodies. Native PTF beta, in either protein fractions or a PTF-Oct-1-DNA complex, can be recognized by polyclonal antibodies raised against recombinant PTF beta. Immunodepletion studies show that PTF beta is required for transcription of both classes of snRNA genes in vitro. In addition, immunoprecipitation analyses demonstrate that substantial and similar molar amounts of TATA-binding protein (TBP) and TFIIIB90 can weakly associate with PTF at low salt conditions, but this association is dramatically reduced at high salt concentrations. Along with our previous demonstration of both physical interactions between PTF gamma/PTF delta and TBP and the involvement of TFIIIB90 in the transcription of class III snRNA genes, these results are consistent with the notion that a TBP-containing complex related to TFIIIB is required for the transcription of class III snRNA genes, and acts through weak interaction with the four-subunit PTF. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 287, "end": 292}, "arguments": [{"role": "Theme", "text": "snRNA", "start": 392, "end": 397}]}, {"trigger": {"text": "recognized", "start": 823, "end": 833}, "arguments": [{"role": "Theme", "text": "PTF beta", "start": 750, "end": 758}]}, {"trigger": {"text": "associate", "start": 1161, "end": 1170}, "arguments": [{"role": "Theme", "text": "TBP", "start": 1132, "end": 1135}]}, {"trigger": {"text": "associate", "start": 1161, "end": 1170}, "arguments": [{"role": "Theme", "text": "TFIIIB90", "start": 1141, "end": 1149}]}, {"trigger": {"text": "physical interactions", "start": 1324, "end": 1345}, "arguments": [{"role": "Theme", "text": "PTF gamma", "start": 1354, "end": 1363}, {"role": "Theme2", "text": "TBP", "start": 1378, "end": 1381}]}, {"trigger": {"text": "physical interactions", "start": 1324, "end": 1345}, "arguments": [{"role": "Theme", "text": "PTF delta", "start": 1364, "end": 1373}, {"role": "Theme2", "text": "TBP", "start": 1378, "end": 1381}]}, {"trigger": {"text": "interaction", "start": 1636, "end": 1647}, "arguments": [{"role": "Theme", "text": "TBP", "start": 1513, "end": 1516}]}], "gene expression": [{"trigger": {"text": "expression", "start": 641, "end": 651}, "arguments": [{"role": "Theme", "text": "PTF beta", "start": 671, "end": 679}]}], "positive regulation": [{"trigger": {"text": "by", "start": 177, "end": 179}, "arguments": [{"role": "Theme", "text": "transcription", "start": 136, "end": 149}]}, {"trigger": {"text": "transcribed", "start": 351, "end": 362}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 351, "end": 362}]}, {"trigger": {"text": "essential", "start": 409, "end": 418}, "arguments": [{"role": "Theme", "text": "transcription", "start": 429, "end": 442}]}, {"trigger": {"text": "required", "start": 942, "end": 950}, "arguments": [{"role": "Cause", "text": "PTF beta", "start": 930, "end": 938}, {"role": "Theme", "text": "transcription", "start": 955, "end": 968}]}, {"trigger": {"text": "required", "start": 1557, "end": 1565}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1574, "end": 1587}]}, {"trigger": {"text": "acts", "start": 1618, "end": 1622}, "arguments": [{"role": "Theme", "text": "required", "start": 1557, "end": 1565}, {"role": "Cause", "text": "interaction", "start": 1636, "end": 1647}]}, {"trigger": {"text": "acts", "start": 1618, "end": 1622}, "arguments": [{"role": "Theme", "text": "required", "start": 1557, "end": 1565}]}], "transcription": [{"trigger": {"text": "transcription", "start": 136, "end": 149}, "arguments": [{"role": "Theme", "text": "small nuclear RNA", "start": 153, "end": 170}]}, {"trigger": {"text": "transcribed", "start": 351, "end": 362}, "arguments": [{"role": "Theme", "text": "snRNA", "start": 392, "end": 397}]}, {"trigger": {"text": "transcription", "start": 429, "end": 442}, "arguments": [{"role": "Theme", "text": "snRNA", "start": 392, "end": 397}]}, {"trigger": {"text": "transcription", "start": 955, "end": 968}, "arguments": [{"role": "Theme", "text": "snRNA", "start": 988, "end": 993}]}, {"trigger": {"text": "transcription", "start": 1421, "end": 1434}, "arguments": [{"role": "Theme", "text": "snRNA", "start": 1448, "end": 1453}]}, {"trigger": {"text": "transcription", "start": 1574, "end": 1587}, "arguments": [{"role": "Theme", "text": "snRNA", "start": 1601, "end": 1606}]}]}}, "schema": []}
{"input": "Induction of bcl-2 expression by phosphorylated CREB proteins during B-cell activation and rescue from apoptosis. \nEngagement of surface immunoglobulin on mature B cells leads to rescue from apoptosis and to proliferation. Levels of bcl-2 mRNA and protein increase with cross-linking of surface immunoglobulin. We have located the major positive regulatory region for control of bcl-2 expression in B cells in the 5'-flanking region. The positive region can be divided into an upstream and a downstream regulatory region. The downstream regulatory region contains a cyclic AMP-responsive element (CRE). We show by antibody supershift experiments and UV cross-linking followed by denaturing polyacrylamide gel electrophoresis that both CREB and ATF family members bind to this region in vitro. Mutations of the CRE site that result in loss of CREB binding also lead to loss of functional activity of the bcl-2 promoter in transient-transfection assays. The presence of an active CRE site in the bcl-2 promoter implies that the regulation of bcl-2 expression is linked to a signal transduction pathway in B cells. Treatment of the mature B-cell line BAL-17 with either anti-immunoglobulin M or phorbol 12-myristate 13-acetate leads to an increase in bcl-2 expression that is mediated by the CRE site. Treatment of the more immature B-cell line, Ramos, with phorbol esters rescues the cells from calcium-dependent apoptosis. bcl-2 expression is increased following phorbol ester treatment, and the increased expression is dependent on the CRE site. These stimuli result in phosphorylation of CREB at serine 133. The phosphorylation of CREB that results in activation is mediated by protein kinase C rather than by protein kinase A. Although the CRE site is necessary, optimal induction of bcl-2 expression requires participation of the upstream regulatory element, suggesting that phosphorylation of CREB alters its interaction with the upstream regulatory element. The CRE site in the bcl-2 promoter appears to play a major role in the induction of bcl-2 expression during the activation of mature B cells and during the rescue of immature B cells from apoptosis. It is possible that the CRE site is responsible for induction of bcl-2 expression in other cell types, particularly those in which protein kinase C is involved. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 270, "end": 283}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 233, "end": 238}]}], "gene expression": [{"trigger": {"text": "expression", "start": 19, "end": 29}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 13, "end": 18}]}, {"trigger": {"text": "Levels", "start": 223, "end": 229}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 233, "end": 238}]}, {"trigger": {"text": "expression", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 379, "end": 384}]}, {"trigger": {"text": "expression", "start": 1046, "end": 1056}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 1040, "end": 1045}]}, {"trigger": {"text": "expression", "start": 1254, "end": 1264}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 1248, "end": 1253}]}, {"trigger": {"text": "expression", "start": 1428, "end": 1438}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 1422, "end": 1427}]}, {"trigger": {"text": "expression", "start": 1792, "end": 1802}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 1786, "end": 1791}]}, {"trigger": {"text": "expression", "start": 2053, "end": 2063}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 2047, "end": 2052}]}, {"trigger": {"text": "expression", "start": 2233, "end": 2243}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 2227, "end": 2232}]}], "negative regulation": [{"trigger": {"text": "loss", "start": 868, "end": 872}, "arguments": [{"role": "Theme", "text": "functional activity", "start": 876, "end": 895}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "expression", "start": 19, "end": 29}]}, {"trigger": {"text": "increase", "start": 256, "end": 264}, "arguments": [{"role": "Theme", "text": "Levels", "start": 223, "end": 229}, {"role": "Cause", "text": "cross-linking", "start": 270, "end": 283}]}, {"trigger": {"text": "increase", "start": 256, "end": 264}, "arguments": [{"role": "Theme", "text": "Levels", "start": 223, "end": 229}]}, {"trigger": {"text": "functional activity", "start": 876, "end": 895}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 903, "end": 908}, {"role": "Site", "text": "promoter", "start": 909, "end": 917}]}, {"trigger": {"text": "increase", "start": 1236, "end": 1244}, "arguments": [{"role": "Theme", "text": "expression", "start": 1254, "end": 1264}]}, {"trigger": {"text": "mediated", "start": 1273, "end": 1281}, "arguments": [{"role": "Theme", "text": "expression", "start": 1254, "end": 1264}]}, {"trigger": {"text": "increased", "start": 1442, "end": 1451}, "arguments": [{"role": "Theme", "text": "expression", "start": 1428, "end": 1438}]}, {"trigger": {"text": "dependent", "start": 1519, "end": 1528}, "arguments": [{"role": "Theme", "text": "expression", "start": 1428, "end": 1438}]}, {"trigger": {"text": "necessary", "start": 1754, "end": 1763}, "arguments": [{"role": "Theme", "text": "optimal induction", "start": 1765, "end": 1782}]}, {"trigger": {"text": "optimal induction", "start": 1765, "end": 1782}, "arguments": [{"role": "Theme", "text": "expression", "start": 1792, "end": 1802}]}, {"trigger": {"text": "requires", "start": 1803, "end": 1811}, "arguments": [{"role": "Theme", "text": "optimal induction", "start": 1765, "end": 1782}]}, {"trigger": {"text": "role", "start": 2022, "end": 2026}, "arguments": [{"role": "CSite", "text": "CRE site", "start": 1967, "end": 1975}, {"role": "Cause", "text": "bcl-2", "start": 1983, "end": 1988}, {"role": "Theme", "text": "induction", "start": 2034, "end": 2043}]}, {"trigger": {"text": "induction", "start": 2034, "end": 2043}, "arguments": [{"role": "Theme", "text": "expression", "start": 2053, "end": 2063}]}, {"trigger": {"text": "induction", "start": 2214, "end": 2223}, "arguments": [{"role": "Theme", "text": "expression", "start": 2233, "end": 2243}]}], "regulation": [{"trigger": {"text": "positive regulatory", "start": 337, "end": 356}, "arguments": [{"role": "Theme", "text": "control", "start": 368, "end": 375}]}, {"trigger": {"text": "control", "start": 368, "end": 375}, "arguments": [{"role": "Theme", "text": "expression", "start": 385, "end": 395}]}, {"trigger": {"text": "regulation", "start": 1026, "end": 1036}, "arguments": [{"role": "Theme", "text": "expression", "start": 1046, "end": 1056}]}, {"trigger": {"text": "responsible", "start": 2198, "end": 2209}, "arguments": [{"role": "Theme", "text": "induction", "start": 2214, "end": 2223}]}, {"trigger": {"text": "involved", "start": 2313, "end": 2321}, "arguments": [{"role": "Theme", "text": "responsible", "start": 2198, "end": 2209}]}], "transcription": [{"trigger": {"text": "Levels", "start": 223, "end": 229}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 233, "end": 238}]}]}}, "schema": []}
{"input": "E3, a hematopoietic-specific transcript directly regulated by the retinoic acid receptor alpha. \nRetinoic acid (RA)-induced maturation mediated by the retinoic acid receptor alpha (RAR alpha) has been implicated in myeloid development. We have used differential hybridization analysis of a cDNA library constructed from the murine RA-inducible MPRO promyelocyte cell line to identify immediate-early genes induced by RA during granulocytic differentiation. E3, one of nine sequences identified, was upregulated in an immediate-early manner, with transcript levels peaking after 60 minutes exposure to RA. E3 transcripts were RA-inducible in HL60 cells, but not in an RA-resistant subclone, HL60R, that harbors a mutated RAR alpha gene. However, when HL60R cells were transduced with a functional copy of the RAR alpha gene, RA induced a 10-fold increase in E3 mRNA levels. E3 transcripts are present in the myeloid, B-lymphoid, and erythroid lineages, absent in nonhematopoietic cells, and encode a highly hydrophobic, potentially phosphorylated polypeptide of unknown function with significant homology to a putative protein expressed in myeloid cells. The murine E3 promoter harbors a single bipartite retinoic acid response element which in transient transfection assays conferred RA sensitivity. These results indicate that E3 is a hematopoietic-specific gene that is an immediate target for the activated RAR alpha during myelopoiesis. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "upregulated", "start": 499, "end": 510}, "arguments": [{"role": "Theme", "text": "E3", "start": 457, "end": 459}]}, {"trigger": {"text": "levels peaking", "start": 557, "end": 571}, "arguments": [{"role": "Theme", "text": "transcript", "start": 546, "end": 556}]}, {"trigger": {"text": "inducible", "start": 628, "end": 637}, "arguments": [{"role": "Theme", "text": "transcripts", "start": 608, "end": 619}]}, {"trigger": {"text": "induced", "start": 827, "end": 834}, "arguments": [{"role": "Theme", "text": "increase", "start": 845, "end": 853}]}, {"trigger": {"text": "increase", "start": 845, "end": 853}, "arguments": [{"role": "Theme", "text": "levels", "start": 865, "end": 871}]}, {"trigger": {"text": "activated", "start": 1400, "end": 1409}, "arguments": [{"role": "Theme", "text": "RAR alpha", "start": 1410, "end": 1419}]}], "regulation": [{"trigger": {"text": "regulated", "start": 49, "end": 58}, "arguments": [{"role": "Theme", "text": "transcript", "start": 29, "end": 39}, {"role": "Cause", "text": "retinoic acid receptor alpha", "start": 66, "end": 94}]}, {"trigger": {"text": "sensitivity", "start": 1287, "end": 1298}, "arguments": [{"role": "Theme", "text": "E3", "start": 1165, "end": 1167}, {"role": "Site", "text": "promoter", "start": 1168, "end": 1176}]}, {"trigger": {"text": "target", "start": 1385, "end": 1391}, "arguments": [{"role": "Theme", "text": "E3", "start": 1328, "end": 1330}, {"role": "Cause", "text": "RAR alpha", "start": 1410, "end": 1419}]}], "transcription": [{"trigger": {"text": "transcript", "start": 29, "end": 39}, "arguments": [{"role": "Theme", "text": "E3", "start": 0, "end": 2}]}, {"trigger": {"text": "transcript", "start": 546, "end": 556}, "arguments": [{"role": "Theme", "text": "E3", "start": 457, "end": 459}]}, {"trigger": {"text": "transcripts", "start": 608, "end": 619}, "arguments": [{"role": "Theme", "text": "E3", "start": 605, "end": 607}]}, {"trigger": {"text": "levels", "start": 865, "end": 871}, "arguments": [{"role": "Theme", "text": "E3", "start": 857, "end": 859}]}, {"trigger": {"text": "transcripts", "start": 876, "end": 887}, "arguments": [{"role": "Theme", "text": "E3", "start": 873, "end": 875}]}]}}, "schema": []}
{"input": "Transcriptional control of steroid-regulated apoptosis in murine thymoma cells. \nEarly studies in murine T cell lines indicated that transcriptional transactivation functions encoded in the glucocorticoid receptor (GR) N-terminal domain are required for glucocorticoid-mediated apoptosis. However, more recent studies in human T cell lines have suggested that the N-terminal domain is not necessary for steroid-regulated apoptosis and that GR-mediated transrepression may be the more critical mechanism. To better understand the contribution of the GR N-terminal transactivation domain in mediating murine thymocyte apoptosis, we stably transfected GR, GR variants, and the androgen receptor (AR) into receptor-negative S49 murine thymoma cells. GR expression levels were shown to be rate-limiting for initiating the apoptotic pathway, and a positive correlation between steroid sensitivity and GR-mediated induction of an integrated mouse mammary tumor virus (MMTV) LTR reporter gene was observed. Analysis of GR chimeric receptors containing the potent VP16 and E1A viral transactivation domains in place of the GR N terminus revealed that even low level expression of these receptors resulted in both enhanced steroid sensitivity and MMTV induction, thus supporting a role for transactivation in apoptosis. In contrast, we found that AR can initiate apoptosis in S49 cells after treatment with 5 alpha-dihydrotestosterone, despite its relative inability to induce high level expression of MMTV. To investigate this further, we examined the steroid-regulated expression of an endogenous thymocyte-specific gene called GIG18. We found that GIG18 was rapidly induced to comparable levels by both AR and GR, demonstrating that AR can indeed function as a transcriptional activator in S49 cells and, moreover, that GIG18 induction may be a marker of early apoptotic events in steroid-treated cells. Taken together, these results support our conclusion that transcriptional transactivation is a necessary signaling component of S49 cell apoptosis, although an additional role for GR-mediated transrepression cannot be excluded. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "transfected", "start": 637, "end": 648}, "arguments": [{"role": "Theme", "text": "GR", "start": 649, "end": 651}]}, {"trigger": {"text": "transfected", "start": 637, "end": 648}, "arguments": [{"role": "Theme", "text": "GR", "start": 653, "end": 655}]}, {"trigger": {"text": "expression", "start": 749, "end": 759}, "arguments": [{"role": "Theme", "text": "GR", "start": 746, "end": 748}]}, {"trigger": {"text": "expression", "start": 1561, "end": 1571}, "arguments": [{"role": "Theme", "text": "GIG18", "start": 1620, "end": 1625}]}], "positive regulation": [{"trigger": {"text": "transactivation", "start": 149, "end": 164}, "arguments": [{"role": "Theme", "text": "glucocorticoid receptor", "start": 190, "end": 213}, {"role": "Site", "text": "N-terminal domain", "start": 219, "end": 236}]}, {"trigger": {"text": "transfected", "start": 637, "end": 648}, "arguments": [{"role": "Theme", "text": "transfected", "start": 637, "end": 648}]}, {"trigger": {"text": "induced", "start": 1659, "end": 1666}, "arguments": [{"role": "Theme", "text": "GIG18", "start": 1641, "end": 1646}, {"role": "Cause", "text": "AR", "start": 1696, "end": 1698}]}, {"trigger": {"text": "induced", "start": 1659, "end": 1666}, "arguments": [{"role": "Theme", "text": "GIG18", "start": 1641, "end": 1646}, {"role": "Cause", "text": "GR", "start": 1703, "end": 1705}]}, {"trigger": {"text": "induction", "start": 1819, "end": 1828}, "arguments": [{"role": "Theme", "text": "GIG18", "start": 1813, "end": 1818}]}]}}, "schema": []}
{"input": "Selenium-mediated inhibition of transcription factor NF-kappa B and HIV-1 LTR promoter activity. \nThe eukaryotic transcription factor NF-kappa B is involved in the inducible expression of various inflammatory genes as well as in HIV-1 replication. Activation of NF-kappa B is induced by prooxidants and several stimuli eliciting oxidative stress, such as cytokines, lipopolysaccharide, UV irradiation and other mediators. Various antioxidants inhibit NF-kappa B activation in response to these stimuli. In this study, we have investigated the effects of selenium, an integral component of glutathione peroxidase (GPX), on NF-kappa B activation. In selenium-deprived Jurkat and ESb-L T lymphocytes, supplementation of selenium led to a substantial increase of GPX activity. Analysis of DNA binding revealed that NF-kappa B activation in response to TNF was significantly inhibited under these conditions. Likewise, reporter gene assays using luciferase constructs driven by the HIV-1 long terminal repeat showed a dose-dependent inhibition of NF-kappa B controlled gene expression by selenium. The effects of selenium were specific for NF-kappa B, since the activity of the transcription factor AP-1 was not suppressed. These data suggest that selenium supplementation may be used to modulate the expression of NF-kappa B target genes and HIV-1. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "increase", "start": 747, "end": 755}, "arguments": [{"role": "Theme", "text": "GPX", "start": 759, "end": 762}]}]}}, "schema": []}
{"input": "Transcriptional and posttranscriptional regulation of erythroid gene expression in anthracycline-induced differentiation of human erythroleukemic cells. \nAclacinomycin (ACLA) and doxorubicin (DOX) were used at subtoxic concentrations to induce erythroid differentiation in the human leukemic cell line K562. Cell hemoglobinization was accompanied by the increased expression of genes encoding gamma-globin and porphobilinogen deaminase (PBGD), an enzyme of heme synthesis. By using run-on assays, ACLA was shown to induce an enhancement of the transcription of erythroid genes, including gamma-globin, PBGD, erythropoietin receptor, and GATA-1 transcription factor. In contrast, in DOX-treated cells, the transcription rate of these genes was unchanged in comparison with control cells. In addition, inhibition of mRNA synthesis with actinomycin D indicated that DOX induced an increased stability of PBGD and GATA-1 mRNAs, whereas ACLA did not affect the half-lives of these mRNAs. Because the increase in erythroid mRNA steady-state level in anthracycline-treated cells was inhibited by cycloheximide, this suggests that transcriptional activation in ACLA-treated cells and mRNA stabilization in DOX-treated cells were dependent on de novo protein synthesis. Finally, GATA-1 protein level was shown to be increased in ACLA-treated but not in DOX-treated cells. These two anthracyclines, although closely related in their structures, appeared to act as differentiation inducers by distinct mechanisms. Indeed, erythroid gene expression was demonstrated to be regulated transcriptionally by ACLA and mainly posttranscriptionally by DOX. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 364, "end": 374}, "arguments": [{"role": "Theme", "text": "PBGD", "start": 437, "end": 441}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 354, "end": 363}, "arguments": [{"role": "Theme", "text": "expression", "start": 364, "end": 374}]}, {"trigger": {"text": "induce an enhancement", "start": 515, "end": 536}, "arguments": [{"role": "Theme", "text": "transcription", "start": 544, "end": 557}]}, {"trigger": {"text": "increased stability", "start": 878, "end": 897}, "arguments": [{"role": "Theme", "text": "PBGD", "start": 901, "end": 905}]}, {"trigger": {"text": "increased stability", "start": 878, "end": 897}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 910, "end": 916}]}, {"trigger": {"text": "increased", "start": 1307, "end": 1316}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1270, "end": 1276}]}], "regulation": [{"trigger": {"text": "unchanged", "start": 743, "end": 752}, "arguments": [{"role": "Theme", "text": "transcription rate", "start": 705, "end": 723}]}, {"trigger": {"text": "affect the half-lives", "start": 945, "end": 966}, "arguments": [{"role": "Theme", "text": "PBGD", "start": 901, "end": 905}]}, {"trigger": {"text": "affect the half-lives", "start": 945, "end": 966}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 910, "end": 916}]}], "transcription": [{"trigger": {"text": "transcription", "start": 544, "end": 557}, "arguments": [{"role": "Theme", "text": "PBGD", "start": 602, "end": 606}]}, {"trigger": {"text": "transcription", "start": 544, "end": 557}, "arguments": [{"role": "Theme", "text": "erythropoietin receptor", "start": 608, "end": 631}]}, {"trigger": {"text": "transcription", "start": 544, "end": 557}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 637, "end": 643}]}, {"trigger": {"text": "transcription rate", "start": 705, "end": 723}, "arguments": [{"role": "Theme", "text": "PBGD", "start": 602, "end": 606}]}, {"trigger": {"text": "transcription rate", "start": 705, "end": 723}, "arguments": [{"role": "Theme", "text": "erythropoietin receptor", "start": 608, "end": 631}]}, {"trigger": {"text": "transcription rate", "start": 705, "end": 723}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 637, "end": 643}]}]}}, "schema": []}
{"input": "Human TAFII 105 is a cell type-specific TFIID subunit related to hTAFII130. \nWe previously characterized Drosophila and human TAF subunits that make up the core TFIID complex found in all cells. Here, we report that differentiated B cells contain a novel substoichiometric TAF of 105 kDa not found associated with TFIID isolated from other cell types. The cDNA encoding hTAFII105 reveals a highly conserved C-terminal domain shared by hTAFII130 and oTAFII110, while the N-terminal coactivator domain has diverged significantly. All cells tested express TAFII105 mRNA, but only B cells contain significant levels of protein associated with TFIID. Transient overexpression of hTAFII105 selectively squelches the transcription of some genes in B cells. These properties suggest that TAFII105 is a cell type-specific subunit of TFIID that may be responsible for mediating transcription by a subset of activators in B cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associated", "start": 623, "end": 633}, "arguments": [{"role": "Theme", "text": "TAFII105", "start": 553, "end": 561}]}], "gene expression": [{"trigger": {"text": "overexpression", "start": 656, "end": 670}, "arguments": [{"role": "Theme", "text": "hTAFII105", "start": 674, "end": 683}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 656, "end": 670}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 656, "end": 670}]}], "transcription": [{"trigger": {"text": "express", "start": 545, "end": 552}, "arguments": [{"role": "Theme", "text": "TAFII105", "start": 553, "end": 561}]}]}}, "schema": []}
{"input": "IL-12-induced activation of NK and T cells occurs in the absence of immediate-early activation gene expression. \nThe responses of lymphocytes to IL-2 and IL-12, involving proliferation, differentiation, and cytokine production, are only partially overlapping, and may depend on induced differential expression of specific sets of genes. Using reverse-transcription PCR differential display, we isolated an mRNA species expressed in IL-2- but not IL-12-stimulated NK cells. This was identified as the mRNA encoding the transcription factor egr-1, which is expressed with fast kinetics in T and NK cells upon IL-2, but not IL-12, stimulation. Analysis of the accumulation of mRNA-encoding members of the AP-1 transcription factor family demonstrated that c-fos and junB are also expressed upon stimulation of NK and T cells with IL-2, but not IL-12, whereas expression of c-jun and junD is not modified by either cytokine. Accordingly, increased AP-1 DNA-binding activity and AP-1-dependent transcriptional activity were detected exclusively in IL-2-stimulated cells. Analysis of the expression of genes reported to regulate cytokine-induced proliferation demonstrated that both IL-2 and IL-12 induce c-myc mRNA accumulation in NK and T cells, whereas only IL-2 induces bcl-2 expression. Our data provide the first demonstration that IL-12-mediated activation of T and NK cells does not involve expression of members of the immediate-early activation genes family (egr-1, c-fos, and junB), AP-1 transcriptional activity, or bcl-2 expression. This indicates that functional differences observed in IL-2- and IL-12-stimulated cells may depend, at least in part, on differential gene regulation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 555, "end": 564}, "arguments": [{"role": "Theme", "text": "egr-1", "start": 539, "end": 544}]}, {"trigger": {"text": "expressed", "start": 777, "end": 786}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 753, "end": 758}]}, {"trigger": {"text": "expressed", "start": 777, "end": 786}, "arguments": [{"role": "Theme", "text": "junB", "start": 763, "end": 767}]}, {"trigger": {"text": "expression", "start": 856, "end": 866}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 870, "end": 875}]}, {"trigger": {"text": "expression", "start": 856, "end": 866}, "arguments": [{"role": "Theme", "text": "junD", "start": 880, "end": 884}]}, {"trigger": {"text": "expression", "start": 1274, "end": 1284}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 1268, "end": 1273}]}, {"trigger": {"text": "expression", "start": 1393, "end": 1403}, "arguments": [{"role": "Theme", "text": "egr-1", "start": 1463, "end": 1468}]}, {"trigger": {"text": "expression", "start": 1393, "end": 1403}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1470, "end": 1475}]}, {"trigger": {"text": "expression", "start": 1393, "end": 1403}, "arguments": [{"role": "Theme", "text": "junB", "start": 1481, "end": 1485}]}, {"trigger": {"text": "expression", "start": 1528, "end": 1538}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 1522, "end": 1527}]}], "positive regulation": [{"trigger": {"text": "upon", "start": 787, "end": 791}, "arguments": [{"role": "Theme", "text": "expressed", "start": 777, "end": 786}]}, {"trigger": {"text": "modified", "start": 892, "end": 900}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 827, "end": 831}, {"role": "Theme", "text": "expression", "start": 856, "end": 866}]}, {"trigger": {"text": "modified", "start": 892, "end": 900}, "arguments": [{"role": "Theme", "text": "expression", "start": 856, "end": 866}]}, {"trigger": {"text": "induce", "start": 1192, "end": 1198}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1177, "end": 1181}, {"role": "Theme", "text": "accumulation", "start": 1210, "end": 1222}]}, {"trigger": {"text": "induce", "start": 1192, "end": 1198}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1210, "end": 1222}]}, {"trigger": {"text": "accumulation", "start": 1210, "end": 1222}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 1199, "end": 1204}]}, {"trigger": {"text": "induces", "start": 1260, "end": 1267}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1255, "end": 1259}, {"role": "Theme", "text": "expression", "start": 1274, "end": 1284}]}]}}, "schema": []}
{"input": "Induction of activator protein (AP)-1 and nuclear factor-kappaB by CD28 stimulation involves both phosphatidylinositol 3-kinase and acidic sphingomyelinase signals. \nA major obstacle in understanding the signaling events that follow CD28 receptor ligation arises from the fact that CD28 acts as a costimulus to TCR engagement, making it difficult to assess the relative contribution of CD28 signals as distinct from those of the TCR. To overcome this problem, we have exploited the observation that activated human T cell blasts can be stimulated via the CD28 surface molecule in the absence of antigenic challenge; thus, we have been able to observe the response of normal T cells to CD28 activation in isolation. Using this system, we observed that CD28 stimulation by B7-transfected CHO cells induced a proliferative response in T cells that was not accompanied by measurable IL-2 production. However, subsequent analysis of transcription factor generation revealed that B7 stimulation induced both activator protein-1 (AP-1) and nuclear factor-kappaB (NF-kappaB) complexes, but not NF-AT. In contrast, engagement of the TCR by class II MHC/superantigen, either with or without CD28 ligation, resulted in the induction of NF-AT, AP-1, and NF-kappaB as well as IL-2 production. Using selective inhibitors, we investigated the signaling pathways involved in the CD28-mediated induction of AP-1 and NF-kappaB. This revealed that NF-kappaB generation was sensitive to chloroquine, an inhibitor of acidic sphingomyelinase, but not to the phosphatidylinositol 3-kinase inhibitor, wortmannin. In contrast, AP-1 generation was inhibited by wortmannin and was also variably sensitive to chloroquine. These data suggest that in activated normal T cells, CD28-derived signals can stimulate proliferation at least in part via NF-kappaB and AP-1 generation, and that this response uses both acidic sphingomyelinase and phosphatidylinositol 3-kinase-linked pathways. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 247, "end": 255}, "arguments": [{"role": "Theme", "text": "CD28", "start": 233, "end": 237}]}, {"trigger": {"text": "ligation", "start": 1186, "end": 1194}, "arguments": [{"role": "Theme", "text": "CD28", "start": 1181, "end": 1185}]}], "gene expression": [{"trigger": {"text": "transfected", "start": 774, "end": 785}, "arguments": [{"role": "Theme", "text": "B7", "start": 771, "end": 773}]}, {"trigger": {"text": "production", "start": 884, "end": 894}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 879, "end": 883}]}, {"trigger": {"text": "production", "start": 1268, "end": 1278}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1263, "end": 1267}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 1483, "end": 1492}, "arguments": [{"role": "Theme", "text": "acidic sphingomyelinase", "start": 1496, "end": 1519}]}], "positive regulation": [{"trigger": {"text": "stimulation", "start": 72, "end": 83}, "arguments": [{"role": "Theme", "text": "CD28", "start": 67, "end": 71}]}, {"trigger": {"text": "activation", "start": 690, "end": 700}, "arguments": [{"role": "Theme", "text": "CD28", "start": 685, "end": 689}]}, {"trigger": {"text": "stimulation", "start": 756, "end": 767}, "arguments": [{"role": "Theme", "text": "CD28", "start": 751, "end": 755}]}, {"trigger": {"text": "transfected", "start": 774, "end": 785}, "arguments": [{"role": "Theme", "text": "transfected", "start": 774, "end": 785}]}, {"trigger": {"text": "accompanied", "start": 853, "end": 864}, "arguments": [{"role": "Cause", "text": "stimulation", "start": 756, "end": 767}, {"role": "Theme", "text": "production", "start": 884, "end": 894}]}, {"trigger": {"text": "induction", "start": 1212, "end": 1221}, "arguments": [{"role": "Theme", "text": "production", "start": 1268, "end": 1278}]}]}}, "schema": []}
{"input": "A critical role of Sp1- and Ets-related transcription factors in maintaining CTL-specific expression of the mouse perforin gene. \nThis study was designed to determine the potential cis-elements involved in transcriptional regulation of the mouse perforin gene. DNase I hypersensitive site (DHS) mapping revealed that the perforin locus contained six DHS within 7.0 kb of the 5' upstream sequence (-7.0 kb) and two DHS in intron 2. The six 5' upstream and one intronic DHS were detected in only perforin-expressing lymphocytes. Chloramphenicol acetyltransferase (CAT) activities directed by 5' upstream promoter were detected preferentially in perforin-expressing cell lines. A construct termed PFP5a containing -795 bp exhibited the highest CAT activity, and PFP9a20 containing only -73 bp also produced significantly high CAT activity in CTLL-R8 cells. The proximal region in PFP9a20 contained two potential Sp1 binding sites (GC box and GT box) and one Ets binding site (EBS). Electrophoretic mobility shift assay showed that each of the cis-elements bound specific protein factors. When single-point mutation was introduced to each GC box, EBS, and GT box in PFP9a20, at least 3-fold less CAT activity was observed in CTLL-R8 cells. To confirm the importance of the three cis-acting elements in the perforin gene expression, point mutation was introduced again to each proximal GC box, EBS, and GT box of PFP5a. The point mutations resulted in a 2.5- to 3-fold reduction of CAT activity. The results suggest that a combination of the three proximal cis-acting elements may constitute a minimal region responsible for CTL-specific expression of perforin. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 1053, "end": 1058}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 909, "end": 912}]}], "gene expression": [{"trigger": {"text": "expression", "start": 90, "end": 100}, "arguments": [{"role": "Theme", "text": "perforin", "start": 114, "end": 122}]}, {"trigger": {"text": "expressing", "start": 503, "end": 513}, "arguments": [{"role": "Theme", "text": "perforin", "start": 494, "end": 502}]}, {"trigger": {"text": "expression", "start": 1316, "end": 1326}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1302, "end": 1310}]}, {"trigger": {"text": "expression", "start": 1633, "end": 1643}, "arguments": [{"role": "Theme", "text": "perforin", "start": 1647, "end": 1655}]}], "negative regulation": [{"trigger": {"text": "less", "start": 1187, "end": 1191}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1192, "end": 1195}]}, {"trigger": {"text": "reduction", "start": 1464, "end": 1473}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1477, "end": 1480}]}], "positive regulation": [{"trigger": {"text": "exhibited", "start": 719, "end": 728}, "arguments": [{"role": "Theme", "text": "CAT", "start": 741, "end": 744}]}, {"trigger": {"text": "produced", "start": 795, "end": 803}, "arguments": [{"role": "Theme", "text": "CAT", "start": 823, "end": 826}]}], "regulation": [{"trigger": {"text": "role", "start": 11, "end": 15}, "arguments": [{"role": "Theme", "text": "expression", "start": 90, "end": 100}]}, {"trigger": {"text": "involved", "start": 194, "end": 202}, "arguments": [{"role": "Theme", "text": "transcriptional regulation", "start": 206, "end": 232}]}, {"trigger": {"text": "transcriptional regulation", "start": 206, "end": 232}, "arguments": [{"role": "Theme", "text": "perforin", "start": 246, "end": 254}]}, {"trigger": {"text": "directed", "start": 578, "end": 586}, "arguments": [{"role": "Theme", "text": "CAT", "start": 562, "end": 565}]}, {"trigger": {"text": "importance", "start": 1251, "end": 1261}, "arguments": [{"role": "Theme", "text": "expression", "start": 1316, "end": 1326}]}, {"trigger": {"text": "resulted", "start": 1435, "end": 1443}, "arguments": [{"role": "Theme", "text": "reduction", "start": 1464, "end": 1473}]}, {"trigger": {"text": "responsible", "start": 1604, "end": 1615}, "arguments": [{"role": "Theme", "text": "expression", "start": 1633, "end": 1643}]}]}}, "schema": []}
{"input": "Soluble factors secreted by activated T-lymphocytes modulate the transcription of the immunosuppressive cytokine TGF-beta 2 in glial cells. \nCoordination of the immune response to injury or disease in the brain is postulated to involve bi-directional discourse between the immune system and the central nervous system. This cross communication involves soluble mediators, including various growth factors, cytokines, and neuropeptides. In this report, we demonstrate that the supernatant from activated T-lymphocytes is able to induce the transcription of a potent cytokine, TGF-beta 2 in glial cells. The activating stimulus invokes signaling mechanisms distinct from known kinase or protease pathways. Activation of TGF-beta 2 transcription correlates with the loss of binding activity for an 80 kDA glial labile repressor protein, GLRP, to a responsive region within the TFG-beta 2 promoter. Although GLRP shares some characteristics with the inducible transcription factor AP-1, it appears to be distinct from known AP-1 family members. These data along with previous observations demonstrating the potent immunosuppressive activity of TGF-beta 2, support a model for a feedback mechanism between the activated T-lymphocytes and astrocytes via TGF-beta 2 to regulate the immune response. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 771, "end": 787}, "arguments": [{"role": "Theme", "text": "GLRP", "start": 834, "end": 838}, {"role": "Theme2", "text": "TFG-beta 2", "start": 874, "end": 884}, {"role": "Site2", "text": "promoter", "start": 885, "end": 893}]}], "negative regulation": [{"trigger": {"text": "loss", "start": 763, "end": 767}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 771, "end": 787}]}], "positive regulation": [{"trigger": {"text": "induce", "start": 528, "end": 534}, "arguments": [{"role": "Theme", "text": "transcription", "start": 539, "end": 552}]}, {"trigger": {"text": "Activation", "start": 704, "end": 714}, "arguments": [{"role": "Theme", "text": "transcription", "start": 729, "end": 742}]}], "regulation": [{"trigger": {"text": "modulate", "start": 52, "end": 60}, "arguments": [{"role": "Theme", "text": "transcription", "start": 65, "end": 78}]}], "transcription": [{"trigger": {"text": "transcription", "start": 65, "end": 78}, "arguments": [{"role": "Theme", "text": "TGF-beta 2", "start": 113, "end": 123}]}, {"trigger": {"text": "transcription", "start": 539, "end": 552}, "arguments": [{"role": "Theme", "text": "TGF-beta 2", "start": 575, "end": 585}]}, {"trigger": {"text": "transcription", "start": 729, "end": 742}, "arguments": [{"role": "Theme", "text": "TGF-beta 2", "start": 718, "end": 728}]}]}}, "schema": []}
{"input": "Regulation of cytokine and cytokine receptor expression by glucocorticoids. \nGlucocorticoids (GCS) profoundly inhibit several aspects of T cell immunity largely through inhibition of cytokine expression at the transcriptional and posttranscriptional levels. GCS were also reported to act indirectly by inducing transforming growth factor-beta expression, which in turn blocks T cell immunity. In exerting their antiproliferative effects, GCS diffuse into target cells where they bind their cytoplasmic receptor, which in turn translocates to the nucleus where it inhibits transcription of cytokine genes through direct binding to the glucocorticoid response elements (GRE), which are located in the promoter region of cytokine genes or, alternatively, through antagonism of the action of transcription factors required for optimal transcriptional activation. In contrast to their inhibitory effects on cytokine expression, GCS up-regulate cytokine receptor expression that correlates with enhanced cytokine effects on target cells. In this review, we summarize the current state of knowledge of the mechanism of action of GCS, including the phenomenon of steroid-induced rebound, which ensues upon GCS withdrawal. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 343, "end": 353}, "arguments": [{"role": "Theme", "text": "transforming growth factor-beta", "start": 311, "end": 342}]}], "positive regulation": [{"trigger": {"text": "inducing", "start": 302, "end": 310}, "arguments": [{"role": "Theme", "text": "expression", "start": 343, "end": 353}]}]}}, "schema": []}
{"input": "The Oct-2 transcription factor. \nThe Oct-2 transcription factor is a member of the POU (Pit-Oct-Unc) family of transcription factors and is expressed only in B lymphocytes and in neuronal cells but not in other cell types. The primary RNA transcript of the gene is subject to alternative splicing to yield different variants which can either activate or repress gene expression. The forms produced in B lymphocytes have a predominantly activating effect on gene expression whereas those produced in neuronal cells have a predominantly inhibitory effect and can repress the expression of both the herpes simplex virus immediate-early genes and the cellular tyrosine hydroxylase gene. Thus Oct-2 plays an important role in the regulation of cellular gene expression in both B cells and neuronal cells as well as in the control of viral latency. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 140, "end": 149}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 37, "end": 42}]}, {"trigger": {"text": "expression", "start": 573, "end": 583}, "arguments": [{"role": "Theme", "text": "tyrosine hydroxylase", "start": 656, "end": 676}]}], "negative regulation": [{"trigger": {"text": "inhibitory effect", "start": 535, "end": 552}, "arguments": [{"role": "Theme", "text": "expression", "start": 573, "end": 583}]}, {"trigger": {"text": "repress", "start": 561, "end": 568}, "arguments": [{"role": "Theme", "text": "expression", "start": 573, "end": 583}]}], "regulation": [{"trigger": {"text": "subject", "start": 265, "end": 272}, "arguments": [{"role": "Theme", "text": "RNA transcript", "start": 235, "end": 249}]}], "transcription": [{"trigger": {"text": "RNA transcript", "start": 235, "end": 249}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 37, "end": 42}]}]}}, "schema": []}
{"input": "Tissue and cell-type specific expression of the tuberous sclerosis gene, TSC2, in human tissues. \nTSC2 is a gene on chromosome 16p13.3 associated with the autosomal dominant neurocutaneous disorder, tuberous sclerosis complex (TSC). By using a partial nucleotide sequence from the cloned TSC2 and polymerase chain reaction methodology, we constructed a digoxigenin-labeled complementary DNA probe to examine TSC2 gene expression in autopsy- or biopsy-derived human tissues by in situ hybridization. TSC2 messenger RNA was widely expressed in various cell types throughout the body, including epithelia, lymphocytes, and cells with endocrine functions, e.g., adrenal cortex and anterior pituitary. It was prominently and selectively (within the central nervous system) expressed in pyramidal cells of the cerebral cortex and other motor neurons, e.g., in spinal cord and brainstem nuclei. Visceral TSC2 expression was comparable in autopsy tissues from patients with and without TSC; TSC2 messenger RNA expression was most prominent in cells with a rapid mitotic rate and turnover, e.g., epithelia and lymphocytes, with central nervous system pyramidal cells and other neurons being an obvious exception, and/or in cells with important secretory/transport functions. This widespread expression of the TSC2 gene supports the view that it encodes a protein vital to cell growth and metabolism or one that functions as a tumor/growth suppressor. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 30, "end": 40}, "arguments": [{"role": "Theme", "text": "TSC2", "start": 73, "end": 77}]}, {"trigger": {"text": "expression", "start": 418, "end": 428}, "arguments": [{"role": "Theme", "text": "TSC2", "start": 408, "end": 412}]}, {"trigger": {"text": "expression", "start": 902, "end": 912}, "arguments": [{"role": "Theme", "text": "TSC2", "start": 897, "end": 901}]}, {"trigger": {"text": "expression", "start": 1282, "end": 1292}, "arguments": [{"role": "Theme", "text": "TSC2", "start": 1300, "end": 1304}]}], "positive regulation": [{"trigger": {"text": "prominent", "start": 1022, "end": 1031}, "arguments": [{"role": "Theme", "text": "expression", "start": 1002, "end": 1012}]}], "transcription": [{"trigger": {"text": "expressed", "start": 529, "end": 538}, "arguments": [{"role": "Theme", "text": "TSC2", "start": 499, "end": 503}]}, {"trigger": {"text": "expressed", "start": 768, "end": 777}, "arguments": [{"role": "Theme", "text": "TSC2", "start": 499, "end": 503}]}, {"trigger": {"text": "expression", "start": 1002, "end": 1012}, "arguments": [{"role": "Theme", "text": "TSC2", "start": 983, "end": 987}]}]}}, "schema": []}
{"input": "Cell specific expression of human Bruton's agammaglobulinemia tyrosine kinase gene (Btk) is regulated by Sp1- and Spi-1/PU.1-family members. \nBruton's agammaglobulinemia tyrosine kinase (Btk) is a cytoplasmic tyrosine kinase involved in the human disease X-linked agammaglobulinemia (XLA). The gene is expressed in all hematopoietic cells with the exception of T-cells and plasma cells. For this expression pattern the first 280 bp upstream of the major transcriptional start site seems to be sufficient. In vitro footprinting analysis within this part of the promoter revealed two Sp1 binding sites as well as a PU-box. The transcription factor Spi-1/PU.1 as well as the closely related factor Spi-B bound to the PU-box in B-cells. In the erythroleukemia cell line K562, due to the absence of Spi-B, only PU.1 bound to the Btk promoter. Mutation of either site reduced the expression in transient transfection experiments. However, mutation of the PU box had no effect in the T-cell line Jurkat, where none of the Spi-1 family members is expressed. In addition Spi-B as well as PU.1 were able to transactivate Btk expression. In fetal liver of PU.1-/- mice, which lack lymphoid and myeloid cells, expression of Btk was reduced two- to threefold but not abolished. Collectively this study shows that expression of the Btk gene is regulated by the combined action of Sp1- and PU.1-family members. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 701, "end": 706}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 646, "end": 651}]}, {"trigger": {"text": "bound", "start": 701, "end": 706}, "arguments": [{"role": "Theme", "text": "Spi-B", "start": 695, "end": 700}]}, {"trigger": {"text": "bound", "start": 811, "end": 816}, "arguments": [{"role": "Theme", "text": "PU.1", "start": 806, "end": 810}, {"role": "Theme2", "text": "Btk", "start": 824, "end": 827}, {"role": "Site2", "text": "promoter", "start": 828, "end": 836}]}], "gene expression": [{"trigger": {"text": "expression", "start": 14, "end": 24}, "arguments": [{"role": "Theme", "text": "Btk", "start": 84, "end": 87}]}, {"trigger": {"text": "expressed", "start": 302, "end": 311}, "arguments": [{"role": "Theme", "text": "Btk", "start": 187, "end": 190}]}, {"trigger": {"text": "absence", "start": 783, "end": 790}, "arguments": [{"role": "Theme", "text": "Spi-B", "start": 794, "end": 799}]}, {"trigger": {"text": "expression", "start": 874, "end": 884}, "arguments": [{"role": "Theme", "text": "Btk", "start": 187, "end": 190}]}, {"trigger": {"text": "expressed", "start": 1039, "end": 1048}, "arguments": [{"role": "Theme", "text": "Spi-1", "start": 1015, "end": 1020}]}, {"trigger": {"text": "expression", "start": 1115, "end": 1125}, "arguments": [{"role": "Theme", "text": "Btk", "start": 1111, "end": 1114}]}, {"trigger": {"text": "expression", "start": 1198, "end": 1208}, "arguments": [{"role": "Theme", "text": "Btk", "start": 1212, "end": 1215}]}, {"trigger": {"text": "expression", "start": 1300, "end": 1310}, "arguments": [{"role": "Theme", "text": "Btk", "start": 1318, "end": 1321}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 862, "end": 869}, "arguments": [{"role": "Theme", "text": "expression", "start": 874, "end": 884}]}, {"trigger": {"text": "reduced", "start": 1220, "end": 1227}, "arguments": [{"role": "Theme", "text": "expression", "start": 1198, "end": 1208}]}, {"trigger": {"text": "abolished", "start": 1254, "end": 1263}, "arguments": [{"role": "Theme", "text": "expression", "start": 1198, "end": 1208}]}], "positive regulation": [{"trigger": {"text": "sufficient", "start": 493, "end": 503}, "arguments": [{"role": "Theme", "text": "expressed", "start": 302, "end": 311}]}, {"trigger": {"text": "transactivate", "start": 1097, "end": 1110}, "arguments": [{"role": "Cause", "text": "Spi-B", "start": 1062, "end": 1067}, {"role": "Theme", "text": "expression", "start": 1115, "end": 1125}]}, {"trigger": {"text": "transactivate", "start": 1097, "end": 1110}, "arguments": [{"role": "Cause", "text": "PU.1", "start": 1079, "end": 1083}, {"role": "Theme", "text": "expression", "start": 1115, "end": 1125}]}], "regulation": [{"trigger": {"text": "regulated", "start": 92, "end": 101}, "arguments": [{"role": "Theme", "text": "expression", "start": 14, "end": 24}, {"role": "Cause", "text": "Sp1", "start": 105, "end": 108}]}, {"trigger": {"text": "regulated", "start": 92, "end": 101}, "arguments": [{"role": "Theme", "text": "expression", "start": 14, "end": 24}, {"role": "Cause", "text": "Spi-1", "start": 114, "end": 119}]}, {"trigger": {"text": "effect", "start": 963, "end": 969}, "arguments": [{"role": "Theme", "text": "expression", "start": 874, "end": 884}]}, {"trigger": {"text": "regulated", "start": 1330, "end": 1339}, "arguments": [{"role": "Theme", "text": "expression", "start": 1300, "end": 1310}, {"role": "Cause", "text": "Sp1", "start": 1366, "end": 1369}]}, {"trigger": {"text": "regulated", "start": 1330, "end": 1339}, "arguments": [{"role": "Theme", "text": "expression", "start": 1300, "end": 1310}, {"role": "Cause", "text": "PU.1", "start": 1375, "end": 1379}]}]}}, "schema": []}
{"input": "Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene [published erratum appears in Mol Cell Biol 1997 Apr;17(4):2351] \nThe interleukin 2 receptor alpha-chain (IL-2R alpha) gene is a key regulator of lymphocyte proliferation. IL-2R alpha is rapidly and potently induced in T cells in response to mitogenic stimuli. Interleukin 2 (IL-2) stimulates IL-2R alpha transcription, thereby amplifying expression of its own high-affinity receptor. IL-2R alpha transcription is at least in part controlled by two positive regulatory regions, PRRI and PRRII. PRRI is an inducible proximal enhancer, located between nucleotides -276 and -244, which contains NF-kappaB and SRE/CArG motifs. PRRII is a T-cell-specific enhancer, located between nucleotides -137 and -64, which binds the T-cell-specific Ets protein Elf-1 and HMG-I(Y) proteins. However, none of these proximal regions account for the induction of IL-2R alpha transcription by IL-2. To find new regulatory regions of the IL-2R alpha gene, 8.5 kb of the 5' end noncoding sequence of the IL-2R alpha gene have been sequenced. We identified an 86-nucleotide fragment that is 90% identical to the recently characterized murine IL-2-responsive element (mIL-2rE). This putative human IL-2rE, designated PRRIII, confers IL-2 responsiveness on a heterologous promoter. PRRIII contains a Stat protein binding site that overlaps with an EBS motif (GASd/EBSd). These are essential for IL-2 inducibility of PRRIII/CAT reporter constructs. IL-2 induced the binding of Stat5a and b proteins to the human GASd element. To confirm the physiological relevance of these findings, we carried out in vivo footprinting experiments which showed that stimulation of IL-2R alpha expression correlated with occupancy of the GASd element. Our data demonstrate a major role of the GASd/EBSd element in IL-2R alpha regulation and suggest that the T-cell-specific Elf-1 factor can serve as a transcriptional repressor. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 16, "end": 20}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 0, "end": 5}, {"role": "Theme2", "text": "interleukin-2 receptor alpha", "start": 74, "end": 102}]}, {"trigger": {"text": "bind", "start": 16, "end": 20}, "arguments": [{"role": "Theme", "text": "Stat5", "start": 10, "end": 15}, {"role": "Theme2", "text": "interleukin-2 receptor alpha", "start": 74, "end": 102}]}, {"trigger": {"text": "binds", "start": 816, "end": 821}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 854, "end": 859}]}, {"trigger": {"text": "binds", "start": 816, "end": 821}, "arguments": [{"role": "Theme", "text": "HMG-I(Y)", "start": 864, "end": 872}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1759, "end": 1769}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 1747, "end": 1758}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 316, "end": 323}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 280, "end": 291}]}, {"trigger": {"text": "induction", "start": 939, "end": 948}, "arguments": [{"role": "Theme", "text": "transcription", "start": 964, "end": 977}, {"role": "Cause", "text": "IL-2", "start": 981, "end": 985}]}, {"trigger": {"text": "stimulation", "start": 1732, "end": 1743}, "arguments": [{"role": "Theme", "text": "expression", "start": 1759, "end": 1769}]}], "regulation": [{"trigger": {"text": "controlled", "start": 539, "end": 549}, "arguments": [{"role": "Theme", "text": "transcription", "start": 505, "end": 518}]}, {"trigger": {"text": "role", "start": 1846, "end": 1850}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1891, "end": 1901}]}, {"trigger": {"text": "regulation", "start": 1891, "end": 1901}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 1879, "end": 1890}]}], "transcription": [{"trigger": {"text": "transcription", "start": 505, "end": 518}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 493, "end": 504}]}, {"trigger": {"text": "transcription", "start": 964, "end": 977}, "arguments": [{"role": "Theme", "text": "IL-2R alpha", "start": 952, "end": 963}]}]}}, "schema": []}
{"input": "Sterol dependent LDL-receptor gene transcription in lymphocytes from normal and CML patients. \nSterol regulatory element (SRE) has been recognized to regulate various key genes coding for especially low density lipoprotein (LDL)-receptor, 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase and HMG-CoA synthase known to play a crucial role in the cholesterol feedback mechanism. The deranged cholesterol feedback mechanism has been widely recognised in initiation as well as progression of various types of cancers including chronic myeloid leukaemia (CML). Consequently, the present study was addressed to understand this phenomenon and revealed the existence of a unique 47 kDa protein factor having affinity for this SRE sequence in lymphocytes from normal subjects as well as its absence in lymphocytes from untreated CML patients. However, this factor appeared when the CML patients achieved complete haematological remission (CHR) through alpha-interferon therapy. Further, an inverse relationship was also observed between sterol modulated LDL-receptor gene transcription and the binding affinity of this 47 kDa factor to the SRE sequence. Based upon these results we propose that alpha-interferon through its receptor initiates phosphatidic acid dependent signalling which in turn regulates the affinity of 47 kDa sterol regulatory element binding factor as well as LDL-receptor gene transcription in lymphocytes from CML patients. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "dependent", "start": 7, "end": 16}, "arguments": [{"role": "Theme", "text": "transcription", "start": 35, "end": 48}]}], "regulation": [{"trigger": {"text": "regulate", "start": 150, "end": 158}, "arguments": [{"role": "Theme", "text": "low density lipoprotein (LDL)-receptor", "start": 199, "end": 237}]}, {"trigger": {"text": "regulate", "start": 150, "end": 158}, "arguments": [{"role": "Theme", "text": "3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase", "start": 239, "end": 296}]}, {"trigger": {"text": "regulate", "start": 150, "end": 158}, "arguments": [{"role": "Theme", "text": "HMG-CoA synthase", "start": 301, "end": 317}]}, {"trigger": {"text": "modulated", "start": 1044, "end": 1053}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1072, "end": 1085}]}], "transcription": [{"trigger": {"text": "transcription", "start": 35, "end": 48}, "arguments": [{"role": "Theme", "text": "LDL-receptor", "start": 17, "end": 29}]}, {"trigger": {"text": "transcription", "start": 1072, "end": 1085}, "arguments": [{"role": "Theme", "text": "LDL-receptor", "start": 1054, "end": 1066}]}, {"trigger": {"text": "transcription", "start": 1399, "end": 1412}, "arguments": [{"role": "Theme", "text": "LDL-receptor", "start": 1381, "end": 1393}]}]}}, "schema": []}
{"input": "Lymphocytes from CML patients lack a 47 kDa factor having affinity for a genomic sterol regulatory sequence. \nDeranged cellular cholesterol homeostasis has been widely recognized in the initiation as well as progression of various types of cancers including chronic myeloid leukaemia (CML). Since the human genomic sterol regulatory element (SRE) has been shown to regulate various key genes involved in this phenomenon, the present study revealed the existence of a unique 47 kDa protein factor having affinity for this SRE sequence in lymphocytes from normal subjects, as well as its absence in lymphocytes from untreated CML patients. However, this factor appeared when these CML patients achieved complete haematological remission (CHR) through alpha-interferon therapy. Furthermore, an inverse relationship was also observed between the LDL receptor gene expression at the transcriptional level and the binding affinity of this 47 kDa protein factor to the SRE sequence. Based upon these results we propose that this factor may have a role in pathophysiology of chronic myeloid leukaemia. ", "output": {"json_structures": {"transcription": [{"trigger": {"text": "expression at the transcriptional level", "start": 860, "end": 899}, "arguments": [{"role": "Theme", "text": "LDL receptor", "start": 842, "end": 854}]}]}}, "schema": []}
{"input": "A novel immunosuppressive factor in bovine colostrum blocks activation of the interleukin 2 gene enhancer at the NFAT site. \nA factor in bovine colostrum (colostrum inhibitory factor, CIF) inhibits interleukin 2 (IL2) production in activated T helper cells by blocking the accumulation of IL2 mRNA. To determine whether CIF blocks at the level of IL2 transcription, we introduced reporter plasmids into the human T leukemia cell line Jurkat by transient transfection. These contained the luciferase gene under the control of either the human IL2 upstream enhancer region (segments -326 to +45) or three repeats of the NFAT element contained within it (segments -255 to -285). Expression of luciferase in these cells was induced by phorbol myristate acetate plus a calcium ionophore. CIF inhibited induction of either construct as did cyclosporine, which is known to block activation of the NFAT element. CIF failed to inhibit several other enhancer elements. The NFAT-controlled luciferase gene system distinguishes CIF from other T cell inhibitory activities present in colostrum, in particular, TGF beta 1 and TGF beta 2 and the glucocorticoids. Stably transfected Jurkat cells behaved similarly to the transiently transfected ones with respect to inhibition by CIF and cyclosporine. The NFAT-luc assay is a useful technique for the rapid, sensitive measurement of CIF or other immunosuppressants with a similar mode of action. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 218, "end": 228}, "arguments": [{"role": "Theme", "text": "IL2", "start": 213, "end": 216}]}], "localization": [{"trigger": {"text": "present", "start": 1060, "end": 1067}, "arguments": [{"role": "Theme", "text": "TGF beta 1", "start": 1097, "end": 1107}]}, {"trigger": {"text": "present", "start": 1060, "end": 1067}, "arguments": [{"role": "Theme", "text": "TGF beta 2", "start": 1112, "end": 1122}]}], "negative regulation": [{"trigger": {"text": "blocks", "start": 53, "end": 59}, "arguments": [{"role": "Theme", "text": "activation", "start": 60, "end": 70}]}, {"trigger": {"text": "inhibits", "start": 189, "end": 197}, "arguments": [{"role": "Theme", "text": "production", "start": 218, "end": 228}, {"role": "Cause", "text": "blocking", "start": 260, "end": 268}]}, {"trigger": {"text": "blocking", "start": 260, "end": 268}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 273, "end": 285}]}, {"trigger": {"text": "blocks", "start": 324, "end": 330}, "arguments": [{"role": "Theme", "text": "transcription", "start": 351, "end": 364}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 60, "end": 70}, "arguments": [{"role": "Theme", "text": "interleukin 2", "start": 78, "end": 91}, {"role": "Site", "text": "enhancer", "start": 97, "end": 105}]}, {"trigger": {"text": "accumulation", "start": 273, "end": 285}, "arguments": [{"role": "Theme", "text": "IL2", "start": 289, "end": 292}]}], "transcription": [{"trigger": {"text": "transcription", "start": 351, "end": 364}, "arguments": [{"role": "Theme", "text": "IL2", "start": 347, "end": 350}]}]}}, "schema": []}
{"input": "Octamer independent activation of transcription from the kappa immunoglobulin germline promoter. \nPrevious analyses of immunoglobulin V region promoters has led to the discovery of a common octamer motif which is functionally important in the tissue-specific and developmentally regulated transcriptional activation of immunoglobulin genes. The germline promoters (Ko) located upstream of the J region gene segments of the kappa locus also contain an octamer motif (containing a single base pair mutation and referred to as the variant octamer) which has been shown previously to bind Oct-1 and Oct-2 transcription factors in vitro. To further elucidate the role of this variant octamer motif in the regulation of germline transcription from the unrearranged kappa locus, we have quantitated the relative binding affinity of Oct-1 and Oct-2 for the variant octamer motif and determined the functional role of this octamer motif in transcriptional activation. We find that, although the variant octamer motif binds Oct-1 and Oct-2 in vitro with 5-fold lower affinity than the consensus octamer motif, mutation of the variant octamer motif to either a consensus octamer or non-octamer motif has no effect on transcriptional activation from the germline promoter. We also find significant differences in activation of germline and V region promoters by kappa enhancers. Our results suggest that the germline promoters and V region promoters differ in their dependence on octamer for activation and respond differently to enhancer activation. These findings have important implications in regulation of germline transcription as well as concomitant activation of the V-J recombination of the kappa light chain locus. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 580, "end": 584}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 585, "end": 590}]}, {"trigger": {"text": "bind", "start": 580, "end": 584}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 595, "end": 600}]}, {"trigger": {"text": "binding affinity", "start": 805, "end": 821}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 825, "end": 830}]}, {"trigger": {"text": "binding affinity", "start": 805, "end": 821}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 835, "end": 840}]}, {"trigger": {"text": "binds", "start": 1008, "end": 1013}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 1014, "end": 1019}]}, {"trigger": {"text": "binds", "start": 1008, "end": 1013}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 1024, "end": 1029}]}]}}, "schema": []}
{"input": "Characterization of the murine cyclin-dependent kinase inhibitor gene p27Kip1. \nThe cyclin-dependent kinase inhibitor p27Kip1 plays an important role in regulating cell-cycle progression. p27Kip1 directly inhibits the catalytic activity of cyclin/cdks (cyclin-dependent kinase) complexes and/or interferes physically with cyclin/cdks activation by CAK. Interestingly, the expression level of p27Kip1 mRNA was maximal in resting Go T-cells and rapidly declined following anti-CD3 activation. We report here the cloning of p27Kip1 gene from murine genomic DNA and the functional analysis of the promoter of the p27Kip1 gene. The gene consists of at least three exons and spans more than 5.6 kb of DNA. Primer extension and nuclease S1 protection analysis revealed two major transcription initiation sites. The promoter region lacked a TATA box but contained potential binding sites for the transcriptional factors including two Sp1, CRE, Myb and NFkB located at positions -153, -178, -286, -875, and -1011, respectively. To analyze the regulatory mechanisms controlling p27Kip1 gene expression, we characterized the 5'-flanking region from nt -1609 to +178. The -326 to -615 region contained positive regulatory elements. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1081, "end": 1091}, "arguments": [{"role": "Theme", "text": "p27Kip1", "start": 1068, "end": 1075}]}], "negative regulation": [{"trigger": {"text": "declined", "start": 451, "end": 459}, "arguments": [{"role": "Theme", "text": "expression level", "start": 372, "end": 388}]}], "regulation": [{"trigger": {"text": "controlling", "start": 1056, "end": 1067}, "arguments": [{"role": "Theme", "text": "expression", "start": 1081, "end": 1091}]}], "transcription": [{"trigger": {"text": "expression level", "start": 372, "end": 388}, "arguments": [{"role": "Theme", "text": "p27Kip1", "start": 392, "end": 399}]}]}}, "schema": []}
{"input": "The state of maturation of monocytes into macrophages determines the effects of IL-4 and IL-13 on HIV replication. \nThe molecular mechanisms of the effects of IL-4 and IL-13 on HIV infection in human monocytes as they matured into monocyte-derived macrophages over 7 days were investigated using HIV-1(BaL), and low passage clinical strains. IL-4 and IL-13 up-regulated the expression of both genomic and spliced HIV mRNA in monocytes cultured on Teflon, as determined by Northern analysis and p24 Ag assay. Using a nuclear run-on assay, IL-4 stimulation was shown to enhance transcription by two- to threefold. IL-4 stimulated nuclear factor-kappaB nuclear translocation and binding before enhancement of HIV RNA expression. Conversely, IL-4 and IL-13 markedly and significantly inhibited HIV replication at the transcriptional level in monocyte-derived macrophages, and this occurred whether these cytokines were added before or after HIV infection. The reversal from stimulation to inhibition occurred after 3 to 5 days of adherence to plastic. IL-4 had no significant effect on HIV reverse transcription. The effect of both cytokines on the monocyte maturation/differentiation (CD11b, CD13, and CD26) and other macrophage markers (CD14 and CD68) was examined. IL-4 enhanced CD11b, but inhibited CD26 expression and delayed CD13 loss. IL-13 had similar effects on CD11b and CD13, but no effect on CD26. Hence, these cytokines do not simply enhance monocyte differentiation, but have complex and slightly divergent effects that impact on HIV replication probably through cell signaling pathways and nuclear factor-kappaB translocation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1304, "end": 1314}, "arguments": [{"role": "Theme", "text": "CD11b", "start": 1278, "end": 1283}]}, {"trigger": {"text": "expression", "start": 1304, "end": 1314}, "arguments": [{"role": "Theme", "text": "CD26", "start": 1299, "end": 1303}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1289, "end": 1298}, "arguments": [{"role": "Cause", "text": "CD11b", "start": 1278, "end": 1283}, {"role": "Theme", "text": "expression", "start": 1304, "end": 1314}]}, {"trigger": {"text": "delayed", "start": 1319, "end": 1326}, "arguments": [{"role": "Cause", "text": "CD11b", "start": 1278, "end": 1283}, {"role": "Theme", "text": "loss", "start": 1332, "end": 1336}]}, {"trigger": {"text": "loss", "start": 1332, "end": 1336}, "arguments": [{"role": "Theme", "text": "CD13", "start": 1327, "end": 1331}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 1269, "end": 1277}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1264, "end": 1268}, {"role": "Theme", "text": "expression", "start": 1304, "end": 1314}]}, {"trigger": {"text": "had similar effects", "start": 1344, "end": 1363}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 1338, "end": 1343}, {"role": "Theme", "text": "CD11b", "start": 1367, "end": 1372}]}, {"trigger": {"text": "had similar effects", "start": 1344, "end": 1363}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 1338, "end": 1343}, {"role": "Theme", "text": "CD13", "start": 1377, "end": 1381}]}], "regulation": [{"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 738, "end": 742}, {"role": "Theme", "text": "CD11b", "start": 1182, "end": 1187}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 738, "end": 742}, {"role": "Theme", "text": "CD13", "start": 1189, "end": 1193}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 738, "end": 742}, {"role": "Theme", "text": "CD26", "start": 1199, "end": 1203}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 738, "end": 742}, {"role": "Theme", "text": "CD14", "start": 1235, "end": 1239}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 738, "end": 742}, {"role": "Theme", "text": "CD68", "start": 1244, "end": 1248}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 747, "end": 752}, {"role": "Theme", "text": "CD11b", "start": 1182, "end": 1187}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 747, "end": 752}, {"role": "Theme", "text": "CD13", "start": 1189, "end": 1193}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 747, "end": 752}, {"role": "Theme", "text": "CD26", "start": 1199, "end": 1203}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 747, "end": 752}, {"role": "Theme", "text": "CD14", "start": 1235, "end": 1239}]}, {"trigger": {"text": "effect", "start": 1113, "end": 1119}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 747, "end": 752}, {"role": "Theme", "text": "CD68", "start": 1244, "end": 1248}]}, {"trigger": {"text": "effect", "start": 1390, "end": 1396}, "arguments": [{"role": "Cause", "text": "IL-13", "start": 1338, "end": 1343}, {"role": "Theme", "text": "CD26", "start": 1400, "end": 1404}]}]}}, "schema": []}
{"input": "A novel SP-1 site in the human interleukin-1 beta promoter confers preferential transcriptional activity in keratinocytes. \nTo investigate the mechanisms of transcriptional activation of interleukin-1beta (IL-1beta) in non-monocytic cells, we constructed a series of reporter plasmids with the bacterial chloramphenicol acetyltransferase gene linked to various parts of the human IL-1beta promoter and performed transient transfection experiments. We identified a promoter segment that activates transcription most efficiently in keratinocytes. Electrophoretic mobility shift assays (EMSA) with a 43-mer oligonucleotide derived from the functionally identified cis-acting element revealed specific complexes. By competition analysis with transcription factor consensus sequence oligonucleotides and by immunosupershift, transcription factor SP-1 or a closely related protein was shown to bind to this regulatory element. The closest match to the known SP-1 consensus sequence within the respective region is a TCCCCTCCCCT motif. Mutation of this motif almost completely, and specifically, abolished the binding of two low-mobility complexes and led to a 95% decrease of constitutive transcriptional activation of a reporter construct IL-1beta (-170/+108). Likewise, activation of this reporter construct by tumor necrosis factor-alpha depended on the SP-1 site. These observations suggest that a so-far-unrecognized SP-1 site in the human IL-1beta promoter may participate in the transcriptional regulation of this gene in keratinocytes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 888, "end": 892}, "arguments": [{"role": "Theme", "text": "SP-1", "start": 841, "end": 845}]}], "positive regulation": [{"trigger": {"text": "transcriptional activation", "start": 157, "end": 183}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 206, "end": 214}]}, {"trigger": {"text": "participate", "start": 1461, "end": 1472}, "arguments": [{"role": "Theme", "text": "transcriptional regulation", "start": 1480, "end": 1506}]}], "regulation": [{"trigger": {"text": "transcriptional regulation", "start": 1480, "end": 1506}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1439, "end": 1447}, {"role": "Site", "text": "promoter", "start": 1448, "end": 1456}]}]}}, "schema": []}
{"input": "Engagement of the Lewis X antigen (CD15) results in monocyte activation. \nWe previously reported that monocyte adhesion to tumor necrosis factor-alpha (TNF-alpha)-treated endothelial cells increased expression of tissue factor and CD36 on monocytes. Using immunological cross-linking to mimic receptor engagement by natural ligands, we now show that CD15 (Lewis X), a monocyte counter-receptor for endothelial selectins may participate in this response. We used cytokine production as a readout for monocyte activation and found that CD15 cross-linking induced TNF-alpha release from peripheral blood monocytes and cells from the monocytic cell line MM6. Quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) showed an increase in steady-state TNF-alpha mRNA after 3 to 4 hours of cross-linking. CD15 cross-linking also concomitantly increased interleukin-1 beta (IL-1 beta) mRNA, while no apparent change was observed in the levels of beta-actin mRNA, indicating specificity. To examine transcriptional regulation of cytokine genes by CD15 engagement, a CAT plasmid reporter construct containing IL-1 beta promoter/enhancer sequences was introduced into MM6. Subsequent cross-linking of CD15 increased CAT activity. CD15 engagement by monoclonal antibody also attenuated IL-1 beta transcript degradation, demonstrating that signaling via CD15 also had posttranscriptional effects. Nuclear extracts of anti-CD15 cross-linked cells demonstrated enhanced levels of the transcriptional factor activator protein-1, minimally changed nuclear factor-kappa B, and did not affect SV40 promoter specific protein-1. We conclude that engagement of CD15 on monocytes results in monocyte activation. In addition to its well-recognized adhesive role, CD15 may function as an important signaling molecule capable of initiating proinflammatory events in monocytes that come into contact with activated endothelium. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 199, "end": 209}, "arguments": [{"role": "Theme", "text": "tissue factor", "start": 213, "end": 226}]}, {"trigger": {"text": "expression", "start": 199, "end": 209}, "arguments": [{"role": "Theme", "text": "CD36", "start": 231, "end": 235}]}], "localization": [{"trigger": {"text": "release", "start": 571, "end": 578}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 561, "end": 570}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 189, "end": 198}, "arguments": [{"role": "Theme", "text": "expression", "start": 199, "end": 209}]}, {"trigger": {"text": "induced", "start": 553, "end": 560}, "arguments": [{"role": "Theme", "text": "release", "start": 571, "end": 578}]}, {"trigger": {"text": "increase", "start": 735, "end": 743}, "arguments": [{"role": "Theme", "text": "mRNA", "start": 770, "end": 774}]}, {"trigger": {"text": "increased", "start": 850, "end": 859}, "arguments": [{"role": "Theme", "text": "mRNA", "start": 891, "end": 895}]}, {"trigger": {"text": "increased", "start": 1209, "end": 1218}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1219, "end": 1222}]}], "regulation": [{"trigger": {"text": "change", "start": 915, "end": 921}, "arguments": [{"role": "Theme", "text": "mRNA", "start": 963, "end": 967}]}, {"trigger": {"text": "affect", "start": 1581, "end": 1587}, "arguments": [{"role": "Theme", "text": "SV40 promoter specific protein-1", "start": 1588, "end": 1620}]}], "transcription": [{"trigger": {"text": "mRNA", "start": 770, "end": 774}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 760, "end": 769}]}, {"trigger": {"text": "mRNA", "start": 891, "end": 895}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 880, "end": 889}]}, {"trigger": {"text": "mRNA", "start": 963, "end": 967}, "arguments": [{"role": "Theme", "text": "beta-actin", "start": 952, "end": 962}]}]}}, "schema": []}
{"input": "Sequence analysis and expression in cultured lymphocytes of the human FOSB gene (G0S3). \nG0S3 is a member of a set of putative G0/G1 switch regulatory genes (G0S genes) selected by screening cDNA libraries prepared from human blood mononuclear cells cultured for 2 hr with lectin and cycloheximide. The sequence shows high homology with the murine FOSB gene, which encodes a component of the AP1 transcriptional regulator. Comparison of cDNA and genomic sequences reveals a 4-exon structure characteristic of the FOS family of genes. Freshly isolated cells show high levels of FOSB/G0S3 and FOS/G0S7 mRNAs, which decline rapidly during incubation in culture medium. The kinetics of expression suggest that the high initial levels are caused by the isolation procedure, and do not reflect constitutive expression. In cells preincubated for a day, levels of FOS mRNA reach a maximum 20 min after the addition of lectin and decline to control levels over the next 3 hr. Levels of FOSB mRNA reach a maximum 40 min after the addition of lectin and decline to control levels over the next 6 hr. In freshly isolated cells, both FOS and FOSB mRNAs increase dramatically in response to the protein synthesis inhibitor cycloheximide. In preincubated cells, the cycloheximide response is decreased, especially in the case of FOSB. These differences in expression of FOS and FOSB suggest different roles and regulation. Regions of low base order-dependent stem-loop potential in the region of the gene are defined. These indicate where base order has been adapted for purposes other than stem-loop stability (e.g., encoding proteins or gene regulation). Regions of low potential in a 68.5-kb genomic segment containing the FOSB gene suggest that the potential may help locate genes in uncharted DNA sequences. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 22, "end": 32}, "arguments": [{"role": "Theme", "text": "FOSB", "start": 70, "end": 74}]}, {"trigger": {"text": "selected", "start": 169, "end": 177}, "arguments": [{"role": "Theme", "text": "G0S3", "start": 89, "end": 93}]}, {"trigger": {"text": "expression", "start": 1341, "end": 1351}, "arguments": [{"role": "Theme", "text": "FOS", "start": 1355, "end": 1358}]}, {"trigger": {"text": "expression", "start": 1341, "end": 1351}, "arguments": [{"role": "Theme", "text": "FOSB", "start": 1363, "end": 1367}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 1277, "end": 1286}, "arguments": [{"role": "Theme", "text": "increase", "start": 1140, "end": 1148}]}], "positive regulation": [{"trigger": {"text": "reach a maximum", "start": 865, "end": 880}, "arguments": [{"role": "Theme", "text": "levels", "start": 846, "end": 852}]}, {"trigger": {"text": "reach a maximum", "start": 987, "end": 1002}, "arguments": [{"role": "Theme", "text": "Levels", "start": 967, "end": 973}]}, {"trigger": {"text": "increase", "start": 1140, "end": 1148}, "arguments": [{"role": "Theme", "text": "FOS", "start": 1121, "end": 1124}]}, {"trigger": {"text": "increase", "start": 1140, "end": 1148}, "arguments": [{"role": "Theme", "text": "FOSB", "start": 1129, "end": 1133}]}], "transcription": [{"trigger": {"text": "levels", "start": 567, "end": 573}, "arguments": [{"role": "Theme", "text": "FOSB", "start": 577, "end": 581}]}, {"trigger": {"text": "levels", "start": 567, "end": 573}, "arguments": [{"role": "Theme", "text": "FOS", "start": 591, "end": 594}]}, {"trigger": {"text": "levels", "start": 846, "end": 852}, "arguments": [{"role": "Theme", "text": "FOS", "start": 856, "end": 859}]}, {"trigger": {"text": "Levels", "start": 967, "end": 973}, "arguments": [{"role": "Theme", "text": "FOSB", "start": 977, "end": 981}]}]}}, "schema": []}
{"input": "V3 loop of human immunodeficiency virus type 1 suppresses interleukin 2-induced T cell growth [published erratum appears in AIDS Res Hum Retroviruses 1997 May 1;13(7):633] \nWe tested the effect of three linear or two loop peptides derived from the V3 region of the HTLV-III BH10 clone or the SF2 strain of human immunodeficiency virus type 1 on IL-2-driven T cell proliferation. V3-BH10, which consists of 42 amino acids and has a loop structure, suppressed IL-2-driven proliferation of all IL-2-dependent cells [Kit225, ED-40515(+), KT-3, 7-day PHA-blasts, and fresh peripheral blood mononuclear cells] tested, whereas it did not suppress the cell growth of IL-2-independent cell lines (Hut102, Molt-4, and Jurkat). This suppressive effect was also seen in IL-2-driven cell growth of CD8-positive lymphocytes purified from 7-day PHA-blasts, indicating that CD4 molecules were not required for the suppression. The treatment with anti-V3 loop monoclonal antibody (902 antibody) completely abolished the suppressive effect of V3-BH10. In addition, V3-BH10 generated the arrest of Kit225 cells and also purified CD8-positive lymphocytes in G1 phase in the presence of IL-2. Neither chromatin condensation nor DNA fragmentation was detected in Kit225 cells cultured with V3-BH10 and IL-2. V3-BH10 neither blocked radiolabeled IL-2 binding to IL-2 receptors nor affected tyrosyl phosphorylation of several cellular proteins (p120, p98, p96, p54, and p38), which is immediately induced by IL-2 stimulation. However, V3-BH10 enhanced IL-2-induced mRNA expression of c-fos but not c-myc or junB. Thus, the binding of V3 loop of gp120 to the cell surface molecule(s) appears to affect intracellular IL-2 signaling, which leads to the suppression of IL-2-induced T cell growth. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1328, "end": 1335}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1323, "end": 1327}]}, {"trigger": {"text": "binding", "start": 1599, "end": 1606}, "arguments": [{"role": "Site", "text": "V3 loop", "start": 1610, "end": 1617}, {"role": "Theme", "text": "gp120", "start": 1621, "end": 1626}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 1302, "end": 1309}, "arguments": [{"role": "Theme", "text": "binding", "start": 1328, "end": 1335}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1375, "end": 1390}, "arguments": [{"role": "Site", "text": "tyrosyl", "start": 1367, "end": 1374}, {"role": "Theme", "text": "p120", "start": 1421, "end": 1425}]}, {"trigger": {"text": "phosphorylation", "start": 1375, "end": 1390}, "arguments": [{"role": "Site", "text": "tyrosyl", "start": 1367, "end": 1374}, {"role": "Theme", "text": "p98", "start": 1427, "end": 1430}]}, {"trigger": {"text": "phosphorylation", "start": 1375, "end": 1390}, "arguments": [{"role": "Site", "text": "tyrosyl", "start": 1367, "end": 1374}, {"role": "Theme", "text": "p96", "start": 1432, "end": 1435}]}, {"trigger": {"text": "phosphorylation", "start": 1375, "end": 1390}, "arguments": [{"role": "Site", "text": "tyrosyl", "start": 1367, "end": 1374}, {"role": "Theme", "text": "p54", "start": 1437, "end": 1440}]}, {"trigger": {"text": "phosphorylation", "start": 1375, "end": 1390}, "arguments": [{"role": "Site", "text": "tyrosyl", "start": 1367, "end": 1374}, {"role": "Theme", "text": "p38", "start": 1446, "end": 1449}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1473, "end": 1480}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1375, "end": 1390}, {"role": "Cause", "text": "IL-2", "start": 1484, "end": 1488}]}, {"trigger": {"text": "enhanced", "start": 1519, "end": 1527}, "arguments": [{"role": "Theme", "text": "induced", "start": 1533, "end": 1540}]}, {"trigger": {"text": "induced", "start": 1533, "end": 1540}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1528, "end": 1532}, {"role": "Theme", "text": "mRNA expression", "start": 1541, "end": 1556}]}], "regulation": [{"trigger": {"text": "affected", "start": 1358, "end": 1366}, "arguments": [{"role": "Theme", "text": "induced", "start": 1473, "end": 1480}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 1541, "end": 1556}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1560, "end": 1565}]}, {"trigger": {"text": "mRNA expression", "start": 1541, "end": 1556}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 1574, "end": 1579}]}, {"trigger": {"text": "mRNA expression", "start": 1541, "end": 1556}, "arguments": [{"role": "Theme", "text": "junB", "start": 1583, "end": 1587}]}]}}, "schema": []}
{"input": "Nuclear factor-kappaB activation in human monocytes stimulated with lipopolysaccharide is inhibited by fibroblast conditioned medium and exogenous PGE2. \nThe nuclear factor kappaB (NF-kappaB) is thought to be crucially involved in the gene activation of several cytokines, including tumor necrosis factor alpha (TNF). Previously, we showed that fibroblast conditioned medium (FCM) is able to inhibit both TNF mRNA accumulation and protein release in peripheral blood-derived human monocytes (PBM) stimulated with lipopolysaccharide (LPS). In this study we have investigated the effect of FCM on the LPS-induced DNA-binding activity of NF-kappaB, by means of electrophoretic shift assay (EMSA). We provide evidence that FCM strongly inhibits the LPS-induced NF-kappaB activation in PBM. Furthermore, we show that exogenous PGE2 mimics the NF-kappaB inhibitory effect of FCM. On the other hand, FCM produced in the presence of indomethacin does not inhibit NF-kappaB activation by LPS. Our results lend further support to the hypothesis that inflammatory and immune responses of monocytes/macrophages may be modulated at the molecular level by signals originating from tissue structural cells such as fibroblasts. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "release", "start": 439, "end": 446}, "arguments": [{"role": "Theme", "text": "TNF", "start": 405, "end": 408}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 392, "end": 399}, "arguments": [{"role": "Theme", "text": "release", "start": 439, "end": 446}]}], "positive regulation": [{"trigger": {"text": "gene activation", "start": 235, "end": 250}, "arguments": [{"role": "Theme", "text": "TNF", "start": 312, "end": 315}]}]}}, "schema": []}
{"input": "Glycation-dependent, reactive oxygen species-mediated suppression of the insulin gene promoter activity in HIT cells. \nProlonged poor glycemic control in non-insulin-dependent diabetes mellitus patients often leads to a decline in insulin secretion from pancreatic beta cells, accompanied by a decrease in the insulin content of the cells. As a step toward elucidating the pathophysiological background of the so-called glucose toxicity to pancreatic beta cells, we induced glycation in HIT-T15 cells using a sugar with strong deoxidizing activity, D-ribose, and examined the effects on insulin gene transcription. The results of reporter gene analyses revealed that the insulin gene promoter is more sensitive to glycation than the control beta-actin gene promoter; approximately 50 and 80% of the insulin gene promoter activity was lost when the cells were kept for 3 d in the presence of 40 and 60 mM D-ribose, respectively. In agreement with this, decrease in the insulin mRNA and insulin content was observed in the glycation-induced cells. Also, gel mobility shift analyses using specific antiserum revealed decrease in the DNA-binding activity of an insulin gene transcription factor, PDX-1/IPF1/STF-1. These effects of D-ribose seemed almost irreversible but could be prevented by addition of 1 mM aminoguanidine or 10 mM N-acetylcysteine, thus suggesting that glycation and reactive oxygen species, generated through the glycation reaction, serve as mediators of the phenomena. These observations suggest that protein glycation in pancreatic beta cells, which occurs in vivo under chronic hyperglycemia, suppresses insulin gene transcription and thus can explain part of the beta cell glucose toxicity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activity", "start": 1134, "end": 1150}, "arguments": [{"role": "Theme", "text": "insulin", "start": 799, "end": 806}, {"role": "Site", "text": "promoter", "start": 812, "end": 820}, {"role": "Theme2", "text": "PDX-1", "start": 1192, "end": 1197}]}], "localization": [{"trigger": {"text": "secretion", "start": 239, "end": 248}, "arguments": [{"role": "Theme", "text": "insulin", "start": 231, "end": 238}]}], "negative regulation": [{"trigger": {"text": "decline", "start": 220, "end": 227}, "arguments": [{"role": "Theme", "text": "secretion", "start": 239, "end": 248}]}, {"trigger": {"text": "lost", "start": 834, "end": 838}, "arguments": [{"role": "Theme", "text": "insulin", "start": 799, "end": 806}, {"role": "Site", "text": "promoter", "start": 812, "end": 820}]}, {"trigger": {"text": "decrease", "start": 952, "end": 960}, "arguments": [{"role": "Theme", "text": "insulin", "start": 968, "end": 975}]}, {"trigger": {"text": "decrease", "start": 952, "end": 960}, "arguments": [{"role": "Theme", "text": "insulin", "start": 985, "end": 992}]}, {"trigger": {"text": "decrease", "start": 1114, "end": 1122}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 1134, "end": 1150}]}, {"trigger": {"text": "prevented", "start": 1276, "end": 1285}, "arguments": [{"role": "Theme", "text": "decrease", "start": 1114, "end": 1122}]}, {"trigger": {"text": "prevented", "start": 1276, "end": 1285}, "arguments": [{"role": "Theme", "text": "lost", "start": 834, "end": 838}]}, {"trigger": {"text": "prevented", "start": 1276, "end": 1285}, "arguments": [{"role": "Theme", "text": "decrease", "start": 952, "end": 960}]}, {"trigger": {"text": "suppresses", "start": 1613, "end": 1623}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1637, "end": 1650}]}], "positive regulation": [{"trigger": {"text": "serve as mediators", "start": 1450, "end": 1468}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 1134, "end": 1150}]}], "regulation": [{"trigger": {"text": "effects", "start": 576, "end": 583}, "arguments": [{"role": "Theme", "text": "transcription", "start": 600, "end": 613}]}], "transcription": [{"trigger": {"text": "transcription", "start": 600, "end": 613}, "arguments": [{"role": "Theme", "text": "insulin", "start": 587, "end": 594}]}, {"trigger": {"text": "transcription", "start": 1637, "end": 1650}, "arguments": [{"role": "Theme", "text": "insulin", "start": 1624, "end": 1631}]}]}}, "schema": []}
{"input": "Differential interaction of nuclear factors with the PRE-I enhancer element of the human IL-4 promoter in different T cell subsets. \nThe immunomodulatory cytokine IL-4 affects cells of most hemopoietic lineages. IL-4 is secreted by activated Th2 but not Th1 cells and plays a major role in the immune response by modulating the differentiation of naive Th cells toward the Th2 phenotype. We have previously identified an enhancer element, PRE-I, that is essential for the function of the human IL-4 promoter. To investigate the mechanisms responsible for tissue-specific expression of the IL-4 gene, we analyzed nuclear factors binding to the PRE-I site and compared the binding activities of these factors to the IL-4 promoter of Th1 and Th2 cells. We show that PRE-I interacts with PMA- and PMA/ionomycin-inducible, cyclosporin A-sensitive nuclear factors. Using anti-C/EBPbeta (NF-IL6), anti-C/EBPdelta (NF-IL6beta), anti-NF-ATc, anti-NF-ATp, anti-Fos, and anti-Jun Abs we demonstrate that the previously identified PRE-I binding factor POS-1 is composed of different transcription factors in different Th cell subsets. In the IL-4-producing Th0-like human Jurkat and mouse EL-4 cells, POS-1 (designated POS-1a) contains NF-IL6beta and Jun. In the mouse Th2 D10 cells and in the human Th2 clones, POS-1 (designated POS-1b) contains NF-IL6beta, Jun, and NF-ATc/p. In contrast, POS-1 was not found in nuclear extracts of human Th1 clones. These findings suggest that PRE-I may play a role in the differential regulation of IL-4 gene expression levels. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 671, "end": 678}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 714, "end": 718}]}], "gene expression": [{"trigger": {"text": "expression", "start": 571, "end": 581}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 589, "end": 593}]}, {"trigger": {"text": "producing", "start": 1135, "end": 1144}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1130, "end": 1134}]}, {"trigger": {"text": "expression", "start": 1534, "end": 1544}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1524, "end": 1528}]}], "localization": [{"trigger": {"text": "secreted", "start": 220, "end": 228}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 212, "end": 216}]}], "regulation": [{"trigger": {"text": "responsible", "start": 539, "end": 550}, "arguments": [{"role": "Theme", "text": "expression", "start": 571, "end": 581}]}, {"trigger": {"text": "role", "start": 1485, "end": 1489}, "arguments": [{"role": "Theme", "text": "regulation", "start": 1510, "end": 1520}]}, {"trigger": {"text": "regulation", "start": 1510, "end": 1520}, "arguments": [{"role": "Theme", "text": "expression", "start": 1534, "end": 1544}]}]}}, "schema": []}
{"input": "Inhibitory effect of growth hormone on TNF-alpha secretion and nuclear factor-kappaB translocation in lipopolysaccharide-stimulated human monocytes. \nSeveral studies have pointed to a link between immune and endocrine systems, including a regulatory function of GH on monocyte activation. The present study demonstrates that human THP-1 promonocytic cells, engineered by gene transfer to constitutively produce human growth hormone (hGH), secreted depressed amounts of TNF-alpha in response to challenge by LPS. The effect of GH appears to occur in an autocrine fashion, since the inhibitory effect on TNF-alpha secretion by constitutive GH production could be abolished in the presence of anti-hGH mAb. The GH-induced inhibitory effect was also observed using normal human monocytes and monocyte-derived macrophages. Inhibition of TNF-alpha production by THP-1-hGH-transfected cells cultured in the presence of LPS is dependent on a selective pathway, since no inhibition of TNF-alpha production was observed when cells were cultured in the presence of PMA. Inhibition of TNF-alpha secretion by LPS-stimulated THP-1-hGH cells was associated with a decrease in nuclear translocation of nuclear factor-kappaB. The capacity of GH to inhibit LPS-induced TNF-alpha production by monocytes without altering other pathways leading to TNF-alpha production may be of potential relevance in septic shock, since GH is available for clinical use. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 842, "end": 852}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 832, "end": 841}]}, {"trigger": {"text": "production", "start": 986, "end": 996}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 976, "end": 985}]}, {"trigger": {"text": "production", "start": 1261, "end": 1271}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1251, "end": 1260}]}, {"trigger": {"text": "production", "start": 1338, "end": 1348}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1328, "end": 1337}]}], "localization": [{"trigger": {"text": "secretion", "start": 49, "end": 58}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 39, "end": 48}]}, {"trigger": {"text": "secreted", "start": 439, "end": 447}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 469, "end": 478}]}, {"trigger": {"text": "secretion", "start": 612, "end": 621}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 602, "end": 611}]}, {"trigger": {"text": "secretion", "start": 1083, "end": 1092}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1073, "end": 1082}]}], "negative regulation": [{"trigger": {"text": "Inhibitory effect", "start": 0, "end": 17}, "arguments": [{"role": "Theme", "text": "secretion", "start": 49, "end": 58}]}, {"trigger": {"text": "depressed amounts", "start": 448, "end": 465}, "arguments": [{"role": "Theme", "text": "in response", "start": 479, "end": 490}]}, {"trigger": {"text": "inhibitory effect", "start": 581, "end": 598}, "arguments": [{"role": "Theme", "text": "secretion", "start": 612, "end": 621}]}, {"trigger": {"text": "abolished", "start": 661, "end": 670}, "arguments": [{"role": "Theme", "text": "inhibitory effect", "start": 581, "end": 598}]}, {"trigger": {"text": "inhibitory effect", "start": 719, "end": 736}, "arguments": [{"role": "Theme", "text": "secretion", "start": 612, "end": 621}]}, {"trigger": {"text": "Inhibition", "start": 818, "end": 828}, "arguments": [{"role": "Theme", "text": "production", "start": 842, "end": 852}]}, {"trigger": {"text": "inhibition", "start": 962, "end": 972}, "arguments": [{"role": "Theme", "text": "production", "start": 986, "end": 996}]}, {"trigger": {"text": "Inhibition", "start": 1059, "end": 1069}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1083, "end": 1092}]}, {"trigger": {"text": "to inhibit", "start": 1228, "end": 1238}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1251, "end": 1260}]}], "positive regulation": [{"trigger": {"text": "in response", "start": 479, "end": 490}, "arguments": [{"role": "Theme", "text": "secreted", "start": 439, "end": 447}]}, {"trigger": {"text": "induced", "start": 1243, "end": 1250}, "arguments": [{"role": "Theme", "text": "production", "start": 1261, "end": 1271}]}, {"trigger": {"text": "leading", "start": 1317, "end": 1324}, "arguments": [{"role": "Theme", "text": "production", "start": 1338, "end": 1348}]}], "regulation": [{"trigger": {"text": "dependent", "start": 919, "end": 928}, "arguments": [{"role": "Theme", "text": "Inhibition", "start": 818, "end": 828}]}]}}, "schema": []}
{"input": "Impaired induction of c-fos/c-jun genes and of transcriptional regulatory proteins binding distinct c-fos/c-jun promoter elements in activated human T cells during aging. \nThe activation of transcriptional factor c-Fos/c-Jun AP-1 is essential for normal T cell responsiveness and is often impaired in T cells during aging. In the present study, we investigated whether aberrancies in the regulation of c-fos/c-jun at the mRNA or protein level might underlie the age-associated impairments of AP-1 in human T cells. Whereas T cells from young subjects stimulated with cross-linked anti-CD3epsilon mAb OKT3 plus PMA or with the lectin PHA plus PMA demonstrated considerable increases in c-Fos protein expression, the expression of c-Fos but not c-Jun was markedly reduced in stimulated T cells from certain elderly subjects. In addition, RNase protection assays revealed that anti-CD3/PMA-stimulated T cells from a substantial proportion of elderly subjects exhibited decreased levels of c-fos and/or c-jun mRNA compared to T cells from young subjects. Using electrophoretic mobility shift assays, the levels of nuclear regulatory proteins recognizing the AP-1 consensus TRE motif, the proximal c-jun TRE-like promoter element, and the c-fos serum response element (SRE) were determined in resting and stimulated T cells. Although the stimulation of T cells from young subjects resulted in coordinated increases of nuclear protein complexes binding the AP-1 TRE, c-jun TRE, and c-fos SRE DNA sequence motifs, age-related reductions in the activation of AP-1 were accompanied by decreased levels of c-jun TRE and c-fos SRE binding complexes. Furthermore, the nuclear protein complexes binding the SRE motif induced in activated T cells of young and elderly subjects contained serum response factor and Elk-1 pointing toward age-related defects in the activation of transcriptional regulatory proteins distinct from c-jun/AP-1. These results suggest that underlying aberrancies in the induction of c-fos/c-jun as well as their nuclear regulatory proteins may contribute to the age-related impairments of AP-1 activation in human T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 83, "end": 90}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 100, "end": 105}, {"role": "Site", "text": "promoter", "start": 112, "end": 120}]}, {"trigger": {"text": "binding", "start": 83, "end": 90}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 106, "end": 111}, {"role": "Site", "text": "promoter", "start": 112, "end": 120}]}, {"trigger": {"text": "cross-linked", "start": 567, "end": 579}, "arguments": [{"role": "Theme", "text": "CD3epsilon", "start": 585, "end": 595}]}, {"trigger": {"text": "binding", "start": 1439, "end": 1446}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1461, "end": 1466}, {"role": "Site", "text": "DNA sequence motifs", "start": 1486, "end": 1505}]}, {"trigger": {"text": "binding", "start": 1439, "end": 1446}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1476, "end": 1481}, {"role": "Site", "text": "DNA sequence motifs", "start": 1486, "end": 1505}]}], "gene expression": [{"trigger": {"text": "expression", "start": 699, "end": 709}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 685, "end": 690}]}, {"trigger": {"text": "expression", "start": 715, "end": 725}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 729, "end": 734}]}, {"trigger": {"text": "expression", "start": 715, "end": 725}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 743, "end": 748}]}, {"trigger": {"text": "levels", "start": 1100, "end": 1106}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1234, "end": 1239}]}], "negative regulation": [{"trigger": {"text": "Impaired", "start": 0, "end": 8}, "arguments": [{"role": "Theme", "text": "induction", "start": 9, "end": 18}]}, {"trigger": {"text": "impaired", "start": 289, "end": 297}, "arguments": [{"role": "Theme", "text": "activation", "start": 176, "end": 186}]}, {"trigger": {"text": "reduced", "start": 762, "end": 769}, "arguments": [{"role": "Theme", "text": "expression", "start": 715, "end": 725}]}, {"trigger": {"text": "decreased", "start": 966, "end": 975}, "arguments": [{"role": "Theme", "text": "levels", "start": 976, "end": 982}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 9, "end": 18}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 22, "end": 27}]}, {"trigger": {"text": "induction", "start": 9, "end": 18}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 28, "end": 33}]}, {"trigger": {"text": "activation", "start": 176, "end": 186}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 213, "end": 218}]}, {"trigger": {"text": "activation", "start": 176, "end": 186}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 219, "end": 224}]}, {"trigger": {"text": "increases", "start": 672, "end": 681}, "arguments": [{"role": "Theme", "text": "expression", "start": 699, "end": 709}]}, {"trigger": {"text": "increases", "start": 1400, "end": 1409}, "arguments": [{"role": "Theme", "text": "binding", "start": 1439, "end": 1446}]}, {"trigger": {"text": "induced", "start": 1704, "end": 1711}, "arguments": [{"role": "Theme", "text": "binding", "start": 1439, "end": 1446}]}, {"trigger": {"text": "induction", "start": 1981, "end": 1990}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1994, "end": 1999}]}, {"trigger": {"text": "induction", "start": 1981, "end": 1990}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 2000, "end": 2005}]}], "regulation": [{"trigger": {"text": "aberrancies in the regulation", "start": 369, "end": 398}, "arguments": [{"role": "Theme", "text": "mRNA", "start": 421, "end": 425}]}, {"trigger": {"text": "aberrancies", "start": 1962, "end": 1973}, "arguments": [{"role": "Theme", "text": "induction", "start": 1981, "end": 1990}]}], "transcription": [{"trigger": {"text": "mRNA", "start": 421, "end": 425}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 402, "end": 407}]}, {"trigger": {"text": "mRNA", "start": 421, "end": 425}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 408, "end": 413}]}, {"trigger": {"text": "levels", "start": 976, "end": 982}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 986, "end": 991}]}, {"trigger": {"text": "levels", "start": 976, "end": 982}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 999, "end": 1004}]}]}}, "schema": []}
{"input": "Interaction of transcription factors RFX1 and MIBP1 with the gamma motif of the negative regulatory element of the hepatitis B virus core promoter. \nThe negative regulatory element (NRE) of the hepatitis B virus (HBV) core promoter contains three subregions which act synergistically to suppress core promoter activity. One of these subregions, NRE gamma, is active in both HeLa cervical carcinoma cells and Huh7 hepatoma cells and was found to be bound by a protein factor present in both cell types. Here we show that the transcription factor RFX1 can bind to NRE gamma and transactivate the core promoter through this site. Mutations which abrogated the gene-suppressive activity of NRE gamma prevented RFX1 from binding to NRE gamma. In addition, RFX1 can bind simultaneously, most likely as a heterodimer, with the transcription factor MIBP1 to NRE gamma. In the absence of a cloned MIBP1 gene for further studies, we hypothesize that RFX1 acts with MIBP1 to negatively regulate the core promoter activity through the NRE gamma site. The ability of RFX1 to transactivate the core promoter raises the possibility that RFX1 may play a dual role in regulating HBV gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Interaction", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "RFX1", "start": 37, "end": 41}]}, {"trigger": {"text": "Interaction", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "MIBP1", "start": 46, "end": 51}]}, {"trigger": {"text": "bind", "start": 554, "end": 558}, "arguments": [{"role": "Theme", "text": "RFX1", "start": 545, "end": 549}]}, {"trigger": {"text": "binding", "start": 716, "end": 723}, "arguments": [{"role": "Theme", "text": "RFX1", "start": 706, "end": 710}]}, {"trigger": {"text": "bind", "start": 760, "end": 764}, "arguments": [{"role": "Theme", "text": "RFX1", "start": 751, "end": 755}]}, {"trigger": {"text": "heterodimer", "start": 798, "end": 809}, "arguments": [{"role": "Theme", "text": "RFX1", "start": 751, "end": 755}, {"role": "Theme2", "text": "MIBP1", "start": 841, "end": 846}]}], "negative regulation": [{"trigger": {"text": "prevented", "start": 696, "end": 705}, "arguments": [{"role": "Theme", "text": "binding", "start": 716, "end": 723}]}]}}, "schema": []}
{"input": "Differentiation-dependent expression of a human carboxylesterase in monocytic cells and transcription factor binding to the promoter. \nCarboxylesterases play an important role in defense and clearance mechanisms of the monocyte/macrophage system. During the differentiation process of cells from the monocytic cell line THP-1 we observed a transient transcriptional upregulation of a human carboxylesterase analyzed by means of Northern blots. In PMA-treated THP-1 cells we could detect three major transcription initiation sites as revealed by Nuclease Protection Assay carried out with two overlapping antisense RNA probes. We have recently cloned the carboxylesterase upstream sequence and showed its basal promoter activity in CHO cells. Using electrophoretic mobility shift analysis we demonstrated that the promoter region spanning base pairs -1 to -275, which contains several putative binding sites for transcription factors, is bound by nuclear factors Sp1 and IRBP but not by C/EBPs. Taken together these data indicate that carboxylesterase gene transcription in THP-1 cells starts at multiple initiation sites and that Sp1 and IRBP may be critical factors for modulating the differentiation-dependent transcription of this human carboxylesterase gene. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 937, "end": 942}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 962, "end": 965}]}, {"trigger": {"text": "bound", "start": 937, "end": 942}, "arguments": [{"role": "Theme", "text": "IRBP", "start": 970, "end": 974}]}]}}, "schema": []}
{"input": "Characterization of the human platelet/endothelial cell adhesion molecule-1 promoter: identification of a GATA-2 binding element required for optimal transcriptional activity. \nPlatelet/endothelial cell adhesion molecule-1 (PECAM-1) is a 130-kD member of the Ig gene superfamily that is expressed on platelets, endothelial cells, and certain leukocyte subsets. To examine the factors controlling vascular-specific expression of PECAM-1, we cloned the 5'-flanking region of the PECAM-1 gene and analyzed its transcriptional activity. 5'-Rapid amplification of cDNA ends (5'-RACE) analysis showed that transcription initiation occurred at several closely spaced nearby sites originating approximately 204 bp upstream from the translation start site. Analysis of the sequence immediately upstream from the transcription initiation site (TIS) showed no canonical TATA or CAAT elements, however an initiator element commonly found in TATA-less promoters encompassed the TIS. 5'-serially truncated PECAM-1 promoter segments cloned in front of a luciferase reporter drove transcription in both a lineage- and orientation-specific manner. Putative cis-acting control elements present within a 300-bp core promoter included two ets sites, an Sp1 site, tandem E-box domains, two GATA-associated sites (CACCC), an AP-2 binding site, and a GATA element at -24. Mutational analysis showed that optimal transcriptional activity required the GATA sequence at position -24, and gel-shift assays further showed that the GATA-2 transcription factor, but not GATA-1, bound to this region of the PECAM-1 promoter. Understanding the cis- and transacting factors that regulate the tissue-specific expression of PECAM-1 should increase our understanding of the mechanisms by which vascular-specific gene expression is achieved. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 1548, "end": 1553}, "arguments": [{"role": "Theme", "text": "GATA-2", "start": 1503, "end": 1509}]}, {"trigger": {"text": "bound", "start": 1548, "end": 1553}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1540, "end": 1546}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 287, "end": 296}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 224, "end": 231}]}, {"trigger": {"text": "expression", "start": 414, "end": 424}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 428, "end": 435}]}, {"trigger": {"text": "expression", "start": 1675, "end": 1685}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 1689, "end": 1696}]}], "regulation": [{"trigger": {"text": "controlling", "start": 384, "end": 395}, "arguments": [{"role": "Theme", "text": "expression", "start": 414, "end": 424}]}, {"trigger": {"text": "regulate", "start": 1646, "end": 1654}, "arguments": [{"role": "Theme", "text": "expression", "start": 1675, "end": 1685}]}]}}, "schema": []}
{"input": "Expression of erythroid-specific genes in megakaryoblastic disorders. \nCurrently available data indicate that erythroid and megakaryocytic differentiation pathways are closely related to each other, and there may exist progenitor cells common to those two lineages may exist. Acute megakaryoblastic leukemia (AML-M7) and transient myeloproliferative disorder in Down's syndrome (TMD) are characterized by rapid growth of abnormal blast cells which express megakaryocytic markers. These blast cells express lineage-specific transcription factors such as GATA-1 common to these lineages and frequently express erythroid-specific mRNAs such as gamma-globin and erythroid delta-aminolevulinate synthase (ALAS-E), indicating that most of the blasts in M7 and TMD cases have erythroid and megakaryocytic phenotypes. These results suggest that blasts in M7 and TMD may correspond to progenitors of both erythroid and megakaryocytic lineages. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "express", "start": 498, "end": 505}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 553, "end": 559}]}], "transcription": [{"trigger": {"text": "express", "start": 600, "end": 607}, "arguments": [{"role": "Theme", "text": "ALAS-E", "start": 700, "end": 706}]}]}}, "schema": []}
{"input": "Cloning of the novel human myeloid-cell-specific C/EBP-epsilon transcription factor. \nChicken NF-M transcription factor, in cooperation with either c-Myb or v-Myb, is active in the combinatorial activation of myeloid-cell-specific genes in heterologous cell types, such as embryonic fibroblasts. In humans, similar effects were observed with homologous members of the CCAAT/enhancer-binding protein (C/EBP) family of transcriptional regulators, especially the human homolog of chicken NF-M, C/EBP-beta (NF-IL6). However, the NF-IL6 gene is expressed in a variety of nonmyeloid cell types and is strongly inducible in response to inflammatory stimuli, making it an unlikely candidate to have an exclusive role as a combinatorial differentiation switch during myelopoiesis in human cells. By using a reverse transcription-PCR-based approach and a set of primers specific for the DNA-binding domains of highly homologous members of the C/EBP family of transcriptional regulators, we have cloned a novel human gene encoding a member of the C/EBP gene family, identified as the human homolog of CRP1, C/EBP-epsilon. A 1.2-kb cDNA encoding full-length human C/EBP-epsilon was cloned from a promyelocyte-late myeloblast-derived lambda gt11 library. Molecular analysis of the cDNA and genomic clones indicated the presence of two exons encoding a protein with an apparent molecular mass of 32 kDa and a pI of 9.5. Primer extension analysis of C/EBP-epsilon mRNA detected a single major transcription start site approximately 200 bp upstream of the start codon. The putative promoter area is similar to those of several other myeloid-cell-specific genes in that it contains no TATAAA box but has a number of purine-rich stretches with multiple sites for the factors of the Ets family of transcriptional regulators. Northern blot analyses indicated a highly restricted mRNA expression pattern, with the strongest expression occurring in promyelocyte and late-myeloblast-like cell lines. Western blot and immunoprecipitation studies using rabbit anti-C/EBP-epsilon antibodies raised against the N-terminal portion of C/EBP-epsilon (amino acids 1 to 115) showed that C/EBP-epsilon is a 32-kDa nuclear phosphoprotein. The human C/EBP-epsilon protein exhibited strong and specific binding to double-stranded DNA containing consensus C/EBP sites. Cotransfection of the C/EBP-epsilon sense and antisense expression constructs together with chloramphenicol acetyltransferase reporter vectors containing myeloid-cell-specific c-mim and human myeloperoxidase promoters suggested a role for C/EBP-epsilon transcription factor in the regulation of a subset of myeloid-cell-specific genes. Transient tranfection of a promyelocyte cell line (NB4) with a C/EBP-epsilon expression plasmid increased cell growth by sevenfold, while antisense C/EBP-epsilon caused a fivefold decrease in clonal growth of these cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 2267, "end": 2274}, "arguments": [{"role": "Theme", "text": "C/EBP-epsilon", "start": 2215, "end": 2228}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 540, "end": 549}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 525, "end": 531}]}, {"trigger": {"text": "tranfection", "start": 2678, "end": 2689}, "arguments": [{"role": "Theme", "text": "C/EBP-epsilon", "start": 2731, "end": 2744}]}, {"trigger": {"text": "antisense", "start": 2806, "end": 2815}, "arguments": [{"role": "Theme", "text": "C/EBP-epsilon", "start": 2816, "end": 2829}]}], "negative regulation": [{"trigger": {"text": "antisense", "start": 2806, "end": 2815}, "arguments": [{"role": "Theme", "text": "C/EBP-epsilon", "start": 2816, "end": 2829}]}], "positive regulation": [{"trigger": {"text": "inducible", "start": 604, "end": 613}, "arguments": [{"role": "Theme", "text": "expressed", "start": 540, "end": 549}]}, {"trigger": {"text": "strongest", "start": 1893, "end": 1902}, "arguments": [{"role": "Theme", "text": "expression", "start": 1864, "end": 1874}]}, {"trigger": {"text": "tranfection", "start": 2678, "end": 2689}, "arguments": [{"role": "Theme", "text": "tranfection", "start": 2678, "end": 2689}]}], "transcription": [{"trigger": {"text": "expression", "start": 1864, "end": 1874}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 525, "end": 531}]}]}}, "schema": []}
{"input": "Transcriptional regulation of the ferritin heavy-chain gene: the activity of the CCAAT binding factor NF-Y is modulated in heme-treated Friend leukemia cells and during monocyte-to-macrophage differentiation. \nThe ferritin H-chain gene promoter regulation was analyzed in heme-treated Friend leukemia cells (FLCs) and during monocyte-to-macrophage differentiation. In the majority of cell lines studied, the regulation of ferritin expression was exerted mostly at the translational level. However, in differentiating erythroid cells, which must incorporate high levels of iron to sustain hemoglobin synthesis, and in macrophages, which are involved in iron storage, transcriptional regulation seemed to be a relevant mechanism. We show here that the minimum region of the ferritin H-gene promoter that is able to confer transcriptional regulation by heme in FLCs to a reporter gene is 77 nucleotides upstream of the TATA box. This cis element binds a protein complex referred to as HRF (heme-responsive factor), which is greatly enhanced both in heme-treated FLCs and during monocyte-to-macrophage differentiation. The CCAAT element present in reverse orientation in this promoter region of the ferritin H-chain gene is necessary for binding and for gene activity, since a single point mutation is able to abolish the binding of HRF and the transcriptional activity in transfected cells. By competition experiments and supershift assays, we identified the induced HRF as containing at least the ubiquitous transcription factor NF-Y. NF-Y is formed by three subunits, A, B, and C, all of which are necessary for DNA binding. Cotransfection with a transdominant negative mutant of the NF-YA subunit abolishes the transcriptional activation by heme, indicating that NF-Y plays an essential role in this activation. We have also observed a differential expression of the NF-YA subunit in heme-treated and control FLCs and during monocyte-to-macrophage differentiation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1234, "end": 1241}, "arguments": [{"role": "Theme", "text": "ferritin H-chain", "start": 1195, "end": 1211}]}, {"trigger": {"text": "binding", "start": 1318, "end": 1325}, "arguments": [{"role": "Theme", "text": "ferritin H-chain", "start": 1195, "end": 1211}]}], "negative regulation": [{"trigger": {"text": "abolish", "start": 1306, "end": 1313}, "arguments": [{"role": "Theme", "text": "binding", "start": 1318, "end": 1325}]}, {"trigger": {"text": "abolishes", "start": 1697, "end": 1706}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 1711, "end": 1737}]}], "positive regulation": [{"trigger": {"text": "necessary", "start": 1220, "end": 1229}, "arguments": [{"role": "Theme", "text": "ferritin H-chain", "start": 1195, "end": 1211}]}, {"trigger": {"text": "necessary", "start": 1220, "end": 1229}, "arguments": [{"role": "Theme", "text": "binding", "start": 1234, "end": 1241}]}, {"trigger": {"text": "transcriptional activation", "start": 1711, "end": 1737}, "arguments": [{"role": "Theme", "text": "ferritin H-chain", "start": 1195, "end": 1211}]}, {"trigger": {"text": "role", "start": 1787, "end": 1791}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 1711, "end": 1737}]}], "regulation": [{"trigger": {"text": "regulation", "start": 245, "end": 255}, "arguments": [{"role": "Theme", "text": "ferritin H-chain", "start": 214, "end": 230}, {"role": "Site", "text": "promoter", "start": 236, "end": 244}]}]}}, "schema": []}
{"input": "Characterization of a mutant cell line that does not activate NF-kappaB in response to multiple stimuli. \nNumerous genes required during the immune or inflammation response as well as the adhesion process are regulated by nuclear factor kappaB (NF-kappaB). Associated with its inhibitor, I kappaB, NF-kappaB resides as an inactive form in the cytoplasm. Upon stimulation by various agents, I kappaB is proteolyzed and NF-kappaB translocates to the nucleus, where it activates its target genes. The transduction pathways that lead to I kappaB inactivation remain poorly understood. In this study, we have characterized a cellular mutant, the 70/Z3-derived 1.3E2 murine pre-B cell line, that does not activate NF-kappaB in response to several stimuli. We demonstrate that upon stimulation by lipopolysaccharide, Taxol, phorbol myristate acetate, interleukin-1, or double-stranded RNA, I kappaB alpha is not degraded, as a result of an absence of induced phosphorylation on serines 32 and 36. Neither a mutation in I kappaB alpha nor a mutation in p50 or relA, the two major subunits of NF-kappaB in this cell line, accounts for this phosphorylation defect. As well as culminating in the inducible phosphorylation of I kappaB alpha on serines 32 and 36, all the stimuli that are inactive on 1.3E2 cells exhibit a sensitivity to the antioxidant pyrrolidine dithiocarbamate (PDTC). In contrast, stimuli such as hyperosmotic shock or phosphatase inhibitors, which use PDTC-insensitive pathways, induce I kappaB alpha degradation in 1.3E2. Analysis of the redox status of 1.3E2 does not reveal any difference from wild-type 70Z/3. We also report that the human T-cell leukemia virus type 1 (HTLV-1)-derived Tax trans-activator induces NF-kappaB activity in 1.3E2, suggesting that this viral protein does not operate via the defective pathway. Finally, we show that two other I kappaB molecules, I kappaB beta and the recently identified I kappaB epsilon, are not degraded in the 1.3E2 cell line following stimulation. Our results demonstrate that 1.3E2 is a cellular transduction mutant exhibiting a defect in a step that is required by several different stimuli to activate NF-kappaB. In addition, this analysis suggests a common step in the signaling pathways that trigger I kappaB alpha, I kappaB beta, and I kappaB epsilon degradation. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "absence", "start": 933, "end": 940}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 952, "end": 967}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 952, "end": 967}, "arguments": [{"role": "Theme", "text": "I kappaB alpha", "start": 883, "end": 897}, {"role": "Site", "text": "serines 32 and 36", "start": 971, "end": 988}]}, {"trigger": {"text": "phosphorylation", "start": 1195, "end": 1210}, "arguments": [{"role": "Theme", "text": "I kappaB alpha", "start": 1214, "end": 1228}]}], "positive regulation": [{"trigger": {"text": "result", "start": 920, "end": 926}, "arguments": [{"role": "Theme", "text": "degraded", "start": 905, "end": 913}, {"role": "Cause", "text": "absence", "start": 933, "end": 940}]}, {"trigger": {"text": "accounts for", "start": 1113, "end": 1125}, "arguments": [{"role": "Theme", "text": "absence", "start": 933, "end": 940}]}, {"trigger": {"text": "culminating", "start": 1166, "end": 1177}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1195, "end": 1210}]}, {"trigger": {"text": "induce", "start": 1489, "end": 1495}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1511, "end": 1522}]}, {"trigger": {"text": "following", "start": 1988, "end": 1997}, "arguments": [{"role": "Theme", "text": "degraded", "start": 1956, "end": 1964}]}, {"trigger": {"text": "trigger", "start": 2260, "end": 2267}, "arguments": [{"role": "Theme", "text": "degradation", "start": 2320, "end": 2331}]}], "protein catabolism": [{"trigger": {"text": "degraded", "start": 905, "end": 913}, "arguments": [{"role": "Theme", "text": "I kappaB alpha", "start": 883, "end": 897}]}, {"trigger": {"text": "degradation", "start": 1511, "end": 1522}, "arguments": [{"role": "Theme", "text": "I kappaB alpha", "start": 1496, "end": 1510}]}, {"trigger": {"text": "degraded", "start": 1956, "end": 1964}, "arguments": [{"role": "Theme", "text": "I kappaB beta", "start": 1888, "end": 1901}]}, {"trigger": {"text": "degraded", "start": 1956, "end": 1964}, "arguments": [{"role": "Theme", "text": "I kappaB epsilon", "start": 1930, "end": 1946}]}, {"trigger": {"text": "degradation", "start": 2320, "end": 2331}, "arguments": [{"role": "Theme", "text": "I kappaB alpha", "start": 2268, "end": 2282}]}, {"trigger": {"text": "degradation", "start": 2320, "end": 2331}, "arguments": [{"role": "Theme", "text": "I kappaB beta", "start": 2284, "end": 2297}]}, {"trigger": {"text": "degradation", "start": 2320, "end": 2331}, "arguments": [{"role": "Theme", "text": "I kappaB epsilon", "start": 2303, "end": 2319}]}], "regulation": [{"trigger": {"text": "operate", "start": 1801, "end": 1808}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 952, "end": 967}, {"role": "Cause", "text": "Tax", "start": 1700, "end": 1703}]}]}}, "schema": []}
{"input": "Transcription mediated by NFAT is highly inducible in effector CD4+ T helper 2 (Th2) cells but not in Th1 cells. \nTranscriptional factors of the NFAT family play an important role in regulating the expression of several cytokine genes during the immune response, such as the genes for interleukin 2 (IL-2) and IL-4, among others. Upon antigen stimulation, precursor CD4+ T helper (pTh) cells proliferate and differentiate into two populations of effector cells (eTh1 and eTh2), each one expressing a specific pattern of cytokines that distinguishes them from their precursors. eTh2 cells are the major source of IL-4, while gamma interferon is produced by eTh1 cells. Here we have used reporter transgenic mice to show that DNA binding and transcriptional activities of NFAT are transiently induced during the differentiation of pTh cells into either eTh1 or eTh2 cells to mediate the expression of IL-2 as a common growth factor in both pathways. However, although NFAT DNA binding is similarly induced in both eTh1 and eTh2 cells upon antigen stimulation, only the NFAT complexes present in eTh2 cells are able to mediate high-level transcription, and relatively little NFAT transcriptional activity was induced in eTh1 cells. In contrast to activated pTh cells, neither eTh1 nor eTh2 cells produced significant IL-2 upon stimulation, but the high levels of NFAT transcriptional activities directly correlate with the IL-4 production induced in response to antigen stimulation in eTh2 cells. These data suggest that activated NFAT is involved in the effector function of eTh2 cells and that the failure of eTh1 cells to produce IL-4 in response to an antigen is due, at least partially, to a failure to induce high-level transcription of the IL-4 gene by NFAT. Regulation of NFAT could be therefore a critical element in the polarization to eTh1 or eTh2. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 198, "end": 208}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 300, "end": 304}]}, {"trigger": {"text": "expression", "start": 198, "end": 208}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 310, "end": 314}]}, {"trigger": {"text": "source", "start": 602, "end": 608}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 612, "end": 616}]}, {"trigger": {"text": "produced", "start": 644, "end": 652}, "arguments": [{"role": "Theme", "text": "gamma interferon", "start": 624, "end": 640}]}, {"trigger": {"text": "expression", "start": 885, "end": 895}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 899, "end": 903}]}, {"trigger": {"text": "produced", "start": 1293, "end": 1301}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1314, "end": 1318}]}, {"trigger": {"text": "production", "start": 1425, "end": 1435}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1420, "end": 1424}]}, {"trigger": {"text": "produce", "start": 1622, "end": 1629}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1630, "end": 1634}]}], "negative regulation": [{"trigger": {"text": "failure", "start": 1597, "end": 1604}, "arguments": [{"role": "Theme", "text": "in response to", "start": 1635, "end": 1649}]}, {"trigger": {"text": "failure", "start": 1694, "end": 1701}, "arguments": [{"role": "Cause", "text": "failure", "start": 1597, "end": 1604}, {"role": "Theme", "text": "induce", "start": 1705, "end": 1711}]}], "positive regulation": [{"trigger": {"text": "mediate", "start": 873, "end": 880}, "arguments": [{"role": "Theme", "text": "expression", "start": 885, "end": 895}]}, {"trigger": {"text": "induced", "start": 1436, "end": 1443}, "arguments": [{"role": "Theme", "text": "production", "start": 1425, "end": 1435}]}, {"trigger": {"text": "induce", "start": 1705, "end": 1711}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1723, "end": 1736}]}], "regulation": [{"trigger": {"text": "role", "start": 175, "end": 179}, "arguments": [{"role": "Theme", "text": "regulating", "start": 183, "end": 193}]}, {"trigger": {"text": "regulating", "start": 183, "end": 193}, "arguments": [{"role": "Theme", "text": "expression", "start": 198, "end": 208}]}, {"trigger": {"text": "in response to", "start": 1635, "end": 1649}, "arguments": [{"role": "Theme", "text": "produce", "start": 1622, "end": 1629}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1723, "end": 1736}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1744, "end": 1748}]}]}}, "schema": []}
{"input": "Constitutive expression of p50 homodimer in freshly isolated human monocytes decreases with in vitro and in vivo differentiation: a possible mechanism influencing human immunodeficiency virus replication in monocytes and mature macrophages. \nHuman immunodeficiency virus type 1 (HIV-1) replicates more efficiently in vitro in differentiated macrophages than in freshly isolated monocytes. We investigated whether this may be partly explained by changes in expression of NF-kappaB with monocyte differentiation. We demonstrated that constitutive expression of NF-kappaB in primary human monocytes changed significantly with differentiation in vitro to monocyte-derived macrophages (MDMs) and differentiation in vivo to alveolar macrophages (AMs). Freshly isolated monocytes constitutively expressed high levels of transcriptionally inactive p50 homodimer which decreased with time in culture in favor of the transcriptionally active p50/p65 and p50/RelB heterodimers. As in MDMs, AMs constitutively expressed p50/p65 and p50/RelB although at lower levels. HIV infection of fresh monocytes failed to induce p50/p65 as seen in MDMs. The replacement of p50 homodimers with transcriptionally active heterodimers following time in culture may partially explain the progressive increase in susceptibility of monocytes to HIV infection during in vitro culture. The change in NF-kappaB components with monocyte differentiation in vivo may also explain the different transcriptional activities of these cell populations in HIV-infected individuals. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 13, "end": 23}, "arguments": [{"role": "Theme", "text": "p50", "start": 27, "end": 30}]}, {"trigger": {"text": "expressed", "start": 788, "end": 797}, "arguments": [{"role": "Theme", "text": "p50", "start": 840, "end": 843}]}, {"trigger": {"text": "expressed", "start": 998, "end": 1007}, "arguments": [{"role": "Theme", "text": "p50", "start": 1008, "end": 1011}]}, {"trigger": {"text": "expressed", "start": 998, "end": 1007}, "arguments": [{"role": "Theme", "text": "p65", "start": 1012, "end": 1015}]}, {"trigger": {"text": "expressed", "start": 998, "end": 1007}, "arguments": [{"role": "Theme", "text": "p50", "start": 1020, "end": 1023}]}, {"trigger": {"text": "expressed", "start": 998, "end": 1007}, "arguments": [{"role": "Theme", "text": "RelB", "start": 1024, "end": 1028}]}], "negative regulation": [{"trigger": {"text": "decreases", "start": 77, "end": 86}, "arguments": [{"role": "Theme", "text": "expression", "start": 13, "end": 23}]}, {"trigger": {"text": "decreased", "start": 860, "end": 869}, "arguments": [{"role": "Theme", "text": "expressed", "start": 788, "end": 797}]}], "positive regulation": [{"trigger": {"text": "in favor of", "start": 891, "end": 902}, "arguments": [{"role": "Theme", "text": "p50", "start": 932, "end": 935}]}, {"trigger": {"text": "in favor of", "start": 891, "end": 902}, "arguments": [{"role": "Theme", "text": "p65", "start": 936, "end": 939}]}, {"trigger": {"text": "in favor of", "start": 891, "end": 902}, "arguments": [{"role": "Theme", "text": "p50", "start": 944, "end": 947}]}, {"trigger": {"text": "in favor of", "start": 891, "end": 902}, "arguments": [{"role": "Theme", "text": "RelB", "start": 948, "end": 952}]}, {"trigger": {"text": "induce", "start": 1098, "end": 1104}, "arguments": [{"role": "Theme", "text": "p50", "start": 1105, "end": 1108}]}, {"trigger": {"text": "induce", "start": 1098, "end": 1104}, "arguments": [{"role": "Theme", "text": "p65", "start": 1109, "end": 1112}]}]}}, "schema": []}
{"input": "Identification of nucleotide sequences that regulate transcription of the MCF13 murine leukemia virus long terminal repeat in activated T cells. \nThe region downstream of the enhancer (DEN) of the long terminal repeat of the mink cell focus-forming murine leukemia virus is important for viral pathogenicity. Another important activity of DEN is its control of transcription in activated T cells, and we have determined that an NF-kappaB site is critical for this activity. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Immune hyperactivation of HIV-1-infected T cells mediated by Tat and the CD28 pathway. \nHuman immunodeficiency virus-type 1 (HIV-1) infection is characterized by a chronic state of immune hyperactivation in patients. Infection of human peripheral blood lymphocytes with HIV-1 in vitro resulted in increased interleukin-2 (IL-2) secretion in response to T cell activation via the CD3 and CD28 receptors. Expression of the HIV-1 transactivator Tat recapitulated this phenotype and was associated with increased IL-2 secretion in response to costimulation with CD3 plus CD28. IL-2 superinduction by Tat occurred at the transcriptional level, was mediated by the CD28-responsive element in the IL-2 promoter, and was exclusively dependent on the 29 amino acids encoded by the second exon of Tat. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "secretion", "start": 328, "end": 337}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 322, "end": 326}]}, {"trigger": {"text": "secretion", "start": 514, "end": 523}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 509, "end": 513}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 297, "end": 306}, "arguments": [{"role": "Theme", "text": "in response to", "start": 338, "end": 352}]}, {"trigger": {"text": "in response to", "start": 338, "end": 352}, "arguments": [{"role": "Theme", "text": "secretion", "start": 328, "end": 337}]}, {"trigger": {"text": "increased", "start": 499, "end": 508}, "arguments": [{"role": "Theme", "text": "secretion", "start": 514, "end": 523}, {"role": "Cause", "text": "CD28", "start": 567, "end": 571}]}, {"trigger": {"text": "superinduction", "start": 578, "end": 592}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 573, "end": 577}]}, {"trigger": {"text": "mediated", "start": 643, "end": 651}, "arguments": [{"role": "Theme", "text": "superinduction", "start": 578, "end": 592}]}, {"trigger": {"text": "dependent", "start": 725, "end": 734}, "arguments": [{"role": "Theme", "text": "superinduction", "start": 578, "end": 592}]}]}}, "schema": []}
{"input": "c-Rel is a target of pentoxifylline-mediated inhibition of T lymphocyte activation. \nThe possible clinical use of the methyl xanthine derivative, pentoxifylline (PF), for the treatment of T cell-dependent diseases is being noted with increasing interest. In this paper, we studied the molecular consequences of PF treatment during lymphocyte activation. We found that in T cells, anti-CD3-induced c-Rel expression was blocked by PF, whereas the induction of other NF-kappaB family members was not significantly affected. However, induction of NF-AT, which has the same signaling requirements as c-Rel induction, was not inhibited by PF. Among genes that respond to these transcription factors, IL-2 mRNA induction was suppressed by PF, whereas IL-2R(alpha) chain mRNA induction was not affected. These observations implicated c-Rel as an IL-2 promoter factor, for which experimental support was obtained from transient transfection experiments. In contrast with the observation in T cells, c-Rel induction was not blocked by PF in B cells. The greater selectivity of PF, compared with FK506, at both the molecular and cellular levels may prove advantageous in manipulating T cell responses in vivo. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 403, "end": 413}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 397, "end": 402}]}, {"trigger": {"text": "induction", "start": 601, "end": 610}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 595, "end": 600}]}, {"trigger": {"text": "induction", "start": 996, "end": 1005}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 990, "end": 995}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 418, "end": 425}, "arguments": [{"role": "Theme", "text": "induced", "start": 389, "end": 396}]}, {"trigger": {"text": "suppressed", "start": 718, "end": 728}, "arguments": [{"role": "Theme", "text": "induction", "start": 704, "end": 713}]}, {"trigger": {"text": "affected", "start": 786, "end": 794}, "arguments": [{"role": "Theme", "text": "induction", "start": 768, "end": 777}]}, {"trigger": {"text": "blocked", "start": 1014, "end": 1021}, "arguments": [{"role": "Theme", "text": "induction", "start": 996, "end": 1005}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 389, "end": 396}, "arguments": [{"role": "Theme", "text": "expression", "start": 403, "end": 413}]}], "regulation": [{"trigger": {"text": "target", "start": 11, "end": 17}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 0, "end": 5}]}], "transcription": [{"trigger": {"text": "induction", "start": 704, "end": 713}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 694, "end": 698}]}, {"trigger": {"text": "induction", "start": 768, "end": 777}, "arguments": [{"role": "Theme", "text": "IL-2R(alpha) chain", "start": 744, "end": 762}]}]}}, "schema": []}
{"input": "A T cell-specific enhancer in the interleukin-3 locus is activated cooperatively by Oct and NFAT elements within a DNase I-hypersensitive site. \nInterleukin-3 (IL-3) is a cytokine that is expressed primarily in activated T cells. Here we identified an inducible T cell-specific enhancer 14 kb upstream of the IL-3 gene that responded to activation of T cell receptor signaling pathways. The IL-3 enhancer spanned an inducible cyclosporin A-sensitive DNase I-hypersensitive site found only in T cells. Four NFAT-like elements exist within the enhancer. The two most active NFAT-like elements were located at the center of the DNase I-hypersensitive site. One of these NFAT-like elements encompassed overlapping Oct- and NFATp/c-binding sites, which functioned in a highly synergistic manner. We suggest that the T cell-specific expression of the IL-3 gene is partly controlled through the enhancer by cooperation between Oct and NFAT family proteins. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 188, "end": 197}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 160, "end": 164}]}, {"trigger": {"text": "expression", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 845, "end": 849}]}], "positive regulation": [{"trigger": {"text": "activated cooperatively", "start": 57, "end": 80}, "arguments": [{"role": "Theme", "text": "interleukin-3", "start": 34, "end": 47}]}, {"trigger": {"text": "inducible", "start": 252, "end": 261}, "arguments": [{"role": "Theme", "text": "IL-3", "start": 309, "end": 313}]}], "regulation": [{"trigger": {"text": "controlled", "start": 865, "end": 875}, "arguments": [{"role": "Theme", "text": "expression", "start": 827, "end": 837}]}, {"trigger": {"text": "through", "start": 876, "end": 883}, "arguments": [{"role": "Cause", "text": "IL-3", "start": 391, "end": 395}, {"role": "CSite", "text": "enhancer", "start": 396, "end": 404}, {"role": "Theme", "text": "controlled", "start": 865, "end": 875}]}]}}, "schema": []}
{"input": "A negative regulatory region containing a glucocorticosteroid response element (nGRE) in the human interleukin-1beta gene. \nInterleukin-1 beta (IL-1beta) is one of the most important inflammatory mediators in human inflammatory and immunological diseases. The regulation of human IL-1beta gene expression has been studied for several years, and a few regulatory elements have been discovered in the promoter region. However, little is known about negative regulation of IL-1beta expression at the transcriptional level, which may play an important role in anti-inflammatory and immunosuppressive effects. We have identified a negative regulatory element located in the region between -685 and -395. Within this region, a 19-bp nuclear factor binding site (-570 to -552) was characterized by DNase I footprinting and electromobility shift assay. A consensus sequence for a negative glucocorticoid response element (nGRE) and a transcription activator protein-2 binding site were noted within this footprint. Functional studies showed a 2.5-fold increase in promoter activity when this 19-bp binding site was deleted in the reporter constructs IL-1beta/CAT and IL-1beta/SV40 promoter/CAT. Dexamethasone (10(-8) M) repressed chloramphenicol acetyltransferase (CAT) production by 75% in the wild-type fragment but not in a deletion mutant lacking the 19-bp site. A protein of about 150 kD that bound to this negative regulatory sequence was identified by UV cross-linking. This is the first description of a negative regulatory region responsive to glucocorticoids in a cytokine gene. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 294, "end": 304}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 280, "end": 288}]}, {"trigger": {"text": "expression", "start": 479, "end": 489}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 470, "end": 478}]}, {"trigger": {"text": "production", "start": 1262, "end": 1272}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1257, "end": 1260}]}], "negative regulation": [{"trigger": {"text": "negative regulation", "start": 447, "end": 466}, "arguments": [{"role": "Theme", "text": "expression", "start": 479, "end": 489}]}, {"trigger": {"text": "repressed", "start": 1212, "end": 1221}, "arguments": [{"role": "Theme", "text": "production", "start": 1262, "end": 1272}]}], "regulation": [{"trigger": {"text": "regulation", "start": 260, "end": 270}, "arguments": [{"role": "Theme", "text": "expression", "start": 294, "end": 304}]}]}}, "schema": []}
{"input": "TRAMP, a novel apoptosis-mediating receptor with sequence homology to tumor necrosis factor receptor 1 and Fas(Apo-1/CD95). \nA novel member of the tumor necrosis factor (TNF) receptor family, designated TRAMP, has been identified. The structural organization of the 393 amino acid long human TRAMP is most homologous to TNF receptor 1. TRAMP is abundantly expressed on thymocytes and lymphocytes. Its extracellular domain is composed of four cysteine-rich domains, and the cytoplasmic region contains a death domain known to signal apoptosis. Overexpression of TRAMP leads to two major responses, NF-kappaB activation and apoptosis. TRAMP-induced cell death is inhibited by an inhibitor of ICE-like proteases, but not by Bcl-2. In addition, TRAMP does not appear to interact with any of the known apoptosis-inducing ligands of the TNF family. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 766, "end": 774}, "arguments": [{"role": "Theme", "text": "TRAMP", "start": 741, "end": 746}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 356, "end": 365}, "arguments": [{"role": "Theme", "text": "TRAMP", "start": 336, "end": 341}]}], "positive regulation": [{"trigger": {"text": "Overexpression", "start": 543, "end": 557}, "arguments": [{"role": "Theme", "text": "TRAMP", "start": 561, "end": 566}]}]}}, "schema": []}
{"input": "Involvement of Egr-1/RelA synergy in distinguishing T cell activation from tumor necrosis factor-alpha-induced NF-kappa B1 transcription. \nNF-kappa B is an important transcription factor required for T cell proliferation and other immunological functions. The NF-kappa B1 gene encodes a 105-kD protein that is the precursor of the p50 component of NF-kappa B. Previously, we and others have demonstrated that NF-kappa B regulates the NF-kappa B1 gene. In this manuscript we have investigated the molecular mechanisms by which T cell lines stimulated with phorbol 12-myristate 13-acetate (PMA) and phytohemagglutin (PHA) display significantly higher levels of NF-kappa B1 encoding transcripts than cells stimulated with tumor necrosis factor-alpha, despite the fact that both stimuli activate NF-kappa B. Characterization of the NF-kappa B1 promoter identified an Egr-1 site which was found to be essential for both the PMA/PHA-mediated induction as well as the synergistic activation observed after the expression of the RelA subunit of NF-kappa B and Egr-1. Furthermore, Egr-1 induction was required for endogenous NF-kappa B1 gene expression, since PMA/PHA-stimulated T cell lines expressing antisense Egr-1 RNA were inhibited in their ability to upregulate NF-kappa B1 transcription. Our studies indicate that transcriptional synergy mediated by activation of both Egr-1 and NF-kappa B may have important ramifications in T cell development by upregulating NF-kappa B1 gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1003, "end": 1013}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1021, "end": 1025}]}, {"trigger": {"text": "expression", "start": 1003, "end": 1013}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1052, "end": 1057}]}, {"trigger": {"text": "expression", "start": 1133, "end": 1143}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 1116, "end": 1127}]}, {"trigger": {"text": "expression", "start": 1477, "end": 1487}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 1460, "end": 1471}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1219, "end": 1228}, "arguments": [{"role": "Theme", "text": "upregulate", "start": 1249, "end": 1259}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 103, "end": 110}, "arguments": [{"role": "Cause", "text": "tumor necrosis factor-alpha", "start": 75, "end": 102}, {"role": "Theme", "text": "transcription", "start": 123, "end": 136}]}, {"trigger": {"text": "higher levels", "start": 642, "end": 655}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 659, "end": 670}]}, {"trigger": {"text": "essential", "start": 896, "end": 905}, "arguments": [{"role": "Cause", "text": "Egr-1", "start": 863, "end": 868}, {"role": "Theme", "text": "induction", "start": 936, "end": 945}]}, {"trigger": {"text": "essential", "start": 896, "end": 905}, "arguments": [{"role": "Cause", "text": "Egr-1", "start": 863, "end": 868}, {"role": "Theme", "text": "synergistic activation", "start": 961, "end": 983}]}, {"trigger": {"text": "induction", "start": 936, "end": 945}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 828, "end": 839}, {"role": "Site", "text": "promoter", "start": 840, "end": 848}, {"role": "Cause", "text": "PHA", "start": 923, "end": 926}]}, {"trigger": {"text": "induction", "start": 936, "end": 945}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 828, "end": 839}, {"role": "Site", "text": "promoter", "start": 840, "end": 848}]}, {"trigger": {"text": "synergistic activation", "start": 961, "end": 983}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1021, "end": 1025}]}, {"trigger": {"text": "synergistic activation", "start": 961, "end": 983}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1052, "end": 1057}]}, {"trigger": {"text": "induction", "start": 1078, "end": 1087}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1072, "end": 1077}]}, {"trigger": {"text": "required", "start": 1092, "end": 1100}, "arguments": [{"role": "Cause", "text": "induction", "start": 1078, "end": 1087}, {"role": "Theme", "text": "expression", "start": 1133, "end": 1143}]}, {"trigger": {"text": "upregulate", "start": 1249, "end": 1259}, "arguments": [{"role": "Cause", "text": "PHA", "start": 1155, "end": 1158}, {"role": "Theme", "text": "transcription", "start": 1272, "end": 1285}]}, {"trigger": {"text": "upregulate", "start": 1249, "end": 1259}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1272, "end": 1285}]}, {"trigger": {"text": "activation", "start": 1349, "end": 1359}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1368, "end": 1373}]}, {"trigger": {"text": "upregulating", "start": 1447, "end": 1459}, "arguments": [{"role": "Theme", "text": "expression", "start": 1477, "end": 1487}]}], "regulation": [{"trigger": {"text": "regulates", "start": 420, "end": 429}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 434, "end": 445}]}], "transcription": [{"trigger": {"text": "transcription", "start": 123, "end": 136}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 111, "end": 122}]}, {"trigger": {"text": "transcription", "start": 1272, "end": 1285}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 1260, "end": 1271}]}]}}, "schema": []}
{"input": "Differentiation of U-937 promonocytic cells by etoposide and ICRF-193, two antitumour DNA topoisomerase II inhibitors with different mechanisms of action. \nWe have compared the action on U-937 human promonocytic leukemia cells of two DNA topoisomerase II inhibitors, namely the epipodophyllotoxin etoposide and the bisdioxopiperazine ICRF-193. One hour pulse-treatment with 3 microM etoposide caused topoisomerase associated, primary DNA breakage, which was rapidly followed by apoptosis. By contrast, these effects were not observed upon pulse-treatment with 6 microM ICRF-193. However, continuous treatments with subcytotoxic concentrations of etoposide (0.15 microM) and ICRF-193 (0.3 microM) produced several similar effects, namely decreased cell proliferation, accumulation of cells at G2, increase in cell mass, and induction of differentiation. Under these conditions, etoposide produced a biphasic activation of protein kinase C, which consisted in an early transient activation (from hours 1 to 6) of the membrane-bound enzyme followed by a later activation (hour 48) of the total, membrane-bound and cytosolic enzyme. By contrast, ICRF-193 only provoked a late activation (from hours 72 to 96) of the total enzyme. When used at differentiation-inducing concentrations, both topoisomerase inhibitors caused a great stimulation of AP-1 binding activity, with maximum value at hour 12 in etoposide-treated cells and at hour 48 in ICRF-193-treated cells. By contrast, the binding activity of the NF-kappa(B) and EGR-1 transcription factors was little affected. It is concluded that topoisomerase II inhibitors may induce the differentiation of promonocytic cells, independently of their capacity to cause DNA strand breaks. However, there are other effects, such as the early activation of protein kinase C, which are probably derived from the production of primary DNA breakage by some anti-topoisomerase drugs. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1479, "end": 1486}, "arguments": [{"role": "Theme", "text": "EGR-1", "start": 1519, "end": 1524}]}], "positive regulation": [{"trigger": {"text": "affected", "start": 1558, "end": 1566}, "arguments": [{"role": "Theme", "text": "binding", "start": 1479, "end": 1486}]}]}}, "schema": []}
{"input": "Nuclear Rel-A and c-Rel protein complexes are differentially distributed within human thymocytes. \nNuclear factor-kappa B (NF-kappa B)/Rel proteins are inducible transcriptional regulators of numerous cellular genes. They are particularly abundant in lymphoid tissues and are thought to be critical for the transcription of genes involved in immune and inflammatory responses. We have reported previously that a nuclear NF-kappa B activity was present in freshly extracted human thymocytes in the absence of in vitro treatment of these cells. In the present report, we identified NF-kappa B proteins extracted from human thymocyte nuclei as being p50/p65 and p50/c-Rel complexes. Immunochemical and immunofluorescent staining of thymus sections using specific Abs allowed visualization of nuclear NF-kappa B proteins in both thymocytes and nonthymocyte cells. This detection suggested a preferential activation of p50/c-Rel in medullary thymocytes, whereas p50/p65 was present in both cortical and medullary regions of human thymus lobules. However, the intensity of p65 labeling was much higher in several thymocytes from the medulla. p65, p50, and c-Rel activities were found in both CD4- and CD8-positive thymocytes. These observations suggest that p65 and c-Rel complexes play distinct roles in gene expression and that both forms of NF-kappa B play critical roles during late stages of the intrathymic maturation of T cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "present", "start": 969, "end": 976}, "arguments": [{"role": "Theme", "text": "p50", "start": 957, "end": 960}]}, {"trigger": {"text": "present", "start": 969, "end": 976}, "arguments": [{"role": "Theme", "text": "p65", "start": 961, "end": 964}]}, {"trigger": {"text": "higher", "start": 1089, "end": 1095}, "arguments": [{"role": "Theme", "text": "p65", "start": 1067, "end": 1070}]}, {"trigger": {"text": "found", "start": 1172, "end": 1177}, "arguments": [{"role": "Theme", "text": "p65", "start": 1136, "end": 1139}]}, {"trigger": {"text": "found", "start": 1172, "end": 1177}, "arguments": [{"role": "Theme", "text": "p50", "start": 1141, "end": 1144}]}, {"trigger": {"text": "found", "start": 1172, "end": 1177}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1150, "end": 1155}]}], "localization": [{"trigger": {"text": "distributed", "start": 61, "end": 72}, "arguments": [{"role": "AtLoc", "text": "Nuclear", "start": 0, "end": 7}, {"role": "Theme", "text": "c-Rel", "start": 18, "end": 23}]}, {"trigger": {"text": "distributed", "start": 61, "end": 72}, "arguments": [{"role": "AtLoc", "text": "Nuclear", "start": 0, "end": 7}, {"role": "Theme", "text": "Rel-A", "start": 8, "end": 13}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 900, "end": 910}, "arguments": [{"role": "Theme", "text": "p50", "start": 914, "end": 917}]}, {"trigger": {"text": "activation", "start": 900, "end": 910}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 918, "end": 923}]}]}}, "schema": []}
{"input": "Alteration of a single serine in the basic domain of the Epstein-Barr virus ZEBRA protein separates its functions of transcriptional activation and disruption of latency. \nThe ZEBRA protein from Epstein-Barr virus (EBV) activates a switch from the latent to the lytic expression program of the virus. ZEBRA, a member of the bZIP family of DNA-binding proteins, is a transcriptional activator capable of inducing expression from viral lytic cycle promoters. It had previously been thought that ZEBRA's capacity to disrupt EBV latency resided primarily in its ability to activate transcription of genes that encode products required for lytic replication. We generated a point mutant of ZEBRA, Z(S186A), that was not impaired in its ability to activate transcription; however, this mutation abolished its ability to initiate the viral lytic cascade. The mutant, containing a serine-to-alanine substitution in the DNA-binding domain of the protein, bound to several known ZEBRA-binding sites and activated transcription from reporters bearing known ZEBRA-responsive promoters but did not disrupt latency in EBV-infected cell lines. Therefore, initiation of the EBV lytic cycle by the ZEBRA protein requires a function in addition to transcriptional activation; a change of serine 186 to alanine in the DNA-binding domain of ZEBRA abolished this additional function and uncovered a new role for the ZEBRA protein in disruption of EBV latency. The additional function that is required for initiation of the lytic viral life cycle is likely to require phosphorylation of serine 186 of the ZEBRA protein, which may influence either DNA recognition or transcriptional activation of lytic viral promoters in a chromatinized viral episome. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recognition", "start": 1629, "end": 1640}, "arguments": [{"role": "Theme", "text": "ZEBRA", "start": 1583, "end": 1588}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1546, "end": 1561}, "arguments": [{"role": "Site", "text": "serine 186", "start": 1565, "end": 1575}, {"role": "Theme", "text": "ZEBRA", "start": 1583, "end": 1588}]}], "regulation": [{"trigger": {"text": "influence", "start": 1608, "end": 1617}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 1546, "end": 1561}, {"role": "Theme", "text": "recognition", "start": 1629, "end": 1640}]}]}}, "schema": []}
{"input": "Activation of the transcription factor NF-kappaB in lipopolysaccharide-stimulated U937 cells. \nDuring the course of serious bacterial infections, lipopolysaccharide (LPS) interacts with monocyte/macrophage receptors, resulting in the generation of inflammatory cytokines. Transcription factor NF-kappaB is crucial in activating the transcription of genes encoding proinflammatory cytokines. In this paper, we demonstrate that the activation of NF-kappaB by LPS in a promonocytic cell line (U937) followed a rather slow kinetics, depending on the rate of IkappaB-alpha inhibitor hydrolysis. No degradation of p105 and p100 inhibitors was observed under these conditions. The transduction pathway leading to NF-kappaB activation in U937 cells involved the intracellular generation of reactive oxygen species (ROS), as demonstrated by the concomitant inhibitory effects of antioxidants on NF-kappaB activation and the emission of a fluorescent probe reacting intracellularly with hydrogen peroxide. This ROS pathway was also characterized by the use of other inhibitors. This finding indicates that phospholipase A2 and 5-lipoxygenase are also involved. However, the NF-kappaB activation pathway involving the acidic sphingomyelinase of the endolysosomial membrane did not seem to participate in the LPS-induced NF-kappaB activation in U937 cells. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Possible role of nuclear factor-kappa B activity in germline C epsilon transcription in a human Burkitt lymphoma B cell line. \nNuclear factor-kappa B (NF-kappa B) plays a broad role in gene regulation, but it is not evident whether NF-kappa B acts as a messenger system for germline C epsilon transcription. We report here that the signaling cascade triggered by interleukin-4 (IL-4) or anti-CD40 monoclonal antibody (mAb) participates in NF-kappa B activation responsible for germline C epsilon transcription in a human Burkitt lymphoma B cell line, DND39. Both IL-4 and anti-CD40 mAb induced activation of phosphatidylinositol 3-kinase (PI3-kinase), translocation of a zeta isoform of protein kinase C, and nuclear expression of NF-kappa B. All such events were abrogated by treatment with LY294002, a specific inhibitor of PI3-kinase. In addition, N-acetyl-L-cysteine (NAC), a potent antioxidant, decreased NF-kappa B activation caused by IL-4, anti-CD40 mAb, or their combination. NAC was also effective in diminishing germline C epsilon transcription, and its potency was higher in cultures costimulated with IL-4 and anti-CD40 mAb than in those stimulated with IL-4 alone. These results indicate that IL-4 and ligation of CD40 induce NF-kappa B expression via at least a mechanism dependent on the PI3-kinase pathway and suggest that NF-kappa B sensitive to NAC may play a role in regulating germline C epsilon transcription. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 1216, "end": 1224}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1228, "end": 1232}]}]}}, "schema": []}
{"input": "T-lymphocytes from individuals with filarial inflammatory disease have increased transendothelial migration in vitro. \nThe in vitro transendothelial migration of circulating filarial antigen-specific T-cells was examined in Wuchereria banerofti infection. Circulating T-cells from individuals with filaria-induced lymphatic pathology (LP) had significantly greater migration through unstimulated HUVEC monolayers than did T-cells from asymptomatic infected (MF) individuals (P = 0.04). In contrast to the MF individuals where no effect was seen, transendothelial migration of 48-hr filarial antigen stimulated T-cells from LP individuals was significantly (P = 0.01) greater than migration of 48-hr media-stimulated T-cells. In six of seven patients examined, inhibition of the VLA-4/VCAM-1 pathway resulted in greater than 50% inhibition of transendothelial migration of T-cells. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Suppression by azelastine hydrochloride of NF-kappa B activation involved in generation of cytokines and nitric oxide. \nThe influence of the anti-allergy agent azelastine hydrochloride (Azeptin) on NF-kappa B activation associated with the generation of cytokines and nitric oxide (NO) was investigated in various kinds of human and mouse cells. Azeptin dose-dependently suppressed both DNA and protein synthesis in human gingival fibroblasts (HF) and also suppressed blastogenesis of human peripheral blood lymphocytes (PBL). Generation of tumor necrosis factor-alpha, interleukin 1-beta, granulocyte-macrophage colony-stimulating factor and interleukin-6 from 10(-5) M Azeptin-treated PBL and human monocytes (HM) was decreased to approximately 1/3 to 2/3 of the control levels. In parallel with the decreased cytokine generation, each cytokine mRNA was less expressed in the presence of 10(-5) M Azeptin. In addition, both inducible nitric oxide synthase-mRNA level and NO generation in mouse peritoneal macrophages were suppressed by 10(-5) M Azeptin. Being compatible with those results, Azeptin (10(-5) M) suppressed activation of NF-kappa B in PBL, HM and HF. These results appear to indicate that suppression of cytokine and NO generation by Azeptin results at least partially from the inhibition of NF-kappa B activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Generation", "start": 527, "end": 537}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 541, "end": 568}]}, {"trigger": {"text": "Generation", "start": 527, "end": 537}, "arguments": [{"role": "Theme", "text": "interleukin 1-beta", "start": 570, "end": 588}]}, {"trigger": {"text": "Generation", "start": 527, "end": 537}, "arguments": [{"role": "Theme", "text": "granulocyte-macrophage colony-stimulating factor", "start": 590, "end": 638}]}, {"trigger": {"text": "Generation", "start": 527, "end": 537}, "arguments": [{"role": "Theme", "text": "interleukin-6", "start": 643, "end": 656}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 720, "end": 729}, "arguments": [{"role": "Theme", "text": "Generation", "start": 527, "end": 537}]}, {"trigger": {"text": "suppressed", "start": 1024, "end": 1034}, "arguments": [{"role": "Theme", "text": "inducible", "start": 926, "end": 935}]}], "transcription": [{"trigger": {"text": "inducible", "start": 926, "end": 935}, "arguments": [{"role": "Theme", "text": "nitric oxide synthase", "start": 936, "end": 957}]}]}}, "schema": []}
{"input": "The T cell activation factor NF-ATc positively regulates HIV-1 replication and gene expression in T cells. \nClinical deterioration in human immunodeficiency virus type 1 (HIV-1) infection is associated with increased levels of viral replication and burden in the peripheral blood and lymphoid organs. T cell activation and ensuing cellular gene activation can be critical for HIV-1 replication. The hypothesis that the nuclear factor of activated T cells (NF-AT) may influence HIV-1 replication is therefore compelling given the tight correlation of HIV-1 transcriptional induction to T cell activation. We report that certain NF-AT(Rel) family members productively bind the kappaB regulatory elements, synergize with NF-kappaB and Tat in transcriptional activation of HIV-1, and enhance HIV-1 replication in T cells. These results link regulatory factors critical to T cell commitment directly to HIV-1 replication. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Differentiation of T-helper lymphocytes: selective regulation by members of the STAT family of transcription factors. \nInterleukin-4 (IL-4) and interleukin-12 (IL-12) control the differentiation of T-helper cells. Here we summarize studies which investigate the mechanism by which these cytokines selectively reprogramme gene expression in T-lymphocytes. Cytokine stimulation leads to the phosphorylation of specific tyrosine residues within the intracellular domain of the corresponding cytokine receptor. These phosphotyrosines serve as docking sites for latent, cytoplasmic transcription factors known as signal transducers and activators of transcription (Stat) proteins. Receptor/Stat interaction is mediated by the src homology 2 (SH2) domain of the corresponding Stat protein. Although Stat binding to the intracellular domain of the cytokine receptor strongly depends on the phosphotyrosine residue, the recruitment of a specific Stat protein is dictated by amino acid residues C-terminal to the phosphotyrosine. Specific docking sites within individual cytokine receptors have been identified for almost all Stat proteins. The direct coupling between cytokine receptor and transcription factor helps to explain how different cytokines elicit distinct patterns of gene expression. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Regulation of the tissue factor gene in human monocytic cells. Role of AP-1, NF-kappa B/Rel, and Sp1 proteins in uninduced and lipopolysaccharide-induced expression. \nTissue factor (TF) expression by peripheral blood monocytes during sepsis initiates intravascular thrombosis. Bacterial lipopolysaccharide (LPS) rapidly induces TF gene transcription in monocytes. The human TF promoter contains binding sites for the transcription factors AP-1, c-Rel/p65, Egr-1, and Sp1. NF-kappa B/Rel proteins have been shown to physically interact with both AP-1 and Sp1 proteins. In this study, we investigated the role of these transcription factors in uninduced and LPS-induced TF gene expression in human monocytic THP-1 cells. Deletional analysis indicated that five Sp1 sites mediated basal expression in uninduced cells. The two AP-1 sites bound c-Fos/c-Jun heterodimers in both unstimulated and LPS-stimulated cells. Maximal LPS induction of the TF promoter required the two AP-1 sites and the kappa B site within the LPS response element. Disruption of the conserved spacing between the proximal AP-1 site and the kappa B site abolished LPS induction. Replacement of the two AP-1 sites with intrinsically bent DNA partially restored LPS induction, suggesting an additional structural role for the AP-1 sites. Synergistic transactivation of the LPS response element in Drosophila Schneider cells by coexpression of c-Fos, c-Jun, c-Rel, and p65 or c-Jun and p65 required the transactivation domains of c-Jun and p65. These data indicated that c-Fos/c-Jun, c-Rel/p65, and Sp1 regulate TF gene expression in human monocytic cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 526, "end": 534}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 554, "end": 557}]}, {"trigger": {"text": "bound", "start": 834, "end": 839}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 840, "end": 845}]}, {"trigger": {"text": "bound", "start": 834, "end": 839}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 846, "end": 851}]}], "gene expression": [{"trigger": {"text": "expression", "start": 186, "end": 196}, "arguments": [{"role": "Theme", "text": "TF", "start": 182, "end": 184}]}, {"trigger": {"text": "expression", "start": 676, "end": 686}, "arguments": [{"role": "Theme", "text": "TF", "start": 668, "end": 670}]}, {"trigger": {"text": "expression", "start": 784, "end": 794}, "arguments": [{"role": "Theme", "text": "TF", "start": 668, "end": 670}]}, {"trigger": {"text": "coexpression", "start": 1394, "end": 1406}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 1410, "end": 1415}]}, {"trigger": {"text": "coexpression", "start": 1394, "end": 1406}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 1417, "end": 1422}]}, {"trigger": {"text": "coexpression", "start": 1394, "end": 1406}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1424, "end": 1429}]}, {"trigger": {"text": "coexpression", "start": 1394, "end": 1406}, "arguments": [{"role": "Theme", "text": "p65", "start": 1435, "end": 1438}]}, {"trigger": {"text": "coexpression", "start": 1394, "end": 1406}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 1442, "end": 1447}]}, {"trigger": {"text": "coexpression", "start": 1394, "end": 1406}, "arguments": [{"role": "Theme", "text": "p65", "start": 1452, "end": 1455}]}, {"trigger": {"text": "expression", "start": 1586, "end": 1596}, "arguments": [{"role": "Theme", "text": "TF", "start": 1578, "end": 1580}]}], "negative regulation": [{"trigger": {"text": "abolished", "start": 1123, "end": 1132}, "arguments": [{"role": "Theme", "text": "induction", "start": 1137, "end": 1146}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 320, "end": 327}, "arguments": [{"role": "Theme", "text": "transcription", "start": 336, "end": 349}]}, {"trigger": {"text": "induced", "start": 660, "end": 667}, "arguments": [{"role": "Theme", "text": "expression", "start": 676, "end": 686}]}, {"trigger": {"text": "mediated", "start": 769, "end": 777}, "arguments": [{"role": "Theme", "text": "expression", "start": 784, "end": 794}]}, {"trigger": {"text": "induction", "start": 924, "end": 933}, "arguments": [{"role": "Theme", "text": "TF", "start": 941, "end": 943}, {"role": "Site", "text": "promoter", "start": 944, "end": 952}]}, {"trigger": {"text": "required", "start": 953, "end": 961}, "arguments": [{"role": "Theme", "text": "induction", "start": 924, "end": 933}]}, {"trigger": {"text": "induction", "start": 1137, "end": 1146}, "arguments": [{"role": "Theme", "text": "TF", "start": 941, "end": 943}, {"role": "Site", "text": "promoter", "start": 944, "end": 952}]}, {"trigger": {"text": "restored", "start": 1220, "end": 1228}, "arguments": [{"role": "Theme", "text": "induction", "start": 1233, "end": 1242}]}, {"trigger": {"text": "induction", "start": 1233, "end": 1242}, "arguments": [{"role": "Theme", "text": "TF", "start": 941, "end": 943}, {"role": "Site", "text": "promoter", "start": 944, "end": 952}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "tissue factor", "start": 18, "end": 31}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "c-Rel", "start": 445, "end": 450}, {"role": "Theme", "text": "induced", "start": 660, "end": 667}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "c-Rel", "start": 445, "end": 450}, {"role": "Theme", "text": "expression", "start": 676, "end": 686}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "p65", "start": 451, "end": 454}, {"role": "Theme", "text": "induced", "start": 660, "end": 667}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "p65", "start": 451, "end": 454}, {"role": "Theme", "text": "expression", "start": 676, "end": 686}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "Egr-1", "start": 456, "end": 461}, {"role": "Theme", "text": "induced", "start": 660, "end": 667}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "Egr-1", "start": 456, "end": 461}, {"role": "Theme", "text": "expression", "start": 676, "end": 686}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "Sp1", "start": 467, "end": 470}, {"role": "Theme", "text": "induced", "start": 660, "end": 667}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Cause", "text": "Sp1", "start": 467, "end": 470}, {"role": "Theme", "text": "expression", "start": 676, "end": 686}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Theme", "text": "induced", "start": 660, "end": 667}]}, {"trigger": {"text": "role", "start": 603, "end": 607}, "arguments": [{"role": "Theme", "text": "expression", "start": 676, "end": 686}]}, {"trigger": {"text": "regulate", "start": 1569, "end": 1577}, "arguments": [{"role": "Cause", "text": "c-Fos", "start": 1537, "end": 1542}, {"role": "Theme", "text": "expression", "start": 1586, "end": 1596}]}, {"trigger": {"text": "regulate", "start": 1569, "end": 1577}, "arguments": [{"role": "Cause", "text": "c-Jun", "start": 1543, "end": 1548}, {"role": "Theme", "text": "expression", "start": 1586, "end": 1596}]}, {"trigger": {"text": "regulate", "start": 1569, "end": 1577}, "arguments": [{"role": "Cause", "text": "c-Rel", "start": 1550, "end": 1555}, {"role": "Theme", "text": "expression", "start": 1586, "end": 1596}]}, {"trigger": {"text": "regulate", "start": 1569, "end": 1577}, "arguments": [{"role": "Cause", "text": "p65", "start": 1556, "end": 1559}, {"role": "Theme", "text": "expression", "start": 1586, "end": 1596}]}, {"trigger": {"text": "regulate", "start": 1569, "end": 1577}, "arguments": [{"role": "Cause", "text": "Sp1", "start": 1565, "end": 1568}, {"role": "Theme", "text": "expression", "start": 1586, "end": 1596}]}], "transcription": [{"trigger": {"text": "transcription", "start": 336, "end": 349}, "arguments": [{"role": "Theme", "text": "TF", "start": 328, "end": 330}]}]}}, "schema": []}
{"input": "Physical interactions between Ets and NF-kappaB/NFAT proteins play an important role in their cooperative activation of the human immunodeficiency virus enhancer in T cells. \nThe transcriptional regulatory elements of many inducible T-cell genes contain adjacent or overlapping binding sites for the Ets and NF-kappaB/NFAT families of transcription factors. Similar arrays of functionally important NF-kappaB/NFAT and Ets binding sites are present in the transcriptional enhancers of human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2), suggesting that this pattern of nuclear protein binding sites reflects an evolutionarily conserved mechanism for regulating inducible T-cell gene expression that has been co-opted during HIV evolution. Despite these findings, the molecular mechanisms by which Ets and NF-kappaB/NFAT proteins cooperatively regulate inducible T-cell gene expression remained unknown. In the studies described in this report, we demonstrated a physical interaction between multiple Ets and NF-kappaB/NFAT proteins both in vitro and in activated normal human T cells. This interaction is mediated by the Ets domain of Ets proteins and the C-terminal region of the Rel homology domains of NF-kappaB/NFAT proteins. In addition, the Ets-NF-kappaB/NFAT interaction requires the presence of DNA binding sites for both proteins, as it is abolished by the DNA intercalating agents propidium iodide and ethidium bromide and enhanced by the presence of synthetic oligonucleotides containing binding sites for Ets and NF-kappaB proteins. A dominant-negative mutant of NF-kappaB p50 that binds DNA but fails to interact with Ets proteins inhibits the synergistic activation of the HIV-1 and HIV-2 enhancers by NF-kappaB (p50 + p65) and Ets-1, suggesting that physical interaction between Ets and NF-kappaB proteins is required for the transcriptional activity of the HIV-1 and HIV-2 enhancers. Taken together, these findings suggest that evolutionarily conserved physical interactions between Ets and NF-kappaB/NFAT proteins are important in regulating the inducible expression of T-cell genes and viruses. These interactions represent a potential target for the development of novel immunosuppressive and antiviral therapies. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 1605, "end": 1610}, "arguments": [{"role": "Theme", "text": "p50", "start": 1596, "end": 1599}]}, {"trigger": {"text": "fails to interact", "start": 1619, "end": 1636}, "arguments": [{"role": "Theme", "text": "p50", "start": 1596, "end": 1599}]}]}}, "schema": []}
{"input": "Oxidant-regulation of gene expression in the chronically inflamed intestine. \nIt is becoming increasingly apparent that the chronic gut inflammation observed in the idiopathic inflammatory bowel diseases (e.g. ulcerative colitis, Crohn's disease) is associated with enhanced production of leukocyte-derived oxidants. Oxidants such as hydrogen peroxide are known to activate certain transcription factors such as nuclear transcription factor kappa beta. Nuclear transcription factor kB (NF-kappa B) is a ubiquitous transcription factor and pleiotropic regulator of numerous genes involved in the immune and inflammatory responses. This transcription factor is activated via the selective phosphorylation, ubiquination and degradation of its inhibitor protein I-kB thereby allowing translocation of NF-kappa B into the nucleus where it upregulates the transcription of a variety of adhesion molecules (e.g. ICAM-1, VCAM-1), cytokines (TNF, IL-1, IL-6) and enzymes (iNOS). The proteolytic degradation of the post-translationally modified I-kappa B is known to be mediated by the 26S proteasome complex. Based upon work from our laboratory, we propose that inhibition of NF-kappa B activation produces significant anti inflammatory activity which may be mediated by the inhibition of transcription of certain pro-inflammatory mediators and adhesion molecules. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "upregulates", "start": 834, "end": 845}, "arguments": [{"role": "Theme", "text": "transcription", "start": 850, "end": 863}]}], "transcription": [{"trigger": {"text": "transcription", "start": 850, "end": 863}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 905, "end": 911}]}, {"trigger": {"text": "transcription", "start": 850, "end": 863}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 913, "end": 919}]}, {"trigger": {"text": "transcription", "start": 850, "end": 863}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 944, "end": 948}]}, {"trigger": {"text": "transcription", "start": 850, "end": 863}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 963, "end": 967}]}]}}, "schema": []}
{"input": "Expression of LAZ3/BCL6 in follicular center (FC) B cells of reactive lymph nodes and FC-derived non-Hodgkin lymphomas. \nChromosomal translocation resulting in abnormal expression of the LAZ3/BCL6 gene in B cells has been implicated in the tumorigenesis of non-Hodgkin lymphoma (NHL). Therefore we studied the expression pattern of LAZ3/BCL6 by in situ hybridization with synthetic oligonucleotide probes in frozen tissue sections from five reactive lymph nodes and 38 B cell and non-B NHL. In addition, we investigated the expression of LAZ3/BCL6 by Northern blot analysis on multiple human tissues. The LAZ3/BCL6 transcript was found in a variety of tissues, including skeletal muscle, peripheral blood leukocytes, and weakly in normal lymph nodes. In the tumor samples, expression of LAZ3/BCL6 was observed in 68% of all B cell NHL and none of the non-B lymphomas. All cases of follicular, mixed small and large cell lymphomas showed LAZ3/BCL6 expression confined to the neoplastic follicles. A follicular expression pattern was also found in all non-malignant reactive lymph nodes. Hence, the expression of LAZ3/BCL6 does not correlate to malignancy, but reflects the origin of B cells from the germinal centers. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 14, "end": 18}]}, {"trigger": {"text": "expression", "start": 169, "end": 179}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 187, "end": 191}]}, {"trigger": {"text": "expression", "start": 310, "end": 320}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 332, "end": 336}]}, {"trigger": {"text": "expression", "start": 524, "end": 534}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 538, "end": 542}]}, {"trigger": {"text": "expression", "start": 773, "end": 783}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 787, "end": 791}]}, {"trigger": {"text": "expression", "start": 947, "end": 957}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 937, "end": 941}]}, {"trigger": {"text": "expression", "start": 1009, "end": 1019}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 937, "end": 941}]}, {"trigger": {"text": "expression", "start": 1097, "end": 1107}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 1111, "end": 1115}]}], "positive regulation": [{"trigger": {"text": "confined", "start": 958, "end": 966}, "arguments": [{"role": "Theme", "text": "expression", "start": 947, "end": 957}]}], "regulation": [{"trigger": {"text": "resulting in abnormal", "start": 147, "end": 168}, "arguments": [{"role": "Theme", "text": "expression", "start": 169, "end": 179}]}], "transcription": [{"trigger": {"text": "found", "start": 630, "end": 635}, "arguments": [{"role": "Theme", "text": "LAZ3", "start": 605, "end": 609}]}]}}, "schema": []}
{"input": "Induction of relA(p65) and I kappa B alpha subunit expression during differentiation of human peripheral blood monocytes to macrophages. \nWe evaluated the expression and DNA binding activity of nuclear factor (NF)-kappa B subunits in human peripheral blood monocytes and in monocyte-derived macrophages (MDMs). Constitutive DNA binding activity consisting of p50 homodimers was detected in nuclear extracts from both cell types. An additional complex composed of p50/RelA(p65) heterodimers appeared only in nuclear extracts from 7-day MDMs. Immunoblot analysis showed that the p50 subunit was constitutively expressed in monocytes and MDMs. In contrast, the RelA(p65) subunit was barely detectable in monocytes, but its level increased markedly in MDMs. Analysis of RelA(p65) mRNA revealed that the stability of RelA(p65) mRNA was significantly higher in MDMs, compared with monocytes. In MDMs, an upregulation of I kappa B alpha synthesis as well as the appearance of a novel M(r) 40,000 form of I kappa B alpha were also observed. These results suggest that macrophage differentiation results in the expression of active p50/RelA(p65) heterodimers with the capacity to activate target gene expression. The parallel induction of I kappa B alpha synthesis may allow for the continuous presence of a cytoplasmic reservoir of p50/RelA(p65) complexes that are readily available for inducer-mediated stimulation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 328, "end": 335}, "arguments": [{"role": "Theme", "text": "p50", "start": 359, "end": 362}]}], "gene expression": [{"trigger": {"text": "expression", "start": 51, "end": 61}, "arguments": [{"role": "Theme", "text": "relA", "start": 13, "end": 17}]}, {"trigger": {"text": "expression", "start": 51, "end": 61}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 27, "end": 42}]}, {"trigger": {"text": "appeared", "start": 490, "end": 498}, "arguments": [{"role": "Theme", "text": "p50", "start": 463, "end": 466}]}, {"trigger": {"text": "appeared", "start": 490, "end": 498}, "arguments": [{"role": "Theme", "text": "RelA", "start": 467, "end": 471}]}, {"trigger": {"text": "appeared", "start": 490, "end": 498}, "arguments": [{"role": "Theme", "text": "p65", "start": 472, "end": 475}]}, {"trigger": {"text": "expressed", "start": 608, "end": 617}, "arguments": [{"role": "Theme", "text": "p50", "start": 577, "end": 580}]}, {"trigger": {"text": "detectable", "start": 687, "end": 697}, "arguments": [{"role": "Theme", "text": "RelA", "start": 658, "end": 662}]}, {"trigger": {"text": "synthesis", "start": 930, "end": 939}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 914, "end": 929}]}, {"trigger": {"text": "appearance", "start": 955, "end": 965}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 997, "end": 1012}]}, {"trigger": {"text": "expression", "start": 1102, "end": 1112}, "arguments": [{"role": "Theme", "text": "p50", "start": 1123, "end": 1126}]}, {"trigger": {"text": "expression", "start": 1102, "end": 1112}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1127, "end": 1131}]}, {"trigger": {"text": "expression", "start": 1102, "end": 1112}, "arguments": [{"role": "Theme", "text": "p65", "start": 1132, "end": 1135}]}, {"trigger": {"text": "synthesis", "start": 1246, "end": 1255}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1230, "end": 1245}]}], "localization": [{"trigger": {"text": "reservoir", "start": 1311, "end": 1320}, "arguments": [{"role": "AtLoc", "text": "cytoplasmic", "start": 1299, "end": 1310}, {"role": "Theme", "text": "p50", "start": 1324, "end": 1327}]}, {"trigger": {"text": "reservoir", "start": 1311, "end": 1320}, "arguments": [{"role": "AtLoc", "text": "cytoplasmic", "start": 1299, "end": 1310}, {"role": "Theme", "text": "RelA", "start": 1328, "end": 1332}]}, {"trigger": {"text": "reservoir", "start": 1311, "end": 1320}, "arguments": [{"role": "AtLoc", "text": "cytoplasmic", "start": 1299, "end": 1310}, {"role": "Theme", "text": "p65", "start": 1333, "end": 1336}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "expression", "start": 51, "end": 61}]}, {"trigger": {"text": "increased", "start": 726, "end": 735}, "arguments": [{"role": "Theme", "text": "RelA", "start": 658, "end": 662}]}, {"trigger": {"text": "higher", "start": 845, "end": 851}, "arguments": [{"role": "Theme", "text": "RelA", "start": 812, "end": 816}]}, {"trigger": {"text": "upregulation", "start": 898, "end": 910}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 930, "end": 939}]}, {"trigger": {"text": "results", "start": 1087, "end": 1094}, "arguments": [{"role": "Theme", "text": "expression", "start": 1102, "end": 1112}]}, {"trigger": {"text": "induction", "start": 1217, "end": 1226}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1246, "end": 1255}]}, {"trigger": {"text": "allow", "start": 1260, "end": 1265}, "arguments": [{"role": "Cause", "text": "induction", "start": 1217, "end": 1226}, {"role": "Theme", "text": "reservoir", "start": 1311, "end": 1320}]}]}}, "schema": []}
{"input": "Two distinct pathways of interleukin-5 synthesis in allergen-specific human T-cell clones are suppressed by glucocorticoids. \nGlucocorticoids (GC) have long been used as the most effective agents for the treatment of allergic diseases accompanied by eosinophilia such as chronic asthma and atopic dermatitis. The development of chronic eosinophilic inflammation is dependent on interleukin-5 (IL-5), a selective eosinophil-activating factor, produced by helper T cells. To delineate the regulatory mechanisms of human IL-5 synthesis, we established allergen-specific CD4+ T-cell clones from asthmatic patients. GC efficiently suppressed IL-5 synthesis of T-cell clones activated via either T-cell receptor (TCR) or IL-2 receptor (IL-2R). Induction of IL-5 mRNA upon TCR and IL-2R stimulation was totally inhibited by dexamethasone. Human IL-5 promoter/enhancer-luciferase gene construct transfected to T-cell clones was transcribed on either TCR or IL-2R stimulation and was clearly downregulated by dexamethasone, indicating that the approximately 500-bp human IL-5 gene segment located 5' upstream of the coding region contains activation-inducible enhancer elements responsible for the regulation by GC. Electrophoretic mobility shift assay analysis suggested that AP-1 and NF-kappaB are among the possible targets of GC actions on TCR-stimulated T cells. NF-AT and NF-kappaB were not significantly induced by IL-2 stimulation. Our results showing that GC suppressed IL-5 production by human CD4+ T cells activated by two distinct stimuli, TCR and IL-2R stimulation, underscore the efficacy of GC in the treatment of allergic diseases via suppression of T-cell IL-5 synthesis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "synthesis", "start": 39, "end": 48}, "arguments": [{"role": "Theme", "text": "interleukin-5", "start": 25, "end": 38}]}, {"trigger": {"text": "produced", "start": 442, "end": 450}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 393, "end": 397}]}, {"trigger": {"text": "synthesis", "start": 523, "end": 532}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 518, "end": 522}]}, {"trigger": {"text": "synthesis", "start": 642, "end": 651}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 637, "end": 641}]}, {"trigger": {"text": "production", "start": 1475, "end": 1485}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1470, "end": 1474}]}, {"trigger": {"text": "synthesis", "start": 1669, "end": 1678}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1664, "end": 1668}]}], "negative regulation": [{"trigger": {"text": "suppressed", "start": 94, "end": 104}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 39, "end": 48}]}, {"trigger": {"text": "suppressed", "start": 626, "end": 636}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 642, "end": 651}]}, {"trigger": {"text": "inhibited", "start": 804, "end": 813}, "arguments": [{"role": "Theme", "text": "Induction", "start": 738, "end": 747}]}, {"trigger": {"text": "downregulated", "start": 983, "end": 996}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 838, "end": 842}]}, {"trigger": {"text": "suppressed", "start": 1459, "end": 1469}, "arguments": [{"role": "Theme", "text": "production", "start": 1475, "end": 1485}]}, {"trigger": {"text": "suppression", "start": 1642, "end": 1653}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1669, "end": 1678}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 738, "end": 747}, "arguments": [{"role": "Theme", "text": "mRNA", "start": 756, "end": 760}]}], "regulation": [{"trigger": {"text": "regulatory", "start": 487, "end": 497}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 523, "end": 532}]}, {"trigger": {"text": "stimulation", "start": 955, "end": 966}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 920, "end": 931}]}, {"trigger": {"text": "efficacy", "start": 1585, "end": 1593}, "arguments": [{"role": "Theme", "text": "suppression", "start": 1642, "end": 1653}]}], "transcription": [{"trigger": {"text": "mRNA", "start": 756, "end": 760}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 751, "end": 755}]}, {"trigger": {"text": "transcribed", "start": 920, "end": 931}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 838, "end": 842}]}]}}, "schema": []}
{"input": "Involvement of an SAF-like transcription factor in the activation of serum amyloid A gene in monocyte/macrophage cells by lipopolysaccharide. \nSerum amyloid A (SAA) has been linked to atherosclerosis because of its ability to remodel high-density lipoprotein by the depletion of apolipoprotein A1, its ability to bind cholesterol, and its presence in the atherosclerotic plaques of coronary and carotid arteries. In the present study, we investigated the induction mechanism of SAA gene in THP-1 monocyte/macrophage cells which play a critical role in the development of atherosclerotic fatty streak and plaque formation. We and others have shown that SAA gene is induced in monocyte/macrophage cells by lipopolysaccharide (LPS). By promoter function analysis, we show that the SAA promoter sequence between -280 and -226 can confer LPS responsiveness. Gel electrophoretic mobility shift assay detected an induced DNA-binding activity in these cells in response to LPS. Characterization of the DNA-binding protein by UV cross-linking, Southwestern blot, and antibody ablation/supershift assays revealed that it is similar to a recently reported nuclear factor designated SAF. These results demonstrated that LPS-mediated SAA gene induction in monocyte/macrophage cells is primarily due to the induction of SAF activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "linked", "start": 174, "end": 180}, "arguments": [{"role": "Theme", "text": "SAA", "start": 160, "end": 163}]}, {"trigger": {"text": "bind", "start": 313, "end": 317}, "arguments": [{"role": "Theme", "text": "SAA", "start": 160, "end": 163}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 55, "end": 65}, "arguments": [{"role": "Theme", "text": "serum amyloid A", "start": 69, "end": 84}]}, {"trigger": {"text": "induction", "start": 455, "end": 464}, "arguments": [{"role": "Theme", "text": "SAA", "start": 478, "end": 481}]}, {"trigger": {"text": "induced", "start": 664, "end": 671}, "arguments": [{"role": "Theme", "text": "SAA", "start": 652, "end": 655}]}, {"trigger": {"text": "induction", "start": 1230, "end": 1239}, "arguments": [{"role": "Theme", "text": "SAA", "start": 1221, "end": 1224}]}], "regulation": [{"trigger": {"text": "Involvement", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "activation", "start": 55, "end": 65}]}, {"trigger": {"text": "responsiveness", "start": 837, "end": 851}, "arguments": [{"role": "Theme", "text": "SAA", "start": 778, "end": 781}, {"role": "Site", "text": "promoter sequence", "start": 782, "end": 799}]}]}}, "schema": []}
{"input": "Oncogenic forms of NOTCH1 lacking either the primary binding site for RBP-Jkappa or nuclear localization sequences retain the ability to associate with RBP-Jkappa and activate transcription. \nTruncated forms of the NOTCH1 transmembrane receptor engineered to resemble mutant forms of NOTCH1 found in certain cases of human T cell leukemia/lymphoma (T-ALL) efficiently induce T-ALL when expressed in the bone marrow of mice. Unlike full-sized NOTCH1, two such truncated forms of the protein either lacking a major portion of the extracellular domain (DeltaE) or consisting only of the intracellular domain (ICN) were found to activate transcription in cultured cells, presumably through RBP-Jkappa response elements within DNA. Both truncated forms also bound to the transcription factor RBP-Jkappa in extracts prepared from human and murine T-ALL cell lines. Transcriptional activation required the presence of a weak RBP-Jkappa-binding site within the NOTCH1 ankyrin repeat region of the intracellular domain. Unexpectedly, a second, stronger RBP-Jkappa-binding site, which lies within the intracellular domain close to the transmembrane region and significantly augments association with RBP-Jkappa, was not needed for oncogenesis or for transcriptional activation. While ICN appeared primarily in the nucleus, DeltaE localized to cytoplasmic and nuclear membranes, suggesting that intranuclear localization is not essential for oncogenesis or transcriptional activation. In support of this interpretation, mutation of putative nuclear localization sequences decreased nuclear localization and increased transcriptional activation by membrane-bound DeltaE. Transcriptional activation by this mutant form of membrane-bound DeltaE was approximately equivalent to that produced by intranuclear ICN. These data are most consistent with NOTCH1 oncogenesis and transcriptional activation being independent of association with RBP-Jkappa at promoter sites. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associate", "start": 137, "end": 146}, "arguments": [{"role": "Theme", "text": "NOTCH1", "start": 19, "end": 25}, {"role": "Theme2", "text": "RBP-Jkappa", "start": 152, "end": 162}]}, {"trigger": {"text": "bound", "start": 753, "end": 758}, "arguments": [{"role": "Theme", "text": "RBP-Jkappa", "start": 787, "end": 797}]}, {"trigger": {"text": "association", "start": 1173, "end": 1184}, "arguments": [{"role": "Theme", "text": "NOTCH1", "start": 19, "end": 25}, {"role": "Theme2", "text": "RBP-Jkappa", "start": 1190, "end": 1200}]}, {"trigger": {"text": "association", "start": 1905, "end": 1916}, "arguments": [{"role": "Theme", "text": "RBP-Jkappa", "start": 1922, "end": 1932}]}], "localization": [{"trigger": {"text": "localization", "start": 1579, "end": 1591}, "arguments": [{"role": "Theme", "text": "NOTCH1", "start": 19, "end": 25}, {"role": "AtLoc", "text": "nuclear", "start": 1571, "end": 1578}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 1561, "end": 1570}, "arguments": [{"role": "Theme", "text": "localization", "start": 1579, "end": 1591}]}], "positive regulation": [{"trigger": {"text": "augments", "start": 1164, "end": 1172}, "arguments": [{"role": "Theme", "text": "association", "start": 1173, "end": 1184}]}]}}, "schema": []}
{"input": "Transcriptional induction of collagenase-1 in differentiated monocyte-like (U937) cells is regulated by AP-1 and an upstream C/EBP-beta site. \nIn this report, we demonstrate that the AP-1 site and a distal promoter element regulate transcriptional induction of collagenase-1 during monocytic differentiation. Chloramphenicol acetyltransferase expression constructs containing regions of the human collagenase-1 promoter were stably or transiently transfected into U937 cells, and reporter activity was assessed at various times after the onset of phorbol 12-myristate 13-acetate (PMA)-mediated differentiation. Rapid and strong induction of promoter activity was lost in constructs with a mutant AP-1 element; however, at 16-96 h post-PMA, the mutant collagenase-1 promoter displayed AP-1 independent PMA-mediated transactivation. The AP-1 mutant constructs also showed delayed transcriptional activation in PMA-treated fibroblasts. Western and supershift analyses indicated that functional Jun and Fos proteins were present in nuclear extracts of PMA-differentiated U937 cells. Promoter deletion constructs demonstrated the potential role of distal promoter sequences in regulating collagenase-1 transcription. In particular, Western, supershift, and promoter deletion analyses suggested a role for CCAAT/enhancer-binding protein-beta (C/EBP-beta) binding site between -2010 and -1954 in regulating transcription of collagenase-1 in monocytic cells. Our findings suggest that distinct regulatory elements, acting somewhat independently of each other, control expression of collagenase-1. In addition, our data suggests that the rapid PMA-mediated induction of collagenase-1 transcription is controlled by a mechanism distinct from that regulating the sustained expression of this proteinase in activated macrophages. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1560, "end": 1570}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 1574, "end": 1587}]}, {"trigger": {"text": "expression", "start": 1762, "end": 1772}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 1661, "end": 1674}]}], "positive regulation": [{"trigger": {"text": "Transcriptional induction", "start": 0, "end": 25}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 29, "end": 42}]}, {"trigger": {"text": "transcriptional induction", "start": 232, "end": 257}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 261, "end": 274}]}, {"trigger": {"text": "transactivation", "start": 814, "end": 829}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 751, "end": 764}, {"role": "Site", "text": "promoter", "start": 765, "end": 773}]}, {"trigger": {"text": "potential role", "start": 1125, "end": 1139}, "arguments": [{"role": "Theme", "text": "regulating", "start": 1172, "end": 1182}]}, {"trigger": {"text": "role", "start": 1291, "end": 1295}, "arguments": [{"role": "Theme", "text": "regulating", "start": 1389, "end": 1399}]}, {"trigger": {"text": "induction", "start": 1648, "end": 1657}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1675, "end": 1688}]}], "regulation": [{"trigger": {"text": "regulated", "start": 91, "end": 100}, "arguments": [{"role": "Theme", "text": "Transcriptional induction", "start": 0, "end": 25}]}, {"trigger": {"text": "regulate", "start": 223, "end": 231}, "arguments": [{"role": "Theme", "text": "transcriptional induction", "start": 232, "end": 257}]}, {"trigger": {"text": "regulating", "start": 1172, "end": 1182}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1197, "end": 1210}]}, {"trigger": {"text": "regulating", "start": 1389, "end": 1399}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1400, "end": 1413}]}, {"trigger": {"text": "control", "start": 1552, "end": 1559}, "arguments": [{"role": "Theme", "text": "expression", "start": 1560, "end": 1570}]}, {"trigger": {"text": "controlled", "start": 1692, "end": 1702}, "arguments": [{"role": "Theme", "text": "induction", "start": 1648, "end": 1657}]}, {"trigger": {"text": "distinct from that regulating", "start": 1718, "end": 1747}, "arguments": [{"role": "Theme", "text": "expression", "start": 1762, "end": 1772}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1197, "end": 1210}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 1183, "end": 1196}]}, {"trigger": {"text": "transcription", "start": 1400, "end": 1413}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 1417, "end": 1430}]}, {"trigger": {"text": "transcription", "start": 1675, "end": 1688}, "arguments": [{"role": "Theme", "text": "collagenase-1", "start": 1661, "end": 1674}]}]}}, "schema": []}
{"input": "A novel genetic system to isolate a dominant negative effector on DNA-binding activity of Oct-2. \nRecent studies have revealed that interactions between transcription factors play an important role in regulation of gene expression in eukaryotic cells. To isolate cDNA clones that dominantly inhibit the DNA-binding activity of Oct-2, chosen as a representative factor, we have developed a novel screening system. This employs an Escherichia coli tester strain carrying a modified lac operon as a reporter gene, with the lac operator sequence replaced by an octamer sequence. Oct-2 expressed in this tester strain represses the expression of the reporter gene and changes the phenotype of the cell from Lac+to Lac-. Introduction of a cDNA expression library prepared from a human T-cell line into the Oct-2-harboring tester strain allowed selection of three Lac+clones out of 1 x 10(5) transformants. One of them, hT86, encoding a putative zinc finger protein was found to derepress beta-galactosidase activity in the Oct-2-harboring tester strain at the transcriptional level. In gel mobility shift assays, hT86 attenuated the intensity of the retarded band composed of the octamer probe and Oct-2, suggesting a dominant negative effect on the DNA-binding activity of Oct-2. The strategy described here provides a new approach for studying protein-protein interactions that govern the complex regulation of gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 70, "end": 77}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 90, "end": 95}]}, {"trigger": {"text": "binding", "start": 307, "end": 314}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 327, "end": 332}]}, {"trigger": {"text": "binding", "start": 1248, "end": 1255}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 1268, "end": 1273}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 581, "end": 590}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 575, "end": 580}]}], "negative regulation": [{"trigger": {"text": "inhibit", "start": 291, "end": 298}, "arguments": [{"role": "Theme", "text": "binding", "start": 307, "end": 314}]}, {"trigger": {"text": "negative effect", "start": 1221, "end": 1236}, "arguments": [{"role": "Theme", "text": "binding", "start": 1248, "end": 1255}]}], "positive regulation": [{"trigger": {"text": "derepress", "start": 972, "end": 981}, "arguments": [{"role": "Theme", "text": "beta-galactosidase", "start": 982, "end": 1000}]}]}}, "schema": []}
{"input": "A negative role for phosphoinositide 3-kinase in T-cell antigen receptor function. \nBACKGROUND: A delicate balance between positive and negative regulatory mechanisms during T-cell activation determines the specificity and magnitude of an immune response. Phosphoinositide 3-kinase (PI 3-kinase) is activated by a diverse set of receptors that determine T-cell function, including the T-cell antigen receptor (TCR), the costimulatory receptor CD28, and negative regulators of T-cell activation such as CTLA-4. PI 3-kinase is also regulated by the haematopoietic cytokines that determine T-cell differentiation and lymphocyte proliferation. PI 3-kinase can thus dynamically influence the outcome of the immune reactions at various stages. In this study, we investigated the importance of PI 3-kinase in TCR-directed T-cell activation using activated or inhibitory versions of PI 3-kinase. RESULTS: Certain aspects of TCR responses such as the induction of transcriptional activity of AP1 and serum response factor were not affected by expression of the mutant forms of PI 3-kinase. We found, however, that PI 3-kinase profoundly influenced the transactivation capacity of 'nuclear factor of activated T cells' (NF-AT) elicited by the TCR: expression of an activated form of PI 3-kinase inhibited TCR-mediated NF-AT responses, whereas expression of a dominant negative mutant of PI 3-kinase potently enhanced TCR-controlled NF-AT induction. These effects of PI 3-kinase were not mediated by previously identified PI 3-kinase effectors, such as protein kinase B, a positive regulator of PI 3-kinase, or the GTPase Rac, and are therefore likely to involve a novel, as yet unknown, effector molecule. CONCLUSIONS: Our results establish that PI 3-kinase can both positively and negatively regulate T-cell function, and uncover a previously unrecognized function for PI 3-kinase in T cells as a selective negative regulator of TCR-signalling events and therefore as a determinant of T-cell homeostasis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1034, "end": 1044}, "arguments": [{"role": "Theme", "text": "PI 3-kinase", "start": 1068, "end": 1079}]}, {"trigger": {"text": "expression", "start": 1238, "end": 1248}, "arguments": [{"role": "Theme", "text": "PI 3-kinase", "start": 1273, "end": 1284}]}], "negative regulation": [{"trigger": {"text": "negative regulators", "start": 453, "end": 472}, "arguments": [{"role": "Theme", "text": "activated", "start": 299, "end": 308}, {"role": "Cause", "text": "CTLA-4", "start": 502, "end": 508}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 299, "end": 308}, "arguments": [{"role": "Theme", "text": "PI 3-kinase", "start": 283, "end": 294}, {"role": "Cause", "text": "CD28", "start": 443, "end": 447}]}, {"trigger": {"text": "activated", "start": 299, "end": 308}, "arguments": [{"role": "Theme", "text": "PI 3-kinase", "start": 283, "end": 294}, {"role": "Cause", "text": "CTLA-4", "start": 502, "end": 508}]}, {"trigger": {"text": "activated", "start": 299, "end": 308}, "arguments": [{"role": "Theme", "text": "PI 3-kinase", "start": 283, "end": 294}]}, {"trigger": {"text": "positive regulator", "start": 1562, "end": 1580}, "arguments": [{"role": "Theme", "text": "PI 3-kinase", "start": 1584, "end": 1595}]}], "regulation": [{"trigger": {"text": "regulated", "start": 530, "end": 539}, "arguments": [{"role": "Theme", "text": "PI 3-kinase", "start": 510, "end": 521}]}]}}, "schema": []}
{"input": "NF-kappa B-independent suppression of HIV expression by ascorbic acid. \nAscorbic acid (ascorbate or vitamin C) has been shown to suppress the induction of HIV in latently infected T lymphocytic cells following stimulation with a tumor promoter (PMA) and inflammatory cytokine (TNF-alpha). To assess whether this inhibition was mediated via modulation of the cellular transcription factor, NF-kappa B, we carried out gel shift analysis on nuclear extracts prepared under different conditions of cell stimulation in the presence or absence of ascorbate, N-acetylcysteine (NAC), or zidovudine (AZT). Pretreatment of ACH-2 T cells by NAC followed by stimulation with PMA, TNF-alpha, or hydrogen peroxide (H2O2) resulted in strong suppression of NF-kappa B activation. In contrast, neither ascorbate nor AZT affected NF-kappa B activity under all three induction conditions in the ACH-2 cell line. Ascorbate and AZT also had no effect on NF-kappa B activation following TNF-alpha- or PMA-induced stimulation of U1 promonocytic cells. These results suggest that the molecular mechanism of HIV inhibition by ascorbate is not mediated via NF-kappa B inhibition, unlike that seen with other antioxidants. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Lineage- and stage-specific expression of runt box polypeptides in primitive and definitive hematopoiesis. \nTranslocations involving the human CBFA2 locus have been associated with leukemia. This gene, originally named AML1, is a human homologue of the Drosophila gene runt that controls early events in fly embryogenesis. To clarify the role of mammalian runt products in normal and leukemic hematopoiesis, we have studied their pattern of expression in mouse hematopoietic tissues in the adult and during ontogeny using an anti-runt box antiserum. In the adult bone marrow, we found expression of runt polypeptides in differentiating myeloid cells and in B lymphocytes. Within the erythroid lineage, runt expression is biphasic, clearly present in the erythroblasts of early blood islands and of the fetal liver, but absent in the adult. Biochemical analysis by Western blotting of fetal and adult hematopoietic populations shows several runt isoforms. At least one of them appears to be myeloid specific. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 707, "end": 717}, "arguments": [{"role": "Theme", "text": "runt", "start": 702, "end": 706}]}, {"trigger": {"text": "absent", "start": 819, "end": 825}, "arguments": [{"role": "Theme", "text": "runt", "start": 702, "end": 706}]}]}}, "schema": []}
{"input": "Cell-to-cell contact activates the long terminal repeat of human immunodeficiency virus 1 through its kappaB motif. \nCell-to-cell contact between peripheral blood lymphocytes and transfected human colonic carcinoma cell line HT29 activates transcription of the long terminal repeats (LTR) of human immunodeficiency virus. HIV-1 LTR transcription is controlled by a complex array of virus-encoded and cellular proteins. Using various constructs expressing a lacZ reporter gene under the control of the intact or three deleted forms of HIV-1 LTR, we obtained evidence that the kappaB regulatory elements located in the U3 region are involved in cell-to-cell activation of HIV-1 LTR. Cell-to-cell contact activates in vitro binding of the nuclear factor kappaB (NF-kappaB) p50/p65 heterodimer to an HIV-1 kappaB oligonucleotide. Cell-to-cell contact activation of NF-kappaB was only partially inhibited by 100 microM pyrrolidine dithiocarbamate and was not correlated with a significant decrease of cellular inhibitor kappaB alpha. NF-kappaB nuclear activation was not detectable before 1 h after cell contact and was dependent on protein synthesis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 721, "end": 728}, "arguments": [{"role": "Theme", "text": "p50", "start": 770, "end": 773}]}, {"trigger": {"text": "binding", "start": 721, "end": 728}, "arguments": [{"role": "Theme", "text": "p65", "start": 774, "end": 777}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 984, "end": 992}, "arguments": [{"role": "Theme", "text": "inhibitor kappaB alpha", "start": 1005, "end": 1027}]}], "positive regulation": [{"trigger": {"text": "activates", "start": 702, "end": 711}, "arguments": [{"role": "Theme", "text": "binding", "start": 721, "end": 728}]}]}}, "schema": []}
{"input": "HIV does not replicate in naive CD4 T cells stimulated with CD3/CD28. \nIn this report, we demonstrate that the T cell tropic strain of HIV, LAI, does not replicate in naive CD4 T cells stimulated by cross-linking CD3 and CD28. In contrast, LAI replicates well in memory CD4 T cells stimulated in the same way. Unlike this physiologically relevant stimulation, PHA stimulates productive LAI replication in both naive and memory T cells. These studies were conducted with highly purified (FACS-isolated) subsets of CD4 T cells identified by expression of both CD45RA and CD62L. Remixing of purified T cells showed that naive T cells do not suppress LAI replication in memory T cells and that memory T cells do not restore LAI expression in naive T cells. The suppression of productive LAI replication in naive T cells is not due to differential expression of viral coreceptors, nor is it due to inhibition of activation of the important HIV transcription factors, nuclear factor-kappaB and activator protein-1. The inherent resistance of naive T cells to productive HIV infection, coupled with their proliferative advantage as demonstrated here, provides a sound basis for proposed clinical therapies using ex vivo expansion and reinfusion of CD4 T cells from HIV-infected adults. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 199, "end": 212}, "arguments": [{"role": "Theme", "text": "CD28", "start": 221, "end": 225}]}]}}, "schema": []}
{"input": "Control of NFATx1 nuclear translocation by a calcineurin-regulated inhibitory domain. \nThe nuclear factor of activated T cells (NFAT) regulates cytokine gene expression in T cells through cis-acting elements located in the promoters of several cytokine genes. NFATx1, which is preferentially expressed in the thymus and peripheral blood leukocytes, is one of four members of the NFAT family of transcription factors. We have performed domain analysis of NFATx1 by examining the effects of deletion mutations. We found that NFATx1 DNA binding activity and interaction with AP-1 polypeptides were dependent on its central Rel similarity region and that transcriptional activation was reduced by deletions of either its N-terminal domain or its C-terminal domain, suggesting the presence of intrinsic transcriptional activation motifs in both regions. We also identified a potent inhibitory sequence within its N-terminal domain. We show that the inactivation of the inhibition was dependent on the activity of calcineurin, a calcium-calmodulin-dependent phosphatase. We also show that calcineurin associated with the N-terminal domain of NFATx1 at multiple docking sites and caused a reduction of size, indicative of dephosphorylation, in NFATx1. We have mapped the inhibitory activity to less than 60 residues, containing motifs that are conserved in all NFAT proteins. Finally, we demonstrate that deletion in NFATx1 of the mapped 60 residues leads to its nuclear translocation independent of calcium signaling. Our results support the model proposing that the N-terminal domain confers calcium-signaling dependence on NFATx1 transactivation activity by regulating its intracellular localization through a protein module that associates with calcineurin and is a target of its phosphatase activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 534, "end": 541}, "arguments": [{"role": "Theme", "text": "NFATx1", "start": 523, "end": 529}]}, {"trigger": {"text": "associated", "start": 1095, "end": 1105}, "arguments": [{"role": "Theme", "text": "NFATx1", "start": 1136, "end": 1142}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 292, "end": 301}, "arguments": [{"role": "Theme", "text": "NFATx1", "start": 260, "end": 266}]}], "localization": [{"trigger": {"text": "translocation", "start": 26, "end": 39}, "arguments": [{"role": "Theme", "text": "NFATx1", "start": 11, "end": 17}, {"role": "ToLoc", "text": "nuclear", "start": 18, "end": 25}]}, {"trigger": {"text": "translocation", "start": 1464, "end": 1477}, "arguments": [{"role": "Theme", "text": "NFATx1", "start": 1410, "end": 1416}, {"role": "ToLoc", "text": "nuclear", "start": 1456, "end": 1463}]}, {"trigger": {"text": "localization", "start": 1683, "end": 1695}, "arguments": [{"role": "Theme", "text": "NFATx1", "start": 1619, "end": 1625}, {"role": "AtLoc", "text": "intracellular", "start": 1669, "end": 1682}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 682, "end": 689}, "arguments": [{"role": "Theme", "text": "transcriptional activation", "start": 651, "end": 677}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 595, "end": 604}, "arguments": [{"role": "Theme", "text": "binding", "start": 534, "end": 541}]}, {"trigger": {"text": "transcriptional activation", "start": 651, "end": 677}, "arguments": [{"role": "Theme", "text": "NFATx1", "start": 523, "end": 529}]}, {"trigger": {"text": "leads", "start": 1443, "end": 1448}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1464, "end": 1477}]}, {"trigger": {"text": "independent", "start": 1478, "end": 1489}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1464, "end": 1477}]}], "regulation": [{"trigger": {"text": "Control", "start": 0, "end": 7}, "arguments": [{"role": "Theme", "text": "translocation", "start": 26, "end": 39}]}, {"trigger": {"text": "regulating", "start": 1654, "end": 1664}, "arguments": [{"role": "Theme", "text": "localization", "start": 1683, "end": 1695}]}, {"trigger": {"text": "through", "start": 1696, "end": 1703}, "arguments": [{"role": "Theme", "text": "regulating", "start": 1654, "end": 1664}]}]}}, "schema": []}
{"input": "Neuronal (type I) nitric oxide synthase regulates nuclear factor kappaB activity and immunologic (type II) nitric oxide synthase expression. \nNitric oxide subserves diverse physiologic roles in the nervous system. NO is produced from at least three different NO synthase (NOS) isoforms: neuronal NOS (nNOS), endothelial NOS, and immunologic NOS (iNOS). We show that nNOS is the predominant isoform constitutively expressed in glia. NO derived from nNOS in glia inhibits the transcription factor nuclear factor kappaB (NF kappaB) as NOS inhibitors enhance basal NF kappaB activation. Pyrrolidine dithiocarbamate (PDTC) is an inhibitor of NF kappaB in most cells; however, we show that PDTC is also a potent scavenger of NO through formation of mononitrosyl iron complexes with PDTC. In Jurkat cells, a human T-cell lymphoma cell line, tumor necrosis factor-alpha (TNF-alpha) induces NF kappaB activation that is inhibited by PDTC. Contrary to the results in Jurkat cells, PDTC did not inhibit tumor necrosis factor-alpha-induced NF kappaB activation in astrocytes; instead PDTC itself induces NF kappaB activation in astrocytes, and this may be related to scavenging of endogenously produced NO by the PDTC iron complex. In astrocytes PDTC also dramatically induces the NF kappaB-dependent enzyme, iNOS, supporting the physiologic relevance of endogenous NO regulation of NF kappaB. NF kappaB activation in glia from mice lacking nNOS responds more rapidly to PDTC compared with astrocytes from wild-type mice. Our data suggest that nNOS in astrocytes regulates NF kappaB activity and iNOS expression, and indicate a novel regulatory role for nNOS in tonically suppressing central nervous system, NF kappaB-regulated genes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 129, "end": 139}, "arguments": [{"role": "Theme", "text": "immunologic (type II) nitric oxide synthase", "start": 85, "end": 128}]}, {"trigger": {"text": "expressed", "start": 413, "end": 422}, "arguments": [{"role": "Theme", "text": "nNOS", "start": 366, "end": 370}]}, {"trigger": {"text": "expression", "start": 1589, "end": 1599}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 1584, "end": 1588}]}], "negative regulation": [{"trigger": {"text": "lacking", "start": 1421, "end": 1428}, "arguments": [{"role": "Theme", "text": "nNOS", "start": 1429, "end": 1433}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 1257, "end": 1264}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 1297, "end": 1301}]}, {"trigger": {"text": "dependent", "start": 1279, "end": 1288}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 1297, "end": 1301}]}], "regulation": [{"trigger": {"text": "regulates", "start": 40, "end": 49}, "arguments": [{"role": "Cause", "text": "Neuronal (type I) nitric oxide synthase", "start": 0, "end": 39}, {"role": "Theme", "text": "expression", "start": 129, "end": 139}]}, {"trigger": {"text": "regulates", "start": 1551, "end": 1560}, "arguments": [{"role": "Cause", "text": "nNOS", "start": 1532, "end": 1536}, {"role": "Theme", "text": "expression", "start": 1589, "end": 1599}]}]}}, "schema": []}
{"input": "Regulation of human epsilon germline transcription: role of B-cell-specific activator protein. \nGermline transcripts initiate from promoters upstream of the immunoglobulin switch region, and are necessary to target the appropriate switch region for recombination and switching. Different cytokines activate transcription at the appropriate germline promoter. Because binding sites for B-cell-specific activator protein (BSAP) are located upstream of several switch regions in the immunoglobulin heavy chain gene cluster, BSAP might play a role in the regulation of germline transcription and isotype switching. We investigated whether BSAP plays a role in the transcriptional regulation of the epsilon germline promoter in human B cells. Our results showed that BSAP plays a role in both IL-4-dependent induction and CD40-mediated upregulation of human epsilon germline transcription. BSAP is unique among the transcription factors that regulate epsilon germline expression, because it is B cell specific, and is at the merging point of two signalling pathways that are critical for IgE switching. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Retinoic acid-induced modulation of IL-2 mRNA production and IL-2 receptor expression on T cells. \nBACKGROUND: Retinoic acid (RA) has important immune-modulating effects on both T and B cell function. Our laboratory has shown that RA can enhance in vitro polyclonal B cell immunoglobulin (Ig) response. Investigating cytokines known to affect B cell differentiation, we have recently shown that IL-6 production is augmented by RA. In the present study we have examined the immune modulating effects of RA on IL-2 mRNA, another important cytokine for B cell immunoglobulin production, the expression of IL-2 receptors on T cells, and the RA nuclear receptors. METHODS: Purified T cells were obtained from adenoidal tissues, and incubated with RA (10(-7) M) or DMSO solvent/media control for 0, 6-8, and 24 h. Total mRNA was extracted from T cells, and using RT-PCR, changes in the production of IL-2 and RA receptors (RAR)-alpha,beta,gamma mRNA were determined. The effects of RA on IL-2-alpha receptor expression was determined by flow cytometry on T cells. CONCLUSION: These studies suggest that RA can augment IL-2 mRNA production by T cells with a possible paracrine effect on IL-2R-alpha expression. These changes appear to be mediated by RAR-alpha. Thus, IL-2 may be another important cytokine modulated by RA in the immune response. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 400, "end": 410}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 395, "end": 399}]}, {"trigger": {"text": "expression", "start": 1002, "end": 1012}, "arguments": [{"role": "Theme", "text": "IL-2-alpha receptor", "start": 982, "end": 1001}]}, {"trigger": {"text": "expression", "start": 1192, "end": 1202}, "arguments": [{"role": "Theme", "text": "IL-2R-alpha", "start": 1180, "end": 1191}]}], "positive regulation": [{"trigger": {"text": "augmented", "start": 414, "end": 423}, "arguments": [{"role": "Theme", "text": "production", "start": 400, "end": 410}]}, {"trigger": {"text": "augment", "start": 1104, "end": 1111}, "arguments": [{"role": "Theme", "text": "production", "start": 1122, "end": 1132}]}, {"trigger": {"text": "mediated", "start": 1231, "end": 1239}, "arguments": [{"role": "Theme", "text": "production", "start": 1122, "end": 1132}, {"role": "Cause", "text": "RAR-alpha", "start": 1243, "end": 1252}]}], "regulation": [{"trigger": {"text": "modulation", "start": 22, "end": 32}, "arguments": [{"role": "Theme", "text": "production", "start": 46, "end": 56}]}, {"trigger": {"text": "immune modulating effects", "start": 473, "end": 498}, "arguments": [{"role": "Theme", "text": "mRNA", "start": 513, "end": 517}]}, {"trigger": {"text": "changes", "start": 865, "end": 872}, "arguments": [{"role": "Theme", "text": "production", "start": 880, "end": 890}]}, {"trigger": {"text": "effects", "start": 965, "end": 972}, "arguments": [{"role": "Theme", "text": "expression", "start": 1002, "end": 1012}]}, {"trigger": {"text": "effect", "start": 1170, "end": 1176}, "arguments": [{"role": "Theme", "text": "expression", "start": 1192, "end": 1202}]}, {"trigger": {"text": "modulated", "start": 1299, "end": 1308}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1260, "end": 1264}]}], "transcription": [{"trigger": {"text": "production", "start": 46, "end": 56}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 36, "end": 40}]}, {"trigger": {"text": "mRNA", "start": 513, "end": 517}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 508, "end": 512}]}, {"trigger": {"text": "production", "start": 880, "end": 890}, "arguments": [{"role": "Theme", "text": "RA receptors (RAR)-alpha", "start": 903, "end": 927}]}, {"trigger": {"text": "production", "start": 880, "end": 890}, "arguments": [{"role": "Theme", "text": "beta", "start": 928, "end": 932}]}, {"trigger": {"text": "production", "start": 880, "end": 890}, "arguments": [{"role": "Theme", "text": "gamma", "start": 933, "end": 938}]}, {"trigger": {"text": "production", "start": 1122, "end": 1132}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1112, "end": 1116}]}]}}, "schema": []}
{"input": "Itk, a T cell-specific tyrosine kinase, is required for CD2-mediated interleukin-2 promoter activation in the human T cell line Jurkat. \nWe investigated the functional role of Itk, a member of the cytoplasmic tyrosine kinase Tec family, in T cell activation. Stimulation of either CD2 or T cell receptor (TCR)/CD3 on Tcells by monoclonal antibody-mediated cross-linking induced tyrosine phosphorylation of Itk, which was maximal as early as 1 min after stimulation. The tyrosine kinase activity in the anti-Itk immunoprecipitate was significantly activated upon these stimulations. Interleukin-2 (IL-2) promoter activity stimulated by cross-linking of CD2, TCR/CD3, and CD28 with antibodies was significantly reduced by transient expression of an Itk mutant lacking the kinase activity. The reduction paralleled a decrease in tyrosine phosphorylation of endogenous wild-type Itk. Stimulation of CD2 or TCR/CD3 induced activation of the nuclear factor of activated T cells (NFAT), the binding site of which is included in the IL-2 gene promoter. The activation of NFAT was also impaired by expression of the Itk mutant. These results demonstrate that Itk plays a role in IL-2 production, indicating a critical involvement of Itk in the initial stage of T cell activation by mediating signals from the TCR/CD3 complex, CD2, and CD28. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 356, "end": 369}, "arguments": [{"role": "Theme", "text": "CD2", "start": 281, "end": 284}]}, {"trigger": {"text": "cross-linking", "start": 635, "end": 648}, "arguments": [{"role": "Theme", "text": "CD2", "start": 652, "end": 655}]}, {"trigger": {"text": "cross-linking", "start": 635, "end": 648}, "arguments": [{"role": "Theme", "text": "CD28", "start": 670, "end": 674}]}], "gene expression": [{"trigger": {"text": "expression", "start": 730, "end": 740}, "arguments": [{"role": "Theme", "text": "Itk", "start": 747, "end": 750}]}, {"trigger": {"text": "expression", "start": 1089, "end": 1099}, "arguments": [{"role": "Theme", "text": "Itk", "start": 1107, "end": 1110}]}, {"trigger": {"text": "production", "start": 1175, "end": 1185}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1170, "end": 1174}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 709, "end": 716}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 621, "end": 631}, {"role": "Cause", "text": "expression", "start": 730, "end": 740}]}, {"trigger": {"text": "decrease", "start": 814, "end": 822}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 835, "end": 850}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 387, "end": 402}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 378, "end": 386}, {"role": "Theme", "text": "Itk", "start": 406, "end": 409}]}, {"trigger": {"text": "phosphorylation", "start": 835, "end": 850}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 826, "end": 834}, {"role": "Theme", "text": "Itk", "start": 875, "end": 878}]}], "positive regulation": [{"trigger": {"text": "required", "start": 43, "end": 51}, "arguments": [{"role": "Cause", "text": "Itk", "start": 0, "end": 3}, {"role": "Theme", "text": "activation", "start": 92, "end": 102}]}, {"trigger": {"text": "activation", "start": 92, "end": 102}, "arguments": [{"role": "Cause", "text": "CD2", "start": 56, "end": 59}, {"role": "Theme", "text": "interleukin-2", "start": 69, "end": 82}]}, {"trigger": {"text": "Stimulation", "start": 259, "end": 270}, "arguments": [{"role": "Theme", "text": "CD2", "start": 281, "end": 284}, {"role": "Cause", "text": "cross-linking", "start": 356, "end": 369}]}, {"trigger": {"text": "induced", "start": 370, "end": 377}, "arguments": [{"role": "Cause", "text": "Stimulation", "start": 259, "end": 270}, {"role": "Theme", "text": "phosphorylation", "start": 387, "end": 402}]}, {"trigger": {"text": "induced", "start": 370, "end": 377}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 387, "end": 402}]}, {"trigger": {"text": "maximal", "start": 421, "end": 428}, "arguments": [{"role": "Theme", "text": "induced", "start": 370, "end": 377}]}, {"trigger": {"text": "stimulated", "start": 621, "end": 631}, "arguments": [{"role": "Theme", "text": "Interleukin-2", "start": 582, "end": 595}, {"role": "Site", "text": "promoter", "start": 603, "end": 611}, {"role": "Cause", "text": "cross-linking", "start": 635, "end": 648}]}, {"trigger": {"text": "stimulated", "start": 621, "end": 631}, "arguments": [{"role": "Theme", "text": "Interleukin-2", "start": 582, "end": 595}, {"role": "Site", "text": "promoter", "start": 603, "end": 611}]}, {"trigger": {"text": "Stimulation", "start": 880, "end": 891}, "arguments": [{"role": "Theme", "text": "CD2", "start": 895, "end": 898}]}, {"trigger": {"text": "included", "start": 1009, "end": 1017}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1025, "end": 1029}, {"role": "Site", "text": "promoter", "start": 1035, "end": 1043}]}], "regulation": [{"trigger": {"text": "plays a role", "start": 1154, "end": 1166}, "arguments": [{"role": "Cause", "text": "Itk", "start": 1150, "end": 1153}, {"role": "Theme", "text": "production", "start": 1175, "end": 1185}]}]}}, "schema": []}
{"input": "Jak3 is associated with CD40 and is critical for CD40 induction of gene expression in B cells. \nCD40 is a receptor that is critical for the survival, growth, differentiation, and isotype switching of B lymphocytes. Although CD40 lacks intrinsic tyrosine kinase activity, its ligation induces protein tyrosine phosphorylation, which is necessary for several CD40-mediated events. We show that engagement of CD40 induces tyrosine phosphorylation and activation of Jak3 as well as of STAT3. Jak3 is constitutively associated with CD40, and this interaction requires a proline-rich sequence in the membrane-proximal region of CD40. Deletion of this sequence abolishes the capacity of CD40 to induce expression of CD23, ICAM-1, and lymphotoxin-alpha genes in B cells. These results indicate that signaling through Jak3 is activated by CD40 and plays an important role in CD40-mediated functions. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associated", "start": 8, "end": 18}, "arguments": [{"role": "Theme", "text": "Jak3", "start": 0, "end": 4}, {"role": "Theme2", "text": "CD40", "start": 24, "end": 28}]}, {"trigger": {"text": "ligation", "start": 275, "end": 283}, "arguments": [{"role": "Theme", "text": "CD40", "start": 224, "end": 228}]}, {"trigger": {"text": "associated", "start": 511, "end": 521}, "arguments": [{"role": "Theme", "text": "Jak3", "start": 488, "end": 492}, {"role": "Theme2", "text": "CD40", "start": 527, "end": 531}]}], "gene expression": [{"trigger": {"text": "expression", "start": 695, "end": 705}, "arguments": [{"role": "Theme", "text": "CD23", "start": 709, "end": 713}]}, {"trigger": {"text": "expression", "start": 695, "end": 705}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 715, "end": 721}]}, {"trigger": {"text": "expression", "start": 695, "end": 705}, "arguments": [{"role": "Theme", "text": "lymphotoxin-alpha", "start": 727, "end": 744}]}], "negative regulation": [{"trigger": {"text": "abolishes", "start": 654, "end": 663}, "arguments": [{"role": "Theme", "text": "induce", "start": 688, "end": 694}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 428, "end": 443}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 419, "end": 427}, {"role": "Theme", "text": "Jak3", "start": 462, "end": 466}]}, {"trigger": {"text": "phosphorylation", "start": 428, "end": 443}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 419, "end": 427}, {"role": "Theme", "text": "STAT3", "start": 481, "end": 486}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 411, "end": 418}, "arguments": [{"role": "Cause", "text": "CD40", "start": 406, "end": 410}, {"role": "Theme", "text": "phosphorylation", "start": 428, "end": 443}]}, {"trigger": {"text": "induces", "start": 411, "end": 418}, "arguments": [{"role": "Cause", "text": "CD40", "start": 406, "end": 410}, {"role": "Theme", "text": "activation", "start": 448, "end": 458}]}, {"trigger": {"text": "activation", "start": 448, "end": 458}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 428, "end": 443}, {"role": "Theme", "text": "Jak3", "start": 462, "end": 466}]}, {"trigger": {"text": "activation", "start": 448, "end": 458}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 428, "end": 443}, {"role": "Theme", "text": "STAT3", "start": 481, "end": 486}]}, {"trigger": {"text": "requires", "start": 554, "end": 562}, "arguments": [{"role": "Theme", "text": "associated", "start": 511, "end": 521}, {"role": "CSite", "text": "proline-rich sequence", "start": 565, "end": 586}, {"role": "Cause", "text": "CD40", "start": 622, "end": 626}]}, {"trigger": {"text": "induce", "start": 688, "end": 694}, "arguments": [{"role": "Cause", "text": "CD40", "start": 680, "end": 684}, {"role": "Theme", "text": "expression", "start": 695, "end": 705}]}], "regulation": [{"trigger": {"text": "role", "start": 858, "end": 862}, "arguments": [{"role": "Theme", "text": "expression", "start": 695, "end": 705}]}]}}, "schema": []}
{"input": "The tumour associated cell surface antigen A6H is costimulatory for human CD4+ but not CD8+ T cells. \nThe A6H monoclonal antibody (mAb) recognizes a 120,000-140,000 MW antigen that is expressed at similar densities on 85-90% of human CD4+ and CD8+ T cells and on renal cell carcinomas. The binding of the A6H mAb induced a costimulatory signal in anti-CD3 activated T cells. In the present report, we show that A6H costimulated cell proliferation and cytokine production in purified CD4+ T cells. Unexpectedly, the CD8+ T-cell subpopulation failed to respond. CD4+ T cells costimulated with the A6H mAb upregulated CD80, CD86, CD71, interleukin-2 (IL-2)R alpha, IL-2R beta and IL-2R gamma, while no corresponding up-regulation of these cell surface molecules was seen in CD8+ T cells. In order to investigate the nature of the A6H mAb costimulus at the transcriptional level we have examined induction of the transcription factors OCT-1, AP-1 and NF-kappa B which are known to be transcriptional regulators of several cytokine and cytokine receptor genes, including the IL-2 and IL-2R genes. Co-ligation of the A6H antigen and the CD3 complex induced expression of the transcription factor AP-1 in CD4+ T cells, whereas no increase in NF-kappa B and octamer-binding (Oct) proteins was seen compared to T cells stimulated with anti-CD3 alone. Furthermore, no induction of AP-1 was seen in A6H costimulated CD8+ T cells. These results suggests that both proximal steps in CD8+ T-cell activation as well as the later phases are unresponsive to A6H ligation. Molecular differences of the A6H molecule or distinct regulation of the A6H transduced AP-1 activation pathway may exist in CD4+ and CD8+ T cell subpopulations. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "upregulated", "start": 603, "end": 614}, "arguments": [{"role": "Theme", "text": "CD80", "start": 615, "end": 619}]}, {"trigger": {"text": "upregulated", "start": 603, "end": 614}, "arguments": [{"role": "Theme", "text": "CD86", "start": 621, "end": 625}]}, {"trigger": {"text": "upregulated", "start": 603, "end": 614}, "arguments": [{"role": "Theme", "text": "CD71", "start": 627, "end": 631}]}, {"trigger": {"text": "upregulated", "start": 603, "end": 614}, "arguments": [{"role": "Theme", "text": "interleukin-2 (IL-2)R alpha", "start": 633, "end": 660}]}, {"trigger": {"text": "upregulated", "start": 603, "end": 614}, "arguments": [{"role": "Theme", "text": "IL-2R beta", "start": 662, "end": 672}]}, {"trigger": {"text": "upregulated", "start": 603, "end": 614}, "arguments": [{"role": "Theme", "text": "IL-2R gamma", "start": 677, "end": 688}]}, {"trigger": {"text": "up-regulation", "start": 713, "end": 726}, "arguments": [{"role": "Theme", "text": "CD80", "start": 615, "end": 619}]}, {"trigger": {"text": "up-regulation", "start": 713, "end": 726}, "arguments": [{"role": "Theme", "text": "CD86", "start": 621, "end": 625}]}, {"trigger": {"text": "up-regulation", "start": 713, "end": 726}, "arguments": [{"role": "Theme", "text": "CD71", "start": 627, "end": 631}]}, {"trigger": {"text": "up-regulation", "start": 713, "end": 726}, "arguments": [{"role": "Theme", "text": "interleukin-2 (IL-2)R alpha", "start": 633, "end": 660}]}, {"trigger": {"text": "up-regulation", "start": 713, "end": 726}, "arguments": [{"role": "Theme", "text": "IL-2R beta", "start": 662, "end": 672}]}, {"trigger": {"text": "up-regulation", "start": 713, "end": 726}, "arguments": [{"role": "Theme", "text": "IL-2R gamma", "start": 677, "end": 688}]}, {"trigger": {"text": "induction", "start": 892, "end": 901}, "arguments": [{"role": "Theme", "text": "OCT-1", "start": 931, "end": 936}]}], "regulation": [{"trigger": {"text": "transcriptional regulators", "start": 980, "end": 1006}, "arguments": [{"role": "Cause", "text": "OCT-1", "start": 931, "end": 936}, {"role": "Theme", "text": "IL-2", "start": 1070, "end": 1074}]}, {"trigger": {"text": "transcriptional regulators", "start": 980, "end": 1006}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1070, "end": 1074}]}]}}, "schema": []}
{"input": "Structure and function analysis of the human myeloid cell nuclear differentiation antigen promoter: evidence for the role of Sp1 and not of c-Myb or PU.1 in myelomonocytic lineage-specific expression. \nThe human myeloid nuclear differentiation antigen (MNDA) is expressed specifically in maturing cells of the myelomonocytic lineage and in monocytes and granulocytes. Epitope enhancement was used to confirm the strict lineage- and stage-specific expression of MNDA in bone marrow as well as in other paraffin-embedded fixed tissues. A 1-kb region of the gene that includes 5' flanking sequence was reported earlier to contain functional promoter activity and was specifically demethylated in expressing cells in contrast to null cells. Further analysis has revealed that this 1-kb fragment promotes higher reporter gene activity in MNDA-expressing cells than non-expressing cells, indicating cell-specific differences in transactivation. This sequence contains consensus elements consistent with myeloid-specific gene expression, including a PU.1 consensus site near the major transcription start site and a cluster of c-Myb sites located several hundred bases upstream of this region. However, analysis of deletion mutants localized nearly all of the promoter activity to a short region (-73 to -16) that did not include the cluster of c-Myb sites. A 4-bp mutation of the core Sp1 consensus element (GC box) (-20) reduced overall promoter activity of the 1-kb fragment. Mutation of the PU.1 site did not significantly affect promoter activity. Only a small region (-35 to +22) including the Sp1 element and transcription start site, but not the PU.1 site was footprinted. The 4-bp mutation of the core Sp1 consensus element abolished footprinting at the site and an antibody super-shift reaction showed that Sp1 is one of the factors binding the consensus site. The Sp1 site also co-localizes with a DNase I hypersensitive site. The results indicate that DNA methylation, chromatin structure, and transactivation at an Sp1 site contribute to the highly restricted expression of this myelomonocytic lineage specific gene. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1836, "end": 1843}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1810, "end": 1813}]}], "gene expression": [{"trigger": {"text": "expression", "start": 189, "end": 199}, "arguments": [{"role": "Theme", "text": "myeloid cell nuclear differentiation antigen", "start": 45, "end": 89}]}, {"trigger": {"text": "expressed", "start": 262, "end": 271}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 253, "end": 257}]}, {"trigger": {"text": "expression", "start": 447, "end": 457}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 461, "end": 465}]}, {"trigger": {"text": "expressing", "start": 838, "end": 848}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 833, "end": 837}]}, {"trigger": {"text": "non-expressing", "start": 860, "end": 874}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 833, "end": 837}]}, {"trigger": {"text": "expression", "start": 1019, "end": 1029}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 833, "end": 837}]}, {"trigger": {"text": "expression", "start": 2066, "end": 2076}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 833, "end": 837}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 1416, "end": 1423}, "arguments": [{"role": "Theme", "text": "promoter activity", "start": 1432, "end": 1449}]}], "positive regulation": [{"trigger": {"text": "contain functional promoter activity", "start": 619, "end": 655}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 461, "end": 465}]}, {"trigger": {"text": "promoter activity", "start": 1253, "end": 1270}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 833, "end": 837}]}, {"trigger": {"text": "promoter activity", "start": 1432, "end": 1449}, "arguments": [{"role": "Theme", "text": "MNDA", "start": 833, "end": 837}]}, {"trigger": {"text": "contribute", "start": 2030, "end": 2040}, "arguments": [{"role": "Theme", "text": "expression", "start": 2066, "end": 2076}]}], "regulation": [{"trigger": {"text": "role", "start": 117, "end": 121}, "arguments": [{"role": "Cause", "text": "Sp1", "start": 125, "end": 128}, {"role": "Theme", "text": "expression", "start": 189, "end": 199}]}, {"trigger": {"text": "role", "start": 117, "end": 121}, "arguments": [{"role": "Cause", "text": "c-Myb", "start": 140, "end": 145}, {"role": "Theme", "text": "expression", "start": 189, "end": 199}]}, {"trigger": {"text": "role", "start": 117, "end": 121}, "arguments": [{"role": "Cause", "text": "PU.1", "start": 149, "end": 153}, {"role": "Theme", "text": "expression", "start": 189, "end": 199}]}, {"trigger": {"text": "affect", "start": 1520, "end": 1526}, "arguments": [{"role": "Theme", "text": "promoter activity", "start": 1432, "end": 1449}]}, {"trigger": {"text": "contribute", "start": 2030, "end": 2040}, "arguments": [{"role": "Theme", "text": "expression", "start": 2066, "end": 2076}]}]}}, "schema": []}
{"input": "Inhibitor (IK) of IFN-gamma induced HLA class II antigens expression also inhibits HLA class II constitutive expression in the human Raji B cell line. \nThe expression of major histocompatibility complex (MHC) class II antigens is constitutive in professional antigen presenting cells (APCs) but can also be induced by interferon-gamma (IFN-gamma) on the majority of the non professional APCs (e.g. fibroblasts). We have recently characterised a new factor called IK which is an efficient inhibitor of IFN-gamma induction of MHC class II antigens expression. Here, we demonstrate a novel role for IK in MHC class II expression since over-expression of this protein by stable transfection into human B cells led to a total disappearance of constitutive MHC class II mRNA expression. The class II transactivator (CIITA) is necessary for both constitutive and IFN-gamma induced MHC class II expressions. Examination of CIITA mRNA in IK stably transfected clones revealed a marked reduction of CIITA mRNA transcription. Taken together these results demonstrate that the IK protein plays a key role in the constitutive expression of MHC class II antigens and that inhibition induced by IK is upstream of CIITA in this regulatory pathway. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "over-expression", "start": 632, "end": 647}, "arguments": [{"role": "Theme", "text": "IK", "start": 596, "end": 598}]}, {"trigger": {"text": "transfected", "start": 939, "end": 950}, "arguments": [{"role": "Theme", "text": "IK", "start": 929, "end": 931}]}], "negative regulation": [{"trigger": {"text": "reduction", "start": 976, "end": 985}, "arguments": [{"role": "Cause", "text": "transfected", "start": 939, "end": 950}, {"role": "Theme", "text": "transcription", "start": 1000, "end": 1013}]}, {"trigger": {"text": "inhibition", "start": 1158, "end": 1168}, "arguments": [{"role": "Cause", "text": "IK", "start": 1180, "end": 1182}, {"role": "Theme", "text": "CIITA", "start": 1198, "end": 1203}]}], "positive regulation": [{"trigger": {"text": "over-expression", "start": 632, "end": 647}, "arguments": [{"role": "Theme", "text": "over-expression", "start": 632, "end": 647}]}, {"trigger": {"text": "transfected", "start": 939, "end": 950}, "arguments": [{"role": "Theme", "text": "transfected", "start": 939, "end": 950}]}], "transcription": [{"trigger": {"text": "mRNA", "start": 921, "end": 925}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 915, "end": 920}]}, {"trigger": {"text": "transcription", "start": 1000, "end": 1013}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 989, "end": 994}]}]}}, "schema": []}
{"input": "An enhancer-blocking element between alpha and delta gene segments within the human T cell receptor alpha/delta locus. \nT cell receptor (TCR) alpha and delta gene segments are organized within a single genetic locus but are differentially regulated during T cell development. An enhancer-blocking element (BEAD-1, for blocking element alpha/delta 1) was localized to a 2.0-kb region 3' of TCR delta gene segments and 5' of TCR alpha joining gene segments within this locus. BEAD-1 blocked the ability of the TCR delta enhancer (Edelta) to activate a promoter when located between the two in a chromatin-integrated construct. We propose that BEAD-1 functions as a boundary that separates the TCR alpha/delta locus into distinct regulatory domains controlled by Edelta and the TCR alpha enhancer, and that it prevents Edelta from opening the chromatin of the TCR alpha joining gene segments for VDJ recombination at an early stage of T cell development. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Quantification of vitamin D receptor mRNA by competitive polymerase chain reaction in PBMC: lack of correspondence with common allelic variants. \nIt has been recently claimed that polymorphism for the vitamin D receptor (VDR) influences several aspects of calcium and bone metabolism. To evaluate the physiologic plausibility of these claims, we compared the abundance of the VDR mRNA in peripheral blood mononuclear cells (PBMCs) between different VDR genotypes using a quantitative reverse transcribed polymerase chain reaction-based method. The method is based on the coamplification of VDR cDNA and an internal standard consisting of known concentrations of a human VDR CDNA mutated at a BglII restriction site; the interassay coefficient of variation is 11%. To validate the method, we made use of earlier receptor binding studies indicating that normal human monocytes and activated, but not resting, lymphocytes expressed the VDR. The concentration of the VDR mRNA was 10(-8) to 10(-7) g/g of total RNA in cell-sorted monocytes and in in vitro activated lymphocytes, but only 10(-12) g/g of total mRNA in resting lymphocytes, establishing that the VDR mRNA determined by our method in PBMCs is due to constitutive expression in monocytes. Following an initial genotype screening of 85 normal volunteers by polymerase chain reaction or restriction fragment length polymorphism analysis, 14 individuals with the Bb genotype, 12 with the bb genotype, and 12 with the BB genotype were selected. The concentration of the VDR mRNA, corrected for the number of monocytes, was similar among the three genotype groups, as were the other variables examined: serum calcitriol, serum osteocalcin, and vertebral and hip bone density. We conclude that VDR polymorphism does not affect the abundance of the VDR mRNA. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 919, "end": 928}, "arguments": [{"role": "Theme", "text": "VDR", "start": 933, "end": 936}]}], "regulation": [{"trigger": {"text": "affect", "start": 1771, "end": 1777}, "arguments": [{"role": "Theme", "text": "abundance", "start": 1782, "end": 1791}]}], "transcription": [{"trigger": {"text": "abundance", "start": 359, "end": 368}, "arguments": [{"role": "Theme", "text": "VDR", "start": 376, "end": 379}]}, {"trigger": {"text": "expression", "start": 1221, "end": 1231}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1155, "end": 1158}]}, {"trigger": {"text": "concentration", "start": 1502, "end": 1515}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1523, "end": 1526}]}, {"trigger": {"text": "abundance", "start": 1782, "end": 1791}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1799, "end": 1802}]}]}}, "schema": []}
{"input": "Regulation of CD95 (Fas) ligand expression by TCR-mediated signaling events. \nStimulation of mature peripheral T cells by TCR engagement results in activation of signals that drive induction of cytokine gene expression and clonal expansion. However, under some conditions, engagement of the TCR leads instead to apoptosis. Recent studies demonstrate that TCR-stimulated apoptosis requires expression of CD95 ligand on activated T cells followed by an interaction between CD95 ligand and the CD95 receptor also expressed on this population. The experiments reported in this study were designed to address the signaling events triggered by TCR engagement that are important for regulating CD95 ligand gene expression. To approach this, we generated a luciferase reporter construct containing elements of the CD95 ligand promoter. Using a previously described mutant of the Jurkat T cell line, we show that proximal signaling events dependent on the presence of the CD45 tyrosine phosphatase are required for TCR-stimulated CD95 ligand expression. Transient transfection studies demonstrate further that TCR-stimulated activation of the Ras signaling pathway is required for optimal activation of CD95 ligand. Next, in an effort to determine critical transcription factors that regulate CD95 ligand expression, we demonstrate a cyclosporin A-sensitive nuclear factor-AT response element in the promoter region of this gene that is critical for optimal CD95 ligand reporter activity in stimulated T cells. Together, these studies begin a dissection of the biochemical events that lead to expression of CD95 ligand, a required step for TCR-induced apoptosis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 451, "end": 462}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 471, "end": 482}]}], "gene expression": [{"trigger": {"text": "expression", "start": 32, "end": 42}, "arguments": [{"role": "Theme", "text": "CD95 (Fas) ligand", "start": 14, "end": 31}]}, {"trigger": {"text": "expression", "start": 389, "end": 399}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 403, "end": 414}]}, {"trigger": {"text": "expression", "start": 704, "end": 714}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 687, "end": 698}]}, {"trigger": {"text": "expression", "start": 1033, "end": 1043}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 1021, "end": 1032}]}, {"trigger": {"text": "expression", "start": 1296, "end": 1306}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 1284, "end": 1295}]}, {"trigger": {"text": "expression", "start": 1584, "end": 1594}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 1598, "end": 1609}]}], "positive regulation": [{"trigger": {"text": "required", "start": 993, "end": 1001}, "arguments": [{"role": "Theme", "text": "stimulated", "start": 1010, "end": 1020}]}, {"trigger": {"text": "stimulated", "start": 1010, "end": 1020}, "arguments": [{"role": "Theme", "text": "expression", "start": 1033, "end": 1043}]}, {"trigger": {"text": "required", "start": 1159, "end": 1167}, "arguments": [{"role": "Theme", "text": "activation", "start": 1180, "end": 1190}]}, {"trigger": {"text": "activation", "start": 1180, "end": 1190}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 1194, "end": 1205}]}, {"trigger": {"text": "critical", "start": 1428, "end": 1436}, "arguments": [{"role": "Theme", "text": "CD95 ligand", "start": 1449, "end": 1460}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 32, "end": 42}]}, {"trigger": {"text": "important for regulating", "start": 662, "end": 686}, "arguments": [{"role": "Theme", "text": "expression", "start": 704, "end": 714}]}, {"trigger": {"text": "regulate", "start": 1275, "end": 1283}, "arguments": [{"role": "Theme", "text": "expression", "start": 1296, "end": 1306}]}]}}, "schema": []}
{"input": "CD40 is a functional activation antigen and B7-independent T cell costimulatory molecule on normal human lung fibroblasts. \nCD40 is an important signaling and activation Ag found on certain bone marrow-derived cells. Recently, CD40 also has been shown to be expressed by mesenchymal cells, including human fibroblasts. Little is known about the role of CD40 in fibroblasts. The current study investigates the hypothesis that CD40 expressed on lung fibroblasts is an activation structure and mechanism for interaction with hemopoietic cells. Communication between resident tissue fibroblasts and T cells is necessary for normal wound healing, and can be pathologic, resulting in tissue fibrosis. Signaling through CD40 with soluble CD40 ligand stimulated fibroblast activation, as evidenced by mobilization of nuclear factor-kappaB and by induction of the proinflammatory and chemoattractant cytokines IL-6 and IL-8. IFN-gamma-primed lung fibroblasts costimulate T lymphocyte proliferation utilizing CD40, but not the well-studied costimulatory molecules B7-1 and B7-2. Data reported herein support the hypothesis that cognate interactions between tissue fibroblasts and infiltrating T lymphocytes, via the CD40/CD40L pathway, augment inflammation and may promote fibrogenesis by activating both cell types. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "found", "start": 173, "end": 178}, "arguments": [{"role": "Theme", "text": "CD40", "start": 124, "end": 128}]}, {"trigger": {"text": "expressed", "start": 258, "end": 267}, "arguments": [{"role": "Theme", "text": "CD40", "start": 227, "end": 231}]}, {"trigger": {"text": "expressed", "start": 430, "end": 439}, "arguments": [{"role": "Theme", "text": "CD40", "start": 425, "end": 429}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 838, "end": 847}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 901, "end": 905}]}, {"trigger": {"text": "induction", "start": 838, "end": 847}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 910, "end": 914}]}]}}, "schema": []}
{"input": "Tap: a novel cellular protein that interacts with tip of herpesvirus saimiri and induces lymphocyte aggregation. \nTip of herpesvirus saimiri associates with Lck and down-regulates Lck-mediated activation. We identified a novel cellular Tip-associated protein (Tap) by a yeast two-hybrid screen. Tap associated with Tip following transient expression in COS-1 cells and stable expression in human Jurkat-T cells. Expression of Tip and Tap in Jurkat-T cells induced dramatic cell aggregation. Aggregation was likely caused by the up-regulated surface expression of adhesion molecules including integrin alpha, L-selectin, ICAM-3, and H-CAM. Furthermore, NF-kappaB transcriptional factor of aggregated cells had approximately 40-fold higher activity than that of parental cells. Thus, Tap is likely to be an important cellular mediator of Tip function in T cell transformation by herpesvirus saimiri. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associates", "start": 141, "end": 151}, "arguments": [{"role": "Theme", "text": "Lck", "start": 157, "end": 160}]}], "gene expression": [{"trigger": {"text": "expression", "start": 549, "end": 559}, "arguments": [{"role": "Theme", "text": "L-selectin", "start": 608, "end": 618}]}, {"trigger": {"text": "expression", "start": 549, "end": 559}, "arguments": [{"role": "Theme", "text": "ICAM-3", "start": 620, "end": 626}]}, {"trigger": {"text": "expression", "start": 549, "end": 559}, "arguments": [{"role": "Theme", "text": "H-CAM", "start": 632, "end": 637}]}], "positive regulation": [{"trigger": {"text": "up-regulated", "start": 528, "end": 540}, "arguments": [{"role": "Theme", "text": "expression", "start": 549, "end": 559}]}]}}, "schema": []}
{"input": "Transactivation by CIITA, the type II bare lymphocyte syndrome-associated factor, requires participation of multiple regions of the TATA box binding protein. \nCIITA is a positive regulator of class II major histocompatibility complex gene transcription that has been found to be defective in one of the five complementation groups of class II major histocompatibility complex-negative cell lines. Its N-terminal region is capable of activating transcription from a reporter gene when fused to a DNA binding domain. We have investigated the mechanism of transactivation mediated by the CIITA activation domain by studying its role in the process of transcription initiation and elongation. Specifically the altered specificity TBP (TATA box binding protein) assay has been used to analyze the response of the CIITA activation domain to mutations in TBP known to disrupt its interaction with its associated general factors. Transactivation by CIITA was extremely sensitive to a mutation in TBP that in yeast is known to abolish VP16-mediated transcription but leaves basal transcription unaffected. A TBP mutant defective in interaction with TBP-associated factor TAFII250 also failed to mediate transactivation through the CIITA activation domain. Certain interactions between TBP and general factors that are specifically required for acidic activation domains were also required for CIITA-mediated transactivation to reach its full potential. Finally, like VP16, CIITA was able to stimulate elongation of transcription. Overall the mechanism of transactivation by the human B-cell-specific CIITA is very similar to that mediated by the herpes virus transactivator VP16 in the ways that have been tested. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 873, "end": 884}, "arguments": [{"role": "Theme", "text": "TBP", "start": 848, "end": 851}]}, {"trigger": {"text": "interaction", "start": 1123, "end": 1134}, "arguments": [{"role": "Theme", "text": "TBP", "start": 1099, "end": 1102}, {"role": "Theme2", "text": "TAFII250", "start": 1162, "end": 1170}]}, {"trigger": {"text": "interactions", "start": 1255, "end": 1267}, "arguments": [{"role": "Theme", "text": "TBP", "start": 1276, "end": 1279}]}], "negative regulation": [{"trigger": {"text": "defective", "start": 279, "end": 288}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 159, "end": 164}]}, {"trigger": {"text": "disrupt", "start": 861, "end": 868}, "arguments": [{"role": "Theme", "text": "interaction", "start": 873, "end": 884}]}]}}, "schema": []}
{"input": "Specific complex formation between the type II bare lymphocyte syndrome-associated transactivators CIITA and RFX5. \nTwo of the genes defective in the five complementation groups identified in the class II-negative bare lymphocyte syndrome or corresponding laboratory mutants have been cloned. One gene encodes a protein, RFX5, that is a member of the RFX family of DNA binding proteins. The other, CIITA, encodes a large protein with a defined acidic transcriptional activation domain; this protein does not interact with DNA. Expression plasmids encoding regions of RFX5 fused to the GAL4 DNA binding domain activated transcription from a reporter construct containing GAL4 sites in a cotransfection assay in the Raji human B cell line. However, these plasmids produced transcriptional activity in HeLa cells only in conjunction with interferon gamma stimulation, a condition in which expression of both CIITA and class II major histocompatibility complex surface proteins are induced. Furthermore, these plasmids were not active in RJ2.2.5, an in vitro mutagenized derivative of Raji in which both copies of CIITA are defective. Transcriptional activation by the RFX5 fusion protein could be restored in RJ2.2.5 by cotransfection with a CIITA expression plasmid. Finally, a direct interaction between RFX5 and CIITA was detected with the yeast two-hybrid and far-Western blot assays. Thus, RFX5 can activate transcription only in cooperation with CIITA. RFX5 and CIITA associate to form a complex capable of activating transcription from class II major histocompatibility complex promoters. In this complex, promoter specificity is determined by the DNA binding domain of RFX5 and the general transcription apparatus is recruited by the acidic activation domain of CIITA. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complex formation", "start": 9, "end": 26}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 99, "end": 104}, {"role": "Theme2", "text": "RFX5", "start": 109, "end": 113}]}, {"trigger": {"text": "interact", "start": 508, "end": 516}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 398, "end": 403}]}, {"trigger": {"text": "interaction", "start": 1283, "end": 1294}, "arguments": [{"role": "Theme", "text": "RFX5", "start": 1303, "end": 1307}, {"role": "Theme2", "text": "CIITA", "start": 1312, "end": 1317}]}, {"trigger": {"text": "associate to form a complex", "start": 1471, "end": 1498}, "arguments": [{"role": "Theme", "text": "RFX5", "start": 1456, "end": 1460}, {"role": "Theme2", "text": "CIITA", "start": 1465, "end": 1470}]}, {"trigger": {"text": "specificity", "start": 1619, "end": 1630}, "arguments": [{"role": "Site", "text": "DNA binding domain", "start": 1652, "end": 1670}, {"role": "Theme", "text": "RFX5", "start": 1674, "end": 1678}]}], "gene expression": [{"trigger": {"text": "expression", "start": 886, "end": 896}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 905, "end": 910}]}, {"trigger": {"text": "expression", "start": 1245, "end": 1255}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 1239, "end": 1244}]}], "negative regulation": [{"trigger": {"text": "defective", "start": 133, "end": 142}, "arguments": [{"role": "Theme", "text": "RFX5", "start": 109, "end": 113}]}, {"trigger": {"text": "defective", "start": 133, "end": 142}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 99, "end": 104}]}, {"trigger": {"text": "defective", "start": 1120, "end": 1129}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 1110, "end": 1115}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 978, "end": 985}, "arguments": [{"role": "Theme", "text": "expression", "start": 886, "end": 896}]}, {"trigger": {"text": "cotransfection", "start": 1217, "end": 1231}, "arguments": [{"role": "Theme", "text": "expression", "start": 1245, "end": 1255}]}]}}, "schema": []}
{"input": "Reactive oxygen species and antioxidants in inflammatory diseases. \nThis paper aims to review the role of free radical-induced tissue damage and antioxidant defence mechanisms in inflammatory diseases that involve pathogenic processes similar to the periodontal diseases. There is a clearly defined and substantial role for free radicals or reactive oxygen species (ROS) in periodontitis, but little research has been performed in this area. This paper reviews the considerable data available relating ROS activity and antioxidant defence to inflammatory diseases and attempts to draw parallels with periodontitis, in an effort to stimulate more periodontal research in this important area. The recent discovery of the transcription factor nuclear factor kappa B (NF-kappa B) is reviewed and several potential pathways for cytokine-induced periodontal tissue damage, mediated by NF-kappa B1 are discussed. Emphasis is placed on cytokines that have been studied in periodontitis, principally TNF-alpha, IL-1, IL-6, IL-8 and beta-interferon. The link between cellular production of such important mediators of inflammation and the antioxidant (AO) thiols, cysteine and reduced glutathione (GSH), is discussed and it is hypothesised that NF-kappa B antagonists may offer important therapeutic benefits. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 1066, "end": 1076}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1008, "end": 1012}]}, {"trigger": {"text": "production", "start": 1066, "end": 1076}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1014, "end": 1018}]}, {"trigger": {"text": "production", "start": 1066, "end": 1076}, "arguments": [{"role": "Theme", "text": "beta-interferon", "start": 1023, "end": 1038}]}, {"trigger": {"text": "production", "start": 1066, "end": 1076}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 991, "end": 1000}]}]}}, "schema": []}
{"input": "Transcriptional activity and constitutive nuclear localization of the ETS protein Elf-1. \nElf-1 is a lymphoid-specific transcription factor that belongs to the ETS protein family. It can bind to DNA target sequences within a variety of cytokine genes. We demonstrate that Elf-1 is constitutively localized in the nucleus which is dependent on the presence of amino acids 86-265. Analysis of Gal4-Elf-1 fusion proteins revealed that the N-terminal 86 amino acids of Elf-1 contain a transcriptional activation domain, the activity of which is attenuated by an internal repression domain. Furthermore, Elf-1 interacts specifically with the E74 target sequence and can stimulate transcription driven by the E74 site independent of mitogenic signaling. Thus, Elf-1 is able to stimulate gene transcription which may be required for the development and activity of lymphocytes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 187, "end": 191}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 90, "end": 95}]}, {"trigger": {"text": "interacts", "start": 605, "end": 614}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 599, "end": 604}]}], "localization": [{"trigger": {"text": "localization", "start": 50, "end": 62}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 42, "end": 49}, {"role": "Theme", "text": "Elf-1", "start": 82, "end": 87}]}, {"trigger": {"text": "localized", "start": 296, "end": 305}, "arguments": [{"role": "Theme", "text": "Elf-1", "start": 272, "end": 277}, {"role": "AtLoc", "text": "nucleus", "start": 313, "end": 320}]}], "positive regulation": [{"trigger": {"text": "dependent", "start": 330, "end": 339}, "arguments": [{"role": "Theme", "text": "localized", "start": 296, "end": 305}]}]}}, "schema": []}
{"input": "Overexpression of HSF2-beta inhibits hemin-induced heat shock gene expression and erythroid differentiation in K562 cells. \nAcquisition of heat shock factor 2 (HSF2) DNA binding activity is accompanied by induced transcription of heat shock genes in hemin-treated K562 cells undergoing erythroid differentiation. Previous studies revealed that HSF2 consists of two alternatively spliced isoforms, HSF2-alpha and HSF2-beta, whose relative abundance is developmentally regulated and varies between different tissues. To investigate whether the molar ratio of HSF2-alpha and HSF2-beta isoforms is crucial for the activation of HSF2 and whether the HSF2 isoforms play functionally distinct roles during the hemin-mediated erythroid differentiation, we generated cell clones expressing different levels of HSF2-alpha and HSF2-beta. We show that in parental K562 cells, the HSF2-alpha isoform is predominantly expressed and HSF2 can be activated upon hemin treatment. In contrast, when HSF2-beta is expressed at levels exceeding those of endogenous HSF2-alpha, the hemin-induced DNA binding activity and transcription of heat shock genes are repressed, whereas overexpression of HSF2-alpha results in an enhanced hemin response. Furthermore, the hemin-induced accumulation of globin, known as a marker of erythroid differentiation, is decreased in cells overexpressing HSF2-beta. We suggest that HSF2-beta acts as a negative regulator of HSF2 activity during hemin-mediated erythroid differentiation of K562 cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 170, "end": 177}, "arguments": [{"role": "Theme", "text": "HSF2", "start": 160, "end": 164}]}], "gene expression": [{"trigger": {"text": "Overexpression", "start": 0, "end": 14}, "arguments": [{"role": "Theme", "text": "HSF2-beta", "start": 18, "end": 27}]}, {"trigger": {"text": "expressing", "start": 770, "end": 780}, "arguments": [{"role": "Theme", "text": "HSF2-alpha", "start": 801, "end": 811}]}, {"trigger": {"text": "expressing", "start": 770, "end": 780}, "arguments": [{"role": "Theme", "text": "HSF2-beta", "start": 816, "end": 825}]}, {"trigger": {"text": "expressed", "start": 904, "end": 913}, "arguments": [{"role": "Theme", "text": "HSF2-alpha", "start": 868, "end": 878}]}, {"trigger": {"text": "expressed", "start": 993, "end": 1002}, "arguments": [{"role": "Theme", "text": "HSF2-alpha", "start": 1043, "end": 1053}]}, {"trigger": {"text": "expressed", "start": 993, "end": 1002}, "arguments": [{"role": "Theme", "text": "HSF2-beta", "start": 980, "end": 989}]}, {"trigger": {"text": "overexpression", "start": 1155, "end": 1169}, "arguments": [{"role": "Theme", "text": "HSF2-alpha", "start": 1173, "end": 1183}]}, {"trigger": {"text": "overexpressing", "start": 1348, "end": 1362}, "arguments": [{"role": "Theme", "text": "HSF2-beta", "start": 1363, "end": 1372}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 1329, "end": 1338}, "arguments": [{"role": "Theme", "text": "overexpressing", "start": 1348, "end": 1362}]}, {"trigger": {"text": "negative regulator", "start": 1410, "end": 1428}, "arguments": [{"role": "Cause", "text": "HSF2-beta", "start": 1390, "end": 1399}, {"role": "Theme", "text": "HSF2", "start": 1432, "end": 1436}]}], "positive regulation": [{"trigger": {"text": "Overexpression", "start": 0, "end": 14}, "arguments": [{"role": "Theme", "text": "Overexpression", "start": 0, "end": 14}]}, {"trigger": {"text": "activation", "start": 610, "end": 620}, "arguments": [{"role": "Theme", "text": "HSF2", "start": 624, "end": 628}]}, {"trigger": {"text": "activated", "start": 930, "end": 939}, "arguments": [{"role": "Theme", "text": "HSF2", "start": 918, "end": 922}]}, {"trigger": {"text": "levels", "start": 1006, "end": 1012}, "arguments": [{"role": "Theme", "text": "expressed", "start": 993, "end": 1002}]}, {"trigger": {"text": "overexpression", "start": 1155, "end": 1169}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 1155, "end": 1169}]}, {"trigger": {"text": "overexpressing", "start": 1348, "end": 1362}, "arguments": [{"role": "Theme", "text": "overexpressing", "start": 1348, "end": 1362}]}], "regulation": [{"trigger": {"text": "accompanied", "start": 190, "end": 201}, "arguments": [{"role": "Theme", "text": "binding", "start": 170, "end": 177}]}, {"trigger": {"text": "regulated", "start": 467, "end": 476}, "arguments": [{"role": "Theme", "text": "HSF2-alpha", "start": 397, "end": 407}]}, {"trigger": {"text": "regulated", "start": 467, "end": 476}, "arguments": [{"role": "Theme", "text": "HSF2-beta", "start": 412, "end": 421}]}, {"trigger": {"text": "varies", "start": 481, "end": 487}, "arguments": [{"role": "Theme", "text": "HSF2-alpha", "start": 397, "end": 407}]}, {"trigger": {"text": "varies", "start": 481, "end": 487}, "arguments": [{"role": "Theme", "text": "HSF2-beta", "start": 412, "end": 421}]}, {"trigger": {"text": "crucial", "start": 594, "end": 601}, "arguments": [{"role": "Cause", "text": "HSF2-alpha", "start": 557, "end": 567}, {"role": "Theme", "text": "activation", "start": 610, "end": 620}]}, {"trigger": {"text": "crucial", "start": 594, "end": 601}, "arguments": [{"role": "Cause", "text": "HSF2-beta", "start": 572, "end": 581}, {"role": "Theme", "text": "activation", "start": 610, "end": 620}]}]}}, "schema": []}
{"input": "Glucocorticoid-mediated repression of cytokine gene transcription in human arteritis-SCID chimeras. \nGiant cell arteritis (GCA) is a vasculitic syndrome that preferentially affects medium and large-sized arteries. Glucocorticoid therapy resolves clinical symptoms within hours to days, but therapy has to be continued over several years to prevent disease relapses. It is not known whether and how glucocorticoids affect the function of the inflammatory infiltrate or why the disease persists subclinically despite chronic treatment. GCA is self-sustained in temporal arteries engrafted into SCID mice, providing a model in which the mechanisms of action and limitations of glucocorticoid therapy can be examined in vivo. Administration of dexamethasone to temporal artery-SCID chimeras for 1 wk induced a partial suppression of T cell and macrophage function as indicated by the reduced tissue concentrations of IL-2, IL-1beta, and IL-6 mRNA, and by the diminished expression of inducible NO synthase. In contrast, synthesis of IFN-gamma mRNA was only slightly decreased, and expression of TGF-beta1 was unaffected. These findings correlated with activation of the IkappaBalpha gene and blockade of the nuclear translocation of NFkappaB in the xenotransplanted tissue. Dose-response experiments suggested that steroid doses currently used in clinical medicine are suboptimal in repressing NFkappaB-mediated cytokine production in the inflammatory lesions. Chronic steroid therapy was able to deplete the T cell products IL-2 and IFN-gamma, whereas the activation of tissue-infiltrating macrophages was only partially affected. IL-1beta transcription was abrogated; in contrast, TGF-beta1 mRNA synthesis was steroid resistant. The persistence of TGF-beta1-transcribing macrophages, despite paralysis of T cell function, may provide an explanation for the chronicity of the disease, and may identify a novel therapeutic target in this inflammatory vasculopathy. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1077, "end": 1087}, "arguments": [{"role": "Theme", "text": "TGF-beta1", "start": 1091, "end": 1100}]}, {"trigger": {"text": "products", "start": 1512, "end": 1520}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1521, "end": 1525}]}, {"trigger": {"text": "products", "start": 1512, "end": 1520}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1530, "end": 1539}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 880, "end": 887}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 913, "end": 917}]}, {"trigger": {"text": "reduced", "start": 880, "end": 887}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 919, "end": 927}]}, {"trigger": {"text": "reduced", "start": 880, "end": 887}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 933, "end": 937}]}, {"trigger": {"text": "decreased", "start": 1062, "end": 1071}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1016, "end": 1025}]}, {"trigger": {"text": "unaffected", "start": 1105, "end": 1115}, "arguments": [{"role": "Theme", "text": "expression", "start": 1077, "end": 1087}]}, {"trigger": {"text": "deplete", "start": 1493, "end": 1500}, "arguments": [{"role": "Theme", "text": "products", "start": 1512, "end": 1520}]}, {"trigger": {"text": "abrogated", "start": 1655, "end": 1664}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1637, "end": 1650}]}, {"trigger": {"text": "persistence", "start": 1731, "end": 1742}, "arguments": [{"role": "Theme", "text": "transcribing", "start": 1756, "end": 1768}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 1148, "end": 1158}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1166, "end": 1178}]}], "regulation": [{"trigger": {"text": "resistant", "start": 1716, "end": 1725}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1694, "end": 1703}]}], "transcription": [{"trigger": {"text": "synthesis", "start": 1016, "end": 1025}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1029, "end": 1038}]}, {"trigger": {"text": "transcription", "start": 1637, "end": 1650}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1628, "end": 1636}]}, {"trigger": {"text": "synthesis", "start": 1694, "end": 1703}, "arguments": [{"role": "Theme", "text": "TGF-beta1", "start": 1679, "end": 1688}]}, {"trigger": {"text": "transcribing", "start": 1756, "end": 1768}, "arguments": [{"role": "Theme", "text": "TGF-beta1", "start": 1746, "end": 1755}]}]}}, "schema": []}
{"input": "Histamine modulates the expression of c-fos through cyclic AMP production via the H2 receptor in the human promonocytic cell line U937. \nWe examined the effects of histamine and its agonists on the expression of the c-fos and c-myc proto-oncogenes at the transcriptional and translational levels in the human promonocytic U937 cell line. Histamine transiently increased cAMP and c-fos expression through H2 receptors. Dibutyryl cAMP also increased c-fos mRNA and protein, and levels remained elevated even after 12 hr of treatment. Dose-dependence studies using histamine and dimaprit showed that the EC50 values for cAMP production and c-fos increase were similar, suggesting that cAMP might be involved in c-fos induction via H2 receptors. Furthermore, studies carried out using H7, a protein kinase A/protein kinase C inhibitor, blocked c-fos induction, whereas no effect was observed with bisindolylmaleimide, a specific protein kinase C inhibitor. No modification of c-myc expression could be detected on treatment with histamine or its analogues. Nevertheless, dibutyryl cAMP induced a down-regulation of the levels of this proto-oncogene. In addition, dibutyryl cAMP inhibited cell growth in a dose-dependent manner, whereas histamine failed to affect proliferation and differentiation of U937 cells. Cells pretreated with dimaprit showed a decrease in the cAMP response to subsequent addition of H2 agonists, whereas the cAMP response to prostaglandin E2 remained unaltered. This homologous mechanism of H2 receptor desensitization was time dependent. These results indicate that histamine activates several mechanisms involved in the induction of differentiation, such as cAMP and c-fos production, but fails to promote differentiation of U937 cells, apparently due to the rapid desensitization of H2 receptors. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 24, "end": 34}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 38, "end": 43}]}, {"trigger": {"text": "expression", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 379, "end": 384}]}, {"trigger": {"text": "expression", "start": 978, "end": 988}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 972, "end": 977}]}, {"trigger": {"text": "production", "start": 1696, "end": 1706}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1690, "end": 1695}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 832, "end": 839}, "arguments": [{"role": "Theme", "text": "induction", "start": 846, "end": 855}]}, {"trigger": {"text": "induced a down-regulation", "start": 1082, "end": 1107}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 972, "end": 977}]}, {"trigger": {"text": "desensitization", "start": 1524, "end": 1539}, "arguments": [{"role": "Theme", "text": "H2 receptor", "start": 1512, "end": 1523}]}, {"trigger": {"text": "desensitization", "start": 1788, "end": 1803}, "arguments": [{"role": "Theme", "text": "H2 receptors", "start": 1807, "end": 1819}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 360, "end": 369}, "arguments": [{"role": "Cause", "text": "increased", "start": 360, "end": 369}, {"role": "Theme", "text": "expression", "start": 385, "end": 395}]}, {"trigger": {"text": "increased", "start": 360, "end": 369}, "arguments": [{"role": "Theme", "text": "H2 receptors", "start": 404, "end": 416}]}, {"trigger": {"text": "increased", "start": 438, "end": 447}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 448, "end": 453}]}, {"trigger": {"text": "remained elevated", "start": 483, "end": 500}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 448, "end": 453}]}, {"trigger": {"text": "increase", "start": 643, "end": 651}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 637, "end": 642}]}, {"trigger": {"text": "induction", "start": 714, "end": 723}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 708, "end": 713}, {"role": "Cause", "text": "H2 receptors", "start": 728, "end": 740}]}, {"trigger": {"text": "induction", "start": 846, "end": 855}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 840, "end": 845}]}, {"trigger": {"text": "activates", "start": 1598, "end": 1607}, "arguments": [{"role": "Theme", "text": "production", "start": 1696, "end": 1706}]}], "regulation": [{"trigger": {"text": "modulates", "start": 10, "end": 19}, "arguments": [{"role": "Theme", "text": "expression", "start": 24, "end": 34}]}, {"trigger": {"text": "modulates", "start": 10, "end": 19}, "arguments": [{"role": "Theme", "text": "H2 receptor", "start": 82, "end": 93}]}, {"trigger": {"text": "effects", "start": 153, "end": 160}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 255, "end": 270}]}, {"trigger": {"text": "EC50 values", "start": 601, "end": 612}, "arguments": [{"role": "Theme", "text": "increase", "start": 643, "end": 651}]}, {"trigger": {"text": "effect", "start": 868, "end": 874}, "arguments": [{"role": "Theme", "text": "induction", "start": 846, "end": 855}]}, {"trigger": {"text": "modification", "start": 956, "end": 968}, "arguments": [{"role": "Theme", "text": "expression", "start": 978, "end": 988}]}], "transcription": [{"trigger": {"text": "transcriptional", "start": 255, "end": 270}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 216, "end": 221}]}, {"trigger": {"text": "transcriptional", "start": 255, "end": 270}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 226, "end": 231}]}]}}, "schema": []}
{"input": "Human cytomegalovirus induces interleukin-8 production by a human monocytic cell line, THP-1, through acting concurrently on AP-1- and NF-kappaB-binding sites of the interleukin-8 gene. \nCytomegalovirus (CMV) infection induced interleukin-8 (IL-8) gene transcription in a human monocytic cell line, THP-1 cells, leading to IL-8 secretion. The functional analysis of the IL-8 gene revealed that both AP-1- and NF-kappaB factor-binding elements were involved in conferring the responsiveness to CMV. Moreover, electrophoretic mobility shift assays demonstrated that CMV induced the formation of NF-kappaB and AP-1 complexes. These results suggest that CMV activates these transcriptional factors, resulting in IL-8 gene expression. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 44, "end": 54}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 30, "end": 43}]}, {"trigger": {"text": "expression", "start": 718, "end": 728}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 708, "end": 712}]}], "localization": [{"trigger": {"text": "secretion", "start": 328, "end": 337}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 323, "end": 327}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 22, "end": 29}, "arguments": [{"role": "Theme", "text": "production", "start": 44, "end": 54}]}, {"trigger": {"text": "induced", "start": 219, "end": 226}, "arguments": [{"role": "Theme", "text": "transcription", "start": 253, "end": 266}]}, {"trigger": {"text": "leading", "start": 312, "end": 319}, "arguments": [{"role": "Cause", "text": "induced", "start": 219, "end": 226}, {"role": "Theme", "text": "secretion", "start": 328, "end": 337}]}, {"trigger": {"text": "resulting", "start": 695, "end": 704}, "arguments": [{"role": "Theme", "text": "expression", "start": 718, "end": 728}]}], "transcription": [{"trigger": {"text": "transcription", "start": 253, "end": 266}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 242, "end": 246}]}]}}, "schema": []}
{"input": "Concomitant downregulation of IgH 3' enhancer activity and c-myc expression in a plasmacytoma x fibroblast environment: implications for dysregulation of translocated c-myc. \nRegulation of immunoglobulin heavy chain (IgH) gene expression is controlled by a B cell-specific promoter, intronic enhancer and additional B cell-specific enhancer elements identified recently in the 3' end of the IgH locus. One of the latter elements, the IgH 3' enhancer, is of particular interest: (1) it is B cell-specific and active only in late B cell development; (2) in rodent plasmacytomas and in some human Burkitt's lymphomas it is part of a locus control region (LCR) that is involved in deregulation of the c-myc oncogene as a result of translocation into the IgH locus; and (3) it has been implicated in the mechanisms that control Ig gene class switch recombination. We have used a somatic cell hybridization approach to genetically analyse regulation of the activity of the IgH 3' enhancer. When mouse MPC11 plasmacytoma cells, in which the IgH 3' enhancer is active, are fused with fibroblasts, Ig expression is extinguished at the level of transcription. Here we show that in a MPC11 plasmacytoma x fibroblast environment, the IgH 3' enhancer is transcriptionally inactive. Furthermore, we demonstrate that binding of several B cell-specific transcription factors, essential for IgH 3' enhancer activity, is lacking, which may explain 3' enhancer inactivity, although the binding of repressors cannot be excluded. Moreover, the high expression level of c-myc, characteristic of the parental MPC11 cells carrying the t(12;15) translocation, is down-regulated in the hybrids to that in unfused fibroblasts. Therefore, inactivation of the IgH 3' enhancer is a multifactorial process affecting several transcription factors that control the cell-specific and developmental activity of the enhancer. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 65, "end": 75}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 59, "end": 64}]}, {"trigger": {"text": "expression", "start": 1528, "end": 1538}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 1548, "end": 1553}]}], "localization": [{"trigger": {"text": "translocated", "start": 154, "end": 166}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 167, "end": 172}]}, {"trigger": {"text": "translocation", "start": 727, "end": 740}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 697, "end": 702}, {"role": "ToLoc", "text": "IgH locus", "start": 750, "end": 759}]}], "negative regulation": [{"trigger": {"text": "downregulation", "start": 12, "end": 26}, "arguments": [{"role": "Theme", "text": "expression", "start": 65, "end": 75}]}, {"trigger": {"text": "down-regulated", "start": 1638, "end": 1652}, "arguments": [{"role": "Theme", "text": "expression", "start": 1528, "end": 1538}]}], "regulation": [{"trigger": {"text": "dysregulation", "start": 137, "end": 150}, "arguments": [{"role": "Theme", "text": "translocated", "start": 154, "end": 166}]}, {"trigger": {"text": "involved", "start": 665, "end": 673}, "arguments": [{"role": "Theme", "text": "deregulation", "start": 677, "end": 689}]}, {"trigger": {"text": "deregulation", "start": 677, "end": 689}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 697, "end": 702}]}, {"trigger": {"text": "result", "start": 717, "end": 723}, "arguments": [{"role": "Theme", "text": "deregulation", "start": 677, "end": 689}, {"role": "Cause", "text": "translocation", "start": 727, "end": 740}]}]}}, "schema": []}
{"input": "ETS1, NFkappaB and AP1 synergistically transactivate the human GM-CSF promoter. \nActivation of helper T cells results in coordinate expression of a number of cytokines involved in differentiation, proliferation and activation of the haematopoietic system. Granulocyte-macrophage colony stimulating factor (GM-CSF) is one such cytokine, whose increased expression results mostly from increases in transcription. Cis-acting elements with NFkappaB, AP1 and ETS-like binding motifs have been identified in the promoter region of the GM-CSF gene, and are important or essential for transcriptional activity following T cell activation. ETS1 is a transcription factor of the ETS family that is expressed in T cells. We have previously shown that ETS1 can transactivate GM-CSF in Jurkat T cells, but only after the cells have been stimulated by treatment with PMA and ionomycin, agents that mimic T cell activation. Thus we proposed that ETS1, which is expressed constitutively in Jurkat cells, may act in concert with PMA/ionomycin inducible factors. Here we show that ETS1 can transactivate a GM-CSF reporter construct in unstimulated Jurkat cells, providing that either NFkappaB or AP1 transcription factors are supplied by co-transfection. We confirm that binding of endogenous NFkappaB and AP1 is induced following PMA/ionomycin treatment of T cells. Transactivation by ETS1, NFkappaB and AP1 is synergistic, and mutation of the individual binding sites reveals that the transcriptional activities of these factors are interdependent. Our results suggest that constitutive ETS1, and inducible NFkappaB and AP1, cooperate as part of a higher order transcriptional complex in activated T cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 352, "end": 362}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 306, "end": 312}]}, {"trigger": {"text": "expressed", "start": 688, "end": 697}, "arguments": [{"role": "Theme", "text": "ETS1", "start": 631, "end": 635}]}, {"trigger": {"text": "expressed", "start": 946, "end": 955}, "arguments": [{"role": "Theme", "text": "ETS1", "start": 931, "end": 935}]}], "positive regulation": [{"trigger": {"text": "synergistically transactivate", "start": 23, "end": 52}, "arguments": [{"role": "Cause", "text": "ETS1", "start": 0, "end": 4}, {"role": "Theme", "text": "GM-CSF", "start": 63, "end": 69}, {"role": "Site", "text": "promoter", "start": 70, "end": 78}]}, {"trigger": {"text": "increased", "start": 342, "end": 351}, "arguments": [{"role": "Theme", "text": "expression", "start": 352, "end": 362}, {"role": "Cause", "text": "increases", "start": 383, "end": 392}]}, {"trigger": {"text": "increases", "start": 383, "end": 392}, "arguments": [{"role": "Theme", "text": "transcription", "start": 396, "end": 409}]}, {"trigger": {"text": "important or essential", "start": 550, "end": 572}, "arguments": [{"role": "CSite", "text": "Cis-acting elements", "start": 411, "end": 430}, {"role": "Cause", "text": "GM-CSF", "start": 529, "end": 535}, {"role": "Theme", "text": "following", "start": 602, "end": 611}]}, {"trigger": {"text": "following", "start": 602, "end": 611}, "arguments": [{"role": "Theme", "text": "transcriptional activity", "start": 577, "end": 601}]}, {"trigger": {"text": "transactivate", "start": 749, "end": 762}, "arguments": [{"role": "Cause", "text": "ETS1", "start": 740, "end": 744}, {"role": "Theme", "text": "GM-CSF", "start": 763, "end": 769}]}], "transcription": [{"trigger": {"text": "transcription", "start": 396, "end": 409}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 306, "end": 312}]}, {"trigger": {"text": "transcriptional activity", "start": 577, "end": 601}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 529, "end": 535}]}]}}, "schema": []}
{"input": "Relief of cyclin A gene transcriptional inhibition during activation of human primary T lymphocytes via CD2 and CD28 adhesion molecules. \nCyclin A transcription is cell cycle regulated and induced by cell proliferative signals. To understand the mechanisms underlined in this regulation in normal human cells, we have analysed in vivo protein-DNA interactions at the Cyclin A locus in primary T lymphocytes. Stimulation of purified T lymphocytes by a combination of monoclonal antibodies directed at CD2 and CD28 adhesion molecules gives rise to a long lasting proliferation in the absence of accessory cells. Cyclin A was observed after 4 days of costimulation with anti CD2 + CD28 whereas stimulation by anti CD2 or anti CD28 alone was not effective. In vivo genomic DMS footprinting revealed upstream of the major transcription initiation sites, the presence of at least three protein binding sites, two of which were constitutively occupied. They bind in vitro respectively ATF-1 and NF-Y proteins. The third site was occupied in quiescent cells or in cells stimulated by anti CD2 or anti CD28 alone. The mitogenic combination of anti CD2 + anti CD28 released the footprint as cells were committed to proliferation. Consistent with theses results, nuclear extracts prepared from quiescent cells formed a specific complex with this element, whereas extracts prepared from cells treated with anti CD2 + anti CD28 failed to do so after cells entered a proliferative state. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interactions", "start": 347, "end": 359}, "arguments": [{"role": "Theme", "text": "Cyclin A", "start": 367, "end": 375}]}, {"trigger": {"text": "bind", "start": 951, "end": 955}, "arguments": [{"role": "Theme", "text": "ATF-1", "start": 978, "end": 983}]}], "negative regulation": [{"trigger": {"text": "Relief", "start": 0, "end": 6}, "arguments": [{"role": "Theme", "text": "transcriptional inhibition", "start": 24, "end": 50}]}, {"trigger": {"text": "transcriptional inhibition", "start": 24, "end": 50}, "arguments": [{"role": "Theme", "text": "cyclin A", "start": 10, "end": 18}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 189, "end": 196}, "arguments": [{"role": "Theme", "text": "transcription", "start": 147, "end": 160}]}, {"trigger": {"text": "effective", "start": 742, "end": 751}, "arguments": [{"role": "Theme", "text": "transcription", "start": 147, "end": 160}]}], "regulation": [{"trigger": {"text": "regulated", "start": 175, "end": 184}, "arguments": [{"role": "Theme", "text": "transcription", "start": 147, "end": 160}]}], "transcription": [{"trigger": {"text": "transcription", "start": 147, "end": 160}, "arguments": [{"role": "Theme", "text": "Cyclin A", "start": 138, "end": 146}]}, {"trigger": {"text": "observed", "start": 623, "end": 631}, "arguments": [{"role": "Theme", "text": "Cyclin A", "start": 610, "end": 618}]}]}}, "schema": []}
{"input": "Biphasic control of NF-kappa B activation induced by the triggering of HLA-DR antigens expressed on B cells. \nThe regulation of NF-kappa B activation following the triggering of HLA-DR antigens by mAb L243 has been studied at various times in Raji cells. Electrophoretic mobility shift assays demonstrated a strong increase of NF-kappa B DNA binding after triggering of HLA-DR antigens. Using TNF-alpha-activity neutralizing antibodies, the authors demonstrated that the upregulation of NF-kappa B was found to depend, at later time point, on an autocrine effect of TNF-alpha secreted following triggering of HLA-DR antigens. In contrast, it was found to be TNF-alpha independent in the early time point. Moreover, the upregulation of NF-kappa B binding activity is regulated by the triggering of selected epitopes of HLA-DR antigens. In fact, mAb L243 but not the staphylococcal superantigens, staphylococcal exotoxin toxic shock syndrome toxin-I or staphylococcal enterotoxin B, regulate the NF-kappa B binding activity. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "secreted", "start": 576, "end": 584}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 566, "end": 575}]}], "positive regulation": [{"trigger": {"text": "following", "start": 585, "end": 594}, "arguments": [{"role": "Theme", "text": "secreted", "start": 576, "end": 584}]}]}}, "schema": []}
{"input": "Comparison of the transactivation domains of Stat5 and Stat6 in lymphoid cells and mammary epithelial cells. \nStat (signal transducers and activators of transcription) and Jak (Janus kinases) proteins are central components in the signal transduction events in hematopoietic and epithelial cells. They are rapidly activated by various cytokines, hormones, and growth factors. Upon ligand binding and cytokine receptor dimerization, Stat proteins are phosphorylated on tyrosine residues by Jak kinases. Activated Stat proteins form homo- or heterodimers, translocate to the nucleus, and induce transcription from responsive genes. Stat5 and Stat6 are transcription factors active in mammary epithelial cells and immune cells. Prolactin activates Stat5, and interleukin-4 (IL-4) activates Stat6. Both cytokines are able to stimulate cell proliferation, differentiation, and survival. We investigated the transactivation potential of Stat6 and found that it is not restricted to lymphocytes. IL-4-dependent activation of Stat6 was also observed in HC11 mammary epithelial cells. In these cells, Stat6 activation led to the induction of the beta-casein gene promoter. The induction of this promoter was confirmed in COS7 cells. The glucocorticoid receptor was able to further enhance IL-4-induced gene transcription through the action of Stat6. Deletion analysis of the carboxyl-terminal region of Stat6 and recombination of this region with a heterologous DNA binding domain allowed the delimitation and characterization of the transactivation domain of Stat6. The potencies of the transactivation domains of Stat5, Stat6, and viral protein VP16 were compared. Stat6 had a transactivation domain which was about 10-fold stronger than that of Stat5. In pre-B cells (Ba/F3), the transactivation domain of Stat6 was IL-4 regulated, independently from its DNA binding function. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1853, "end": 1860}, "arguments": [{"role": "Site", "text": "transactivation domain", "start": 1774, "end": 1796}, {"role": "Theme", "text": "Stat6", "start": 1800, "end": 1805}]}], "negative regulation": [{"trigger": {"text": "restricted", "start": 962, "end": 972}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 902, "end": 917}]}], "positive regulation": [{"trigger": {"text": "active", "start": 672, "end": 678}, "arguments": [{"role": "Theme", "text": "Stat5", "start": 630, "end": 635}]}, {"trigger": {"text": "active", "start": 672, "end": 678}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 640, "end": 645}]}, {"trigger": {"text": "activates", "start": 735, "end": 744}, "arguments": [{"role": "Cause", "text": "Prolactin", "start": 725, "end": 734}, {"role": "Theme", "text": "Stat5", "start": 745, "end": 750}]}, {"trigger": {"text": "activates", "start": 777, "end": 786}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 771, "end": 775}, {"role": "Theme", "text": "Stat6", "start": 787, "end": 792}]}, {"trigger": {"text": "transactivation", "start": 902, "end": 917}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 931, "end": 936}]}, {"trigger": {"text": "activation", "start": 1004, "end": 1014}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 989, "end": 993}, {"role": "Theme", "text": "Stat6", "start": 1018, "end": 1023}]}, {"trigger": {"text": "activation", "start": 1098, "end": 1108}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 1092, "end": 1097}]}, {"trigger": {"text": "enhance", "start": 1272, "end": 1279}, "arguments": [{"role": "Cause", "text": "glucocorticoid receptor", "start": 1228, "end": 1251}, {"role": "Theme", "text": "Stat6", "start": 1334, "end": 1339}]}, {"trigger": {"text": "independently", "start": 1826, "end": 1839}, "arguments": [{"role": "Theme", "text": "regulated", "start": 1815, "end": 1824}, {"role": "Cause", "text": "binding", "start": 1853, "end": 1860}]}], "regulation": [{"trigger": {"text": "regulated", "start": 1815, "end": 1824}, "arguments": [{"role": "Site", "text": "transactivation domain", "start": 1774, "end": 1796}, {"role": "Theme", "text": "Stat6", "start": 1800, "end": 1805}, {"role": "Cause", "text": "IL-4", "start": 1810, "end": 1814}]}]}}, "schema": []}
{"input": "The immediate-early gene product Egr-1 regulates the human interleukin-2 receptor beta-chain promoter through noncanonical Egr and Sp1 binding sites. \nThe interleukin-2 IL-2 receptor beta-chain (IL-2Rbeta) is an essential component of the receptors for IL-2 and IL-15. Although IL-2Rbeta is constitutively expressed by lymphocytes, its expression can be further induced by a number of stimuli, including phorbol 12-myristate 13-acetate (PMA). We have now characterized factors that bind to an enhancer region located between nucleotides -170 and -139 of the human IL-2Rbeta promoter. Both Sp1 and Sp3 bound to the 5' portion of this region, whereas a PMA-inducible factor (PIF) mainly bound to its 3' portion and bound to the Sp binding motifs as well. In Jurkat T cells, induction of PIF DNA binding activity was rapidly induced, required de novo protein synthesis, and was sustained at a high level for at least 23 h. Interestingly, PIF was constitutively activated in human T-cell leukemia virus type 1-transformed MT-2 cells. In this paper, we demonstrate that PIF is Egr-1 based on its recognition by anti-Egr-1 antisera in gel mobility shift assays, even though the IL-2Rbeta DNA binding motif differed substantially from the canonical Egr-1 binding site. In addition, Egr-1 bound to the Sp binding site. In Jurkat cells, both sites were required for maximal IL-2Rbeta promoter activity, and in HeLaS3 cells, transfection of Egr-1 could drive activity of a reporter construct containing both sites. Moreover, Sp1 and Egr-1 could form a complex with kinetics that correlated with the production of Egr-1 in Jurkat cells upon PMA stimulation. Thus, Sp1 and Egr-1 physically and functionally cooperate to mediate maximal IL-2Rbeta promoter activity. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 482, "end": 486}, "arguments": [{"role": "Theme", "text": "IL-2Rbeta", "start": 564, "end": 573}, {"role": "Site", "text": "promoter", "start": 574, "end": 582}]}, {"trigger": {"text": "bound", "start": 601, "end": 606}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 589, "end": 592}]}, {"trigger": {"text": "bound", "start": 601, "end": 606}, "arguments": [{"role": "Theme", "text": "Sp3", "start": 597, "end": 600}]}, {"trigger": {"text": "recognition", "start": 1091, "end": 1102}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1072, "end": 1077}]}, {"trigger": {"text": "bound", "start": 1281, "end": 1286}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1275, "end": 1280}]}, {"trigger": {"text": "form a complex", "start": 1535, "end": 1549}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1515, "end": 1518}, {"role": "Theme2", "text": "Egr-1", "start": 1523, "end": 1528}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 306, "end": 315}, "arguments": [{"role": "Theme", "text": "IL-2Rbeta", "start": 278, "end": 287}]}, {"trigger": {"text": "transfection", "start": 1415, "end": 1427}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1431, "end": 1436}]}, {"trigger": {"text": "production", "start": 1589, "end": 1599}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1603, "end": 1608}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 362, "end": 369}, "arguments": [{"role": "Theme", "text": "expressed", "start": 306, "end": 315}]}, {"trigger": {"text": "required", "start": 1344, "end": 1352}, "arguments": [{"role": "Theme", "text": "IL-2Rbeta", "start": 1365, "end": 1374}, {"role": "Site", "text": "promoter", "start": 1375, "end": 1383}]}, {"trigger": {"text": "transfection", "start": 1415, "end": 1427}, "arguments": [{"role": "Theme", "text": "transfection", "start": 1415, "end": 1427}]}, {"trigger": {"text": "mediate", "start": 1708, "end": 1715}, "arguments": [{"role": "Cause", "text": "Sp1", "start": 1653, "end": 1656}, {"role": "Theme", "text": "IL-2Rbeta", "start": 1724, "end": 1733}]}, {"trigger": {"text": "mediate", "start": 1708, "end": 1715}, "arguments": [{"role": "Cause", "text": "Egr-1", "start": 1661, "end": 1666}, {"role": "Theme", "text": "IL-2Rbeta", "start": 1724, "end": 1733}]}], "regulation": [{"trigger": {"text": "through", "start": 102, "end": 109}, "arguments": [{"role": "Theme", "text": "interleukin-2 receptor beta-chain", "start": 59, "end": 92}]}]}}, "schema": []}
{"input": "Anti-Ehrlichia chaffeensis antibody complexed with E. chaffeensis induces potent proinflammatory cytokine mRNA expression in human monocytes through sustained reduction of IkappaB-alpha and activation of NF-kappaB. \nEhrlichia chaffeensis is an obligatory intracellular bacterium that infects monocytes and macrophages and is the etiologic agent of human ehrlichiosis in the United States. Our previous studies showed that the exposure of human monocytes to E. chaffeensis induces the expression of interleukin-1beta (IL-1beta), IL-8, and IL-10 genes in vitro but not the expression of tumor necrosis factor alpha (TNF-alpha) and IL-6 mRNAs. In this study, the effect of anti-E. chaffeensis antibody complexed with E. chaffeensis on the expression of major proinflammatory cytokines in human monocytes was examined. Human monocytic cell line THP-1 was treated with E. chaffeensis which had been preincubated with human anti-E. chaffeensis serum for 2 h, and the levels of cytokine mRNAs were evaluated by competitive reverse transcription-PCR. Anti-E. chaffeensis antibody complexed with E. chaffeensis significantly enhanced mRNA expression of IL-1beta in THP-1 cells. The expression of TNF-alpha and IL-6 mRNAs was also induced. The levels of secreted IL-1beta, TNF-alpha, and IL-6 during 24 h of stimulation were comparable to those induced by Escherichia coli lipopolysaccharide at 1 microg/ml. Fab fragment of anti-E. chaffeensis immunoglobulin G complexed with E. chaffeensis did not induce any of these three cytokines, indicating that ehrlichial binding is required for IL-1beta mRNA expression and that binding of the immune complex to the Fc gamma receptor is required for TNF-alpha and IL-6 mRNA expression and enhanced IL-1beta mRNA expression. Furthermore, prolonged degradation of IkappaB-alpha and activation of NF-kappaB were demonstrated in THP-1 cells exposed to anti-E. chaffeensis serum and E. chaffeensis. This result implies that development of anti-E. chaffeensis antibody in patients can result in the production of major proinflammatory cytokines, which may play an important role in the pathophysiology of ehrlichiosis and immune responses to it. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1611, "end": 1618}, "arguments": [{"role": "Theme", "text": "Fc gamma receptor", "start": 1648, "end": 1665}]}], "gene expression": [{"trigger": {"text": "expression", "start": 484, "end": 494}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 517, "end": 525}]}, {"trigger": {"text": "expression", "start": 484, "end": 494}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 528, "end": 532}]}, {"trigger": {"text": "expression", "start": 484, "end": 494}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 538, "end": 543}]}], "negative regulation": [{"trigger": {"text": "reduction", "start": 159, "end": 168}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 172, "end": 185}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 472, "end": 479}, "arguments": [{"role": "Theme", "text": "expression", "start": 484, "end": 494}]}, {"trigger": {"text": "induces", "start": 472, "end": 479}, "arguments": [{"role": "Theme", "text": "expression", "start": 571, "end": 581}]}, {"trigger": {"text": "enhanced", "start": 1116, "end": 1124}, "arguments": [{"role": "Theme", "text": "mRNA expression", "start": 1125, "end": 1140}]}, {"trigger": {"text": "induced", "start": 1221, "end": 1228}, "arguments": [{"role": "Theme", "text": "expression", "start": 1173, "end": 1183}]}, {"trigger": {"text": "induce", "start": 1489, "end": 1495}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1253, "end": 1261}]}, {"trigger": {"text": "induce", "start": 1489, "end": 1495}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1263, "end": 1272}]}, {"trigger": {"text": "induce", "start": 1489, "end": 1495}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1278, "end": 1282}]}, {"trigger": {"text": "required", "start": 1564, "end": 1572}, "arguments": [{"role": "Theme", "text": "expression", "start": 1591, "end": 1601}]}, {"trigger": {"text": "required", "start": 1669, "end": 1677}, "arguments": [{"role": "Cause", "text": "binding", "start": 1611, "end": 1618}, {"role": "Theme", "text": "expression", "start": 1706, "end": 1716}]}, {"trigger": {"text": "enhanced", "start": 1721, "end": 1729}, "arguments": [{"role": "Cause", "text": "binding", "start": 1611, "end": 1618}, {"role": "Theme", "text": "expression", "start": 1744, "end": 1754}]}, {"trigger": {"text": "demonstrated", "start": 1841, "end": 1853}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1779, "end": 1790}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 1779, "end": 1790}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1794, "end": 1807}]}], "transcription": [{"trigger": {"text": "expression", "start": 571, "end": 581}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 614, "end": 623}]}, {"trigger": {"text": "expression", "start": 571, "end": 581}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 629, "end": 633}]}, {"trigger": {"text": "mRNA expression", "start": 1125, "end": 1140}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1144, "end": 1152}]}, {"trigger": {"text": "expression", "start": 1173, "end": 1183}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1187, "end": 1196}]}, {"trigger": {"text": "expression", "start": 1173, "end": 1183}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1201, "end": 1205}]}, {"trigger": {"text": "expression", "start": 1591, "end": 1601}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1577, "end": 1585}]}, {"trigger": {"text": "expression", "start": 1706, "end": 1716}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1682, "end": 1691}]}, {"trigger": {"text": "expression", "start": 1706, "end": 1716}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1696, "end": 1700}]}, {"trigger": {"text": "expression", "start": 1744, "end": 1754}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1730, "end": 1738}]}]}}, "schema": []}
{"input": "S-allyl cysteine inhibits activation of nuclear factor kappa B in human T cells. \nReactive oxygen species are involved in signal transduction pathways leading to nuclear factor kappa B (NF-kappa B) activation which has been implicated in the regulation of gene transcription. We recently reported that a garlic compound, S-allyl cysteine (SAC), protects bovine pulmonary artery endothelial cells from oxidant injury induced by hydrogen peroxide (H2O2). In this study we determined the effects of SAC on NF-kappa B activation in human T lymphocytes (Jurkat cells) induced by tumor necrosis factor alpha (TNF- alpha) and H2O2. Activated NF-kappa B in nuclear extracts was measured by an electrophoretic mobility shift assay using 32P-labeled probe. SAC consistently exhibited a dose-dependent inhibition of NF-kappa B activation induced by both TNF-alpha and H2O2. Supershift with specific antibodies to NF-kappa B subunits confirmed that the inducible retarded bands observed in the EMSA and p65-p50 heterodimer of the NF-kappa B/Rel protein. Our data suggest that SAC may act via antioxidant mechanisms to block NF-kappa B activation in Jurkat cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "heterodimer", "start": 999, "end": 1010}, "arguments": [{"role": "Theme", "text": "p65", "start": 991, "end": 994}, {"role": "Theme2", "text": "p50", "start": 995, "end": 998}]}]}}, "schema": []}
{"input": "Effect of adenovirus 2 on cellular gene activation in blood-derived monocytes and macrophages. \nWe have investigated the effect of adenovirus 2 (Ad2) infection on human monocytes and monocyte-derived macrophages with regard to expression of TNF-alpha and IL-1 beta. In monocytes, the virus was bound to the surface without being internalized. On the other hand, Ad2 was internalized by macrophages. No virus replication and no transcription of the Ad2 early genes was observed in either of the cells. Ad2 infection induced transient increase in the mRNA levels for TNF-alpha and IL-1 beta in both monocytes and in macrophages, although the kinetics of the transcription was slightly different. The production of both cytokines, measured by ELISA tests, was enhanced in monocytes. In macrophages, a slight enhancement of TNF-alpha production was seen, whereas IL-1 beta was not detected. The data indicate that cellular genes might be activated by Ad2 virus infection in nonpermissive cells where no viral gene products could be detected. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 227, "end": 237}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 241, "end": 250}]}, {"trigger": {"text": "expression", "start": 227, "end": 237}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 255, "end": 264}]}, {"trigger": {"text": "production", "start": 698, "end": 708}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 565, "end": 574}]}, {"trigger": {"text": "production", "start": 698, "end": 708}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 579, "end": 588}]}, {"trigger": {"text": "production", "start": 830, "end": 840}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 820, "end": 829}]}, {"trigger": {"text": "detected", "start": 877, "end": 885}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 859, "end": 868}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 515, "end": 522}, "arguments": [{"role": "Theme", "text": "increase", "start": 533, "end": 541}]}, {"trigger": {"text": "increase", "start": 533, "end": 541}, "arguments": [{"role": "Theme", "text": "mRNA levels", "start": 549, "end": 560}]}, {"trigger": {"text": "enhanced", "start": 757, "end": 765}, "arguments": [{"role": "Theme", "text": "production", "start": 698, "end": 708}]}, {"trigger": {"text": "enhancement", "start": 805, "end": 816}, "arguments": [{"role": "Theme", "text": "production", "start": 830, "end": 840}]}], "regulation": [{"trigger": {"text": "effect", "start": 121, "end": 127}, "arguments": [{"role": "Theme", "text": "expression", "start": 227, "end": 237}]}], "transcription": [{"trigger": {"text": "mRNA levels", "start": 549, "end": 560}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 565, "end": 574}]}, {"trigger": {"text": "mRNA levels", "start": 549, "end": 560}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 579, "end": 588}]}]}}, "schema": []}
{"input": "Activation of nuclear factor-kappa B by beta-amyloid peptides and interferon-gamma in murine microglia. \nAn increasing body of evidence suggests that amyloid-beta (A beta) peptides and microglia are crucially involved in the pathogenesis of Alzheimer's disease. In an effort to further elucidate the biological effects of A beta towards microglia, we investigated the ability of A beta peptides to activate nuclear factor (NF)-kappa B in the N9 murine microglial cell line. Co-stimulation of microglia with suboptimal concentrations of A beta(25-35) and 100 U/ml IFN gamma resulted in the detection of a specific NF-kappa B DNA-binding activity in nuclear extracts, as determined in gel mobility shift assays. This response required at least 120 min to be evident and supershift experiments revealed that the NF-kappa B complex contains both RelA and p50. Accordingly, immunoblot experiments showed that amongst NF-kappa B/Rel proteins, RelA and p50 are mobilized to the nucleus following microglial cell stimulation with A beta(25-35) plus IFN gamma. Higher concentrations of A beta(25-35) were effective by themselves in inducing NF-kappa B activation, both in the N9 microglial cell line and in rat primary microglia, as well as in human monocytes. For purposes of comparison, microglia were also stimulated with bacterial LPS, a known NF-kappa B inducer. As expected, LPS strongly induced the formation of two NF-kappa B DNA-binding activities, one of which was identified as RelA/p50. The LPS response was also more rapid, as it was already evident by 40 min and remained sustained for up to 3 h. Collectively, these findings indicate that NF-kappa B activation might constitute one of the mechanisms underlying the inducible expression of kappa B-dependent genes in microglia stimulated by A beta peptides and IFN gamma, or by LPS. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1429, "end": 1436}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1480, "end": 1484}]}, {"trigger": {"text": "binding", "start": 1429, "end": 1436}, "arguments": [{"role": "Theme", "text": "p50", "start": 1485, "end": 1488}]}], "localization": [{"trigger": {"text": "mobilized", "start": 954, "end": 963}, "arguments": [{"role": "Theme", "text": "RelA", "start": 937, "end": 941}, {"role": "ToLoc", "text": "nucleus", "start": 971, "end": 978}]}, {"trigger": {"text": "mobilized", "start": 954, "end": 963}, "arguments": [{"role": "Theme", "text": "p50", "start": 946, "end": 949}, {"role": "ToLoc", "text": "nucleus", "start": 971, "end": 978}]}], "positive regulation": [{"trigger": {"text": "following", "start": 979, "end": 988}, "arguments": [{"role": "Theme", "text": "mobilized", "start": 954, "end": 963}]}, {"trigger": {"text": "induced the formation", "start": 1385, "end": 1406}, "arguments": [{"role": "Theme", "text": "binding", "start": 1429, "end": 1436}]}]}}, "schema": []}
{"input": "AP-1 derived from mature monocytes and astrocytes preferentially interacts with the HTLV-I promoter central 21 bp repeat. \nCharacterization of the cellular transcription factors interacting with the human T cell lymphotropic virus type I (HTLV-I) long terminal repeat (LTR) is essential to dissecting the mechanisms involved in viral transcription that may be pertinent to the oncogenic and neuropathogenic processes associated with HTLV-I infection in both the immune and nervous systems. Electrophoretic mobility shift (EMS) analyses utilizing oligonucleotides homologous to each of the 21 bp repeat elements reacted with nuclear extracts derived from cell lines of lymphocytic, monocytic, neuronal, and glial cell origin have demonstrated differential binding of cellular factors to the three 21 bp repeats (1-4). ATF/CREB and Sp family members interacted with the 21 bp repeats to form DNA-protein complexes common to all cell types examined. However, a unique DNA-protein complex was detected when the promoter central 21 bp repeat was reacted with nuclear extracts derived from either the U-373 MG glioblastoma cell line or the THP-1 mature monocytic cell line. Based on nucleotide sequence requirements and immunoreactivity, we demonstrate that this DNA-protein complex is comprised of the AP-1 components, Fos and Jun. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Of the GATA-binding proteins, only GATA-4 selectively regulates the human IL-5 gene promoter in IL-5 producing cells which express multiple GATA-binding proteins. \nInterleukin-5 (IL-5) is produced by T lymphocytes and known to support B cell growth and eosinophilic differentiation of the progenitor cells. Using ATL-16T cells which express IL-5 mRNA, we have identified a region, within the human IL-5 gene promoter, that regulates IL-5 gene transcription. This cis-acting sequence contains the core binding motif, (A/T)GATA(A/G), for GATA-binding family proteins and thus suggests the involvement of these family members. In this report, we describe the cloning of human GATA-4 (hGATA-4) and show that hGATA-4 selectively interacts with the -70 GATA site within the IL-5 proximal promoter region. By promoter deletion and mutation analyses, we established this region as a positive regulatory element. Cotransfection experiments revealed that both hGATA-4 and PMA/A23187 stimulation are necessary for the IL-5 promoter activation. The requirement of another regulatory element called CLE0, which lies downstream of the -70 GATA site, was also demonstrated. ATL-16T cells express mRNA of three GATA-binding proteins, hGATA-2, hGATA-3 and hGATA-4, and each of them has a potential to bind to the consensus (A/T)GATA(G/ A) motif. However, using ATL-16T nuclear extract, we demonstrated that GATA-4 is the only GATA-binding protein that forms specific DNA-protein complex with the -70 GATA site. The electrophoretic mobility shift assay with extracts of COS cells expressing GATA-binding proteins showed that GATA-4 has the highest binding affinity to the -70 GATA site among the three GATA-binding proteins. When the transactivation ability was compared among the three, GATA-4 showed the highest activity. These results demonstrate the selective role of GATA-4 in the transcriptional regulation of the IL-5 gene in a circumstance where multiple members of the GATA-binding proteins are expressed. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 724, "end": 733}, "arguments": [{"role": "Theme", "text": "hGATA-4", "start": 704, "end": 711}, {"role": "Site2", "text": "-70 GATA site", "start": 743, "end": 756}, {"role": "Theme2", "text": "IL-5", "start": 768, "end": 772}]}, {"trigger": {"text": "bind", "start": 1284, "end": 1288}, "arguments": [{"role": "Theme", "text": "hGATA-2", "start": 1218, "end": 1225}]}, {"trigger": {"text": "bind", "start": 1284, "end": 1288}, "arguments": [{"role": "Theme", "text": "hGATA-3", "start": 1227, "end": 1234}]}, {"trigger": {"text": "bind", "start": 1284, "end": 1288}, "arguments": [{"role": "Theme", "text": "hGATA-4", "start": 1239, "end": 1246}]}, {"trigger": {"text": "forms specific DNA-protein complex", "start": 1435, "end": 1469}, "arguments": [{"role": "Theme", "text": "GATA-4", "start": 1390, "end": 1396}]}, {"trigger": {"text": "has the highest binding affinity", "start": 1614, "end": 1646}, "arguments": [{"role": "Theme", "text": "GATA-4", "start": 1607, "end": 1613}]}], "gene expression": [{"trigger": {"text": "producing", "start": 101, "end": 110}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 96, "end": 100}]}, {"trigger": {"text": "produced", "start": 188, "end": 196}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 179, "end": 183}]}, {"trigger": {"text": "express", "start": 1173, "end": 1180}, "arguments": [{"role": "Theme", "text": "hGATA-2", "start": 1218, "end": 1225}]}, {"trigger": {"text": "express", "start": 1173, "end": 1180}, "arguments": [{"role": "Theme", "text": "hGATA-3", "start": 1227, "end": 1234}]}, {"trigger": {"text": "express", "start": 1173, "end": 1180}, "arguments": [{"role": "Theme", "text": "hGATA-4", "start": 1239, "end": 1246}]}], "positive regulation": [{"trigger": {"text": "necessary", "start": 989, "end": 998}, "arguments": [{"role": "Cause", "text": "hGATA-4", "start": 950, "end": 957}, {"role": "Theme", "text": "activation", "start": 1021, "end": 1031}]}, {"trigger": {"text": "activation", "start": 1021, "end": 1031}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1007, "end": 1011}, {"role": "Site", "text": "promoter", "start": 1012, "end": 1020}]}, {"trigger": {"text": "requirement", "start": 1037, "end": 1048}, "arguments": [{"role": "Theme", "text": "activation", "start": 1021, "end": 1031}]}], "regulation": [{"trigger": {"text": "regulates", "start": 54, "end": 63}, "arguments": [{"role": "Cause", "text": "GATA-4", "start": 35, "end": 41}, {"role": "Theme", "text": "IL-5", "start": 74, "end": 78}, {"role": "Site", "text": "promoter", "start": 84, "end": 92}]}, {"trigger": {"text": "regulates", "start": 423, "end": 432}, "arguments": [{"role": "CSite", "text": "region", "start": 373, "end": 379}, {"role": "Cause", "text": "IL-5", "start": 398, "end": 402}, {"role": "Theme", "text": "transcription", "start": 443, "end": 456}]}, {"trigger": {"text": "role", "start": 1846, "end": 1850}, "arguments": [{"role": "Cause", "text": "GATA-4", "start": 1854, "end": 1860}, {"role": "Theme", "text": "transcriptional regulation", "start": 1868, "end": 1894}]}, {"trigger": {"text": "transcriptional regulation", "start": 1868, "end": 1894}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1902, "end": 1906}]}], "transcription": [{"trigger": {"text": "express", "start": 333, "end": 340}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 341, "end": 345}]}, {"trigger": {"text": "transcription", "start": 443, "end": 456}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 433, "end": 437}]}]}}, "schema": []}
{"input": "Inducible expression and phosphorylation of coactivator BOB.1/OBF.1 in T cells [see comments] \nBOB.1/OBF.1 is a transcriptional coactivator that is constitutively expressed in B cells and interacts with the Oct1 and Oct2 transcription factors. Upon activation of Jurkat T cells and primary murine thymocytes with phorbol esters and ionomycin, BOB.1/OBF.1 expression and transactivation function were induced. BOB.1/OBF.1 was phosphorylated at Ser184 both in vivo and in vitro, and this modification was required for inducible activation. Mutation of Ser184 also diminished transactivation function in B cells, suggesting that the activating phosphorylation that is inducible in T cells is constitutively present in B cells. Thus, BOB.1/OBF.1 is a transcriptional coactivator that is critically regulated by posttranslational modifications to mediate cell type-specific gene expression. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacts", "start": 188, "end": 197}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 95, "end": 100}, {"role": "Theme2", "text": "Oct1", "start": 207, "end": 211}]}, {"trigger": {"text": "interacts", "start": 188, "end": 197}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 95, "end": 100}, {"role": "Theme2", "text": "Oct2", "start": 216, "end": 220}]}], "gene expression": [{"trigger": {"text": "expression", "start": 10, "end": 20}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 56, "end": 61}]}, {"trigger": {"text": "expressed", "start": 163, "end": 172}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 95, "end": 100}]}, {"trigger": {"text": "expression", "start": 355, "end": 365}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 343, "end": 348}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 25, "end": 40}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 56, "end": 61}]}, {"trigger": {"text": "phosphorylated", "start": 425, "end": 439}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 409, "end": 414}, {"role": "Site", "text": "Ser184", "start": 443, "end": 449}]}], "positive regulation": [{"trigger": {"text": "Inducible", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "expression", "start": 10, "end": 20}]}, {"trigger": {"text": "Inducible", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 25, "end": 40}]}, {"trigger": {"text": "induced", "start": 400, "end": 407}, "arguments": [{"role": "Theme", "text": "expression", "start": 355, "end": 365}]}, {"trigger": {"text": "required", "start": 503, "end": 511}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 409, "end": 414}, {"role": "Cause", "text": "phosphorylated", "start": 425, "end": 439}]}, {"trigger": {"text": "activating", "start": 630, "end": 640}, "arguments": [{"role": "Theme", "text": "phosphorylated", "start": 425, "end": 439}]}, {"trigger": {"text": "inducible", "start": 665, "end": 674}, "arguments": [{"role": "Theme", "text": "activating", "start": 630, "end": 640}]}], "regulation": [{"trigger": {"text": "regulated", "start": 794, "end": 803}, "arguments": [{"role": "Theme", "text": "BOB.1", "start": 730, "end": 735}]}]}}, "schema": []}
{"input": "Role of the X2 box in activated transcription from the DRA promoter in B cells. \nWe investigated the function of the evolutionary conserved X2 box in the promoter of the HLA-DRA gene from the human major histocompatibility complex (MHC) in resting and activated B cells. NF-X2, which contains members of the AP-1/ATF/CREB families of transcription factors, interacts with the X2 box (5'-TGCGTCA-3') from positions -97 to -91 in the DRA promoter. In resting Raji cells, little to no binding to the X2 box was observed. In sharp contrast, in B cells treated with the phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA), strong interactions between the X2 box and NF-X2 containing c-Fos were observed. As determined by transient expression and RNA analyses, the activation of protein kinase C (PKC) also increased rates of transcription from the wild-type DRA promoter but not from a DRA promoter bearing clustered point mutations in the X2 box. Since the co-expression with a dominant negative c-Fos abolished the responsiveness to TPA, we conclude that activated transcription of the DRA gene depends on interactions between the X2 box and NF-X2, which contains c-Fos. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "co-expression", "start": 958, "end": 971}, "arguments": [{"role": "Theme", "text": "c-Fos", "start": 997, "end": 1002}]}]}}, "schema": []}
{"input": "Rescue by cytokines of apoptotic cell death induced by IL-2 deprivation of human antigen-specific T cell clones. \nThe control of cell survival and cell death is of central importance in tissues with high cell turnover such as the lymphoid system. We have examined the effect of cytokines on IL-2 deprivation-induced apoptosis of human antigen-specific T helper clones with different cytokine production profiles. We found that IL-2, interferon-alpha (IFN-alpha), and IFN-beta inhibited IL-2 deprivation apoptosis in Th0, Th1, and Th2 clones. We also found that IL-2 protects T cell clones from IL-2 deprivation apoptosis accompanying active proliferation and enhanced expression of P53, Rb and Bcl-xL proteins. In contrast, IFN-alpha/beta rescued T cell clones from apoptosis without active proliferation, and expression of apoptosis-associated proteins tested so far was unaffected. This may be due to the fact that T cells treated with IL-2 contained those located in S + G2/M phases of the cell cycle, whereas the vast majority of T cells treated with IFN-alpha/beta were located in G0/G1 phase. IFN-alpha/beta specifically induced tyrosine phosphorylation and translocation into nucleus of signal transducers and activators of transcription (STAT) 2 protein in the T cell clones. In addition, over-expression of STAT2 by transfection of the cDNA prevented apoptosis of the T cell clones. Our present study shows that IFN-alpha and -beta mediate anti-apoptotic effect through other pathways than that of IL-2 in growth factor deprivation apoptosis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 668, "end": 678}, "arguments": [{"role": "Theme", "text": "P53", "start": 682, "end": 685}]}, {"trigger": {"text": "expression", "start": 668, "end": 678}, "arguments": [{"role": "Theme", "text": "Rb", "start": 687, "end": 689}]}, {"trigger": {"text": "expression", "start": 668, "end": 678}, "arguments": [{"role": "Theme", "text": "Bcl-xL", "start": 694, "end": 700}]}, {"trigger": {"text": "over-expression", "start": 1297, "end": 1312}, "arguments": [{"role": "Theme", "text": "STAT2", "start": 1316, "end": 1321}]}], "localization": [{"trigger": {"text": "translocation", "start": 1164, "end": 1177}, "arguments": [{"role": "ToLoc", "text": "nucleus", "start": 1183, "end": 1190}, {"role": "Theme", "text": "signal transducers and activators of transcription (STAT) 2", "start": 1194, "end": 1253}]}], "negative regulation": [{"trigger": {"text": "deprivation", "start": 60, "end": 71}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 55, "end": 59}]}, {"trigger": {"text": "deprivation", "start": 296, "end": 307}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 291, "end": 295}]}, {"trigger": {"text": "deprivation", "start": 491, "end": 502}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 486, "end": 490}]}, {"trigger": {"text": "deprivation", "start": 599, "end": 610}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 594, "end": 598}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1144, "end": 1159}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1135, "end": 1143}, {"role": "Theme", "text": "signal transducers and activators of transcription (STAT) 2", "start": 1194, "end": 1253}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 659, "end": 667}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 561, "end": 565}, {"role": "Theme", "text": "expression", "start": 668, "end": 678}]}, {"trigger": {"text": "induced", "start": 1127, "end": 1134}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1144, "end": 1159}]}, {"trigger": {"text": "induced", "start": 1127, "end": 1134}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1164, "end": 1177}]}, {"trigger": {"text": "over-expression", "start": 1297, "end": 1312}, "arguments": [{"role": "Theme", "text": "over-expression", "start": 1297, "end": 1312}]}]}}, "schema": []}
{"input": "Association between expression of intercellular adhesion molecule-1 and integration of human T-cell-leukemia virus type 1 in adult T-cell leukemia cells. \nIt is known that the expression levels of intercellular adhesion molecule-1 (ICAM-1) in adult T cell leukemia(ATL) cells are high, whereas those in T-lymphoid cells are not. In order to investigate the factors that influence the induction of ICAM-1 molecules, Northern blot analysis to measure the expression level of ICAM-1 mRNAs and Southern blot hybridization to analyze the integration of human T-cell-leukemia virus type 1 (HTLV-1) provirus were done. The levels of ICAM-1 mRNA expression of ATL cells were generally higher than those of T-lymphoid cells. However, ILT-mat cells and ATL16T(-) cells, although they were ATL cells, showed rather low surface ICAM-1 expression and ICAM-1 mRNA expression. Southern blot hybridization showed that only two and four bands were found in ILT-mat and ATL16T(-) cells, respectively, whereas > 10 bands were detected in other ATL cells. These results suggest that monoclonal integration of HTLV-1 provirus to the genome of T cell, especially the number of integration sites, is one of the factors for induction of ICAM-1 molecules. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 20, "end": 30}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 34, "end": 67}]}, {"trigger": {"text": "expression", "start": 176, "end": 186}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 232, "end": 238}]}, {"trigger": {"text": "expression", "start": 823, "end": 833}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 816, "end": 822}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 384, "end": 393}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 397, "end": 403}]}, {"trigger": {"text": "induction", "start": 1200, "end": 1209}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1213, "end": 1219}]}], "regulation": [{"trigger": {"text": "influence", "start": 370, "end": 379}, "arguments": [{"role": "Theme", "text": "induction", "start": 384, "end": 393}]}], "transcription": [{"trigger": {"text": "expression", "start": 453, "end": 463}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 473, "end": 479}]}, {"trigger": {"text": "expression", "start": 638, "end": 648}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 626, "end": 632}]}, {"trigger": {"text": "expression", "start": 850, "end": 860}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 838, "end": 844}]}]}}, "schema": []}
{"input": "Transcription factor binding sites downstream of the human immunodeficiency virus type 1 transcription start site are important for virus infectivity. \nWhen transcriptionally active, the human immunodeficiency virus (HIV) promoter contains a nucleosome-free region encompassing both the promoter/enhancer region and a large region (255 nucleotides [nt]) downstream of the transcription start site. We have previously identified new binding sites for transcription factors downstream of the transcription start site (nt 465 to 720): three AP-1 sites (I, II, and III), an AP3-like motif (AP3-L), a downstream binding factor (DBF) site, and juxtaposed Sp1 sites. Here, we show that the DBF site is an interferon-responsive factor (IRF) binding site and that the AP3-L motif binds the T-cell-specific factor NF-AT. Mutations that abolish the binding of each factor to its cognate site are introduced in an infectious HIV-1 molecular clone to study their effect on HIV-1 transcription and replication. Individual mutation of the DBF or AP3-L site as well as the double mutation AP-1(III)/AP3-L did not affect HIV-1 replication compared to that of the wild-type virus. In contrast, proviruses carrying mutations in the Sp1 sites were totally defective in terms of replication. Virus production occurred with slightly delayed kinetics for viruses containing combined mutations in the AP-1(III), AP3-L, and DBF sites and in the AP3-L and DBF-sites, whereas viruses mutated in the AP-1(I,II,III) and AP3-L sites and in the AP-1(I,II,III), AP3-L, and DBF sites exhibited a severely defective replicative phenotype. No RNA-packaging defect could be measured for any of the mutant viruses as determined by quantification of their HIV genomic RNA. Measurement of the transcriptional activity of the HIV-1 promoter after transient transfection of the HIV-1 provirus DNA or of long terminal repeat-luciferase constructs showed a positive correlation between the transcriptional and the replication defects for most mutants. ", "output": {"json_structures": {}}, "schema": []}
{"input": "The role of nuclear factor-kappa B in cytokine gene regulation. \nTranscription factors are DNA-binding proteins that regulate gene expression. Nuclear factor-kappa B (NF-kappa B) is a critical transcription factor for maximal expression of many cytokines that are involved in the pathogenesis of inflammatory diseases, such as adult respiratory distress syndrome (ARDS) and sepsis syndrome. Activation and regulation of NF-kappa B are tightly controlled by a group of inhibitory proteins (I kappa B) that sequester NF-kappa B in the cytoplasm of immune/inflammatory effector cells. NF-kappa B activation involves signaled phosphorylation, ubiquitination, and proteolysis of I kappa B. Liberated NF-kappa B migrates to the nucleus, where it binds to specific promoter sites and activates gene transcription. The activation of NF-kappa B initiates both extracellular and intracellular regulatory events that result in autoregulation of the inflammatory cascade through modulation of NF-kappa B activation. Recently, activation of NF-kappa B has been linked to ARDS and has been shown to be a critical proximal step in the initiation of neutrophilic inflammation in animal models. Activation of NF-kappa B can be inhibited in vivo by treatment with antioxidants, corticosteroids, and the induction of endotoxin tolerance. Identification of more specific and efficacious inhibitors of NF-kappa B activation might prove beneficial for the treatment of cytokine-mediated inflammatory diseases. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Role of ascorbate in the activation of NF-kappaB by tumour necrosis factor-alpha in T-cells. \nThe first product of ascorbate oxidation, the ascorbate free radical (AFR), acts in biological systems mainly as an oxidant, and through its role in the plasma membrane redox system exerts different effects on the cell. We have investigated the role of ascorbate, AFR and dehydroascorbate (DHA) in the activation of the NF-kappaB transcription factor in Jurkat T-cells stimulated by tumour necrosis factor-alpha (TNF-alpha). Here we show, by electrophoretic mobility shift assays, that ascorbate increases the binding of NF-kappaB to DNA in TNF-alpha-stimulated Jurkat cells. The ability of ascorbate to enhance cytoplasmic inhibitory IkBalpha protein degradation correlates completely with its capacity to induce NF-kappaB binding to DNA and to potentiate NF-kappaB-mediated transactivation of the HIV-1 long terminal repeat promoter in TNF-alpha-stimulated Jurkat cells but not in cells stimulated with PMA plus ionomycin. AFR behaves like ascorbate, while DHA and ascorbate phosphate do not affect TNF-alpha-mediated NF-kappaB activation. These results provide new evidence for a possible relationship between the activation of the electron-transport system at the plasma membrane by ascorbate or its free radical and redox-dependent gene transcription in T-cells. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "enhance", "start": 698, "end": 705}, "arguments": [{"role": "Theme", "text": "degradation", "start": 746, "end": 757}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 746, "end": 757}, "arguments": [{"role": "Theme", "text": "IkBalpha", "start": 729, "end": 737}]}]}}, "schema": []}
{"input": "Pancreatic islet expression studies and polymorphic DNA markers in the genes encoding hepatocyte nuclear factor-3alpha, -3beta, -3gamma, -4gamma, and -6. \nThe genes encoding the functionally related hepatocyte nuclear factors HNF-1alpha and HNF-4alpha play a critical role in normal pancreatic beta-cell function. Mutations in these liver-enriched transcription factors result in two forms of early-onset type 2 diabetes (maturity-onset diabetes of the young [MODY]), MODY3 and MODY1, which are characterized by impaired glucose-stimulated insulin secretion, early disease onset, and autosomal dominant inheritance. The transcriptional hierarchy of HNFs suggests that other proteins of the regulatory cascade might be responsible for other forms of MODY and/or late-onset type 2 diabetes. In this study, we show that HNF-3alpha, -3beta, -3gamma, -4gamma, and -6 are expressed in pancreatic beta-cells. We report the identification and characterization of simple tandem repeat DNA polymorphisms in the genes encoding HNF-3alpha, -3beta, -3gamma, -4gamma, and -6 and the mapping of HNF-6 to chromosome bands 15q21.1-21.2 by fluorescence in situ hybridization. These markers will be useful to study the role of genetic variation in these genes in the pathogenesis of type 2 diabetes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression studies", "start": 17, "end": 35}, "arguments": [{"role": "Theme", "text": "-3beta", "start": 120, "end": 126}]}, {"trigger": {"text": "expression studies", "start": 17, "end": 35}, "arguments": [{"role": "Theme", "text": "-3gamma", "start": 128, "end": 135}]}, {"trigger": {"text": "expression studies", "start": 17, "end": 35}, "arguments": [{"role": "Theme", "text": "-4gamma", "start": 137, "end": 144}]}, {"trigger": {"text": "expression studies", "start": 17, "end": 35}, "arguments": [{"role": "Theme", "text": "-6", "start": 150, "end": 152}]}, {"trigger": {"text": "expression studies", "start": 17, "end": 35}, "arguments": [{"role": "Theme", "text": "hepatocyte nuclear factor-3alpha", "start": 86, "end": 118}]}, {"trigger": {"text": "expressed", "start": 866, "end": 875}, "arguments": [{"role": "Theme", "text": "HNF-3alpha", "start": 817, "end": 827}]}, {"trigger": {"text": "expressed", "start": 866, "end": 875}, "arguments": [{"role": "Theme", "text": "-3beta", "start": 829, "end": 835}]}, {"trigger": {"text": "expressed", "start": 866, "end": 875}, "arguments": [{"role": "Theme", "text": "-3gamma", "start": 837, "end": 844}]}, {"trigger": {"text": "expressed", "start": 866, "end": 875}, "arguments": [{"role": "Theme", "text": "-4gamma", "start": 846, "end": 853}]}, {"trigger": {"text": "expressed", "start": 866, "end": 875}, "arguments": [{"role": "Theme", "text": "-6", "start": 859, "end": 861}]}]}}, "schema": []}
{"input": "RP1, a new member of the adenomatous polyposis coli-binding EB1-like gene family, is differentially expressed in activated T cells. \nCross-linking of the CD3 and CD28 molecules on T lymphocytes represents one of the most effective signals for T lymphocyte activation and triggering of their cytotoxic effector function. To identify genes that are expressed in T cells after stimulation, mRNA from T lymphocytes that had been activated by the simultaneous stimulation of the CD3 and CD28 trigger molecules was transcribed for a differential mRNA display analysis into cDNA and was compared with cDNA from CD28- or CD3-activated or resting lymphocytes. Differential expression was confirmed subsequently by Northern blot analysis. One of the cDNA fragments expressed specifically in CD3- and CD28-activated T cells was designated RP1. The predictive protein-coding region of RP1 had a significant homology to members of the recently found adenomatous polyposis coli (APC) protein-binding EB1 gene family, which codes for yet unknown protein(s). Bacterially expressed RP1 protein revealed specific binding to wild-type but not to mutated APC protein. The rapid up-regulation of RP1 mRNA in properly activated T cells suggests that this gene might belong to the immediate/early gene family, which controls the signal transduction cascade downstream of the TCR. As the expression level of the RP1 gene in activated T cells and a spectrum of tumor-derived cell lines correlates with the proliferative status of the cells, members of the EB1-like gene family may not only be involved in the tumorigenesis of colorectal cancers but may also play a role in the proliferative control of normal cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Cross-linking", "start": 133, "end": 146}, "arguments": [{"role": "Theme", "text": "CD28", "start": 162, "end": 166}]}, {"trigger": {"text": "binding", "start": 1095, "end": 1102}, "arguments": [{"role": "Theme", "text": "RP1", "start": 1065, "end": 1068}, {"role": "Theme2", "text": "APC", "start": 1135, "end": 1138}]}, {"trigger": {"text": "binding", "start": 1095, "end": 1102}, "arguments": [{"role": "Theme", "text": "RP1", "start": 1065, "end": 1068}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 100, "end": 109}, "arguments": [{"role": "Theme", "text": "RP1", "start": 0, "end": 3}]}, {"trigger": {"text": "expressed", "start": 1055, "end": 1064}, "arguments": [{"role": "Theme", "text": "RP1", "start": 1065, "end": 1068}]}, {"trigger": {"text": "expression", "start": 1364, "end": 1374}, "arguments": [{"role": "Theme", "text": "RP1", "start": 1388, "end": 1391}]}], "positive regulation": [{"trigger": {"text": "up-regulation", "start": 1158, "end": 1171}, "arguments": [{"role": "Theme", "text": "RP1", "start": 1175, "end": 1178}]}]}}, "schema": []}
{"input": "Induction of human immunodeficiency virus type 1 expression in monocytic cells by Cryptococcus neoformans and Candida albicans. \nBecause candidiasis and cryptococcosis are common in human immunodeficiency virus (HIV)-infected persons, the effect of Cryptococcus neoformans and Candida albicans on HIV expression in monocytic cells was examined. Stimulation of the latently HIV-infected myelomonocytic cell line OM-10.1 with C. neoformans and C. albicans in the presence of pooled human serum caused a ratio-dependent increase in HIV production. Induction of HIV by C. neoformans was enhanced by anti-capsular antibody, while induction by both organisms was inhibited by anti-TNF-alpha antibody. In THP-1 cells transfected with HIV plasmid constructs, both organisms induced transcription from the HIV long terminal repeat that was dependent on intact NF-kappaB binding sequences. Thus, C. neoformans and C. albicans enhance HIV expression in monocytic cells through a TNF-alpha- and NF-kappaB-dependent mechanism. In HIV-infected patients, such enhancement may further impair host immunity and could accelerate the course of HIV disease. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Bcl-2 protein inhibits bufalin-induced apoptosis through inhibition of mitogen-activated protein kinase activation in human leukemia U937 cells. \nIn a previous study, we demonstrated that bufalin, which is an active principle of Chinese medicine, chan'su, caused apoptosis in human leukemia U937 cells by anomalous activation of mitogen-activated protein kinase (MAPK) via the signaling pathway of Ras, Raf-1, and MAPK kinase-1. Here, we report the effect of overexpression of bcl-2 in U937 cells on the signaling pathway of apoptosis that is induced by bufalin. The results indicated that the apoptosis induced by bufalin in U937 cells was significantly inhibited by overexpression of the Bcl-2 protein. No significant difference was detected in the activation of MAPK kinase-1 that is induced by bufalin in wild-type or Bcl-2-overexpressed U937 cells; however, the activation of MAPK by bufalin was significantly attenuated in the cells overexpressing Bcl-2. Bufalin treatment activated activator protein-1 transcriptional activity; however, this activation was decreased to 40% in bcl-2-overexpressed U937 cells. These results indicate that Bcl-2 acts downstream of MAPK kinase-1 but upstream of MAPK and suggest that, in the signaling pathway of the apoptotic process induced by bufalin, the transcriptional activity of activator protein-1 may be down-regulated through the inhibition of MAPK activity by Bcl-2. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "overexpression", "start": 459, "end": 473}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 477, "end": 482}]}, {"trigger": {"text": "overexpression", "start": 668, "end": 682}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 690, "end": 695}]}, {"trigger": {"text": "overexpressed", "start": 828, "end": 841}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 822, "end": 827}]}, {"trigger": {"text": "overexpressing", "start": 939, "end": 953}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 954, "end": 959}]}, {"trigger": {"text": "overexpressed", "start": 1090, "end": 1103}, "arguments": [{"role": "Theme", "text": "bcl-2", "start": 1084, "end": 1089}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 459, "end": 473}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 459, "end": 473}]}, {"trigger": {"text": "overexpression", "start": 668, "end": 682}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 668, "end": 682}]}, {"trigger": {"text": "activation", "start": 751, "end": 761}, "arguments": [{"role": "Theme", "text": "MAPK kinase-1", "start": 765, "end": 778}]}, {"trigger": {"text": "overexpressed", "start": 828, "end": 841}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 828, "end": 841}]}, {"trigger": {"text": "overexpressing", "start": 939, "end": 953}, "arguments": [{"role": "Theme", "text": "overexpressing", "start": 939, "end": 953}]}, {"trigger": {"text": "overexpressed", "start": 1090, "end": 1103}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 1090, "end": 1103}]}], "regulation": [{"trigger": {"text": "acts", "start": 1150, "end": 1154}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1144, "end": 1149}, {"role": "Cause", "text": "MAPK kinase-1", "start": 1169, "end": 1182}]}]}}, "schema": []}
{"input": "A shortened life span of EKLF-/- adult erythrocytes, due to a deficiency of beta-globin chains, is ameliorated by human gamma-globin chains. \nUsing homologous recombination, both EKLF alleles in murine embryonic stem (ES) cells were inactivated. These EKLF-/- ES cells were capable of undergoing in vitro differentiation to form definitive erythroid colonies that were similar in size and number to those formed by wild-type ES cells. However, the EKLF-/- colonies were poorly hemoglobinized and enucleated erythrocytes in these colonies contained numerous Heinz bodies. Reverse transcriptase-polymerase chain reaction (RT-PCR) analyses revealed that adult and embryonic globin genes were appropriately regulated, with the exception of beta h1-globin, which continued to be expressed at a very low level. The ratio of adult beta-globin/alpha-globin mRNA in the mutant ES cells was 1/15 of that in wild-type ES cells. When the EKLF-/- cells were injected into blastocysts, they did not contribute at a detectable level to the mature erythrocyte compartment of the chimeric animals, based on analysis of glucose phosphate isomerase-1 (GPI-1) isozymes and hemoglobins that distinguish ES cell-derived erythrocytes from host blastocyst-derived erythrocytes. In contrast, semiquantitative RT-PCR analysis of RNA from reticulocytes of the same chimeric animals suggested that the ES cell-derived reticulocytes were present at a level of 6% to 8%. This indicated that the EKLF-/- erythrocytes in adult animals must be short-lived, apparently due to the imbalance of beta- versus alpha-globin chains, leading to the precipitation of excess alpha-globin chains to form Heinz bodies. Consistent with this hypothesis, the short life span was ameliorated by introduction into the EKLF-/- ES cells of a human LCR/gamma-globin gene, as evidenced by the presence of ES cell-derived reticulocytes as well as mature erythrocytes in the blood of the chimeric animals. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 774, "end": 783}, "arguments": [{"role": "Theme", "text": "beta h1-globin", "start": 736, "end": 750}]}], "localization": [{"trigger": {"text": "precipitation", "start": 1608, "end": 1621}, "arguments": [{"role": "Theme", "text": "alpha-globin", "start": 1632, "end": 1644}, {"role": "AtLoc", "text": "Heinz bodies", "start": 1660, "end": 1672}]}], "negative regulation": [{"trigger": {"text": "deficiency", "start": 62, "end": 72}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 76, "end": 87}]}, {"trigger": {"text": "continued to", "start": 758, "end": 770}, "arguments": [{"role": "Theme", "text": "expressed", "start": 774, "end": 783}]}], "positive regulation": [{"trigger": {"text": "leading", "start": 1593, "end": 1600}, "arguments": [{"role": "Theme", "text": "precipitation", "start": 1608, "end": 1621}]}, {"trigger": {"text": "excess", "start": 1625, "end": 1631}, "arguments": [{"role": "Theme", "text": "alpha-globin", "start": 1632, "end": 1644}]}], "regulation": [{"trigger": {"text": "regulated", "start": 703, "end": 712}, "arguments": [{"role": "Theme", "text": "beta h1-globin", "start": 736, "end": 750}]}]}}, "schema": []}
{"input": "Induction of nuclear factor kappa B/Rel nuclear activity in human peripheral blood T lymphocytes by anti-HLA class I monoclonal antibodies. \nMonoclonal antibodies against either monomorphic or polymorphic determinants of class I antigen induced in PBMC and highly purified T lymphocytes the nuclear activity of NF-kappa B/Rel complexes. These included both p50/p50 and p50/p65 dimers, recognized by specific antibodies in EMSA. The induced complexes were detectable in extracts of cells incubated with anti-class I monoclonal antibody (mAb) for 1.5 h; the induction was maximal at 5 h, persistent at 16 h and no longer observed at 40 h. The mAb failed to induce NF-kappa B/Rel nuclear activity in cells incubated in the presence of 3,4-dichloroisocoumarin, an inhibitor of I kappa B-alpha degradation. Together, these results suggest that class I triggering can induce the activity of NF-kappa B/Rel nuclear activity in peripheral blood T lymphocytes, thereby modulating the expression of genes regulated by these transcription factors. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recognized", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "p50", "start": 357, "end": 360}]}, {"trigger": {"text": "recognized", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "p50", "start": 369, "end": 372}]}, {"trigger": {"text": "recognized", "start": 385, "end": 395}, "arguments": [{"role": "Theme", "text": "p65", "start": 373, "end": 376}]}], "gene expression": [{"trigger": {"text": "detectable", "start": 455, "end": 465}, "arguments": [{"role": "Theme", "text": "p50", "start": 357, "end": 360}]}, {"trigger": {"text": "detectable", "start": 455, "end": 465}, "arguments": [{"role": "Theme", "text": "p50", "start": 369, "end": 372}]}, {"trigger": {"text": "detectable", "start": 455, "end": 465}, "arguments": [{"role": "Theme", "text": "p65", "start": 373, "end": 376}]}], "negative regulation": [{"trigger": {"text": "inhibitor", "start": 760, "end": 769}, "arguments": [{"role": "Theme", "text": "degradation", "start": 789, "end": 800}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 789, "end": 800}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 773, "end": 788}]}]}}, "schema": []}
{"input": "Cyclosporin A interferes with the inducible degradation of NF-kappa B inhibitors, but not with the processing of p105/NF-kappa B1 in T cells. \nThe transcription factor NF-kappa B controls the induction of numerous cytokine promoters during the activation of T lymphocytes. Inhibition of T cell activation by the immunosuppressants cyclosporin A (CsA) and FK506 exerts a suppressive effect on the induction of these NF-kappa B-controlled cytokine promoters. We show for human Jurkat T leukemia cells, as well as human and mouse primary T lymphocytes, that this inhibitory effect is accompanied by an impaired nuclear translocation of the Rel proteins c-Rel, RelA/p65 and NF-kappa B1/p50, whereas the nuclear appearance of RelB remains unaffected. CsA does not interfere with the synthesis of Rel proteins, but prevents the inducible degradation of cytosolic NF-kappa B inhibitors I kappa B alpha and I kappa B beta upon T cell activation. CsA neither inhibits the processing of the NF-kappa B1 precursor p105 to p50, nor does it \"stabilize\" the C-terminal portion of p105, I kappa B gamma, which is degraded during p105 processing to mature p50. These results indicate that CsA interferes with a specific event in the signal-induced degradation of I kappa B alpha and I kappa B beta, but does not affect the processing of NF-kappa B1/p105 to p50. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "translocation", "start": 616, "end": 629}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 608, "end": 615}, {"role": "Theme", "text": "c-Rel", "start": 650, "end": 655}]}, {"trigger": {"text": "translocation", "start": 616, "end": 629}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 608, "end": 615}, {"role": "Theme", "text": "RelA", "start": 657, "end": 661}]}, {"trigger": {"text": "translocation", "start": 616, "end": 629}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 608, "end": 615}, {"role": "Theme", "text": "p50", "start": 682, "end": 685}]}, {"trigger": {"text": "appearance", "start": 707, "end": 717}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 699, "end": 706}, {"role": "Theme", "text": "RelB", "start": 721, "end": 725}]}], "negative regulation": [{"trigger": {"text": "impaired", "start": 599, "end": 607}, "arguments": [{"role": "Theme", "text": "translocation", "start": 616, "end": 629}]}, {"trigger": {"text": "unaffected", "start": 734, "end": 744}, "arguments": [{"role": "Theme", "text": "appearance", "start": 707, "end": 717}]}, {"trigger": {"text": "prevents", "start": 809, "end": 817}, "arguments": [{"role": "Theme", "text": "degradation", "start": 832, "end": 843}]}, {"trigger": {"text": "\"stabilize\"", "start": 1028, "end": 1039}, "arguments": [{"role": "Theme", "text": "degraded", "start": 1098, "end": 1106}]}, {"trigger": {"text": "interferes", "start": 1177, "end": 1187}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1232, "end": 1243}]}], "positive regulation": [{"trigger": {"text": "inducible", "start": 822, "end": 831}, "arguments": [{"role": "Theme", "text": "degradation", "start": 832, "end": 843}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 832, "end": 843}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 879, "end": 894}]}, {"trigger": {"text": "degradation", "start": 832, "end": 843}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 899, "end": 913}]}, {"trigger": {"text": "degraded", "start": 1098, "end": 1106}, "arguments": [{"role": "Theme", "text": "I kappa B gamma", "start": 1072, "end": 1087}]}, {"trigger": {"text": "degradation", "start": 1232, "end": 1243}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1247, "end": 1262}]}, {"trigger": {"text": "degradation", "start": 1232, "end": 1243}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 1267, "end": 1281}]}]}}, "schema": []}
{"input": "EBF and E47 collaborate to induce expression of the endogenous immunoglobulin surrogate light chain genes. \nEarly B cell factor (EBF) and E47 participate in the transcriptional control of early B lymphocyte differentiation. With the aim of identifying genetic targets for these transcription factors, we stably transfected cDNAs encoding EBF or a covalent homodimer of E47, individually or together, into immature hematopoietic Ba/F3 cells, which lack both factors. In combination, EBF and E47 induce efficient expression of the endogenous immunoglobulin surrogate light chain genes, lambda5 and VpreB, whereas other pre-B cell-specific genes remain silent. Multiple functionally important EBF and E47 binding sites were identified in the lambda5 promoter/enhancer region, indicating that lambda5 is a direct genetic target for these transcription factors. Taken together, these data suggest that EBF and E47 synergize to activate expression of a subset of genes that define an early stage of the B cell lineage. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "transfected", "start": 311, "end": 322}, "arguments": [{"role": "Theme", "text": "EBF", "start": 338, "end": 341}]}, {"trigger": {"text": "transfected", "start": 311, "end": 322}, "arguments": [{"role": "Theme", "text": "E47", "start": 369, "end": 372}]}, {"trigger": {"text": "lack", "start": 447, "end": 451}, "arguments": [{"role": "Theme", "text": "EBF", "start": 338, "end": 341}]}, {"trigger": {"text": "lack", "start": 447, "end": 451}, "arguments": [{"role": "Theme", "text": "E47", "start": 369, "end": 372}]}, {"trigger": {"text": "expression", "start": 511, "end": 521}, "arguments": [{"role": "Theme", "text": "lambda5", "start": 584, "end": 591}]}, {"trigger": {"text": "expression", "start": 511, "end": 521}, "arguments": [{"role": "Theme", "text": "VpreB", "start": 596, "end": 601}]}], "positive regulation": [{"trigger": {"text": "transfected", "start": 311, "end": 322}, "arguments": [{"role": "Theme", "text": "transfected", "start": 311, "end": 322}]}, {"trigger": {"text": "induce", "start": 494, "end": 500}, "arguments": [{"role": "Cause", "text": "EBF", "start": 482, "end": 485}, {"role": "Theme", "text": "expression", "start": 511, "end": 521}]}, {"trigger": {"text": "induce", "start": 494, "end": 500}, "arguments": [{"role": "Cause", "text": "E47", "start": 490, "end": 493}, {"role": "Theme", "text": "expression", "start": 511, "end": 521}]}], "regulation": [{"trigger": {"text": "target", "start": 817, "end": 823}, "arguments": [{"role": "Cause", "text": "EBF", "start": 482, "end": 485}, {"role": "Theme", "text": "lambda5", "start": 789, "end": 796}]}, {"trigger": {"text": "target", "start": 817, "end": 823}, "arguments": [{"role": "Cause", "text": "E47", "start": 490, "end": 493}, {"role": "Theme", "text": "lambda5", "start": 789, "end": 796}]}]}}, "schema": []}
{"input": "Nuclear levels of NF-kappaB correlate with syncytium-forming capacity of 8e51 cells, expressing a defective HIV virus. \nThe double NF-kappaB site identified in the LTR of the human immunodeficiency virus-1 (HIV-1) has been demonstrated to be necessary for efficient viral transcription. In this report we present the characterisation of NF-kappaB subunits engaged in complexes binding to the HIV-1 NF-kappaB site in human 8e51 T-cells, that harbour a defective HIV-1. At least four different specific NF-kappaB complexes are present in the nucleus of these cells. With the use of specific antibodies we have determined the composition of each complex using electrophoretic mobility shift assays. The results show the presence of several NF-kappaB family members, with the transactivating RelA being engaged in multiple complexes. The importance of NF-kappaB complexes in viral functions has been established comparing the level of NF-kappaB DNA-binding complexes with syncytia-forming activity of 8e51 cells. In fact, 8e51 cells that had almost lost their syncytia-forming capacity were found to contain at least 10 times less active NF-kappaB DNA-binding complex than the actively fusing cells. The correlation is specific as the level of at least three other transcription factors did not change. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Differential interaction of nuclear factors with the leukocyte-specific pp52 promoter in B and T cells. \nThe leukocyte-specific, cytoskeleton-binding pp52 (LSP-1, WP-34) protein is widely expressed in multiple leukocyte lineages, including B and T lymphocytes, granulocytes, and macrophages. We previously detected a tissue-specific promoter preceding the exon encoding the N terminus of the pp52 leukocyte protein. Here we describe the functional characterization of this promoter and identification of the factors in B and T cells that regulate its activity. The pp52 promoter contains an initiator specifying the unique 5' terminus of pp52 mRNA, tandem pairs of Ets and SP1 motifs, and a lone C/EBP motif. All these motifs are essential and collectively control transcriptional activity. DNA binding studies and Ab supershift assays revealed that different combinations of factors interact with these motifs in B cells vs T cells. The Ets motifs are preferentially bound by PU-1 in B cell extracts from all stages of development, whereas a different Ets family member reacts with these motifs in T cell extracts. The C/EBP motif is bound by Ig/EBP-1 in pre-B cell and T cell extracts, but is replaced by nuclear factor-IL-6beta or a nuclear factor-IL-6beta-Ig/EBP-1 heterodimer in plasmacytoma cell extracts. Despite its reported role as a negative regulator of transcription, Ig/EBP-1 appears to exert a stimulatory effect on this promoter. These findings reveal the features controlling the pp52 promoter in B and T cells and provide the foundation for determining the regulation of this promoter in other leukocyte lineages. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 884, "end": 892}, "arguments": [{"role": "Theme", "text": "pp52", "start": 565, "end": 569}, {"role": "Site", "text": "initiator", "start": 591, "end": 600}]}, {"trigger": {"text": "interact", "start": 884, "end": 892}, "arguments": [{"role": "Theme", "text": "pp52", "start": 565, "end": 569}, {"role": "Site", "text": "C/EBP motif", "start": 696, "end": 707}]}, {"trigger": {"text": "bound", "start": 968, "end": 973}, "arguments": [{"role": "Theme", "text": "PU-1", "start": 977, "end": 981}]}, {"trigger": {"text": "bound", "start": 1135, "end": 1140}, "arguments": [{"role": "Theme", "text": "Ig/EBP-1", "start": 1144, "end": 1152}]}, {"trigger": {"text": "replaced", "start": 1195, "end": 1203}, "arguments": [{"role": "Theme", "text": "nuclear factor-IL-6beta", "start": 1207, "end": 1230}]}, {"trigger": {"text": "replaced", "start": 1195, "end": 1203}, "arguments": [{"role": "Theme", "text": "nuclear factor-IL-6beta", "start": 1236, "end": 1259}]}, {"trigger": {"text": "replaced", "start": 1195, "end": 1203}, "arguments": [{"role": "Theme", "text": "Ig/EBP-1", "start": 1260, "end": 1268}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 188, "end": 197}, "arguments": [{"role": "Theme", "text": "LSP-1", "start": 156, "end": 161}]}], "positive regulation": [{"trigger": {"text": "exert a stimulatory effect", "start": 1400, "end": 1426}, "arguments": [{"role": "Theme", "text": "pp52", "start": 565, "end": 569}, {"role": "Site", "text": "promoter", "start": 570, "end": 578}, {"role": "Cause", "text": "Ig/EBP-1", "start": 1380, "end": 1388}]}], "regulation": [{"trigger": {"text": "specifying", "start": 601, "end": 611}, "arguments": [{"role": "Cause", "text": "pp52", "start": 565, "end": 569}, {"role": "CSite", "text": "initiator", "start": 591, "end": 600}, {"role": "Site", "text": "5' terminus", "start": 623, "end": 634}, {"role": "Theme", "text": "pp52", "start": 638, "end": 642}]}, {"trigger": {"text": "controlling", "start": 1480, "end": 1491}, "arguments": [{"role": "Theme", "text": "pp52", "start": 1496, "end": 1500}, {"role": "Site", "text": "promoter", "start": 1501, "end": 1509}]}, {"trigger": {"text": "regulation", "start": 1574, "end": 1584}, "arguments": [{"role": "Theme", "text": "pp52", "start": 1496, "end": 1500}, {"role": "Site", "text": "promoter", "start": 1501, "end": 1509}]}]}}, "schema": []}
{"input": "Transcription factor GATA-3 is differentially expressed in murine Th1 and Th2 cells and controls Th2-specific expression of the interleukin-5 gene. \nInterleukin-5 (IL-5), which is produced by CD4(+) T helper 2 (Th2) cells, but not by Th1 cells, plays a key role in the development of eosinophilia in asthma. Despite increasing evidence that the outcome of many diseases is determined by the ratio of the two subsets of CD4(+) T helper cells, Th1 and Th2, the molecular basis for Th1- and Th2- specific gene expression remains to be elucidated. We previously established a critical role for the transcription factor GATA-3 in IL-5 promoter activation in EL-4 cells, which express both Th1- and Th2-type cytokines. Our studies reported here demonstrate that GATA-3 is critical for expression of the IL-5 gene in bona fide Th2 cells. Whereas mutations in the GATA-3 site abolished antigen- or cAMP- stimulated IL-5 promoter activation in Th2 cells, ectopic expression of GATA-3 in Th1 cells or in a non-lymphoid, non-IL-5-producing cell line activated the IL-5 promoter. During the differentiation of naive CD4(+) T cells isolated from T cell receptor transgenic mice, GATA-3 gene expression was up-regulated in developing Th2 cells, but was down-regulated in Th1 cells, and antigen- or cAMP-activated Th2 cells (but not Th1 cells) expressed the GATA-3 protein. Thus, GATA-3 may play an important role in the balance between Th1 and Th2 subsets in immune responses. Inhibition of GATA-3 activity has therapeutic potential in the treatment of asthma and other hypereosinophilic diseases. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 46, "end": 55}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 21, "end": 27}]}, {"trigger": {"text": "expression", "start": 110, "end": 120}, "arguments": [{"role": "Theme", "text": "interleukin-5", "start": 128, "end": 141}]}, {"trigger": {"text": "produced", "start": 180, "end": 188}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 164, "end": 168}]}, {"trigger": {"text": "expression", "start": 779, "end": 789}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 797, "end": 801}]}, {"trigger": {"text": "expression", "start": 954, "end": 964}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 968, "end": 974}]}, {"trigger": {"text": "producing", "start": 1019, "end": 1028}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1014, "end": 1018}]}, {"trigger": {"text": "expression", "start": 1178, "end": 1188}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 1166, "end": 1172}]}, {"trigger": {"text": "expressed", "start": 1329, "end": 1338}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 1343, "end": 1349}]}], "negative regulation": [{"trigger": {"text": "abolished", "start": 868, "end": 877}, "arguments": [{"role": "Theme", "text": "activation", "start": 921, "end": 931}]}, {"trigger": {"text": "down-regulated", "start": 1239, "end": 1253}, "arguments": [{"role": "Theme", "text": "expression", "start": 1178, "end": 1188}]}, {"trigger": {"text": "Inhibition", "start": 1463, "end": 1473}, "arguments": [{"role": "Theme", "text": "GATA-3", "start": 1477, "end": 1483}]}], "positive regulation": [{"trigger": {"text": "critical role", "start": 572, "end": 585}, "arguments": [{"role": "Cause", "text": "GATA-3", "start": 615, "end": 621}, {"role": "Theme", "text": "activation", "start": 639, "end": 649}]}, {"trigger": {"text": "activation", "start": 639, "end": 649}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 625, "end": 629}, {"role": "Site", "text": "promoter", "start": 630, "end": 638}]}, {"trigger": {"text": "critical", "start": 766, "end": 774}, "arguments": [{"role": "Cause", "text": "GATA-3", "start": 756, "end": 762}, {"role": "Theme", "text": "expression", "start": 779, "end": 789}]}, {"trigger": {"text": "activation", "start": 921, "end": 931}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 907, "end": 911}, {"role": "Site", "text": "promoter", "start": 912, "end": 920}]}, {"trigger": {"text": "activated", "start": 1039, "end": 1048}, "arguments": [{"role": "Cause", "text": "expression", "start": 954, "end": 964}, {"role": "Theme", "text": "IL-5", "start": 1053, "end": 1057}, {"role": "Site", "text": "promoter", "start": 1058, "end": 1066}]}, {"trigger": {"text": "activated", "start": 1039, "end": 1048}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1053, "end": 1057}, {"role": "Site", "text": "promoter", "start": 1058, "end": 1066}]}, {"trigger": {"text": "up-regulated", "start": 1193, "end": 1205}, "arguments": [{"role": "Theme", "text": "expression", "start": 1178, "end": 1188}]}], "regulation": [{"trigger": {"text": "controls", "start": 88, "end": 96}, "arguments": [{"role": "Cause", "text": "GATA-3", "start": 21, "end": 27}, {"role": "Theme", "text": "expression", "start": 110, "end": 120}]}]}}, "schema": []}
{"input": "Inhibition of human immunodeficiency virus type 1 replication in vitro by a novel combination of anti-Tat single-chain intrabodies and NF-kappa B antagonists. \nHuman immunodeficiency virus type 1 (HIV-1) Tat, an early regulatory protein that is critical for viral gene expression and replication, transactivates the HIV-1 long terminal repeat (LTR) via its binding to the transactivation response element (TAR) and, along with other cellular factors, increases viral transcription initiation and elongation. Tat also superactivates the HIV-1 promoter through a TAR-independent mechanism, including tumor necrosis factor alpha-induced and protein kinase C (PKC)-dependent activation of NF-kappa B, and inhibitors of Tat and NF-kappa B cooperatively down-regulate this Tat-mediated LTR superactivation. In this study, a combined pharmacologic and genetic strategy using two PKC (NF-kappa B) inhibitors, pentoxifylline (PTX) and Go-6976, and a stably expressed anti-Tat single-chain intracellular antibody (sFv intrabody) was employed to obtain cooperative inhibition of both HIV-1 LTR-driven gene expression and HIV-1 replication. Treatment of cells with PTX and Go-6976 resulted in cooperative inhibition of both HIV-1 LTR-driven gene expression and HIV-1 replication. In addition, the combined use of anti-Tat sFv intrabodies and the two NF-kappa B inhibitors retained the virus in the latent state for as long as 45 days. The combined treatment resulted in more durable inhibition of HIV-1 replication than was seen with the NF-kappa B inhibitors alone or the anti-Tat sFv intrabodies alone. Together, these results suggest that in future clinical gene therapy trials, a combined pharmacologic and genetic strategy like the one reported here may improve the survival of transduced cells and prolong clinical benefit. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 357, "end": 364}, "arguments": [{"role": "Theme", "text": "Tat", "start": 204, "end": 207}]}]}}, "schema": []}
{"input": "Transcription factors in immune-mediated disease. \nA large amount of detailed information about the intracellular proteins regulating NF-kappa B activation and the cellular response to NF-kappa B activation has emerged recently. Several small molecules, an antisense oligonucleotide, and gene therapeutic agents that inhibit NF-kappa b activation have been described. Despite this, there are still significant gaps in our understanding of this process and its consequences. In contrast, the characterization of transcription factors selectively regulating cytokine production by CD4+ T cell subsets is at a very early stage. Three interacting proteins have recently been shown to contribute to subset-restricted expression of the IL-4 gene. There are other elements regulating IL-4 gene expression, however, and the relative importance of these recently identified proteins has yet to be determined. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 712, "end": 722}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 730, "end": 734}]}, {"trigger": {"text": "expression", "start": 787, "end": 797}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 777, "end": 781}]}], "regulation": [{"trigger": {"text": "contribute", "start": 680, "end": 690}, "arguments": [{"role": "Theme", "text": "expression", "start": 712, "end": 722}]}, {"trigger": {"text": "regulating", "start": 766, "end": 776}, "arguments": [{"role": "Theme", "text": "expression", "start": 787, "end": 797}]}]}}, "schema": []}
{"input": "CholecystokininB receptor from human Jurkat lymphoblastic T cells is involved in activator protein-1-responsive gene activation. \nThe aim of this study was to analyze the role of cholecystokinin (CCK(B)) receptor in human lymphoblastic Jurkat T cells. We investigated the trophic effect resulting from activation of such a receptor by using the reporter gene strategy. For this purpose, we transiently transfected Jurkat T cells with the reporter plasmid p[(TRE)3-tk-Luc] and found that CCK-8 was able to dose-dependently induce luciferase expression related to activator protein-1 (AP-1) activation with a maximal response identical to that obtained with compounds known to activate AP-1 complex (quantitatively, the same level of induction was obtained with 1 nM 12-O-tetradecanoylphorbol-13-acetate, 100 microM diacylglycerol, or 4 nM epidermal growth factor). The involvement of the CCK(B) receptor in such a stimulation was demonstrated by the inhibiting effect of the selective CCK(B) receptor antagonist PD-135,158. This effect was confirmed in COS-7 cells transfected with the cDNA of CCK(B) receptor cloned from Jurkat T cells. To better understand the AP-1-dependent luciferase expression in Jurkat T cells, we tested two specific inhibitors of serine/threonine phosphatases-1 and -2A: okadaic acid and calyculin A. These compounds strongly increased the phorbol-12-myristate-13-acetate response, whereas we have not observed a contribution of phosphatase inhibitors on a CCK-8-induced luciferase activity. To confirm that CCK(B) receptors are involved in AP-1 response, we investigated the CCK-8 effect on interleukin-2 expression, a natural endogenous gene regulated by several factors, including AP-1. In Jurkat T cells activated by phorbol-12-myristate-13-acetate and phytohemagglutinin, CCK-8 induced IL-2 expression. This induction was abolished by PD-135,158. Our results indicate that CCK-8 exerts a trophic effect in Jurkat T cells through stimulation of CCK(B) receptors by modulation of expression of AP-1-regulated genes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 540, "end": 550}, "arguments": [{"role": "Theme", "text": "luciferase", "start": 529, "end": 539}]}, {"trigger": {"text": "expression", "start": 1188, "end": 1198}, "arguments": [{"role": "Theme", "text": "luciferase", "start": 1177, "end": 1187}]}, {"trigger": {"text": "expression", "start": 1631, "end": 1641}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 1617, "end": 1630}]}, {"trigger": {"text": "expression", "start": 1821, "end": 1831}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1816, "end": 1820}]}], "negative regulation": [{"trigger": {"text": "inhibiting effect", "start": 949, "end": 966}, "arguments": [{"role": "Theme", "text": "induce", "start": 522, "end": 528}]}, {"trigger": {"text": "antagonist", "start": 1000, "end": 1010}, "arguments": [{"role": "Theme", "text": "CCK(B) receptor", "start": 984, "end": 999}]}, {"trigger": {"text": "inhibitors", "start": 1241, "end": 1251}, "arguments": [{"role": "Theme", "text": "serine/threonine phosphatases-1", "start": 1255, "end": 1286}]}, {"trigger": {"text": "inhibitors", "start": 1241, "end": 1251}, "arguments": [{"role": "Theme", "text": "-2A", "start": 1291, "end": 1294}]}, {"trigger": {"text": "abolished", "start": 1852, "end": 1861}, "arguments": [{"role": "Theme", "text": "induced", "start": 1808, "end": 1815}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 302, "end": 312}, "arguments": [{"role": "Theme", "text": "(CCK(B)) receptor", "start": 195, "end": 212}]}, {"trigger": {"text": "induce", "start": 522, "end": 528}, "arguments": [{"role": "Theme", "text": "expression", "start": 540, "end": 550}]}, {"trigger": {"text": "induction was obtained", "start": 732, "end": 754}, "arguments": [{"role": "Theme", "text": "expression", "start": 540, "end": 550}]}, {"trigger": {"text": "dependent", "start": 1167, "end": 1176}, "arguments": [{"role": "Theme", "text": "expression", "start": 1188, "end": 1198}]}, {"trigger": {"text": "induced", "start": 1488, "end": 1495}, "arguments": [{"role": "Theme", "text": "luciferase", "start": 1496, "end": 1506}]}, {"trigger": {"text": "induced", "start": 1808, "end": 1815}, "arguments": [{"role": "Theme", "text": "expression", "start": 1821, "end": 1831}]}, {"trigger": {"text": "stimulation", "start": 1959, "end": 1970}, "arguments": [{"role": "Theme", "text": "CCK(B) receptors", "start": 1974, "end": 1990}]}], "regulation": [{"trigger": {"text": "involvement", "start": 868, "end": 879}, "arguments": [{"role": "Theme", "text": "induce", "start": 522, "end": 528}, {"role": "Cause", "text": "CCK(B) receptor", "start": 887, "end": 902}]}, {"trigger": {"text": "effect", "start": 1607, "end": 1613}, "arguments": [{"role": "Theme", "text": "expression", "start": 1631, "end": 1641}]}, {"trigger": {"text": "regulated", "start": 1669, "end": 1678}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 1617, "end": 1630}]}]}}, "schema": []}
{"input": "Epstein-Barr virus binding to CD21 activates the initial viral promoter via NF-kappaB induction. \nEpstein-Barr virus (EBV), an oncogenic human herpesvirus, binds to and infects normal human B lymphocytes via CD21, the CR2 complement receptor. Studies of the mechanisms that enable EBV to infect nonactivated, noncycling B cells provide compelling evidence for a sequence of events in which EBV binding to CD21 on purified resting human B cells rapidly activates the NF-kappaB transcription factor, which, in turn, binds to and mediates transcriptional activation of Wp, the initial viral latent gene promoter. Thus, EBV binding to its cellular receptor on resting B cells triggers an NF-kappaB-dependent intracellular signaling pathway which is required for infection. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Activation of transcription factor NF-kappa B by phagocytic stimuli in human neutrophils. \nPhagocytosis represents an important physiological trigger for the inducible expression of several genes in human neutrophils. Here, we report that a DNA-binding activity primarily consisting of the classical NF-kappa B heterodimer, p50/RelA, is induced in phagocytosing neutrophils. Under these conditions, NF-kappa B activation was found to be a rapid and transient response, reaching a maximum by 10-15 min, and returning to near-basal levels by 30 min. In neutrophils undergoing the phagocytosis of opsonized yeasts, the onset of NF-kappa B activation was paralleled by a decline in immunoreactive I kappa B-alpha protein levels, and the cellular I kappa B-alpha pool was replenished by 30 min, in agreement with our gel shift data. We conclude that NF-kappa B activation could constitute one of the mechanisms whereby the expression of kappa B-responsive genes is enhanced in phagocytosing neutrophils. To our knowledge, this represents the first demonstration that phagocytic stimuli can induce NF-kappa B activation in human neutrophils. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 245, "end": 252}, "arguments": [{"role": "Theme", "text": "p50", "start": 324, "end": 327}]}, {"trigger": {"text": "binding", "start": 245, "end": 252}, "arguments": [{"role": "Theme", "text": "RelA", "start": 328, "end": 332}]}], "negative regulation": [{"trigger": {"text": "decline", "start": 667, "end": 674}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 693, "end": 708}]}, {"trigger": {"text": "replenished", "start": 767, "end": 778}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 742, "end": 757}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 337, "end": 344}, "arguments": [{"role": "Theme", "text": "binding", "start": 245, "end": 252}]}]}}, "schema": []}
{"input": "Surfactant protein A activates NF-kappa B in the THP-1 monocytic cell line. \nThe expression of many genes for which products are involved in inflammation is controlled by the transcriptional regulator nuclear factor (NF)-kappa B. Because surfactant protein (SP) A is involved in local host defense in the lung and alters immune cell function by modulating the expression of proinflammatory cytokines as well as surface proteins involved in inflammation, we hypothesized that SP-A exerts its action, at least in part, via activation of NF-kappa B. We used gel shift assays to determine whether SP-A activated NF-kappa B in the THP-1 cell line, a human monocytic cell line. Activation of NF-kappa B in THP-1 cells by SP-A doses as low as 1 microgram/ml occurred within 30 min of SP-A treatment, peaked at 60 min, and then declined. This activation is inhibited by known inhibitors of NF-kappa B or by simultaneous treatment of the cells with surfactant lipids. Moreover, the NF-kappa B inhibitors blocked SP-A-dependent increases in tumor necrosis factor-alpha mRNA levels. These observations suggest a mechanism by which SP-A plays a role in the pathogenesis of some lung conditions and point to potential therapeutic measures that could be used to prevent SP-A induced inflammation in the lung. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "blocked", "start": 995, "end": 1002}, "arguments": [{"role": "Theme", "text": "increases", "start": 1018, "end": 1027}]}], "positive regulation": [{"trigger": {"text": "increases", "start": 1018, "end": 1027}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 1031, "end": 1058}]}]}}, "schema": []}
{"input": "alpha-Tocopheryl succinate inhibits monocytic cell adhesion to endothelial cells by suppressing NF-kappa B mobilization. \nThe adherence of monocytes to activated endothelium is an early event in atherogenesis. Because antioxidants have been considered to be of antiatherosclerotic potential, we investigated the effects of alpha-tocopherol (TCP) and its acetate and succinate esters on monocyte adhesion to cytokine-stimulated human umbilical vein endothelial cells (HUVEC). Endothelial cells were treated with TCP, alpha-tocopherol acetate (TCP acetate), or alpha-tocopheryl succinate (TCP succinate) before stimulation with tumor necrosis factor-alpha (TNF-alpha; 10 U/ml, 6 h) or interleukin-1 beta (IL-1 beta; 10 U/ml, 6 h). Cytokine-stimulated cell surface expression of vascular cell adhesion molecule-1 (VCAM-1, CD106) and E-selectin (ELAM-1, CD62E), but not of intercellular adhesion molecule-1 (ICAM-1, CD54), was time- and dose-dependently inhibited by TCP succinate but not by TCP or TCP acetate. TCP succinate (200 microM, 24 h) reduced TNF-induced VCAM-1 and E-selectin expression from a specific mean fluorescence intensity of 151 +/- 28 to 12 +/- 4 channels and from 225 +/- 38 to 79 +/- 21 channels, respectively. Succinate alone had no effect. Decreased adhesion molecule expression was associated with a reduction of monocytic cell adhesion. TCP succinate (20 microM, 72 h), but not TCP (200 microM, 72 h), reduced U-937 cell adhesion to TNF-alpha-stimulated (10 U/ml, 6 h) HUVEC by 30% (P < 0.025) and to IL-1 beta-stimulated HUVEC by 56% (P < 0.010). Electrophoretic mobility-shift assays of HUVEC nuclear proteins revealed a decrease in TNF-alpha-stimulated nuclear factor-kappa B (NF-kappa B) activation after pretreatment of HUVEC with TCP succinate but not with TCP, TCP acetate, or succinate alone. In conclusion, we demonstrate that the vitamin E derivative TCP succinate prevents monocytic cell adhesion to cytokine-stimulated endothelial cells by inhibiting the activation of NF-kappa B, further emphasizing the antiatherosclerotic potential of lipid soluble antioxidants. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 762, "end": 772}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 811, "end": 817}]}, {"trigger": {"text": "expression", "start": 762, "end": 772}, "arguments": [{"role": "Theme", "text": "ELAM-1", "start": 842, "end": 848}]}, {"trigger": {"text": "expression", "start": 762, "end": 772}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 904, "end": 910}]}, {"trigger": {"text": "expression", "start": 1083, "end": 1093}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1061, "end": 1067}]}, {"trigger": {"text": "expression", "start": 1083, "end": 1093}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1072, "end": 1082}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 950, "end": 959}, "arguments": [{"role": "Theme", "text": "expression", "start": 762, "end": 772}]}, {"trigger": {"text": "reduced", "start": 1041, "end": 1048}, "arguments": [{"role": "Theme", "text": "induced", "start": 1053, "end": 1060}]}, {"trigger": {"text": "Decreased", "start": 1261, "end": 1270}, "arguments": [{"role": "Theme", "text": "expression", "start": 1083, "end": 1093}]}], "positive regulation": [{"trigger": {"text": "stimulated", "start": 738, "end": 748}, "arguments": [{"role": "Theme", "text": "expression", "start": 762, "end": 772}]}, {"trigger": {"text": "induced", "start": 1053, "end": 1060}, "arguments": [{"role": "Theme", "text": "expression", "start": 1083, "end": 1093}]}], "regulation": [{"trigger": {"text": "effect", "start": 1253, "end": 1259}, "arguments": [{"role": "Theme", "text": "expression", "start": 1083, "end": 1093}]}]}}, "schema": []}
{"input": "Distinct mechanisms for N-acetylcysteine inhibition of cytokine-induced E-selectin and VCAM-1 expression. \nWe have examined the effects of N-acetyl-L-cysteine (NAC), a well-characterized, thiol-containing antioxidant, on agonist-induced monocytic cell adhesion to endothelial cells (EC). NAC inhibited interleukin-1 (IL-1 beta)-induced, but not basal, adhesion with 50% inhibition at approximately 20 mM. Monocytic cell adhesion to EC in response to tumor necrosis factor-alpha (TNF-alpha), lipopolysaccharide (LPS), alpha-thrombin, or phorbol 12-myristate 13-acetate (PMA) was similarly inhibited by NAC. Unlike published studies with pyrrolidinedithiocarbamate, which specifically inhibited vascular cell adhesion molecule 1 (VCAM-1), NAC inhibited IL-1 beta-induced mRNA and cell surface expression of both E-selectin and VCAM-1. NAC had no effect on the half-life of E-selectin or VCAM-1 mRNA. Although NAC reduced nuclear factor-kappa B (NF-kappa B) activation in EC as measured by gel-shift assays using an oligonucleotide probe corresponding to the consensus NF-kappa B binding sites of the VCAM-1 gene (VCAM-NF-kappa B), the antioxidant had no appreciable effect when an oligomer corresponding to the consensus NF-kappa B binding site of the E-selectin gene (E-selectin-NF-kappa B) was used. Because NF-kappa B has been reported to be redox sensitive, we studied the effects of NAC on the EC redox environment. NAC caused an expected dramatic increase in the reduced glutathione (GSH) levels in EC. In vitro studies demonstrated that whereas the binding affinity of NF-kappa B to the VCAM-NF-kappa B oligomer peaked at a GSH-to-oxidized glutathione (GSSG) ratio of approximately 200 and decreased at higher ratios, the binding to the E-selectin-NF-kappa B oligomer appeared relatively unaffected even at ratios > 400, i.e., those achieved in EC treated with 40 mM NAC. These results suggest that NF-kappa B binding to its consensus sequences in the VCAM-1 and E-selectin gene exhibits marked differences in redox sensitivity, allowing for differential gene expression regulated by the same transcription factor. Our data also demonstrate that NAC increases the GSH-to-GSSG ratio within the EC suggesting one possible mechanism through which this antioxidant inhibits agonist-induced monocyte adhesion to EC. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1915, "end": 1922}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1957, "end": 1963}]}, {"trigger": {"text": "binding", "start": 1915, "end": 1922}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1968, "end": 1978}]}], "gene expression": [{"trigger": {"text": "expression", "start": 94, "end": 104}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 72, "end": 82}]}, {"trigger": {"text": "expression", "start": 94, "end": 104}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 87, "end": 93}]}, {"trigger": {"text": "expression", "start": 791, "end": 801}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 810, "end": 820}]}, {"trigger": {"text": "expression", "start": 791, "end": 801}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 825, "end": 831}]}, {"trigger": {"text": "expression", "start": 2065, "end": 2075}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1957, "end": 1963}]}, {"trigger": {"text": "expression", "start": 2065, "end": 2075}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1968, "end": 1978}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 41, "end": 51}, "arguments": [{"role": "Theme", "text": "induced", "start": 64, "end": 71}]}, {"trigger": {"text": "inhibited", "start": 683, "end": 692}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 728, "end": 734}]}, {"trigger": {"text": "inhibited", "start": 741, "end": 750}, "arguments": [{"role": "Theme", "text": "induced", "start": 761, "end": 768}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 64, "end": 71}, "arguments": [{"role": "Theme", "text": "expression", "start": 94, "end": 104}]}, {"trigger": {"text": "induced", "start": 761, "end": 768}, "arguments": [{"role": "Cause", "text": "IL-1 beta", "start": 751, "end": 760}, {"role": "Theme", "text": "mRNA", "start": 769, "end": 773}]}], "regulation": [{"trigger": {"text": "effect on the half-life", "start": 844, "end": 867}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 871, "end": 881}]}, {"trigger": {"text": "effect on the half-life", "start": 844, "end": 867}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 885, "end": 891}]}, {"trigger": {"text": "regulated", "start": 2076, "end": 2085}, "arguments": [{"role": "Theme", "text": "expression", "start": 2065, "end": 2075}]}], "transcription": [{"trigger": {"text": "mRNA", "start": 769, "end": 773}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 810, "end": 820}]}, {"trigger": {"text": "mRNA", "start": 769, "end": 773}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 825, "end": 831}]}]}}, "schema": []}
{"input": "Human monocyte binding to fibronectin enhances IFN-gamma-induced early signaling events. \nLeukocyte integrins are fundamentally important in modulating adhesion to extracellular matrix components and to other cells. This integrin-mediated adhesion controls leukocyte arrest and extravasation during the onset of inflammatory responses. Moreover, integrin-ligand interactions trigger signaling pathways that may influence leukocyte phenotype and function at sites of inflammation. In the current studies, we evaluated the combinatorial effects of monocyte adhesion and IFN-gamma on intracellular signaling pathways. IFN-gamma triggers a well-defined signal transduction pathway, which although not directly stimulated by monocyte adherence to fibronectin or arginine-glycine-aspartate (RGD)-coated substrata, was enhanced significantly in these matrix-adherent cells. Compared with monocytes in suspension or adherent on plastic surfaces, monocytes adherent to fibronectin or RGD exhibited a greater than threefold increase in steady state levels of IFN-gamma-induced mRNA for the high affinity Fc gammaRI receptor. By electrophoretic mobility shift assays, this increase in mRNA was associated with a 5- to 10-fold increase in the STAT1-containing DNA-binding complex that binds to Fc gammaRI promoter elements. Furthermore, the tyrosine phosphorylation of STAT1 and the tyrosine kinases JAK1 and JAK2 was enhanced significantly in RGD-adherent monocytes compared with control cells. These results suggest a novel mechanism by which integrin-mediated cell adhesion can modulate the magnitude of cytokine-induced signal transduction pathways, thereby amplifying cellular events leading to monocyte activation and inflammation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding complex", "start": 1252, "end": 1267}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1231, "end": 1236}]}, {"trigger": {"text": "binds", "start": 1273, "end": 1278}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1231, "end": 1236}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1338, "end": 1353}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1329, "end": 1337}, {"role": "Theme", "text": "STAT1", "start": 1357, "end": 1362}]}, {"trigger": {"text": "phosphorylation", "start": 1338, "end": 1353}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1329, "end": 1337}, {"role": "Theme", "text": "JAK1", "start": 1388, "end": 1392}]}, {"trigger": {"text": "phosphorylation", "start": 1338, "end": 1353}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 1329, "end": 1337}, {"role": "Theme", "text": "JAK2", "start": 1397, "end": 1401}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 1014, "end": 1022}, "arguments": [{"role": "Theme", "text": "levels", "start": 1039, "end": 1045}]}, {"trigger": {"text": "induced", "start": 1059, "end": 1066}, "arguments": [{"role": "Theme", "text": "levels", "start": 1039, "end": 1045}, {"role": "Cause", "text": "IFN-gamma", "start": 1049, "end": 1058}]}, {"trigger": {"text": "increase", "start": 1162, "end": 1170}, "arguments": [{"role": "Theme", "text": "high affinity Fc gammaRI receptor", "start": 1080, "end": 1113}]}, {"trigger": {"text": "increase", "start": 1215, "end": 1223}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1231, "end": 1236}]}, {"trigger": {"text": "enhanced", "start": 1406, "end": 1414}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1338, "end": 1353}]}], "transcription": [{"trigger": {"text": "levels", "start": 1039, "end": 1045}, "arguments": [{"role": "Theme", "text": "high affinity Fc gammaRI receptor", "start": 1080, "end": 1113}]}]}}, "schema": []}
{"input": "The carboxyl-terminal cytoplasmic domain of CD36 is required for oxidized low-density lipoprotein modulation of NF-kappaB activity by tumor necrosis factor-alpha. \nThe binding of oxidized low-density lipoprotein (Ox LDL) by monocyte-macrophages causes pleiotropic effects, including changes in gene expression, and is thought to represent an early event in atherogenesis. The integral membrane glycoprotein CD36 appears to play a physiological role in binding and uptake of Ox LDL by monocyte-macrophages, although the molecular events associated with CD36-Ox LDL interaction are unknown. To approach this issue, we used CD36 transfected Chinese hampster ovary (CHO) cells, exposed them to Ox LDL, and determined changes in the activity of the transcription factor NF-kappaB. We report here that Ox LDL enhanced DNA binding activity of nuclear extracts to an NF-kappaB sequence following activation of CD36-producing CHO cells with the proinflammatory cytokine tumor necrosis factor-alpha (TNF-alpha). This enhanced DNA binding activity was inhibited by coincubation of CD36 transfected cells with the human CD36-specific antibody OKM5. We also determined that activation of NF-kappaB DNA binding activity required an intact carboxyl-terminal cytoplasmic segment on CD36. Our results support the idea that human CD36 mediates signal transduction events in response to Ox LDL. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 564, "end": 575}, "arguments": [{"role": "Theme", "text": "CD36", "start": 552, "end": 556}]}], "gene expression": [{"trigger": {"text": "producing", "start": 907, "end": 916}, "arguments": [{"role": "Theme", "text": "CD36", "start": 902, "end": 906}]}]}}, "schema": []}
{"input": "Transcriptional regulation during myelopoiesis. \nThe coordinated production of all blood cells from a common stem cell is a highly regulated process involving successive stages of commitment and differentiation. From analyses of mice deficient in transcription factor genes and from the characterizations of chromosome breakpoints in human leukemias, it has become evident that transcription factors are important regulators of hematopoiesis. During myelopoiesis, which includes the development of granulocytic and monocytic lineages, transcription factors from several families are active, including AML1/CBF beta, C/EBP, Ets, c-Myb, HOX, and MZF-1. Few of these factors are expressed exclusively in myeloid cells; instead it appears that they cooperatively regulate transcription of myeloid-specific genes. Here we discuss recent advances in transcriptional regulation during myelopoiesis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 676, "end": 685}, "arguments": [{"role": "Theme", "text": "AML1", "start": 601, "end": 605}]}, {"trigger": {"text": "expressed", "start": 676, "end": 685}, "arguments": [{"role": "Theme", "text": "CBF beta", "start": 606, "end": 614}]}, {"trigger": {"text": "expressed", "start": 676, "end": 685}, "arguments": [{"role": "Theme", "text": "c-Myb", "start": 628, "end": 633}]}, {"trigger": {"text": "expressed", "start": 676, "end": 685}, "arguments": [{"role": "Theme", "text": "MZF-1", "start": 644, "end": 649}]}], "positive regulation": [{"trigger": {"text": "active", "start": 583, "end": 589}, "arguments": [{"role": "Theme", "text": "AML1", "start": 601, "end": 605}]}, {"trigger": {"text": "active", "start": 583, "end": 589}, "arguments": [{"role": "Theme", "text": "CBF beta", "start": 606, "end": 614}]}, {"trigger": {"text": "active", "start": 583, "end": 589}, "arguments": [{"role": "Theme", "text": "c-Myb", "start": 628, "end": 633}]}, {"trigger": {"text": "active", "start": 583, "end": 589}, "arguments": [{"role": "Theme", "text": "MZF-1", "start": 644, "end": 649}]}]}}, "schema": []}
{"input": "Rel/NF-kappa B transcription factors and the control of apoptosis. \nThe process of apoptosis is used to eliminate unwanted cells from a wide variety of organisms. Various extracellular signals, often converging in common intracellular pathways, can induce apoptosis in a cell-type-specific fashion. Recent work from several laboratories has demonstrated that Rel/NF-kappa B transcription factors regulate apoptosis in many cell types. In most cells, Rel/NF-kappa B transcription factors appear to mediate survival signals that protect cells from apoptosis; however, under some circumstances, activation of these factors may also promote apoptosis. ", "output": {"json_structures": {}}, "schema": []}
{"input": "The role of Rel/NF-kappa B proteins in viral oncogenesis and the regulation of viral transcription. \nRel/NF-kappa B is a ubiquitous transcription factor that consists of multiple polypeptide subunits, and is subject to complex regulatory mechanisms that involve protein-protein interactions, phosphorylation, ubiquitination, proteolytic degradation, and nucleocytoplasmic translocation. The sophisticated control of Rel/NF-kappa B activity is not surprising since this transcription factor is involved in a wide array of cellular responses to extracellular cues, associated with growth, development, apoptosis, and pathogen invasion. Thus, it is not unexpected that this versatile cellular homeostatic switch would be affected by a variety of viral pathogens, which have evolved mechanisms to utilize various aspects of Rel/NF-kappa B activity to facilitate their replication, cell survival and possibly evasion of immune responses. This review will cover the molecular mechanisms that are utilized by mammalian oncogenic viruses to affect the activity of Rel/NF-kappa B transcription factors and the role of Rel/NF-kappa B in the regulation of viral gene expression and replication. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Abnormal apoptosis and cell cycle progression in humans exposed to methyl tertiary-butyl ether and benzene contaminating water. \n1. In this study we hypothesized that in individuals with certain genetic makeup, MTBE, benzene or their metabolites act as adducts and may induce programmed cell death. 2. Our study involved a group of 60 male and female subjects who were exposed to MTBE and benzene-contaminated water concentrations up to 76 PPB for MTBE and 14 PPB for benzene, for a period of 5 to 8 years. For comparison, we recruited a control group consisting of 32 healthy males and females with similar age distribution and without a history of exposure to MTBE or benzene. 3. Peripheral blood lymphocytes (PBL) of both groups were tested for the percentage of apoptotic cells and cell cycle progression using flow cytometry. 4. When apoptotic lymphocytes from exposed individuals were compared to apoptotic lymphocytes from the control group, statistically-significant differences between each mean group were detected (26.4 +/- 1.8 and 12.1 +/- 1.3, respectively), indicating an increased rate of apoptosis in 80.5% of exposed individuals (P < 0.0001, Mann-Whitney U-Test). MTBE and benzene-induced apoptosis is attributed to a discrete block within the cell cycle progression. Because cell cycle analysis showed that in PBL from chemically-exposed individuals, between 20-50% of cells were accumulated at the S-G2/M boundaries. 5. One of the signaling molecules which mediates programmed cell death is nuclear factor Kappa-B (NF-kappa B). NF-kappa B was examined as one of the many molecular mechanisms for mediating cell death by MTBE and benzene. Indeed, addition of inhibitors of NF-kappa B activation pyrrolidine dithiocarbamate (PDTC), to the lymphocytes of the chemically-exposed group was capable of inhibiting programmed cell death by 40%. This reversal of apoptosis almost to the control level by inhibitor of NF-kappa B activation may indicate involvement of this signaling molecule in MTBE and benzene induction of programmed cell death. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Activation of a novel gene in 3q21 and identification of intergenic fusion transcripts with ecotropic viral insertion site I in leukemia. \nWe have identified a novel gene, GR6, located within the leukemia breakpoint region of 3q21, that is normally expressed in early fetal development but not in adult peripheral blood. GR6 is activated in the UCSD-AML1 cell line and in a leukemic sample, both of which carry a t(3;3)(q21;q26). In UCSD-AML1, we have also identified fusion transcripts between the ecotropic viral insertion site I (EVI1) gene in 3q26 and GR6 and between EVI1 and Ribophorin I that maps 30 kb telomeric to GR6 in 3q21. All fusions splice the 5' ends of the 3q21 genes into exon 2 of the EVI1 gene, an event that is similar to the normal intergenic splicing of MDS1-EVI1 and to those previously documented in leukemias with t(3;21) and t(3;12), in which acute myelogenous leukemia 1-EVI1 fusions and ETV6-EVI1 fusions, respectively, occur. The Ribophorin I-EVI1 fusion in particular may be a common occurrence in t(3;3). ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 249, "end": 258}, "arguments": [{"role": "Theme", "text": "GR6", "start": 172, "end": 175}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 328, "end": 337}, "arguments": [{"role": "Theme", "text": "GR6", "start": 321, "end": 324}]}]}}, "schema": []}
{"input": "Alcohol-induced regulation of nuclear regulatory factor-kappa beta in human monocytes. \nAcute ethanol exposure has the capacity to modulate immune functions, particularly, to down regulate monocyte production of inflammatory cytokines. However, the intracellular mechanisms for these effects of ethanol are yet to be understood. Considering that nuclear regulatory factor-kappa beta (NF-kappa B)/Rel is a common regulatory element of the promoter region of the inflammatory cytokine genes, herein, we tested the hypothesis that acute ethanol affects NF-kappa B activation in human monocytes. Adherence-isolated monocytes showed constitutive DNA binding activity of NF-kappa B. A clinically relevant dose (25 mM) of acute ethanol treatment in vitro increased NF-kappa B binding activity in monocytes with a preferential induction of the inhibitory, p50/p50, NF-kappa B/Rel homodimer, and resulted in no induction of the p65/p50 heterodimer. In contrast, lipopolysaccharide stimulation primarily induced the p65/p50 heterodimer that has been shown to result in gene activation. Thus, such unique activation of the inhibitory p50/p50 homodimer by acute ethanol treatment may result in inhibition rather than activation of NF-kappa B-regulated inflammatory cytokine genes. Consequently, these results suggest that physiologically relevant concentrations of ethanol may affect production of inflammatory cytokines, such as tumor necrosis factor-alpha, interleukin-1 beta, and interleukin-6 by disrupting NF-kappa B signaling in monocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 1372, "end": 1382}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 1418, "end": 1445}]}, {"trigger": {"text": "production", "start": 1372, "end": 1382}, "arguments": [{"role": "Theme", "text": "interleukin-1 beta", "start": 1447, "end": 1465}]}, {"trigger": {"text": "production", "start": 1372, "end": 1382}, "arguments": [{"role": "Theme", "text": "interleukin-6", "start": 1471, "end": 1484}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 819, "end": 828}, "arguments": [{"role": "Theme", "text": "p50", "start": 848, "end": 851}]}, {"trigger": {"text": "induced", "start": 994, "end": 1001}, "arguments": [{"role": "Theme", "text": "p65", "start": 1006, "end": 1009}]}, {"trigger": {"text": "induced", "start": 994, "end": 1001}, "arguments": [{"role": "Theme", "text": "p50", "start": 1010, "end": 1013}]}, {"trigger": {"text": "activation", "start": 1094, "end": 1104}, "arguments": [{"role": "Theme", "text": "p50", "start": 1123, "end": 1126}]}], "regulation": [{"trigger": {"text": "affect", "start": 1365, "end": 1371}, "arguments": [{"role": "Theme", "text": "production", "start": 1372, "end": 1382}]}]}}, "schema": []}
{"input": "Four P-like elements are required for optimal transcription of the mouse IL-4 gene: involvement of a distinct set of nuclear factor of activated T cells and activator protein-1 family proteins. \nWe previously identified the P sequence as a critical regulatory element of the human IL-4 promoter. In the mouse IL-4 promoter, there are five elements homologous to the human P sequence designated conserved lymphokine element 0 (CLE0), P, P2, P3 and P4. To characterize the role of these P-like elements and their binding factors in the native promoter, we did transient transfection and electrophoretic mobility shift assays (EMSA). Transfection of EL-4 cells with the IL-4 promoter-reporter constructs carrying mutated P-like elements showed that four P-like elements, CLE0, P, P2 and P4, but not P3, were required for optimal activation of the IL-4 promoter. EMSA showed that both constitutive and inducible complexes bound to CLE0, P, P2 and P4, whereas only a constitutive complex bound to P3. In competition and antibody supershift assays in EMSA, complexes formed with P or P2 proved to contain nuclear factor of activated T cells (NFAT) family proteins as major components. Activator protein (AP)-1 family proteins interacted with CLE0, P, P2 and P4. NFAT/AP-1 complex formed only with P and P2. Cross-competition assays among the P-like elements revealed element-specific and common complexes. Six tandem repeats of the P element linked to the SV40 promoter responded to phorbol 12-myristate 13-acetate, while that of other elements did not. It would thus appear that components of each P-like element-binding complexes are not identical and may coordinately contribute to transcriptional activity. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "required", "start": 25, "end": 33}, "arguments": [{"role": "Theme", "text": "transcription", "start": 46, "end": 59}]}, {"trigger": {"text": "activation", "start": 826, "end": 836}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 844, "end": 848}, {"role": "Site", "text": "promoter", "start": 849, "end": 857}]}], "transcription": [{"trigger": {"text": "transcription", "start": 46, "end": 59}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 73, "end": 77}]}]}}, "schema": []}
{"input": "The ability of BHRF1 to inhibit apoptosis is dependent on stimulus and cell type. \nThe development of resistance to host defense mechanisms such as tumor necrosis factor (TNF)- and Fas-mediated apoptosis of transformed or virus-infected cells may be a critical component in the development of disease. To find genes that protect cells from apoptosis, we used an expression cloning strategy and identified BHRF1, an Epstein-Barr virus (EBV) early-lytic-cycle protein with distant homology to Bcl-2, as an anti-apoptosis protein. Expression of BHRF1 in MCF-Fas cells conferred nearly complete resistance against both anti-Fas antibody and TNF-mediated apoptosis. In addition, BHRF1 protected these cells from monocyte-mediated killing but failed to protect them from killing mediated by lymphokine-activated killer cells. The ability of BHRF1 to protect MCF-Fas cells from apoptosis induced by various stimuli was identical to that of Bcl-2 and Bcl-xL. Moreover, the mechanism of action of BHRF1 resembled that of Bcl-2 and Bcl-xL as it inhibited TNF- and anti-Fas-induced activation of two enzymes participating in the apoptosis pathway, cytosolic phospholipase A2 and caspase-3/CPP32, but did not interfere with the activation of NF-kappaB-like transcription factors. A putative function of BHRF1 in EBV-infected epithelial cells may be to protect virus-infected cells from TNF- and/or anti-Fas- induced cell death in order to maximize virus production. Surprisingly, expression of neither BHRF1 nor Bcl-2 in a B-cell line, BJAB, protected the cells from anti-Fas-mediated apoptosis even though they increased the survival of serum-starved cells. Thus, the protective role of BHRF1 against apoptosis resembles that of Bcl-2 in being cell type specific and dependent on the apoptotic stimulus. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 528, "end": 538}, "arguments": [{"role": "Theme", "text": "BHRF1", "start": 542, "end": 547}]}, {"trigger": {"text": "expression", "start": 1468, "end": 1478}, "arguments": [{"role": "Theme", "text": "BHRF1", "start": 1490, "end": 1495}]}, {"trigger": {"text": "expression", "start": 1468, "end": 1478}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1500, "end": 1505}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1035, "end": 1044}, "arguments": [{"role": "Cause", "text": "Bcl-2", "start": 1012, "end": 1017}, {"role": "Theme", "text": "activation", "start": 1071, "end": 1081}]}, {"trigger": {"text": "inhibited", "start": 1035, "end": 1044}, "arguments": [{"role": "Cause", "text": "Bcl-xL", "start": 1022, "end": 1028}, {"role": "Theme", "text": "activation", "start": 1071, "end": 1081}]}, {"trigger": {"text": "inhibited", "start": 1035, "end": 1044}, "arguments": [{"role": "Cause", "text": "BHRF1", "start": 988, "end": 993}, {"role": "Theme", "text": "activation", "start": 1071, "end": 1081}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 1071, "end": 1081}, "arguments": [{"role": "Theme", "text": "cytosolic phospholipase A2", "start": 1137, "end": 1163}]}, {"trigger": {"text": "activation", "start": 1071, "end": 1081}, "arguments": [{"role": "Theme", "text": "caspase-3", "start": 1168, "end": 1177}]}]}}, "schema": []}
{"input": "NF-AT activation induced by a CAML-interacting member of the tumor necrosis factor receptor superfamily. \nActivation of the nuclear factor of activated T cells transcription factor (NF-AT) is a key event underlying lymphocyte action. The CAML (calcium-modulator and cyclophilin ligand) protein is a coinducer of NF-AT activation when overexpressed in Jurkat T cells. A member of the tumor necrosis factor receptor superfamily was isolated by virtue of its affinity for CAML. Cross-linking of this lymphocyte-specific protein, designated TACI (transmembrane activator and CAML-interactor), on the surface of transfected Jurkat cells with TACI-specific antibodies led to activation of the transcription factors NF-AT, AP-1, and NFkappaB. TACI-induced activation of NF-AT was specifically blocked by a dominant-negative CAML mutant, thus implicating CAML as a signaling intermediate. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "affinity", "start": 456, "end": 464}, "arguments": [{"role": "Theme", "text": "CAML", "start": 469, "end": 473}]}], "gene expression": [{"trigger": {"text": "overexpressed", "start": 334, "end": 347}, "arguments": [{"role": "Theme", "text": "CAML", "start": 238, "end": 242}]}], "positive regulation": [{"trigger": {"text": "overexpressed", "start": 334, "end": 347}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 334, "end": 347}]}]}}, "schema": []}
{"input": "The DNA binding domain of the A-MYB transcription factor is responsible for its B cell-specific activity and binds to a B cell 110-kDa nuclear protein. \nExpression studies as well as the use of transgenic animals have demonstrated that the A-MYB transcription factor plays central and specific role in the regulation of mature B cell proliferation and/or differentiation. Furthermore, it is highly expressed in Burkitt's lymphoma cells and may participate in the pathogenesis of this disease. We have therefore investigated the transcriptional activity of A-MYB and its regulation in several human lymphoid cell lines using co-transfection assays and show that A-MYB is transcriptionally active in all the B cell lines studied, but not in T cells. In particular the best responder cell line was the Burkitt's cell line Namalwa. The activity of A-MYB in B and not T cells was observed when either an artificial construct or the c-MYC promoter was used as a reporter. Furthermore, the functional domains responsible for DNA binding, transactivation, and negative regulation, previously characterized in a fibroblast context, were found to have similar activity in B cells. The region of A-MYB responsible for the B cell specific activity was defined to be the N-terminal 218 amino acids containing the DNA binding domain. Finally, a 110-kDa protein has been identified in the nuclei of all the B, but not T, cell lines that specifically binds to this A-MYB N-terminal domain. We hypothesize that this 110-kDa protein may be a functionally important B cell-specific co-activator of A-MYB. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 109, "end": 114}, "arguments": [{"role": "Site", "text": "DNA binding domain", "start": 4, "end": 22}, {"role": "Theme", "text": "A-MYB", "start": 30, "end": 35}]}, {"trigger": {"text": "binding", "start": 1022, "end": 1029}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 844, "end": 849}]}, {"trigger": {"text": "binds", "start": 1435, "end": 1440}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 1449, "end": 1454}, {"role": "Site", "text": "N-terminal domain", "start": 1455, "end": 1472}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 398, "end": 407}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 240, "end": 245}]}], "negative regulation": [{"trigger": {"text": "negative regulation", "start": 1052, "end": 1071}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 844, "end": 849}]}], "positive regulation": [{"trigger": {"text": "transcriptionally active", "start": 670, "end": 694}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 661, "end": 666}]}, {"trigger": {"text": "responder", "start": 771, "end": 780}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 661, "end": 666}]}, {"trigger": {"text": "observed", "start": 875, "end": 883}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 844, "end": 849}]}, {"trigger": {"text": "co-activator", "start": 1563, "end": 1575}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 1579, "end": 1584}]}], "regulation": [{"trigger": {"text": "regulation", "start": 570, "end": 580}, "arguments": [{"role": "Theme", "text": "A-MYB", "start": 556, "end": 561}]}]}}, "schema": []}
{"input": "Evidence that calcineurin is rate-limiting for primary human lymphocyte activation. \nCyclosporine (CsA) is both a clinical immunosuppressive drug and a probe to dissect intracellular signaling pathways. In vitro, CsA inhibits lymphocyte gene activation by inhibiting the phosphatase activity of calcineurin (CN). In clinical use, CsA treatment inhibits 50-75% of CN activity in circulating leukocytes. We modeled this degree of CN inhibition in primary human leukocytes in vitro in order to study the effect of partial CN inhibition on the downstream signaling events that lead to gene activation. In CsA-treated leukocytes stimulated by calcium ionophore, the degree of reduction in CN activity was accompanied by a similar degree of inhibition of each event tested: dephosphorylation of nuclear factor of activated T cell proteins, nuclear DNA binding, activation of a transfected reporter gene construct, IFN-gamma and IL-2 mRNA accumulation, and IFN-gamma production. Furthermore, the degree of CN inhibition was reflected by a similar degree of reduction in lymphocyte proliferation and IFN-gamma production in the allogeneic mixed lymphocyte cultures. These data support the conclusion that CN activity is rate-limiting for the activation of primary human T lymphocytes. Thus, the reduction of CN activity observed in CsA-treated patients is accompanied by a similar degree of reduction in lymphocyte gene activation, and accounts for the immunosuppression observed. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 960, "end": 970}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 950, "end": 959}]}, {"trigger": {"text": "production", "start": 1102, "end": 1112}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1092, "end": 1101}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 735, "end": 745}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 932, "end": 944}]}, {"trigger": {"text": "inhibition", "start": 735, "end": 745}, "arguments": [{"role": "Theme", "text": "production", "start": 960, "end": 970}]}, {"trigger": {"text": "reduction", "start": 1050, "end": 1059}, "arguments": [{"role": "Theme", "text": "production", "start": 1102, "end": 1112}]}], "positive regulation": [{"trigger": {"text": "accumulation", "start": 932, "end": 944}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 908, "end": 917}]}, {"trigger": {"text": "accumulation", "start": 932, "end": 944}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 922, "end": 926}]}]}}, "schema": []}
{"input": "Cooperation of binding sites for STAT6 and NF kappa B/rel in the IL-4-induced up-regulation of the human IgE germline promoter. \nIg heavy chain class switching is directed by cytokines inducing transcription from unrearranged CH genes. Subsequently, such primed cells can undergo switch recombination to express the selected new isotype. In the case of IgE class switching, IL-4 activates the IgE germline promoter by inducing the interaction of the transcription factor STAT6 (IL-4STAT) with a responsive DNA element in the proximal region of the promoter. This study describes the characterization of two additional cis-acting elements that interact with members of the NF kappa B/rel transcription factor family in an IL-4-independent fashion. Electrophoretic mobility shift assays show that the nucleoprotein complex formed on the upstream site (NF kappa B1) contains the classical p50/p65 heterodimer. The complex on the proximal site (NF kappa B2) appears to be composed of p50 and relB. IgE germline promoter reporter gene constructs carrying point mutations in the NF kappa B2 site were largely unresponsive to IL-4 stimulation in transient transfection experiments, while plasmids with similar mutations in the NF kappa B1 site responded to cytokine stimulation better than the wild-type promoter. The NF kappa B2 effect was dependent on the presence of the STAT6 binding site, demonstrating that the NF kappa B2 motif is necessary but not sufficient for mediating cytokine up-regulation. In addition, the combination of a NF kappa B/rel binding site and the STAT6 response element conferred IL-4 inducibility to a heterologous minimal promoter, while the individual sites had no effect. The available data suggest that the NF kappa B2 nucleoprotein complex may cooperate with DNA-bound STAT6 to achieve IL-4-dependent activation of the human IgE germline gene. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interaction", "start": 431, "end": 442}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 471, "end": 476}]}, {"trigger": {"text": "complex formed", "start": 813, "end": 827}, "arguments": [{"role": "Theme", "text": "p50", "start": 886, "end": 889}, {"role": "Theme2", "text": "p65", "start": 890, "end": 893}]}, {"trigger": {"text": "bound", "start": 1790, "end": 1795}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 1796, "end": 1801}]}], "positive regulation": [{"trigger": {"text": "Cooperation", "start": 0, "end": 11}, "arguments": [{"role": "CSite", "text": "binding sites", "start": 15, "end": 28}, {"role": "Cause", "text": "STAT6", "start": 33, "end": 38}, {"role": "Theme", "text": "up-regulation", "start": 78, "end": 91}]}, {"trigger": {"text": "up-regulation", "start": 78, "end": 91}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 65, "end": 69}, {"role": "Theme", "text": "IgE", "start": 105, "end": 108}, {"role": "Site", "text": "germline promoter", "start": 109, "end": 126}]}, {"trigger": {"text": "inducing", "start": 418, "end": 426}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 374, "end": 378}, {"role": "Theme", "text": "interaction", "start": 431, "end": 442}]}, {"trigger": {"text": "conferred", "start": 1591, "end": 1600}, "arguments": [{"role": "Theme", "text": "inducibility", "start": 1606, "end": 1618}]}, {"trigger": {"text": "inducibility", "start": 1606, "end": 1618}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1601, "end": 1605}]}, {"trigger": {"text": "effect", "start": 1689, "end": 1695}, "arguments": [{"role": "Theme", "text": "inducibility", "start": 1606, "end": 1618}]}], "regulation": [{"trigger": {"text": "dependent", "start": 1334, "end": 1343}, "arguments": [{"role": "Theme", "text": "NF kappa B2", "start": 1311, "end": 1322}]}]}}, "schema": []}
{"input": "Dual effects of LPS antibodies on cellular uptake of LPS and LPS-induced proinflammatory functions. \nHuman phagocytes recognize bacterial LPS (endotoxin) through membrane CD14 (mCD14), a proinflammatory LPS receptor. This study tested the hypothesis that anti-LPS Abs neutralize endotoxin by blocking cellular uptake through mCD14. Ab-associated changes in the uptake and cellular distribution of FITC-LPS were assessed by flow cytometry and laser scanning confocal microscopy in human CD14-transfected Chinese hamster ovary fibroblasts (CHO-CD14 cells) and human peripheral blood monocytes. LPS core- and O-side chain-specific mAbs inhibited mCD14-mediated LPS uptake by both cell types in the presence of serum. O-side chain-specific mAb concurrently enhanced complement-dependent LPS uptake by monocytes through complement receptor-1 (CR1) and uptake by CHO-CD14 cells involving another heat-labile serum factor(s) and cell-associated recognition molecule(s). Core-specific mAb inhibited mCD14-mediated uptake of homologous and heterologous LPS, while producing less concurrent enhancement of non-mCD14-mediated LPS uptake. The modulation by anti-LPS mAbs of mCD14-mediated LPS uptake was associated with inhibition of LPS-induced nuclear factor-kappaB (NF-kappaB) translocation and TNF-alpha secretion in CHO-CD14 cells and monocytes, respectively, while mAb enhancement of non-mCD14-mediated LPS uptake stimulated these activities. LPS-specific Abs thus mediate anti-inflammatory and proinflammatory functions, respectively, by preventing target cell uptake of LPS through mCD14 and augmenting uptake through CR1 or other cell receptors. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "secretion", "start": 1296, "end": 1305}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1286, "end": 1295}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 1208, "end": 1218}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1296, "end": 1305}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1226, "end": 1233}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1296, "end": 1305}]}, {"trigger": {"text": "stimulated", "start": 1408, "end": 1418}, "arguments": [{"role": "Theme", "text": "induced", "start": 1226, "end": 1233}]}]}}, "schema": []}
{"input": "Human neutrophils express GH-N gene transcripts and the pituitary transcription factor Pit-1b. \nSince GH stimulates the development and function of granulocytes, we investigated the expression of GH in granulocyte subsets. By immunocytochemistry, 25 +/- 7% of the human neutrophils were shown to express immunoreactive GH, whereas eosinophils were negative. Reversed transcription (RT)-PCR analysis demonstrated GH mRNA in neutrophils. Restriction analysis revealed that neutrophils express the GH-N gene but not the GH-V gene. Furthermore, we demonstrated by western blot analysis that neutrophils express an alternatively spliced variant of the pituitary transcription factor Pit-1, designated Pit-1b. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "express", "start": 18, "end": 25}, "arguments": [{"role": "Theme", "text": "Pit-1b", "start": 87, "end": 93}]}, {"trigger": {"text": "expression", "start": 182, "end": 192}, "arguments": [{"role": "Theme", "text": "GH", "start": 196, "end": 198}]}, {"trigger": {"text": "express", "start": 296, "end": 303}, "arguments": [{"role": "Theme", "text": "GH", "start": 319, "end": 321}]}, {"trigger": {"text": "negative", "start": 348, "end": 356}, "arguments": [{"role": "Theme", "text": "GH", "start": 319, "end": 321}]}, {"trigger": {"text": "express", "start": 483, "end": 490}, "arguments": [{"role": "Theme", "text": "GH-N", "start": 495, "end": 499}]}, {"trigger": {"text": "express", "start": 483, "end": 490}, "arguments": [{"role": "Theme", "text": "GH-V", "start": 517, "end": 521}]}, {"trigger": {"text": "express", "start": 599, "end": 606}, "arguments": [{"role": "Theme", "text": "Pit-1b", "start": 696, "end": 702}]}], "transcription": [{"trigger": {"text": "express", "start": 18, "end": 25}, "arguments": [{"role": "Theme", "text": "GH-N", "start": 26, "end": 30}]}, {"trigger": {"text": "demonstrated", "start": 399, "end": 411}, "arguments": [{"role": "Theme", "text": "GH", "start": 412, "end": 414}]}]}}, "schema": []}
{"input": "Interleukin-7 upregulates the interleukin-2-gene expression in activated human T lymphocytes at the transcriptional level by enhancing the DNA binding activities of both nuclear factor of activated T cells and activator protein-1. \nIn the present report, we studied the role of the stromal-derived cytokine interleukin-7 (IL-7) in the IL-2-gene regulation in activated T lymphocytes. Production of IL-2 requires the formation of transcription factors involved in the IL-2-gene regulation. T-cell receptor (TCR)/CD3 engagement results in the activation of nuclear factor of activated T cells (NFAT), activator protein-1 (AP-1), and nuclear factor kappaB (NFkappaB), whereas the CD28 responsive complex (CD28RC) is activated in response to the CD28 signal. Costimulation of phytohemagglutinin/anti-CD28 activated T lymphocytes with IL-7 induces a fivefold enhanced IL-2-mRNA accumulation and a 2.5-fold enhanced protein secretion. The IL-2-gene transcription rate is increased 3.4-fold, indicating that the effect of IL-7 is in part mediated at the transcriptional level. The molecular mechanisms underlying the IL-7 effect involve the upregulation of the DNA binding activity of NFAT (60%) and AP-1 (120%), without affecting the activities of NFkappaB and CD28RC, which was confirmed by transfection assays. We also show that the IL-7-induced enhancement of the AP-1-DNA binding activity is not cyclosporin A-sensitive. Since AP-1 is part of the NFAT complex, we conclude that the IL-7-signaling pathway is involved in the activation of the fos and jun proteins of which AP-1 consists. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Production", "start": 384, "end": 394}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 398, "end": 402}]}], "positive regulation": [{"trigger": {"text": "upregulates", "start": 14, "end": 25}, "arguments": [{"role": "Theme", "text": "at the transcriptional level", "start": 93, "end": 121}]}, {"trigger": {"text": "enhanced", "start": 854, "end": 862}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 873, "end": 885}]}, {"trigger": {"text": "accumulation", "start": 873, "end": 885}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 863, "end": 867}]}, {"trigger": {"text": "increased", "start": 965, "end": 974}, "arguments": [{"role": "Theme", "text": "transcription", "start": 943, "end": 956}]}, {"trigger": {"text": "mediated", "start": 1031, "end": 1039}, "arguments": [{"role": "Theme", "text": "transcription", "start": 943, "end": 956}, {"role": "Cause", "text": "IL-7", "start": 1015, "end": 1019}]}, {"trigger": {"text": "activation", "start": 1522, "end": 1532}, "arguments": [{"role": "Theme", "text": "fos", "start": 1540, "end": 1543}]}], "regulation": [{"trigger": {"text": "role", "start": 270, "end": 274}, "arguments": [{"role": "Cause", "text": "IL-7", "start": 322, "end": 326}, {"role": "Theme", "text": "regulation", "start": 345, "end": 355}]}, {"trigger": {"text": "regulation", "start": 345, "end": 355}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 335, "end": 339}]}, {"trigger": {"text": "requires", "start": 403, "end": 411}, "arguments": [{"role": "Theme", "text": "Production", "start": 384, "end": 394}]}, {"trigger": {"text": "involved", "start": 451, "end": 459}, "arguments": [{"role": "Theme", "text": "regulation", "start": 477, "end": 487}]}, {"trigger": {"text": "regulation", "start": 477, "end": 487}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 467, "end": 471}]}, {"trigger": {"text": "involved", "start": 1506, "end": 1514}, "arguments": [{"role": "Theme", "text": "activation", "start": 1522, "end": 1532}]}], "transcription": [{"trigger": {"text": "at the transcriptional level", "start": 93, "end": 121}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 30, "end": 43}]}, {"trigger": {"text": "transcription", "start": 943, "end": 956}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 933, "end": 937}]}]}}, "schema": []}
{"input": "Monochloramine inhibits phorbol ester-inducible neutrophil respiratory burst activation and T cell interleukin-2 receptor expression by inhibiting inducible protein kinase C activity. \nMonochloramine derivatives are long lived physiological oxidants produced by neutrophils during the respiratory burst. The effects of chemically prepared monochloramine (NH2Cl) on protein kinase C (PKC) and PKC-mediated cellular responses were studied in elicited rat peritoneal neutrophils and human Jurkat T cells. Neutrophils pretreated with NH2Cl (30-50 microM) showed a marked decrease in the respiratory burst activity induced by phorbol 12-myristate 13-acetate (PMA), which is a potent PKC activator. These cells, however, were viable and showed a complete respiratory burst upon arachidonic acid stimulation, which induces the respiratory burst by a PKC-independent mechanism. The NH2Cl-treated neutrophils showed a decrease in both PKC activity and PMA-induced phosphorylation of a 47-kDa protein, which corresponds to the cytosolic factor of NADPH oxidase, p47(phox). Jurkat T cells pretreated with NH2Cl (20-70 microM) showed a decrease in the expression of the interleukin-2 receptor alpha chain following PMA stimulation. This was also accompanied by a decrease in both PKC activity and nuclear transcription factor-kappaB activation, also without loss of cell viability. These results show that NH2Cl inhibits PKC-mediated cellular responses through inhibition of the inducible PKC activity. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1140, "end": 1150}, "arguments": [{"role": "Theme", "text": "interleukin-2 receptor alpha chain", "start": 1158, "end": 1192}]}], "negative regulation": [{"trigger": {"text": "decrease", "start": 909, "end": 917}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 955, "end": 970}]}, {"trigger": {"text": "decrease", "start": 1124, "end": 1132}, "arguments": [{"role": "Theme", "text": "expression", "start": 1140, "end": 1150}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 955, "end": 970}, "arguments": [{"role": "Theme", "text": "p47(phox)", "start": 1052, "end": 1061}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 947, "end": 954}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 955, "end": 970}]}]}}, "schema": []}
{"input": "HIV-1 Vpr suppresses immune activation and apoptosis through regulation of nuclear factor kappa B [see comments] \nThe HIV-1 accessory gene product Vpr can influence viral pathogenesis by affecting viral replication as well as host cell transcription and proliferation. We have investigated the effects of Vpr on host cell activation and confirm that it influences cellular proliferation. However, we have also found that Vpr modulates T-cell receptor (TCR)-triggered apoptosis in a manner similar to that of glucocorticoids. In the absence of TCR-mediated activation, Vpr induces apoptosis whereas in its presence, Vpr interrupts the expected induction of apoptosis. This regulation of apoptosis is linked to Vpr suppression of NF-kappa B activity via the induction of I kappa B, an inhibitor of NF-kappa B. Further, Vpr suppresses expression of IL-2, IL-10, IL-12, TNF alpha and IL-4, all of which are NF-kappa B-dependent. The effects of Vpr could be reversed by RU486. Our finding that Vpr can regulate NF-kappa B supports the hypothesis that some aspects of viral pathogenesis are the consequence of cell dysregulation by Vpr. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 832, "end": 842}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 846, "end": 850}]}, {"trigger": {"text": "expression", "start": 832, "end": 842}, "arguments": [{"role": "Theme", "text": "IL-10", "start": 852, "end": 857}]}, {"trigger": {"text": "expression", "start": 832, "end": 842}, "arguments": [{"role": "Theme", "text": "TNF alpha", "start": 866, "end": 875}]}, {"trigger": {"text": "expression", "start": 832, "end": 842}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 880, "end": 884}]}], "negative regulation": [{"trigger": {"text": "suppresses", "start": 821, "end": 831}, "arguments": [{"role": "Cause", "text": "Vpr", "start": 817, "end": 820}, {"role": "Theme", "text": "expression", "start": 832, "end": 842}]}, {"trigger": {"text": "reversed", "start": 953, "end": 961}, "arguments": [{"role": "Theme", "text": "Vpr", "start": 940, "end": 943}]}], "regulation": [{"trigger": {"text": "dependent", "start": 914, "end": 923}, "arguments": [{"role": "Theme", "text": "expression", "start": 832, "end": 842}]}]}}, "schema": []}
{"input": "The tax protein of human T-cell leukemia virus type 1 mediates the transactivation of the c-sis/platelet-derived growth factor-B promoter through interactions with the zinc finger transcription factors Sp1 and NGFI-A/Egr-1. \nTranscriptional up-regulation of the c-sis/platelet-derived growth factor-B (PDGF-B) proto-oncogene by the Tax protein of human T-cell leukemia virus type 1 has been implicated as one possible mechanism of cellular transformation by human T-cell leukemia virus type 1. In previous work, we identified an essential site in the c-sis/PDGF-B promoter, Tax-responsive element 1 (TRE1), necessary for transactivation by Tax. We also identified Sp1, Sp3, and NGFI-A/Egr-1 as the primary nuclear transcription factors binding to TRE1 which mediate Tax responsiveness. In the present work, we have investigated the mechanism(s) whereby Tax transactivates the c-sis/PDGF-B proto-oncogene. In vitro transcription assays showed that Tax was able to significantly increase the transcriptional activity of a template containing the -257 to +74 region of the c-sis/PDGF-B promoter. Electrophoretic mobility shift assay analysis showed that Tax increased the DNA binding activity of both Sp1 and NGFI-A/Egr-1 using a TRE1 probe. Analysis of Tax mutants showed that two mutants, IEXC29S and IEXL320G, were unable to significantly transactivate the c-sis/PDGF-B promoter. Finally, co-immunoprecipitation analysis revealed that Tax is able to stably bind to both Sp1 and NGFI-A/Egr-1. Interestingly, co-immunoprecipitation analysis also revealed that Tax mutant IEXC29S is unable to interact with NGFI-A/Egr-1, whereas Tax mutant IEXL320G is able to interact with NGFI-A/Egr-1. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interactions", "start": 146, "end": 158}, "arguments": [{"role": "Theme", "text": "tax", "start": 4, "end": 7}, {"role": "Theme2", "text": "Sp1", "start": 202, "end": 205}]}, {"trigger": {"text": "interactions", "start": 146, "end": 158}, "arguments": [{"role": "Theme", "text": "tax", "start": 4, "end": 7}, {"role": "Theme2", "text": "NGFI-A", "start": 210, "end": 216}]}, {"trigger": {"text": "binding", "start": 736, "end": 743}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 664, "end": 667}]}, {"trigger": {"text": "binding", "start": 736, "end": 743}, "arguments": [{"role": "Theme", "text": "Sp3", "start": 669, "end": 672}]}, {"trigger": {"text": "binding", "start": 736, "end": 743}, "arguments": [{"role": "Theme", "text": "NGFI-A", "start": 678, "end": 684}]}, {"trigger": {"text": "binding activity", "start": 1173, "end": 1189}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1198, "end": 1201}]}, {"trigger": {"text": "binding activity", "start": 1173, "end": 1189}, "arguments": [{"role": "Theme", "text": "NGFI-A", "start": 1206, "end": 1212}]}, {"trigger": {"text": "bind", "start": 1457, "end": 1461}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1435, "end": 1438}, {"role": "Theme2", "text": "Sp1", "start": 1470, "end": 1473}]}, {"trigger": {"text": "bind", "start": 1457, "end": 1461}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1435, "end": 1438}, {"role": "Theme2", "text": "NGFI-A", "start": 1478, "end": 1484}]}, {"trigger": {"text": "interact", "start": 1590, "end": 1598}, "arguments": [{"role": "Theme", "text": "NGFI-A", "start": 1604, "end": 1610}]}, {"trigger": {"text": "interact", "start": 1657, "end": 1665}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1678, "end": 1683}]}], "positive regulation": [{"trigger": {"text": "transactivation", "start": 67, "end": 82}, "arguments": [{"role": "Theme", "text": "c-sis", "start": 90, "end": 95}, {"role": "Site", "text": "promoter", "start": 129, "end": 137}, {"role": "Cause", "text": "interactions", "start": 146, "end": 158}]}, {"trigger": {"text": "Transcriptional up-regulation", "start": 225, "end": 254}, "arguments": [{"role": "Theme", "text": "c-sis", "start": 262, "end": 267}, {"role": "Cause", "text": "Tax", "start": 332, "end": 335}]}, {"trigger": {"text": "transactivates", "start": 857, "end": 871}, "arguments": [{"role": "Cause", "text": "Tax", "start": 853, "end": 856}, {"role": "Theme", "text": "c-sis", "start": 876, "end": 881}]}, {"trigger": {"text": "increase", "start": 977, "end": 985}, "arguments": [{"role": "Cause", "text": "Tax", "start": 947, "end": 950}, {"role": "Theme", "text": "transcriptional activity", "start": 990, "end": 1014}]}, {"trigger": {"text": "increased", "start": 1155, "end": 1164}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1151, "end": 1154}, {"role": "Theme", "text": "binding activity", "start": 1173, "end": 1189}]}, {"trigger": {"text": "transactivate", "start": 1339, "end": 1352}, "arguments": [{"role": "Theme", "text": "c-sis", "start": 1357, "end": 1362}, {"role": "Site", "text": "promoter", "start": 1370, "end": 1378}]}], "transcription": [{"trigger": {"text": "transcriptional activity", "start": 990, "end": 1014}, "arguments": [{"role": "Theme", "text": "c-sis", "start": 1070, "end": 1075}]}]}}, "schema": []}
{"input": "Induction of endothelial cell surface adhesion molecules by tumor necrosis factor is blocked by protein tyrosine phosphatase inhibitors: role of the nuclear transcription factor NF-kappa B. \nRecent studies from our laboratory have indicated that protein tyrosine phosphatase (PTPase) inhibitors can down-modulate the tumor necrosis factor (TNF)-mediated activation of the nuclear transcription factor NF-kappa B in ML-1a, a monocytic cell line (Singh and Aggarwal, J. Biol. Chem. 1995: 270: 10631). Since TNF is one of the major inducers of various adhesion molecules in human endothelial cells and their expression is known to require the activation of NF-kappa B, we examined the effect of PTPase inhibitors on the TNF-mediated induction of intracellular adhesion molecule (ICAM)-1, vascular cell adhesion molecule (VCAM)-1 and endothelial leukocyte adhesion molecule (ELAM)-1. Like ML-1a, human dermal microvessel endothelial cells (MVEC) treated with TNF rapidly activated (within 30 min) NF-kappa B; this effect was completely abolished by co-treatment with phenylarsine oxide (PAO), a specific inhibitor of PTPase. The induction of ICAM-1, VCAM-1, and ELAM-1 by TNF in MVEC occurred within 6 h and was also completely down-regulated by PAO in a dose-dependent manner. PAO was found to be effective even when added 3 h after TNF, suggesting a rapid mode of action of this inhibitor. Besides PAO, other inhibitors of PTPase, including pervanadate and diamide, also blocked TNF-dependent NF-kappa B activation and induction of all the three adhesion proteins. Consistent with these results, the attachment of monocytes to MVEC was also blocked by the PTPase inhibitors. Thus, overall, our results demonstrate that a PTPase is involved either directly or indirectly in the pathway leading to the induction of endothelial cell adhesion molecules by TNF. Because of their role in cell adhesion, PTPase may provide a novel target of drug development for treatment of inflammation, atherogenesis, and tumor metastasis. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "down-regulated", "start": 1224, "end": 1238}, "arguments": [{"role": "Theme", "text": "induction", "start": 1125, "end": 1134}]}, {"trigger": {"text": "blocked", "start": 1469, "end": 1476}, "arguments": [{"role": "Theme", "text": "induction", "start": 1517, "end": 1526}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 730, "end": 739}, "arguments": [{"role": "Theme", "text": "intracellular adhesion molecule (ICAM)-1", "start": 743, "end": 783}]}, {"trigger": {"text": "induction", "start": 730, "end": 739}, "arguments": [{"role": "Theme", "text": "vascular cell adhesion molecule (VCAM)-1", "start": 785, "end": 825}]}, {"trigger": {"text": "induction", "start": 730, "end": 739}, "arguments": [{"role": "Theme", "text": "endothelial leukocyte adhesion molecule (ELAM)-1", "start": 830, "end": 878}]}, {"trigger": {"text": "induction", "start": 1125, "end": 1134}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1138, "end": 1144}]}, {"trigger": {"text": "induction", "start": 1125, "end": 1134}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1146, "end": 1152}]}, {"trigger": {"text": "induction", "start": 1125, "end": 1134}, "arguments": [{"role": "Theme", "text": "ELAM-1", "start": 1158, "end": 1164}]}, {"trigger": {"text": "induction", "start": 1517, "end": 1526}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1138, "end": 1144}]}, {"trigger": {"text": "induction", "start": 1517, "end": 1526}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1146, "end": 1152}]}, {"trigger": {"text": "induction", "start": 1517, "end": 1526}, "arguments": [{"role": "Theme", "text": "ELAM-1", "start": 1158, "end": 1164}]}], "regulation": [{"trigger": {"text": "effect", "start": 682, "end": 688}, "arguments": [{"role": "Theme", "text": "induction", "start": 730, "end": 739}]}]}}, "schema": []}
{"input": "The spatial distribution of human immunoglobulin genes within the nucleus: evidence for gene topography independent of cell type and transcriptional activity. \nThe three-dimensional positioning of immunoglobulin (Ig) genes within the nucleus of human cells was investigated using in situ hybridization and confocal microscopy. The visualization of heavy and light chain genes in B-lymphoid cells showed that the three Ig genes are differentially and nonrandomly distributed in different nuclear subvolumes: the kappa genes were found to be preferentially confined to an outer nuclear volume, whereas the gamma and lambda genes consistently occupied more central positions within the nucleus, the lambda genes being more interior when compared with the gamma genes. The data further show that these overall topographical distributions are independent of gene transcriptional activity and are conserved in different cell types. Although subtle gene movements within those defined topographical regions cannot be excluded by this study, the results indicate that tissue specificity of gene expression is not accompanied by drastic changes in gene nuclear topography, rather suggesting that gene organization within the nucleus may be primarily dependent on structural constraints imposed on the respective chromosomes. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Transcriptional activation of the vascular cell adhesion molecule-1 gene in T lymphocytes expressing human T-cell leukemia virus type 1 Tax protein. \nRecruitment and extravasation of T cells through the blood-brain barrier are favored by adhesion molecule-mediated interactions of circulating T cells with endothelial cells. Since a common pathological finding in human T-cell leukemia virus type 1 (HTLV-1)-associated diseases is the infiltration of HTLV-1-infected T lymphocytes into various organs, we have looked for the profile of adhesion molecules expressed by HTLV-1-transformed T cells. Flow cytometry analysis indicated that these cells were expressing high levels of vascular cell adhesion molecule 1 (VCAM-1 [CD106]), a 110-kDa member of the immunoglobulin gene superfamily, first identified on endothelial cells stimulated with inflammatory cytokines. This adhesion molecule was also expressed by T cells obtained from one patient with HTLV-1-associated myelopathy/tropical spastic paraparesis but not by activated T cells isolated from one normal blood donor. The role of the viral trans-activator Tax protein in the induction of VCAM-1 was first indicated by the detection of this adhesion molecule on Jurkat T-cell clones stably expressing the tax gene. The effect of Tax on VCAM-1 gene transcription was next confirmed in JPX-9 cells, a subclone of Jurkat cells, carrying the tax sequences under the control of an inducible promoter. Furthermore, deletion and mutation analyses of the VCAM-1 promoter performed with chloramphenicol acetyltransferase constructs revealed that Tax was trans activating the VCAM-1 promoter via two NF-kappaB sites present at bp -72 and -57 in the VCAM-1 gene promoter, with both of them being required for the Tax-induced expression of this adhesion molecule. Finally, gel mobility shift assays demonstrated the nuclear translocation of proteins specifically bound to these two NF-kappaB motifs, confirming that VCAM-1 was induced on Tax-expressing cells in a kappaB-dependent manner. Collectively, these results therefore suggest that the exclusive Tax-induced expression of VCAM-1 on T cells may represent a pivotal event in the progression of HTLV-1-associated diseases. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "via", "start": 1637, "end": 1640}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1592, "end": 1595}, {"role": "Site2", "text": "NF-kappaB sites", "start": 1645, "end": 1660}, {"role": "Theme2", "text": "VCAM-1", "start": 1694, "end": 1700}]}], "gene expression": [{"trigger": {"text": "expressing", "start": 90, "end": 100}, "arguments": [{"role": "Theme", "text": "Tax", "start": 136, "end": 139}]}, {"trigger": {"text": "expressing", "start": 652, "end": 662}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 713, "end": 719}]}, {"trigger": {"text": "identified", "start": 793, "end": 803}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 713, "end": 719}]}, {"trigger": {"text": "expressed", "start": 897, "end": 906}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 713, "end": 719}]}, {"trigger": {"text": "detection", "start": 1178, "end": 1187}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1144, "end": 1150}]}, {"trigger": {"text": "expressing", "start": 1245, "end": 1255}, "arguments": [{"role": "Theme", "text": "tax", "start": 1260, "end": 1263}]}, {"trigger": {"text": "expression", "start": 1769, "end": 1779}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1694, "end": 1700}]}, {"trigger": {"text": "expressing", "start": 1985, "end": 1995}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1981, "end": 1984}]}, {"trigger": {"text": "expression", "start": 2109, "end": 2119}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 2123, "end": 2129}]}], "positive regulation": [{"trigger": {"text": "Transcriptional activation", "start": 0, "end": 26}, "arguments": [{"role": "Theme", "text": "vascular cell adhesion molecule-1", "start": 34, "end": 67}]}, {"trigger": {"text": "high levels", "start": 663, "end": 674}, "arguments": [{"role": "Theme", "text": "expressing", "start": 652, "end": 662}]}, {"trigger": {"text": "induction", "start": 1131, "end": 1140}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1144, "end": 1150}]}, {"trigger": {"text": "trans activating", "start": 1600, "end": 1616}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1621, "end": 1627}, {"role": "Site", "text": "promoter", "start": 1628, "end": 1636}, {"role": "Cause", "text": "via", "start": 1637, "end": 1640}]}, {"trigger": {"text": "required", "start": 1740, "end": 1748}, "arguments": [{"role": "CSite", "text": "NF-kappaB sites", "start": 1645, "end": 1660}, {"role": "Cause", "text": "VCAM-1", "start": 1694, "end": 1700}, {"role": "Theme", "text": "induced", "start": 1761, "end": 1768}]}, {"trigger": {"text": "induced", "start": 1761, "end": 1768}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1757, "end": 1760}, {"role": "Theme", "text": "expression", "start": 1769, "end": 1779}]}, {"trigger": {"text": "induced", "start": 1970, "end": 1977}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1959, "end": 1965}]}, {"trigger": {"text": "induced", "start": 2101, "end": 2108}, "arguments": [{"role": "Cause", "text": "Tax", "start": 2097, "end": 2100}, {"role": "Theme", "text": "expression", "start": 2109, "end": 2119}]}], "regulation": [{"trigger": {"text": "role", "start": 1078, "end": 1082}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1112, "end": 1115}, {"role": "Theme", "text": "induction", "start": 1131, "end": 1140}]}, {"trigger": {"text": "effect", "start": 1274, "end": 1280}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1284, "end": 1287}, {"role": "Theme", "text": "transcription", "start": 1303, "end": 1316}]}, {"trigger": {"text": "dependent", "start": 2014, "end": 2023}, "arguments": [{"role": "Theme", "text": "induced", "start": 1970, "end": 1977}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1303, "end": 1316}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1291, "end": 1297}]}]}}, "schema": []}
{"input": "Blockade of T-cell activation by dithiocarbamates involves novel mechanisms of inhibition of nuclear factor of activated T cells. \nDithiocarbamates (DTCs) have recently been reported as powerful inhibitors of NF-kappaB activation in a number of cell types. Given the role of this transcription factor in the regulation of gene expression in the inflammatory response, NF-kappaB inhibitors have been suggested as potential therapeutic drugs for inflammatory diseases. We show here that DTCs inhibited both interleukin 2 (IL-2) synthesis and membrane expression of antigens which are induced during T-cell activation. This inhibition, which occurred with a parallel activation of c-Jun transactivating functions and expression, was reflected by transfection experiments at the IL-2 promoter level, and involved not only the inhibition of NF-kappaB-driven reporter activation but also that of nuclear factor of activated T cells (NFAT). Accordingly, electrophoretic mobility shift assays (EMSAs) indicated that pyrrolidine DTC (PDTC) prevented NF-kappaB, and NFAT DNA-binding activity in T cells stimulated with either phorbol myristate acetate plus ionophore or antibodies against the CD3-T-cell receptor complex and simultaneously activated the binding of AP-1. Furthermore, PDTC differentially targeted both NFATp and NFATc family members, inhibiting the transactivation functions of NFATp and mRNA induction of NFATc. Strikingly, Western blotting and immunocytochemical experiments indicated that PDTC promoted a transient and rapid shuttling of NFATp and NFATc, leading to their accelerated export from the nucleus of activated T cells. We propose that the activation of an NFAT kinase by PDTC could be responsible for the rapid shuttling of the NFAT, therefore transiently converting the sustained transactivation of this transcription factor that occurs during lymphocyte activation, and show that c-Jun NH2-terminal kinase (JNK) can act by directly phosphorylating NFATp. In addition, the combined inhibitory effects on NFAT and NF-KB support a potential use of DTCs as immunosuppressants. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "synthesis", "start": 526, "end": 535}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 520, "end": 524}]}, {"trigger": {"text": "expression", "start": 714, "end": 724}, "arguments": [{"role": "Theme", "text": "c-Jun", "start": 678, "end": 683}]}], "localization": [{"trigger": {"text": "shuttling", "start": 1534, "end": 1543}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1547, "end": 1552}]}, {"trigger": {"text": "export", "start": 1593, "end": 1599}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1547, "end": 1552}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 490, "end": 499}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 526, "end": 535}]}], "phosphorylation": [{"trigger": {"text": "phosphorylating", "start": 1954, "end": 1969}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1970, "end": 1975}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 664, "end": 674}, "arguments": [{"role": "Theme", "text": "expression", "start": 714, "end": 724}]}, {"trigger": {"text": "promoted", "start": 1503, "end": 1511}, "arguments": [{"role": "Theme", "text": "shuttling", "start": 1534, "end": 1543}]}, {"trigger": {"text": "leading to their accelerated", "start": 1564, "end": 1592}, "arguments": [{"role": "Cause", "text": "promoted", "start": 1503, "end": 1511}, {"role": "Theme", "text": "export", "start": 1593, "end": 1599}]}, {"trigger": {"text": "phosphorylating", "start": 1954, "end": 1969}, "arguments": [{"role": "Cause", "text": "JNK", "start": 1929, "end": 1932}, {"role": "Theme", "text": "phosphorylating", "start": 1954, "end": 1969}]}], "regulation": [{"trigger": {"text": "targeted", "start": 1294, "end": 1302}, "arguments": [{"role": "Theme", "text": "NFATp", "start": 1308, "end": 1313}]}]}}, "schema": []}
{"input": "Suppression of nuclear factor kappa B and CD18-mediated leukocyte adhesion to the corneal endothelium by dexamethasone. \nPURPOSE: To demonstrate that leukocyte adhesion to cultured corneal endothelial cells is mediated by the CD18 antigen, and to determine whether dexamethasone directly suppresses adhesion by inhibiting activation of nuclear factor kappa B (NFkappaB). METHODS: Cultured bovine corneal endothelium was stimulated for 6 hours by 40 micron/ml tumor necrosis factor alpha (TNFalpha). Dexamethasone was added 1 hour before TNFalpha stimulation in the dexamethasone group. After stimulation, neutrophils separated from a healthy human volunteer were added with or without anti-CD18 antibody. The culture plate was settled for 15 minutes at 37 degrees C, and then neutrophils were activated by N-formyl-methionyl-leucyl-phenylalanine for 5 minutes. Nonadherent neutrophils were removed by sealing and inverting the culture well. The intracellular localization of NFkappaB after TNFalpha simulation was determined by confocal immunocytochemistry using an anti-p65 antibody. RESULTS: Neutrophil adhesion to cultured corneal endothelial cells increased significantly on exposure to TNFalpha (451.4+/-45.4 cells/mm2, n = 16) compared to control (156.7+/-27.3 cells/mm2, n = 16, P < 0.01). This increased adhesion was suppressed by the addition of anti-CD18 antibody (157.6+/-25.1 cells/mm2, n = 8, P < 0.01) and by pretreatment with 10(-7) M dexamethasone (207.9+/-31.5 cells/mm2, n = 10, P < 0.01). Immunocytochemistry 60 minutes after stimulation revealed that NFkappaB was located in the cytoplasm in unstimulated cells; however, the addition of TNFalpha caused NFkappaB to translocate into the nucleus. Pretreatment with dexamethasone tapered NFkappaB translocation into the nucleus. CONCLUSIONS: Leukocyte adhesion to the corneal endothelium was shown to be mediated by CD18 expressed on activated leukocytes. Pretreatment of the endothelium with dexamethasone inhibited leukocyte adhesion; this may be due in part to the suppression of NFkappaB entry into the nucleus. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 1888, "end": 1897}, "arguments": [{"role": "Theme", "text": "CD18", "start": 1883, "end": 1887}]}]}}, "schema": []}
{"input": "Helenalin, an anti-inflammatory sesquiterpene lactone from Arnica, selectively inhibits transcription factor NF-kappaB [see comments] \nAlcoholic extracts prepared form Arnicae flos, the collective name for flowerheads from Arnica montana and A. chamissonis ssp. foliosa, are used therapeutically as anti-inflammatory remedies. The active ingredients mediating the pharmacological effect are mainly sesquiterpene lactones, such as helenalin, 11alpha,13-dihydrohelenalin, chamissonolid and their ester derivatives. While these compounds affect various cellular processes, current data do not fully explain how sesquiterpene lactones exert their anti-inflammatory effect. We show here that helenalin, and, to a much lesser degree, 11alpha,13-dihydrohelenalin and chamissonolid, inhibit activation of transcription factor NF-kappaB. This difference in efficacy, which correlates with the compounds' anti-inflammatory potency in vivo, may be explained by differences in structure and conformation. NF-kappaB, which resides in an inactive, cytoplasmic complex in unstimulated cells, is activated by phosphorylation and degradation of its inhibitory subunit, IkappaB. Helenalin inhibits NF-kappaB activation in response to four different stimuli in T-cells, B-cells and epithelial cells and abrogates kappaB-driven gene expression. This inhibition is selective, as the activity of four other transcription factors, Oct-1, TBP, Sp1 and STAT 5 was not affected. We show that inhibition is not due to a direct modification of the active NF-kappaB heterodimer. Rather, helenalin modifies the NF-kappaB/IkappaB complex, preventing the release of IkappaB. These data suggest a molecular mechanism for the anti-inflammatory effect of sesquiterpene lactones, which differs from that of other nonsteroidal anti-inflammatory drugs (NSAIDs), indomethacin and acetyl salicylic acid. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "affected", "start": 1443, "end": 1451}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 1408, "end": 1413}]}, {"trigger": {"text": "affected", "start": 1443, "end": 1451}, "arguments": [{"role": "Theme", "text": "TBP", "start": 1415, "end": 1418}]}, {"trigger": {"text": "affected", "start": 1443, "end": 1451}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1420, "end": 1423}]}]}}, "schema": []}
{"input": "Nuclear accumulation of NFAT4 opposed by the JNK signal transduction pathway. \nThe nuclear factor of activated T cells (NFAT) group of transcription factors is retained in the cytoplasm of quiescent cells. NFAT activation is mediated in part by induced nuclear import. This process requires calcium-dependent dephosphorylation of NFAT caused by the phosphatase calcineurin. The c-Jun amino-terminal kinase (JNK) phosphorylates NFAT4 on two sites. Mutational removal of the JNK phosphorylation sites caused constitutive nuclear localization of NFAT4. In contrast, JNK activation in calcineurin-stimulated cells caused nuclear exclusion of NFAT4. These findings show that the nuclear accumulation of NFAT4 promoted by calcineurin is opposed by the JNK signal transduction pathway. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "accumulation", "start": 8, "end": 20}, "arguments": [{"role": "AtLoc", "text": "Nuclear", "start": 0, "end": 7}, {"role": "Theme", "text": "NFAT4", "start": 24, "end": 29}]}, {"trigger": {"text": "localization", "start": 527, "end": 539}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 519, "end": 526}, {"role": "Theme", "text": "NFAT4", "start": 543, "end": 548}]}, {"trigger": {"text": "exclusion", "start": 625, "end": 634}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 617, "end": 624}, {"role": "Theme", "text": "NFAT4", "start": 638, "end": 643}]}, {"trigger": {"text": "accumulation", "start": 682, "end": 694}, "arguments": [{"role": "AtLoc", "text": "nuclear", "start": 674, "end": 681}, {"role": "Theme", "text": "NFAT4", "start": 698, "end": 703}]}], "negative regulation": [{"trigger": {"text": "opposed", "start": 30, "end": 37}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 8, "end": 20}]}, {"trigger": {"text": "opposed", "start": 731, "end": 738}, "arguments": [{"role": "Theme", "text": "promoted", "start": 704, "end": 712}]}], "phosphorylation": [{"trigger": {"text": "phosphorylates", "start": 412, "end": 426}, "arguments": [{"role": "Theme", "text": "NFAT4", "start": 427, "end": 432}]}], "positive regulation": [{"trigger": {"text": "caused", "start": 499, "end": 505}, "arguments": [{"role": "Theme", "text": "localization", "start": 527, "end": 539}]}, {"trigger": {"text": "caused", "start": 610, "end": 616}, "arguments": [{"role": "Theme", "text": "exclusion", "start": 625, "end": 634}]}, {"trigger": {"text": "promoted", "start": 704, "end": 712}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 682, "end": 694}]}]}}, "schema": []}
{"input": "Hypoxia enhances induction of endothelial ICAM-1: role for metabolic acidosis and proteasomes. \nIntercellular adhesion molecule 1 (ICAM-1) is an important molecule in promotion of polymorphonuclear neutrophil transendothelial migration during inflammation. Coincident with many inflammatory diseases is tissue hypoxia. Thus we hypothesized that combinations of hypoxia and inflammatory stimuli may differentially regulate expression of endothelial ICAM-1. Human endothelial cells were exposed to hypoxia in the presence or absence of added lipopolysaccharide (LPS) and examined for expression of functional ICAM-1. Although hypoxia alone did not induce ICAM-1, the combination of LPS and hypoxia enhanced (3 +/- 0.4-fold over normoxia) ICAM-1 expression. Combinations of hypoxia and LPS significantly increased lymphocyte binding, and such increases were inhibited by addition of anti-ICAM-1 antibodies or antisense oligonucleotides. Hypoxic endothelia showed a > 10-fold increase in sensitivity to inhibitors of proteasome activation, and combinations of hypoxia and LPS enhanced proteasome-dependent cytoplasmic-to-nuclear localization of the nuclear transcription factor-kappa B p65 (Rel A) subunit. Such proteasome activation correlated with hypoxia-evoked decreases in both extracellular and intracellular pH. We conclude from these studies that endothelial hypoxia provides a novel, proteasome-dependent stimulus for ICAM-1 induction. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 422, "end": 432}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 448, "end": 454}]}, {"trigger": {"text": "expression", "start": 582, "end": 592}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 607, "end": 613}]}, {"trigger": {"text": "expression", "start": 743, "end": 753}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 736, "end": 742}]}], "localization": [{"trigger": {"text": "localization", "start": 1125, "end": 1137}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1117, "end": 1124}, {"role": "Theme", "text": "Rel A", "start": 1187, "end": 1192}]}], "positive regulation": [{"trigger": {"text": "enhances", "start": 8, "end": 16}, "arguments": [{"role": "Theme", "text": "induction", "start": 17, "end": 26}]}, {"trigger": {"text": "induction", "start": 17, "end": 26}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 42, "end": 48}]}, {"trigger": {"text": "induce", "start": 646, "end": 652}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 653, "end": 659}]}, {"trigger": {"text": "enhanced", "start": 696, "end": 704}, "arguments": [{"role": "Theme", "text": "expression", "start": 743, "end": 753}]}, {"trigger": {"text": "enhanced", "start": 1072, "end": 1080}, "arguments": [{"role": "Theme", "text": "localization", "start": 1125, "end": 1137}]}, {"trigger": {"text": "stimulus", "start": 1410, "end": 1418}, "arguments": [{"role": "Theme", "text": "induction", "start": 1430, "end": 1439}]}, {"trigger": {"text": "induction", "start": 1430, "end": 1439}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1423, "end": 1429}]}], "regulation": [{"trigger": {"text": "regulate", "start": 413, "end": 421}, "arguments": [{"role": "Theme", "text": "expression", "start": 422, "end": 432}]}, {"trigger": {"text": "dependent", "start": 1092, "end": 1101}, "arguments": [{"role": "Theme", "text": "localization", "start": 1125, "end": 1137}]}, {"trigger": {"text": "dependent", "start": 1400, "end": 1409}, "arguments": [{"role": "Theme", "text": "stimulus", "start": 1410, "end": 1418}]}]}}, "schema": []}
{"input": "Modulation of mRNA expression of a novel human myeloid-selective CCAAT/enhancer binding protein gene (C/EBP epsilon). \nHuman C/EBP epsilon is a newly cloned gene coding for a CCAAT/enhancer binding protein that may be involved in the regulation of myeloid differentiation. Our studies showed that levels of C/EBP epsilon mRNA were markedly increased in NB4 cells (promyelocytic leukemia line), because they were induced by 9-cis retinoic acid (9-cis RA) to differentiate towards granulocytes. Accumulation of C/EBP epsilon mRNA occurred as early as 1 hour after exposure of NB4 cells to 9-cis RA (5 x 10(-7) mol/L); and at 48 hours, levels were increased by 5.1-fold. Dose-response studies showed that 10(-7) to 10(-6) mol/L 9-cis RA (12 hours) resulted in peak levels of C/EBP epsilon mRNA; but even 10(-10) mol/L 9-cis RA increased levels of these transcripts. NB4 cells pulse-exposed (30 minutes) to all-trans retinoic acid (ATRA), washed, and cultured (3 days) with either dimethylsulfoxide (DMSO) or hexamethylene bisacetamide (HMBA) had a prominent increase in levels of C/EBP epsilon mRNA and an increase in granulocytic differentiation, but exposure to either DMSO or HMBA alone had no effect on base levels of C/EBP epsilon and did not induce differentiation. Macrophage-differentiation of NB4 reduced levels of C/EBP epsilon mRNA. Nuclear run-off assays and half-life studies showed that accumulation of C/EBP epsilon mRNA by 9-cis RA was due to enhanced transcription. Furthermore, this C/EBP epsilon mRNA accumulation did not require synthesis of new protein factors because 9-cis RA induced C/EBP epsilon mRNA accumulation in the absence of new protein synthesis. ATRA also induced expression of C/EBP epsilon protein in NB4 cells, as shown by Western blotting. In contrast to the increase of C/EBP epsilon in 9-cis RA-mediated granulocytic differentiation, the DMSO-induced differentiation of HL-60 cells down the granulocytic pathway was associated with an initial reduction of C/EBP epsilon mRNA levels. In summary, we have discovered that expression of C/EBP epsilon mRNA is markedly enhanced as the NB4 promyelocytes are induced by retinoids to differentiate towards granulocytes. This induction of C/EBP epsilon mRNA expression is transcriptionally mediated and occurs in the absence of synthesis of additional protein factors. We suspect that the C/EBP epsilon promoter/enhancer contains a retinoic acid-response element that is directly stimulated by retinoids. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1695, "end": 1705}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1709, "end": 1722}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 1303, "end": 1310}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1321, "end": 1334}]}, {"trigger": {"text": "reduction", "start": 1980, "end": 1989}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1993, "end": 2006}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 340, "end": 349}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 307, "end": 320}]}, {"trigger": {"text": "induced", "start": 412, "end": 419}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 307, "end": 320}]}, {"trigger": {"text": "occurred", "start": 528, "end": 536}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 509, "end": 522}]}, {"trigger": {"text": "increased", "start": 645, "end": 654}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 509, "end": 522}]}, {"trigger": {"text": "resulted in peak levels", "start": 745, "end": 768}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 772, "end": 785}]}, {"trigger": {"text": "increased levels", "start": 824, "end": 840}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 772, "end": 785}]}, {"trigger": {"text": "had a prominent increase", "start": 1039, "end": 1063}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1077, "end": 1090}]}, {"trigger": {"text": "accumulation", "start": 1398, "end": 1410}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1414, "end": 1427}]}, {"trigger": {"text": "due to", "start": 1449, "end": 1455}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1398, "end": 1410}, {"role": "Cause", "text": "enhanced", "start": 1456, "end": 1464}]}, {"trigger": {"text": "enhanced", "start": 1456, "end": 1464}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1465, "end": 1478}]}, {"trigger": {"text": "accumulation", "start": 1517, "end": 1529}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1498, "end": 1511}]}, {"trigger": {"text": "not require", "start": 1534, "end": 1545}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1517, "end": 1529}]}, {"trigger": {"text": "induced", "start": 1596, "end": 1603}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1623, "end": 1635}]}, {"trigger": {"text": "accumulation", "start": 1623, "end": 1635}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1604, "end": 1617}]}, {"trigger": {"text": "induced", "start": 1687, "end": 1694}, "arguments": [{"role": "Theme", "text": "expression", "start": 1695, "end": 1705}]}, {"trigger": {"text": "increase", "start": 1794, "end": 1802}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1806, "end": 1819}]}, {"trigger": {"text": "enhanced", "start": 2101, "end": 2109}, "arguments": [{"role": "Theme", "text": "expression", "start": 2056, "end": 2066}]}, {"trigger": {"text": "induction", "start": 2204, "end": 2213}, "arguments": [{"role": "Theme", "text": "expression", "start": 2236, "end": 2246}]}, {"trigger": {"text": "transcriptionally mediated", "start": 2250, "end": 2276}, "arguments": [{"role": "Theme", "text": "induction", "start": 2204, "end": 2213}]}, {"trigger": {"text": "stimulated", "start": 2458, "end": 2468}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 2367, "end": 2380}, {"role": "Site", "text": "retinoic acid-response element", "start": 2410, "end": 2440}]}], "regulation": [{"trigger": {"text": "Modulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "mRNA expression", "start": 14, "end": 29}]}, {"trigger": {"text": "had no effect", "start": 1187, "end": 1200}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1219, "end": 1232}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 14, "end": 29}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 102, "end": 115}]}, {"trigger": {"text": "transcription", "start": 1465, "end": 1478}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 1414, "end": 1427}]}, {"trigger": {"text": "expression", "start": 2056, "end": 2066}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 2070, "end": 2083}]}, {"trigger": {"text": "expression", "start": 2236, "end": 2246}, "arguments": [{"role": "Theme", "text": "C/EBP epsilon", "start": 2217, "end": 2230}]}]}}, "schema": []}
{"input": "Regulation of nuclear factor-kappa B and its inhibitor I kappa B-alpha/MAD-3 in monocytes by Mycobacterium tuberculosis and during human tuberculosis. \nBlood monocytes from patients with active tuberculosis are activated in vivo, as evidenced by an increase in the stimulated release of proinflammatory cytokines, such as TNF-alpha, and the spontaneous expression of IL-2R. Further, monocytes from patients demonstrate an augmented susceptibility to a productive infection with HIV-1 in vitro. Mycobacterium tuberculosis and its components are strong signals to activate monocytes to production of cytokines. In this study we examined the basis of activation of monocytes during active tuberculosis and by M. tuberculosis. We found a constitutive degradation of I kappa B-alpha, the major cytoplasmic inhibitor of nuclear factor kappa B (NF-kappa B), in freshly isolated PBMC and monocytes from patients with tuberculosis. In contrast, I kappa B-alpha levels in PBMC and monocytes from healthy subjects or from patients with nontuberculous pulmonary conditions were intact. Further, by electrophoretic mobility shift assay, NF-kappa B was activated in monocytes from tuberculous patients. The expression of I kappa B-alpha gene, which is responsive to activation by NF-kappa B, was up-regulated in PBMC and monocytes from patients, but not in mononuclear cells from healthy subjects or those with nontuberculous lung diseases. By contrast, the expression of other adherence-associated early genes, such as IL-8 and IL-1 beta, was not up-regulated in PBMC of tuberculous patients. Further, M. tuberculosis and its tuberculin, purified protein derivative, induced the degradation of I kappa B-alpha and the expression of I kappa B-alpha mRNA, and purified protein derivative induced the activation of NF-kappa B in monocytes. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "spontaneous expression", "start": 341, "end": 363}, "arguments": [{"role": "Theme", "text": "IL-2R", "start": 367, "end": 372}]}, {"trigger": {"text": "expression", "start": 1193, "end": 1203}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 1207, "end": 1222}]}, {"trigger": {"text": "expression", "start": 1444, "end": 1454}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1506, "end": 1510}]}, {"trigger": {"text": "expression", "start": 1444, "end": 1454}, "arguments": [{"role": "Theme", "text": "IL-1 beta", "start": 1515, "end": 1524}]}], "localization": [{"trigger": {"text": "release", "start": 276, "end": 283}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 322, "end": 331}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 249, "end": 257}, "arguments": [{"role": "Theme", "text": "release", "start": 276, "end": 283}]}, {"trigger": {"text": "increase", "start": 249, "end": 257}, "arguments": [{"role": "Theme", "text": "spontaneous expression", "start": 341, "end": 363}]}, {"trigger": {"text": "stimulated", "start": 265, "end": 275}, "arguments": [{"role": "Theme", "text": "release", "start": 276, "end": 283}]}, {"trigger": {"text": "activation", "start": 1252, "end": 1262}, "arguments": [{"role": "Theme", "text": "expression", "start": 1193, "end": 1203}]}, {"trigger": {"text": "up-regulated", "start": 1282, "end": 1294}, "arguments": [{"role": "Theme", "text": "expression", "start": 1193, "end": 1203}]}, {"trigger": {"text": "up-regulated", "start": 1534, "end": 1546}, "arguments": [{"role": "Theme", "text": "expression", "start": 1444, "end": 1454}]}, {"trigger": {"text": "induced", "start": 1654, "end": 1661}, "arguments": [{"role": "Cause", "text": "tuberculin", "start": 1613, "end": 1623}, {"role": "Theme", "text": "degradation", "start": 1666, "end": 1677}]}, {"trigger": {"text": "induced", "start": 1654, "end": 1661}, "arguments": [{"role": "Cause", "text": "tuberculin", "start": 1613, "end": 1623}, {"role": "Theme", "text": "expression", "start": 1705, "end": 1715}]}, {"trigger": {"text": "induced", "start": 1654, "end": 1661}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1666, "end": 1677}]}, {"trigger": {"text": "induced", "start": 1654, "end": 1661}, "arguments": [{"role": "Theme", "text": "expression", "start": 1705, "end": 1715}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 747, "end": 758}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 762, "end": 777}]}, {"trigger": {"text": "intact", "start": 1066, "end": 1072}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 936, "end": 951}]}, {"trigger": {"text": "degradation", "start": 1666, "end": 1677}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 1681, "end": 1696}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 55, "end": 70}]}], "transcription": [{"trigger": {"text": "expression", "start": 1705, "end": 1715}, "arguments": [{"role": "Theme", "text": "I kappa B-alpha", "start": 1719, "end": 1734}]}]}}, "schema": []}
{"input": "Expression of c-fos correlates with IFN-alpha responsiveness in Philadelphia chromosome positive chronic myelogenous leukemia. \nThis study evaluates (i) constitutive levels of oncogene and p53 transcripts in chronic phase CML patients and (ii) their modulations subsequent to in vivo therapy with rIFN-alpha 2c. Peripheral blood mononuclear cells (pbmc) and bone marrow cells of 26 patients were examined for c-fos, c-myc, p53 and the hybrid bcr/abl mRNA levels. Results indicated that (i) constitutive c-fos transcript levels are significantly higher in patients subsequently responding to IFN-alpha therapy (p < 0.01) and positively correlated with the proportion of lymphocytes (r = 0.6895, p < 0.01) and negatively with the proportion of immature cells (r = -0.568, p < 0.01) contained in the pbmc preparations tested, (ii) constitutive mRNA levels of the hybrid bcr/abl, c-myc and p53 are positively correlated with each other, but failed to relate to disease parameters, and (iii) acute and chronic in vivo exposure to IFN-alpha is accompanied by upregulation of c-fos and downregulation of c-myc mRNA levels in responder patients. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "Expression", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 14, "end": 19}]}], "negative regulation": [{"trigger": {"text": "downregulation", "start": 1079, "end": 1093}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 1097, "end": 1102}]}], "positive regulation": [{"trigger": {"text": "accompanied by upregulation", "start": 1038, "end": 1065}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1069, "end": 1074}]}], "transcription": [{"trigger": {"text": "levels", "start": 166, "end": 172}, "arguments": [{"role": "Theme", "text": "p53", "start": 189, "end": 192}]}, {"trigger": {"text": "levels", "start": 455, "end": 461}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 409, "end": 414}]}, {"trigger": {"text": "levels", "start": 455, "end": 461}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 416, "end": 421}]}, {"trigger": {"text": "levels", "start": 455, "end": 461}, "arguments": [{"role": "Theme", "text": "p53", "start": 423, "end": 426}]}]}}, "schema": []}
{"input": "Molecular cloning and functional characterization of murine cDNA encoding transcription factor NFATc. \nTranscription factors of the NFAT (nuclear factor of activated T cells) family play important roles in immune and inflammatory responses by regulating the expression of genes encoding cytokines and immunoregulatory proteins. Here we describe cloning and characterization of full-length cDNA encoding murine (m) NFATc which predicts that the protein has all the conserved structural motifs of NFAT family members, including the rel homology domain, the NFAT homology domain and the nuclear translocation signals. mNFATc complexed with AP-1 bound specifically to the murine IL-2 NFAT recognition sequence and activated transcription from the co-transfected IL-2 promoter in COS-7 cells. Northern blot analysis showed that the cDNA probe hybridized with a 4.5 kb transcript which is highly inducible in murine T cells. By Northern and in situ hybridization, mNFATc transcript was detected from the early stage of development. In the mouse embryo, mNFATc transcript was strongly expressed in thymus, lung and submandibular gland and weakly in skeletal muscle and heart suggesting that mNFATc may have a role both in embryogenesis and in mature T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complexed", "start": 622, "end": 631}, "arguments": [{"role": "Theme", "text": "mNFATc", "start": 615, "end": 621}, {"role": "Theme2", "text": "AP-1", "start": 637, "end": 641}]}, {"trigger": {"text": "bound", "start": 642, "end": 647}, "arguments": [{"role": "Theme", "text": "mNFATc", "start": 615, "end": 621}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 710, "end": 719}, "arguments": [{"role": "Cause", "text": "bound", "start": 642, "end": 647}, {"role": "Theme", "text": "transcription", "start": 720, "end": 733}]}], "transcription": [{"trigger": {"text": "transcription", "start": 720, "end": 733}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 758, "end": 762}]}, {"trigger": {"text": "detected", "start": 980, "end": 988}, "arguments": [{"role": "Theme", "text": "mNFATc", "start": 958, "end": 964}]}, {"trigger": {"text": "expressed", "start": 1078, "end": 1087}, "arguments": [{"role": "Theme", "text": "mNFATc", "start": 1047, "end": 1053}]}]}}, "schema": []}
{"input": "Phosphatidylinositol 3-kinase couples the interleukin-2 receptor to the cell cycle regulator E2F. \nCell cycle progression initiated by interleukin-2 (IL-2) in T cells is critical for lymphoproliferation and an immune response. Phosphatidyl inositol 3-kinase (PI3K) is activated by IL-2. However, nuclear targets for PI3K are not known. Here we identify the cell cycle regulator E2F as an IL-2 target in T lymphocytes and PI3K as the critical signaling pathway. We eliminate both Stat5 and Raf/MEK pathways from E2F regulation. Protein kinase B (PKB) is activated by IL-2 via PI3K. The expression of an active PKB is sufficient to induce E2F activity. Inhibition of PI3K inhibits phosphorylation of Rb, induction of cyclin D3, and degradation of p27kip1. These results establish a crucial PI3K/PKB-mediated link between the IL-2 teceptor and the cell cycle machinery. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 585, "end": 595}, "arguments": [{"role": "Theme", "text": "PKB", "start": 609, "end": 612}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 670, "end": 678}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 679, "end": 694}]}, {"trigger": {"text": "inhibits", "start": 670, "end": 678}, "arguments": [{"role": "Theme", "text": "degradation", "start": 730, "end": 741}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 679, "end": 694}, "arguments": [{"role": "Theme", "text": "Rb", "start": 698, "end": 700}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 553, "end": 562}, "arguments": [{"role": "Theme", "text": "PKB", "start": 545, "end": 548}, {"role": "Cause", "text": "IL-2", "start": 566, "end": 570}, {"role": "CSite", "text": "PI3K", "start": 575, "end": 579}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 730, "end": 741}, "arguments": [{"role": "Theme", "text": "p27kip1", "start": 745, "end": 752}]}]}}, "schema": []}
{"input": "Thiol modulation inhibits the interleukin (IL)-1-mediated activation of an IL-1 receptor-associated protein kinase and NF-kappa B. \nThe interleukin-1 receptor type I (IL-1RI) is associated with other proteins thus forming a complex system by which IL-1 exerts its various signals. The initiating event is still uncertain, but activation of a recently described receptor-associated protein kinase is one of the earliest events detectable (Martin et al., Eur.J.Immunol.1994.24: 1566). IL-1 signaling is commonly accompanied by oxidative processes and is thought to be subject to redox regulation. We therefore investigated whether the activation of the IL-1RI-associated protein kinase could be a target for redox regulation and whether an altered activity of the kinase could influence IL-1-mediated NF-kappa B activation. A murine T cell line, EL4, was stimulated with IL-1 with and without pretreatment with different compounds known to influence the cellular redox status. Thiol modifying agents like diamide, menadione, pyrrolidine dithiocarbamate (PDTC), diethyl dithiocarbamate or phenylarsine oxide inhibited the IL-1-induced activation of the IL-1RI-associated protein kinase. N-Acetylcysteine, alpha,alpha'-dipyridyl, aminotriazole or nitrofurantoin did not show any effect. The inhibition by PDTC was reversible unless glutathione synthesis was blocked by buthionine sulfoximine. The described conditions which inhibited or prevented the activation of the IL-1RI-associated kinase similarly impaired the activation of NF-kappa B in EL4 cells. From these observations we conclude that free thiols in the IL-1RI complex are essential for the activation of the IL-1RI-associated protein kinase and that this process is mandatory for IL-1 signaling leading to NF-kappa B activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associated", "start": 178, "end": 188}, "arguments": [{"role": "Theme", "text": "IL-1RI", "start": 167, "end": 173}]}]}}, "schema": []}
{"input": "ATF1 and CREB trans-activate a cell cycle regulated histone H4 gene at a distal nuclear matrix associated promoter element. \nProteins of the ATF/CREB class of transcription factors stimulate gene expression of several cell growth-related genes through protein kinase A-related cAMP response elements. The promoter activity of cell cycle regulated histone H4 genes is regulated by at least four principal cis-acting elements which mediate G1/S phase control and/or enhancement of transcription during the cell cycle. Using protein-DNA interaction assays we show that the H4 promoter contains two ATF/CREB recognition motifs which interact with CREB, ATF1, and ATF2 but not with ATF4/CREB2. One ATF/CRE motif is located in the distal promoter at the nuclear matrix-associated Site IV, and the second motif is present in the proximal promoter at Site I. Both ATF/CRE motifs overlap binding sequences for the multifunctional YY1 transcription factor, which has previously been shown to be nuclear matrix associated. Subnuclear fractionation reveals that there are two ATF1 isoforms which appear to differ with respect to DNA binding activity and partition selectively between nuclear matrix and nonmatrix compartments, consistent with the role of the nuclear matrix in regulating gene expression. Site-directed mutational studies demonstrate that Site I and Site IV together support ATF1- and CREB-induced trans-activation of the H4 promoter. Thus, our data establish that ATF/CREB factors functionally modulate histone H4 gene transcription at distal and proximal promoter elements. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 629, "end": 637}, "arguments": [{"role": "Theme", "text": "ATF1", "start": 649, "end": 653}]}, {"trigger": {"text": "interact", "start": 629, "end": 637}, "arguments": [{"role": "Theme", "text": "ATF2", "start": 659, "end": 663}]}, {"trigger": {"text": "interact", "start": 629, "end": 637}, "arguments": [{"role": "Theme", "text": "ATF4", "start": 677, "end": 681}]}, {"trigger": {"text": "binding", "start": 1121, "end": 1128}, "arguments": [{"role": "Theme", "text": "ATF1", "start": 1064, "end": 1068}]}], "positive regulation": [{"trigger": {"text": "trans-activate", "start": 14, "end": 28}, "arguments": [{"role": "Cause", "text": "ATF1", "start": 0, "end": 4}, {"role": "Theme", "text": "regulated", "start": 42, "end": 51}]}, {"trigger": {"text": "trans-activate", "start": 14, "end": 28}, "arguments": [{"role": "Theme", "text": "regulated", "start": 42, "end": 51}]}, {"trigger": {"text": "mediate", "start": 430, "end": 437}, "arguments": [{"role": "Theme", "text": "enhancement", "start": 464, "end": 475}]}, {"trigger": {"text": "enhancement", "start": 464, "end": 475}, "arguments": [{"role": "Theme", "text": "transcription", "start": 479, "end": 492}]}, {"trigger": {"text": "support", "start": 1371, "end": 1378}, "arguments": [{"role": "Theme", "text": "trans-activation", "start": 1402, "end": 1418}]}, {"trigger": {"text": "trans-activation", "start": 1402, "end": 1418}, "arguments": [{"role": "Cause", "text": "ATF1", "start": 1379, "end": 1383}, {"role": "Theme", "text": "H4", "start": 1426, "end": 1428}, {"role": "Site", "text": "promoter", "start": 1429, "end": 1437}]}, {"trigger": {"text": "trans-activation", "start": 1402, "end": 1418}, "arguments": [{"role": "Theme", "text": "H4", "start": 1426, "end": 1428}, {"role": "Site", "text": "promoter", "start": 1429, "end": 1437}]}, {"trigger": {"text": "at", "start": 1538, "end": 1540}, "arguments": [{"role": "Theme", "text": "modulate", "start": 1499, "end": 1507}]}], "regulation": [{"trigger": {"text": "regulated", "start": 42, "end": 51}, "arguments": [{"role": "Theme", "text": "histone H4", "start": 52, "end": 62}]}, {"trigger": {"text": "regulated", "start": 337, "end": 346}, "arguments": [{"role": "Theme", "text": "histone H4", "start": 347, "end": 357}]}, {"trigger": {"text": "regulated", "start": 367, "end": 376}, "arguments": [{"role": "Theme", "text": "regulated", "start": 337, "end": 346}]}, {"trigger": {"text": "modulate", "start": 1499, "end": 1507}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1524, "end": 1537}]}], "transcription": [{"trigger": {"text": "transcription", "start": 479, "end": 492}, "arguments": [{"role": "Theme", "text": "histone H4", "start": 347, "end": 357}]}, {"trigger": {"text": "transcription", "start": 1524, "end": 1537}, "arguments": [{"role": "Theme", "text": "histone H4", "start": 1508, "end": 1518}]}]}}, "schema": []}
{"input": "IL-2 and IL-7 induce heterodimerization of STAT5 isoforms in human peripheral blood T lymphoblasts. \nDespite differences in T cell responses induced by interleukin (IL)-2 and IL-7, both cytokines modulate T cell functions by activation of signal transducers and activators of transcription (STAT) proteins. We examined the contribution of the two isoforms of STAT5, STAT5A and STAT5B, to IL-2- and IL-7-induced activation of human peripheral blood T lymphoblasts. Both cytokines induced assembly of STAT5A and STAT5B containing complexes capable of binding to the interferon-gamma activation sequence (GAS), and these complexes rapidly translocated (within 1 min) into the nucleus of IL-2- or IL-7-treated cells. The kinetics of this translocation were delayed in IL-7-treated as compared to IL-2-treated cells. IL-2 and IL-7 were equivalent in their ability to induce tyrosine phosphorylation of STAT5A and STAT5B and to facilitate binding of these STATs to an immobilized GAS element. Both IL-2 and IL-7 induced substantial amounts of STAT5A/STAT5B heterodimerization. Moreover, we observed constitutive association of STAT3 with each STAT5 isomer. These data suggest that IL-2 and IL-7 induce assembly of STAT heterodimers in a similar manner and that subsequent cellular responses may be driven by induction of similar sets of genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complexes", "start": 528, "end": 537}, "arguments": [{"role": "Theme", "text": "STAT5A", "start": 499, "end": 505}, {"role": "Theme2", "text": "STAT5B", "start": 510, "end": 516}]}, {"trigger": {"text": "binding", "start": 549, "end": 556}, "arguments": [{"role": "Theme", "text": "STAT5A", "start": 499, "end": 505}]}, {"trigger": {"text": "binding", "start": 549, "end": 556}, "arguments": [{"role": "Theme", "text": "STAT5B", "start": 510, "end": 516}]}, {"trigger": {"text": "binding", "start": 933, "end": 940}, "arguments": [{"role": "Theme", "text": "STAT5A", "start": 897, "end": 903}]}, {"trigger": {"text": "binding", "start": 933, "end": 940}, "arguments": [{"role": "Theme", "text": "STAT5B", "start": 908, "end": 914}]}, {"trigger": {"text": "heterodimerization", "start": 1051, "end": 1069}, "arguments": [{"role": "Theme", "text": "STAT5A", "start": 1037, "end": 1043}, {"role": "Theme2", "text": "STAT5B", "start": 1044, "end": 1050}]}, {"trigger": {"text": "association", "start": 1106, "end": 1117}, "arguments": [{"role": "Theme", "text": "STAT5A", "start": 1037, "end": 1043}]}, {"trigger": {"text": "association", "start": 1106, "end": 1117}, "arguments": [{"role": "Theme", "text": "STAT5B", "start": 1044, "end": 1050}]}], "localization": [{"trigger": {"text": "translocated", "start": 636, "end": 648}, "arguments": [{"role": "Theme", "text": "STAT5A", "start": 499, "end": 505}, {"role": "ToLoc", "text": "nucleus", "start": 673, "end": 680}]}, {"trigger": {"text": "translocated", "start": 636, "end": 648}, "arguments": [{"role": "Theme", "text": "STAT5B", "start": 510, "end": 516}, {"role": "ToLoc", "text": "nucleus", "start": 673, "end": 680}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 878, "end": 893}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 869, "end": 877}, {"role": "Theme", "text": "STAT5A", "start": 897, "end": 903}]}, {"trigger": {"text": "phosphorylation", "start": 878, "end": 893}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 869, "end": 877}, {"role": "Theme", "text": "STAT5B", "start": 908, "end": 914}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 479, "end": 486}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 388, "end": 392}, {"role": "Theme", "text": "complexes", "start": 528, "end": 537}]}, {"trigger": {"text": "induced", "start": 479, "end": 486}, "arguments": [{"role": "Cause", "text": "IL-7", "start": 398, "end": 402}, {"role": "Theme", "text": "complexes", "start": 528, "end": 537}]}, {"trigger": {"text": "treated", "start": 698, "end": 705}, "arguments": [{"role": "Theme", "text": "translocated", "start": 636, "end": 648}, {"role": "Cause", "text": "IL-2", "start": 684, "end": 688}]}, {"trigger": {"text": "induce", "start": 862, "end": 868}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 812, "end": 816}, {"role": "Theme", "text": "phosphorylation", "start": 878, "end": 893}]}, {"trigger": {"text": "induce", "start": 862, "end": 868}, "arguments": [{"role": "Cause", "text": "IL-7", "start": 821, "end": 825}, {"role": "Theme", "text": "phosphorylation", "start": 878, "end": 893}]}, {"trigger": {"text": "facilitate", "start": 922, "end": 932}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 812, "end": 816}, {"role": "Theme", "text": "binding", "start": 933, "end": 940}]}, {"trigger": {"text": "facilitate", "start": 922, "end": 932}, "arguments": [{"role": "Cause", "text": "IL-7", "start": 821, "end": 825}, {"role": "Theme", "text": "binding", "start": 933, "end": 940}]}]}}, "schema": []}
{"input": "Molecular mechanisms of anoxia/reoxygenation-induced neutrophil adherence to cultured endothelial cells. \nThe objectives of this study were to (1) determine the time course of neutrophil adhesion to monolayers of human umbilical vein endothelial cells (HUVECs) that were exposed to 60 minutes of anoxia followed by 30 to 600 minutes of reoxygenation and (2) define the mechanisms responsible for both the early (minutes) and late (hours) hyperadhesivity of postanoxic HUVECs to human neutrophils. The results clearly demonstrate that anoxia/reoxygenation (A/R) leads to a biphasic increase in neutrophil adhesion to HUVECs, with peak responses occurring at 30 minutes (phase 1) and 240 minutes (phase 2) after reoxygenation. Oxypurinol and catalase inhibited phase-1 adhesion, suggesting a role for xanthine oxidase and H2O2. In comparison, platelet activating factor (PAF) contributed to both phases of neutrophil adhesion. Anti-intercellular adhesion molecule-1 (ICAM-1) and anti-P-selectin antibodies (monoclonal antibodies [mAbs]) attenuated phase-1 neutrophil adhesion, consistent with roles for constitutively expressed ICAM-1 and enhanced surface expression of preformed P-selectin. Phase-2 neutrophil adhesion was attenuated by an anti-E-selectin mAb, indicating a dominant role of this adhesion molecule in the late phase response. Pretreatment with actinomycin D and cycloheximide or with competing ds-oligonucleotides containing the nuclear factor-kappa B or activator protein-1 cognate DNA sequences significantly attenuated phase-2 response, suggesting a role for de novo macromolecule synthesis. Surface expression of ICAM-1, P-selectin, and E-selectin on HUVECs correlated with the phase-1 and -2 neutrophil adhesion responses. Collectively, these findings indicate that A/R elicits a two-phase neutrophil-endothelial cell adhesion response that involves transcription-independent and transcription-dependent surface expression of different endothelial cell adhesion molecules. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressed", "start": 1116, "end": 1125}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1126, "end": 1132}]}, {"trigger": {"text": "expression", "start": 1154, "end": 1164}, "arguments": [{"role": "Theme", "text": "P-selectin", "start": 1178, "end": 1188}]}, {"trigger": {"text": "expression", "start": 1618, "end": 1628}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1632, "end": 1638}]}, {"trigger": {"text": "expression", "start": 1618, "end": 1628}, "arguments": [{"role": "Theme", "text": "P-selectin", "start": 1640, "end": 1650}]}, {"trigger": {"text": "expression", "start": 1618, "end": 1628}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1656, "end": 1666}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 1137, "end": 1145}, "arguments": [{"role": "Theme", "text": "expression", "start": 1154, "end": 1164}]}], "regulation": [{"trigger": {"text": "roles", "start": 1091, "end": 1096}, "arguments": [{"role": "Theme", "text": "expressed", "start": 1116, "end": 1125}]}, {"trigger": {"text": "roles", "start": 1091, "end": 1096}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 1137, "end": 1145}]}]}}, "schema": []}
{"input": "c-Rel and p65 subunits bind to an upstream NF-kappaB site in human granulocyte macrophage-colony stimulating factor promoter involved in phorbol ester response in 5637 cells. \nTo further clarify the complex transcriptional regulation of the human GM-CSF gene, which was extensively investigated in activated T cells, we have studied the role of an upstream NF-kappaB like site in the 5637 non-lymphoid cell line, which derives from a bladder carcinoma and constitutively produces GM-CSF. This sequence, named the A element, has an active role on GM-CSF transcription and is responsive to the tumor promoter PMA in transient transfection experiments. We describe here a heterodimeric binding complex of NF-kappaB subunits (c-Rel and p65) which is identical to the one obtained using the HIV-LTR-kappaB site as recognition sequence and different from the one (c-Rel and p50) observed with nuclear extracts from Mo T-lymphoid HTLV-II infected cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 23, "end": 27}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 0, "end": 5}]}, {"trigger": {"text": "bind", "start": 23, "end": 27}, "arguments": [{"role": "Theme", "text": "p65", "start": 10, "end": 13}]}, {"trigger": {"text": "heterodimeric binding complex", "start": 669, "end": 698}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 722, "end": 727}, {"role": "Theme2", "text": "p65", "start": 732, "end": 735}]}, {"trigger": {"text": "heterodimeric binding complex", "start": 669, "end": 698}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 858, "end": 863}, {"role": "Theme2", "text": "p50", "start": 868, "end": 871}]}, {"trigger": {"text": "complex", "start": 691, "end": 698}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 722, "end": 727}]}, {"trigger": {"text": "complex", "start": 691, "end": 698}, "arguments": [{"role": "Theme", "text": "p65", "start": 732, "end": 735}]}], "gene expression": [{"trigger": {"text": "produces", "start": 471, "end": 479}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 480, "end": 486}]}], "regulation": [{"trigger": {"text": "transcriptional regulation", "start": 207, "end": 233}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 247, "end": 253}]}, {"trigger": {"text": "role", "start": 538, "end": 542}, "arguments": [{"role": "Theme", "text": "transcription", "start": 553, "end": 566}]}], "transcription": [{"trigger": {"text": "transcription", "start": 553, "end": 566}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 546, "end": 552}]}]}}, "schema": []}
{"input": "Cyclosporin A inhibits monocyte tissue factor activation in cardiac transplant recipients. \nBACKGROUND: Fibrin deposition and thrombosis have been implicated in both allograft rejection and vasculopathy after cardiac transplantation. Because monocytes play a pivotal role in the pathophysiology of intravascular coagulation activation through their ability to synthesize tissue factor (TF), we asked (1) whether monocyte TF activation occurs in cardiac transplant recipients and (2) whether monocyte TF expression is affected by treatment with cyclosporin A (CsA). METHODS AND RESULTS: We measured levels of TF activity in peripheral blood mononuclear cells and highly purified monocytes/macrophages from 10 consecutive cardiac transplant recipients and 10 healthy control subjects. TF activity generated by both unstimulated and endotoxin-stimulated cells was significantly higher in transplant recipients than in control subjects (P<.05). Increased monocyte TF expression in transplant recipients was shown to be adversely affected by treatment with CsA: TF induction was markedly reduced by CsA serum concentrations reaching peak CsA drug levels. Inhibition of TF induction in the presence of high CsA blood concentrations was also observed when stimulation of cells was performed with interferon-gamma or interleukin-1beta. As shown by reverse transcription-polymerase chain reaction and electrophoretic mobility shift assay, respectively, treatment with CsA leads to decreased TF mRNA expression and reduced activation of the NF-kappaB transcription factor, which is known to contribute to the induction of the TF promotor in human monocytes. CONCLUSIONS: This study demonstrates that TF activation, occurring in mononuclear cells of cardiac transplant recipients, is inhibited by treatment with CsA. Inhibition of monocyte TF induction by CsA may contribute to its successful use in cardiac transplant medicine and might be useful in managing further settings of vascular pathology also known to involve TF expression and NF-kappaB activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "synthesize", "start": 360, "end": 370}, "arguments": [{"role": "Theme", "text": "TF", "start": 386, "end": 388}]}, {"trigger": {"text": "expression", "start": 503, "end": 513}, "arguments": [{"role": "Theme", "text": "TF", "start": 500, "end": 502}]}, {"trigger": {"text": "expression", "start": 963, "end": 973}, "arguments": [{"role": "Theme", "text": "TF", "start": 960, "end": 962}]}, {"trigger": {"text": "expression", "start": 2013, "end": 2023}, "arguments": [{"role": "Theme", "text": "TF", "start": 2010, "end": 2012}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 14, "end": 22}, "arguments": [{"role": "Theme", "text": "activation", "start": 46, "end": 56}]}, {"trigger": {"text": "adversely affected", "start": 1015, "end": 1033}, "arguments": [{"role": "Theme", "text": "Increased", "start": 941, "end": 950}]}, {"trigger": {"text": "reduced", "start": 1083, "end": 1090}, "arguments": [{"role": "Theme", "text": "induction", "start": 1060, "end": 1069}]}, {"trigger": {"text": "Inhibition", "start": 1150, "end": 1160}, "arguments": [{"role": "Theme", "text": "induction", "start": 1167, "end": 1176}]}, {"trigger": {"text": "when", "start": 1244, "end": 1248}, "arguments": [{"role": "Theme", "text": "induction", "start": 1167, "end": 1176}]}, {"trigger": {"text": "decreased", "start": 1472, "end": 1481}, "arguments": [{"role": "Theme", "text": "expression", "start": 1490, "end": 1500}]}, {"trigger": {"text": "inhibited", "start": 1773, "end": 1782}, "arguments": [{"role": "Theme", "text": "activation", "start": 1693, "end": 1703}]}, {"trigger": {"text": "Inhibition", "start": 1806, "end": 1816}, "arguments": [{"role": "Theme", "text": "induction", "start": 1832, "end": 1841}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 46, "end": 56}, "arguments": [{"role": "Theme", "text": "tissue factor", "start": 32, "end": 45}]}, {"trigger": {"text": "activation", "start": 424, "end": 434}, "arguments": [{"role": "Theme", "text": "TF", "start": 421, "end": 423}]}, {"trigger": {"text": "occurs", "start": 435, "end": 441}, "arguments": [{"role": "Theme", "text": "activation", "start": 424, "end": 434}]}, {"trigger": {"text": "generated", "start": 795, "end": 804}, "arguments": [{"role": "Theme", "text": "TF", "start": 783, "end": 785}]}, {"trigger": {"text": "Increased", "start": 941, "end": 950}, "arguments": [{"role": "Theme", "text": "expression", "start": 963, "end": 973}]}, {"trigger": {"text": "induction", "start": 1060, "end": 1069}, "arguments": [{"role": "Theme", "text": "TF", "start": 1057, "end": 1059}]}, {"trigger": {"text": "induction", "start": 1167, "end": 1176}, "arguments": [{"role": "Theme", "text": "TF", "start": 1164, "end": 1166}]}, {"trigger": {"text": "contribute", "start": 1581, "end": 1591}, "arguments": [{"role": "Theme", "text": "induction", "start": 1599, "end": 1608}]}, {"trigger": {"text": "induction", "start": 1599, "end": 1608}, "arguments": [{"role": "Theme", "text": "TF", "start": 1616, "end": 1618}, {"role": "Site", "text": "promotor", "start": 1619, "end": 1627}]}, {"trigger": {"text": "activation", "start": 1693, "end": 1703}, "arguments": [{"role": "Theme", "text": "TF", "start": 1690, "end": 1692}]}, {"trigger": {"text": "induction", "start": 1832, "end": 1841}, "arguments": [{"role": "Theme", "text": "TF", "start": 1829, "end": 1831}]}], "regulation": [{"trigger": {"text": "affected", "start": 517, "end": 525}, "arguments": [{"role": "Theme", "text": "expression", "start": 503, "end": 513}]}], "transcription": [{"trigger": {"text": "expression", "start": 1490, "end": 1500}, "arguments": [{"role": "Theme", "text": "TF", "start": 1482, "end": 1484}]}]}}, "schema": []}
{"input": "Agonistic activity of a CD40-specific single-chain Fv constructed from the variable regions of mAb G28-5. \nA single-chain Fv (sFv) was expressed from the variable regions of the CD40-specific mAb G28-5. The molecule bound CD40 with a high affinity (2.2 nM) and was a monomer in solution. Surprisingly, G28-5 sFv was a potent CD40 agonist that rapidly crosslinked CD40 on the cell surface but did not crosslink CD40-Ig in solution. G28-5 sFv was a more potent agonist than G28-5 IgG and was able to stimulate CD40 responses by B cells and monocytes. G28-5 IgG partially blocked, whereas G28-5 sFv augmented CD40 responses during stimulation with natural ligand (gp39-CD8 fusion protein). These results indicate that the functional activity of ligands built from the binding site of G28-5 is highly dependent upon the size and physical properties of the molecule both in solution and on the cell surfaces. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bound", "start": 216, "end": 221}, "arguments": [{"role": "Theme", "text": "CD40", "start": 222, "end": 226}]}, {"trigger": {"text": "crosslinked", "start": 351, "end": 362}, "arguments": [{"role": "Theme", "text": "CD40", "start": 363, "end": 367}]}, {"trigger": {"text": "crosslink", "start": 400, "end": 409}, "arguments": [{"role": "Theme", "text": "CD40", "start": 410, "end": 414}]}]}}, "schema": []}
{"input": "Competent transcription initiation by RNA polymerase II in cell-free extracts from xeroderma pigmentosum groups B and D in an optimized RNA transcription assay. \nThe human autosomal recessive disease, xeroderma pigmentosum (XP), can result from mutations in any one of seven genes, designated XPA through XPG. Of these, the XPB and XPD genes encode proteins that are subunits of a general transcription factor, TFIIH, involved in both nucleotide excision repair (NER) and initiation of mRNA transcription by RNA polymerase II. In humans, mutation of the XPB or XPD gene impairs NER, resulting in hyper-sensitivity to sunlight and greatly increased skin tumor formation. However, no transcription deficiency has been demonstrated in either XP-B or XP-D. We have employed an optimized cell-free RNA transcription assay to analyze transcription activity of XP-B and XP-D. Although the growth rate was normal, the XP-B and XP-D cells contained reduced amounts of TFIIH. Extracts prepared from XP-B and XP-D lymphoblastoid cells exhibited similar transcription activity from the adenovirus major late promoter when compared to that in extracts from normal cells. Thus, we conclude that the XP-B and XP-D lymphoblastoid cells do not have impaired RNA transcription activity. We consider the possible consequences of the reduced cellular content of TFIIH for the clinical symptoms in XP-B or XP-D patients, and discuss a 'conditional phenotype' that may involve an impairment of cellular function only under certain growth conditions. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Cyclosporin A inhibits early mRNA expression of G0/G1 switch gene 2 (G0S2) in cultured human blood mononuclear cells. \nCyclosporin A (CsA) may achieve its immunosuppressive effects by inhibiting the calcium- and calmodulin-dependent phosphatase calcineurin which is required for activation of target genes by members of the NFAT (nuclear factor of activated T cells) transcription factor family. Among these target genes is the gene encoding interleukin-2 (IL2), a cytokine facilitating progression through the G1 phase of the cell cycle. However, IL2 does not reverse CsA inhibition, suggesting that at least one other NFAT-sensitive gene may be involved. The human G0/G1 switch gene, G0S2, has potential NFAT-binding sites in the 5' flank and encodes a small basic potential phosphoprotein of unknown function. Using a sensitive, reverse transcription-polymerase chain reaction (RT-PCR) assay, G0S2 mRNA levels were assayed in cultured blood mononuclear cells. Freshly isolated cells contain high levels of G0S2 mRNA which rapidly decline. This \"spontaneous stimulation\" is also noted with some other G0S genes and has been attributed to some aspect of the isolation procedure. In cells that have been preincubated to lower mRNA levels, there is a transient increase in G0S2 mRNA, peaking between 1-2 h, in response to Concanavalin-A (ConA), or to the combination of phorbol ester (TPA), and the calcium ionophore, ionomycin. Both these responses are inhibited by CsA. Our results suggest that G0S2 expression is required to commit cells to enter the G1 phase of the cell cycle, and that, while not excluding other possible targets, early inhibition of G0S2 expression by CsA may be important in achieving immunosuppression. G0S2 may be of value as a reporter gene for analyzing the mechanism of action of CsA and its influence on the positive and negative selection of lymphocytes in response to self and not-self antigens. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1501, "end": 1511}, "arguments": [{"role": "Theme", "text": "G0S2", "start": 1496, "end": 1500}]}, {"trigger": {"text": "expression", "start": 1660, "end": 1670}, "arguments": [{"role": "Theme", "text": "G0S2", "start": 1655, "end": 1659}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 14, "end": 22}, "arguments": [{"role": "Theme", "text": "mRNA expression", "start": 29, "end": 44}]}, {"trigger": {"text": "inhibited", "start": 1453, "end": 1462}, "arguments": [{"role": "Theme", "text": "increase", "start": 1260, "end": 1268}]}, {"trigger": {"text": "inhibition", "start": 1641, "end": 1651}, "arguments": [{"role": "Theme", "text": "expression", "start": 1660, "end": 1670}]}], "positive regulation": [{"trigger": {"text": "high", "start": 994, "end": 998}, "arguments": [{"role": "Theme", "text": "levels", "start": 999, "end": 1005}]}, {"trigger": {"text": "stimulation", "start": 1060, "end": 1071}, "arguments": [{"role": "Theme", "text": "G0S", "start": 1103, "end": 1106}]}, {"trigger": {"text": "increase", "start": 1260, "end": 1268}, "arguments": [{"role": "Theme", "text": "G0S2", "start": 1272, "end": 1276}]}], "transcription": [{"trigger": {"text": "mRNA expression", "start": 29, "end": 44}, "arguments": [{"role": "Theme", "text": "G0S2", "start": 69, "end": 73}]}, {"trigger": {"text": "levels", "start": 906, "end": 912}, "arguments": [{"role": "Theme", "text": "G0S2", "start": 896, "end": 900}]}, {"trigger": {"text": "levels", "start": 999, "end": 1005}, "arguments": [{"role": "Theme", "text": "G0S2", "start": 1009, "end": 1013}]}]}}, "schema": []}
{"input": "Estrogen receptor diminishes DNA-binding activities of chicken GATA-1 and CACCC-binding proteins. \nThe estrogen receptor (ER) repressed erythroid differentiation and erythroid-specific gene expression. In this study, we investigated the effect of ER alpha (referred to throughout as ER) on DNA-binding activities of transcription factors involved in regulating the expression of erythroid-specific genes, and, in particular, the histone H5 gene. Using electrophoretic mobility shift assays, we found that in the presence of rabbit reticulocyte lysate, human ER reduced the binding activities of chicken immature erythrocyte nuclear extracted proteins to GATA and CACCC sites in the H5 promoter and enhancer. In contrast, the binding activities of NF1 and Sp1 were not affected by ER. Binding of ER to an estrogen response element was enhanced by addition of rabbit reticulocyte lysate. This lysate was also necessary for ER to diminish the DNA-binding activity of GATA-1. These results suggest that additional factor(s) are necessary for full ER function. Both GATA-1 and CACCC-binding proteins are critical for the developmentally regulated expression of erythroid-specific genes. We hypothesize that interference in DNA-binding activities of GATA-1 and CACCC-binding proteins is the mechanism by which the ER inhibits regulation of these genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding activities", "start": 33, "end": 51}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 63, "end": 69}]}, {"trigger": {"text": "binding activities", "start": 725, "end": 743}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 755, "end": 758}]}, {"trigger": {"text": "Binding", "start": 784, "end": 791}, "arguments": [{"role": "Theme", "text": "ER", "start": 795, "end": 797}]}, {"trigger": {"text": "binding activity", "start": 944, "end": 960}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 964, "end": 970}]}, {"trigger": {"text": "binding activities", "start": 1222, "end": 1240}, "arguments": [{"role": "Theme", "text": "GATA-1", "start": 1244, "end": 1250}]}], "gene expression": [{"trigger": {"text": "expression", "start": 365, "end": 375}, "arguments": [{"role": "Theme", "text": "histone H5", "start": 429, "end": 439}]}], "negative regulation": [{"trigger": {"text": "diminishes", "start": 18, "end": 28}, "arguments": [{"role": "Cause", "text": "Estrogen receptor", "start": 0, "end": 17}, {"role": "Theme", "text": "binding activities", "start": 33, "end": 51}]}, {"trigger": {"text": "to diminish", "start": 924, "end": 935}, "arguments": [{"role": "Theme", "text": "binding activity", "start": 944, "end": 960}, {"role": "Cause", "text": "GATA-1", "start": 964, "end": 970}]}, {"trigger": {"text": "interference", "start": 1202, "end": 1214}, "arguments": [{"role": "Theme", "text": "binding activities", "start": 1222, "end": 1240}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 834, "end": 842}, "arguments": [{"role": "Theme", "text": "Binding", "start": 784, "end": 791}]}, {"trigger": {"text": "necessary", "start": 907, "end": 916}, "arguments": [{"role": "Theme", "text": "to diminish", "start": 924, "end": 935}]}, {"trigger": {"text": "necessary", "start": 1024, "end": 1033}, "arguments": [{"role": "Theme", "text": "ER", "start": 1043, "end": 1045}]}], "regulation": [{"trigger": {"text": "involved in regulating", "start": 338, "end": 360}, "arguments": [{"role": "Theme", "text": "expression", "start": 365, "end": 375}]}, {"trigger": {"text": "not affected", "start": 764, "end": 776}, "arguments": [{"role": "Theme", "text": "binding activities", "start": 725, "end": 743}, {"role": "Cause", "text": "ER", "start": 780, "end": 782}]}]}}, "schema": []}
{"input": "Constitutive expression c-fos, c-jun, and NF kappa B mRNA is in nucleated fetal blood cells and up-regulation of c-fos and c-jun with anti-CD3 stimulation. \nFetal and neonatal lymphocytes are relatively resistant to activation and cytokine production when stimulated either via their T-cell antigen receptors or lectins. The molecular mechanism(s) responsible for this phenomenon have not been clearly elucidated. We have hypothesized that such defects in fetal/neonatal T-cell activation may be due to lack of expression of the transcriptional regulatory elements required for T-cell activation. We used reverse transcriptase-polymerase chain reaction to examine both fetal and term neonatal cord bloods for mRNA expression of three transcription factors implicated in T-cell activation: c-jun, c-fos, and NF kappa B (p50 subunit). We demonstrate that mRNAs for all three of these regulatory factors are expressed in fetal blood cells by the 27th week of gestation and in term cord bloods. Activation of term infant cord blood mononuclear cells with anti-CD3 monoclonal antibodies resulted in up-regulation of both c-jun and c-fos mRNAs within 15 min of stimulation. However, secretion of IL-2 by anti-CD3-stimulated cord blood mononuclear cells was still blunted compared with control cells from adults. We conclude that fetal nucleated blood cells constitutively express important genes for cytokine regulation and are able to increase intracellular accumulation of the mRNAs for these factors in response to anti-CD3 stimulation. Thus, qualitative differences in the capacity to regulate these factors could not be shown in fetal blood cells. Quantitative experiments comparing binding of these transcription factors to the IL-2 promoter are currently under investigation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1682, "end": 1689}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1116, "end": 1121}, {"role": "Theme2", "text": "IL-2", "start": 1728, "end": 1732}, {"role": "Site2", "text": "promoter", "start": 1733, "end": 1741}]}, {"trigger": {"text": "binding", "start": 1682, "end": 1689}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1126, "end": 1131}, {"role": "Theme2", "text": "IL-2", "start": 1728, "end": 1732}, {"role": "Site2", "text": "promoter", "start": 1733, "end": 1741}]}], "gene expression": [{"trigger": {"text": "mRNA expression", "start": 709, "end": 724}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 789, "end": 794}]}], "localization": [{"trigger": {"text": "secretion", "start": 1177, "end": 1186}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1190, "end": 1194}]}], "positive regulation": [{"trigger": {"text": "up-regulation", "start": 96, "end": 109}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 113, "end": 118}]}, {"trigger": {"text": "up-regulation", "start": 96, "end": 109}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 123, "end": 128}]}, {"trigger": {"text": "resulted in up-regulation", "start": 1082, "end": 1107}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1116, "end": 1121}]}, {"trigger": {"text": "resulted in up-regulation", "start": 1082, "end": 1107}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1126, "end": 1131}]}, {"trigger": {"text": "blunted", "start": 1257, "end": 1264}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1177, "end": 1186}]}, {"trigger": {"text": "increase", "start": 1430, "end": 1438}, "arguments": [{"role": "Theme", "text": "accumulation", "start": 1453, "end": 1465}]}, {"trigger": {"text": "accumulation", "start": 1453, "end": 1465}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1116, "end": 1121}]}, {"trigger": {"text": "accumulation", "start": 1453, "end": 1465}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1126, "end": 1131}]}], "regulation": [{"trigger": {"text": "regulate", "start": 1583, "end": 1591}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 1116, "end": 1121}]}, {"trigger": {"text": "regulate", "start": 1583, "end": 1591}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 1126, "end": 1131}]}], "transcription": [{"trigger": {"text": "expression", "start": 13, "end": 23}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 24, "end": 29}]}, {"trigger": {"text": "expression", "start": 13, "end": 23}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 31, "end": 36}]}, {"trigger": {"text": "mRNA expression", "start": 709, "end": 724}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 789, "end": 794}]}, {"trigger": {"text": "mRNA expression", "start": 709, "end": 724}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 796, "end": 801}]}, {"trigger": {"text": "mRNA expression", "start": 709, "end": 724}, "arguments": [{"role": "Theme", "text": "p50", "start": 819, "end": 822}]}, {"trigger": {"text": "expressed", "start": 905, "end": 914}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 789, "end": 794}]}, {"trigger": {"text": "expressed", "start": 905, "end": 914}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 796, "end": 801}]}, {"trigger": {"text": "expressed", "start": 905, "end": 914}, "arguments": [{"role": "Theme", "text": "p50", "start": 819, "end": 822}]}]}}, "schema": []}
{"input": "Replication of human immunodeficiency virus-1 in primary human T cells is dependent on the autocrine secretion of tumor necrosis factor through the control of nuclear factor-kappa B activation. \nTumor necrosis factor (TNF)-alpha controls T-cell activation and is a major inducer of human immunodeficiency virus (HIV)-1 replication in chronically infected cells. Therefore, we have investigated its role in primary cultures of HIV-infected human T lymphocytes by using neutralizing anti-TNF-alpha antibodies or TNF-alpha. Primary resting T lymphocytes produced TNF-alpha and supported HIV replication after T-cell receptor activation. Addition of neutralizing anti-TNF-alpha antibodies drastically reduced p24 antigen release and prevented CD4+ cell depletion associated with infection. Anti-TNF-alpha also prevented nuclear factor-kappa B (NF-kappa B) activation, and a good correlation between this inhibition and inhibition of HIV replication was observed. Moreover, supplementing the cultures with high doses of IL-2 reverted anti-TNF-alpha inhibition of cell proliferation but did not affect the inhibition of HIV p24 antigen release or NF-kappa B activation in the same cultures. Moreover, anti-TNF-alpha inhibited HIV-1 long terminal repeat (LTR)-driven transcription of a reporter gene in primary T cells in response to activation, either in the presence or the absence of HIV-1 Tat. Our results support an important role for autocrine TNF-alpha secretion in controlling HIV replication in primary T cells because of its ability to maintain NF-kappa B elevated in the nucleus of T cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "produced", "start": 551, "end": 559}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 560, "end": 569}]}], "localization": [{"trigger": {"text": "release", "start": 717, "end": 724}, "arguments": [{"role": "Theme", "text": "p24", "start": 705, "end": 708}]}, {"trigger": {"text": "release", "start": 1130, "end": 1137}, "arguments": [{"role": "Theme", "text": "p24", "start": 1118, "end": 1121}]}, {"trigger": {"text": "secretion", "start": 1453, "end": 1462}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1443, "end": 1452}]}], "negative regulation": [{"trigger": {"text": "neutralizing", "start": 646, "end": 658}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 664, "end": 673}]}, {"trigger": {"text": "reduced", "start": 697, "end": 704}, "arguments": [{"role": "Theme", "text": "release", "start": 717, "end": 724}]}, {"trigger": {"text": "inhibition", "start": 1100, "end": 1110}, "arguments": [{"role": "Theme", "text": "release", "start": 1130, "end": 1137}]}], "regulation": [{"trigger": {"text": "affect", "start": 1089, "end": 1095}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1015, "end": 1019}, {"role": "Theme", "text": "inhibition", "start": 1100, "end": 1110}]}]}}, "schema": []}
{"input": "A thiol antioxidant regulates IgE isotype switching by inhibiting activation of nuclear factor-kappaB. \nThe binding site for nuclear factor-kappaB (NF-kappaB) is present at the promoter region of the germline Cepsilon gene, but there is little information on whether this factor is involved in regulating IgE synthesis by human B cells. Accordingly, we studied the role of NF-kappaB in germline Cepsilon transcription by using two human Burkitt's lymphoma B cell lines, DND39 and DG75. In both cell lines, n-acetyl-L-cysteine (NAC), a potent thiol antioxidant, inhibited the triggering of the nuclear expression of NF-kappaB by IL-4 and by anti-CD40 monoclonal antibody. Although IL-4 activated signal transducers and activators of transcription (STAT) 6 in addition to NF-kappaB, NAC treatment or the transfection of decoy oligodeoxynucleotides for NF-kappaB or STAT6 only partly blocked IL-4-induced germline Cepsilon transcription. However, these two decoy oligodeoxynucleotides together almost completely abrogated IL-4-induced germline Cepsilon transcription. Of note, CD40-mediated enhancement of IL-4-driven germline Cepsilon transcription was markedly decreased by NAC or by a decoy oligodeoxynucleotide for NF-kappaB. The effect of NAC was also examined on deletional switch recombination underlying the isotype switch to IgE. NAC inhibited the generation of Smu/Sepsilon switch fragments in normal human B cells costimulated with IL-4 and anti-CD40 monoclonal antibody. It also abolished IL-4-induced upregulation of CD40 but promoted upregulation of CD23. These results suggest that coordination of NF-kappaB and STAT6 may be required for induction of germline Cepsilon transcription by IL-4, and that CD40-mediated NF-kappaB activation may be important in regulating both enhancement of germline Cepsilon transcription and class switching to IgE. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "abolished", "start": 1488, "end": 1497}, "arguments": [{"role": "Theme", "text": "upregulation", "start": 1511, "end": 1523}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 685, "end": 694}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 680, "end": 684}, {"role": "Theme", "text": "signal transducers and activators of transcription (STAT) 6", "start": 695, "end": 754}]}, {"trigger": {"text": "upregulation", "start": 1511, "end": 1523}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1498, "end": 1502}, {"role": "Theme", "text": "CD40", "start": 1527, "end": 1531}]}, {"trigger": {"text": "promoted", "start": 1536, "end": 1544}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1498, "end": 1502}, {"role": "Theme", "text": "upregulation", "start": 1545, "end": 1557}]}, {"trigger": {"text": "upregulation", "start": 1545, "end": 1557}, "arguments": [{"role": "Theme", "text": "CD23", "start": 1561, "end": 1565}]}]}}, "schema": []}
{"input": "Cellular and molecular mechanisms of IL-5 synthesis in atopic diseases: a study with allergen-specific human helper T cells. \nBACKGROUND: Cytokines produced by helper T cells are intimately involved in chronic allergic diseases associated with eosinophilic inflammation. OBJECTIVE: We investigated the production of IL-5, a potent growth factor and chemotactic factor for eosinophils, by CD4+ T lymphocytes in patients with asthma. METHODS: Allergen-specific T cell clones and T cell hybridomas were established from the peripheral blood lymphocytes of patients with asthma, and the responses to various stimuli were determined. RESULTS: After nonspecific stimulation, IL-5 production by CD4+ T cells from both atopic and nonatopic subjects with asthma was significantly enhanced compared with that by cells from healthy controls. Peripheral blood mononuclear cells from atopic asthma patients both proliferated and produced IL-5 after incubation with mite allergen, suggesting that mite-specific helper T cells were involved in the eosinophilic inflammation of atopic asthma. A human IL-5 promoter/enhancer luciferase gene construct transfected into IL-5-producing T cell clones was clearly transcribed after stimulation, indicating that the 515 base pair IL-5 gene segment upstream of the coding region was sufficient to respond to activating signals in human helper T cells. The same gene segment was not transcribed in IL-5-nonproducing T cell clones, suggesting that human T cell IL-5 synthesis is regulated at the transcriptional level. Experiments with T cell hybridomas confirmed these findings and suggested that a unique transcription factor may be essential for human IL-5 gene transcription. CONCLUSION: Enhanced IL-5 production by helper T cells seems to cause the eosinophilic inflammation of both atopic and nonatopic asthma. Elucidation of IL-5-specific regulatory mechanisms may facilitate the development of novel treatments for allergic diseases associated with eosinophilic inflammation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "synthesis", "start": 42, "end": 51}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 37, "end": 41}]}, {"trigger": {"text": "production", "start": 302, "end": 312}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 316, "end": 320}]}, {"trigger": {"text": "production", "start": 674, "end": 684}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 669, "end": 673}]}, {"trigger": {"text": "produced", "start": 916, "end": 924}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 925, "end": 929}]}, {"trigger": {"text": "producing", "start": 1156, "end": 1165}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1151, "end": 1155}]}, {"trigger": {"text": "nonproducing", "start": 1428, "end": 1440}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1423, "end": 1427}]}, {"trigger": {"text": "synthesis", "start": 1490, "end": 1499}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1485, "end": 1489}]}, {"trigger": {"text": "production", "start": 1730, "end": 1740}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1725, "end": 1729}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 771, "end": 779}, "arguments": [{"role": "Theme", "text": "production", "start": 674, "end": 684}]}, {"trigger": {"text": "after incubation with", "start": 930, "end": 951}, "arguments": [{"role": "Theme", "text": "produced", "start": 916, "end": 924}]}, {"trigger": {"text": "after", "start": 1204, "end": 1209}, "arguments": [{"role": "Theme", "text": "transcribed", "start": 1192, "end": 1203}]}, {"trigger": {"text": "sufficient to respond", "start": 1309, "end": 1330}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1257, "end": 1261}, {"role": "Site", "text": "segment", "start": 1267, "end": 1274}]}, {"trigger": {"text": "essential", "start": 1659, "end": 1668}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1689, "end": 1702}]}, {"trigger": {"text": "Enhanced", "start": 1716, "end": 1724}, "arguments": [{"role": "Theme", "text": "production", "start": 1730, "end": 1740}]}], "regulation": [{"trigger": {"text": "regulated", "start": 1503, "end": 1512}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 1490, "end": 1499}, {"role": "Cause", "text": "transcriptional level", "start": 1520, "end": 1541}]}], "transcription": [{"trigger": {"text": "transcribed", "start": 1192, "end": 1203}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1085, "end": 1089}]}, {"trigger": {"text": "not transcribed", "start": 1404, "end": 1419}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1085, "end": 1089}]}, {"trigger": {"text": "transcriptional level", "start": 1520, "end": 1541}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1485, "end": 1489}]}, {"trigger": {"text": "transcription", "start": 1689, "end": 1702}, "arguments": [{"role": "Theme", "text": "IL-5", "start": 1679, "end": 1683}]}]}}, "schema": []}
{"input": "Regulation of NF-kappa B activity by I kappa B alpha and I kappa B beta stability. \nTranscription factor NF-kappa B must be released from cytoplasmic inhibitory molecules (I kappa Bs) in order to move to the nucleus and to activate its target genes. Little is known about the mechanisms regulating the maintenance of constitutive nuclear NF-kappa B in some cell-types and of sustained nuclear NF-kappa B activity after stimulation. Increased turnover has been implicated in the regulation of constitutive NF-kappa B activity in mature B cells. We therefore compared the turnover of I kappa B alpha and I kappa B beta in mature B cells and HeLa cells. Both proteins display a high turnover in B cells although I kappa B beta is considerably more stable than I kappa B alpha. The half-life of both inhibitors is increased in HeLa cells. In contrast, all other NF-kappa B/I kappa B molecules tested are relatively stable in both cell-types. The elevated turnover of endogenous I kappa B alpha in Namalwa cells is inhibited by a proteasome inhibitor and thus seems to be driven by the same degradation machinery as the slower turnover in non-B cells. Furthermore, we investigated the processes involved in persistent activation of NF-kappa B. TNF-alpha signaling leads to a rapid depletion of cellular I kappa B beta pools. I kappa B alpha is efficiently resynthesized whereas I kappa B beta levels stay low for a prolonged time. NF-kappa B binding activity can be detected for several hours after stimulation. We found that removal of the TNF-alpha containing medium causes a rapid decrease in nuclear NF-kappa B. A phosphoform of newly synthesized I kappa B alpha is visible when degradation by the proteasome is inhibited and new I kappa B alpha displays the same properties regarding phosphorylation and degradation in response to a second inducer. There is no significant difference in the turnover of pre- and post-inductive I kappa B alpha. These observations suggest that resynthesis of I kappa B alpha and removal of the stimulus are obligatory steps for the inactivation of nuclear NF kappa B. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "resynthesized", "start": 1351, "end": 1364}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1320, "end": 1335}]}, {"trigger": {"text": "levels stay low", "start": 1388, "end": 1403}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 1373, "end": 1387}]}, {"trigger": {"text": "synthesized", "start": 1634, "end": 1645}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1646, "end": 1661}]}, {"trigger": {"text": "resynthesis", "start": 1976, "end": 1987}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1991, "end": 2006}]}], "negative regulation": [{"trigger": {"text": "depletion", "start": 1276, "end": 1285}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 1298, "end": 1312}]}, {"trigger": {"text": "removal", "start": 1521, "end": 1528}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1536, "end": 1545}]}, {"trigger": {"text": "inhibited", "start": 1711, "end": 1720}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1678, "end": 1689}]}], "phosphorylation": [{"trigger": {"text": "phosphoform", "start": 1613, "end": 1624}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1646, "end": 1661}]}, {"trigger": {"text": "phosphorylation", "start": 1784, "end": 1799}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1729, "end": 1744}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 810, "end": 819}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 709, "end": 723}]}, {"trigger": {"text": "increased", "start": 810, "end": 819}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 757, "end": 772}]}, {"trigger": {"text": "leads", "start": 1259, "end": 1264}, "arguments": [{"role": "Theme", "text": "depletion", "start": 1276, "end": 1285}]}, {"trigger": {"text": "when", "start": 1673, "end": 1677}, "arguments": [{"role": "Theme", "text": "phosphoform", "start": 1613, "end": 1624}, {"role": "Cause", "text": "inhibited", "start": 1711, "end": 1720}]}, {"trigger": {"text": "by", "start": 1690, "end": 1692}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1678, "end": 1689}]}, {"trigger": {"text": "in response to", "start": 1816, "end": 1830}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1784, "end": 1799}]}, {"trigger": {"text": "in response to", "start": 1816, "end": 1830}, "arguments": [{"role": "Theme", "text": "degradation", "start": 1804, "end": 1815}]}], "protein catabolism": [{"trigger": {"text": "stability", "start": 72, "end": 81}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 37, "end": 52}]}, {"trigger": {"text": "stability", "start": 72, "end": 81}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 57, "end": 71}]}, {"trigger": {"text": "degradation", "start": 1678, "end": 1689}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1646, "end": 1661}]}, {"trigger": {"text": "degradation", "start": 1804, "end": 1815}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 1729, "end": 1744}]}]}}, "schema": []}
{"input": "Control of NF-kappa B activity by the I kappa B beta inhibitor. \nThe transcription factor NF-kappa B is maintained in an inactive cytoplasmic state by I kappa B inhibitors. In mammalian cells, I kappa B alpha and I kappa B beta proteins have been purified and shown to be the inhibitors of NF-kappa B through their association with the p65 or c-Rel subunits. In addition, we have isolated a third NF-kappa B inhibitor, I kappa B epsilon (1). Upon treatment with a large variety of inducers, I kappa B alpha, I kappa B beta are proteolytically degraded, resulting in NF-kappa B translocation into the nucleus. Here we show that in E29.1 T cell hybridoma I kappa B alpha and I kappa B beta are equally associated with p65 and that I kappa B beta is degraded in response to TNF alpha in contrast to what has been originally published. Our data also suggest that, unlike I kappa B alpha, I kappa B beta is constitutively phosphorylated and resynthesized as a hypophosphorylated form. The absence of slow migrating forms of I kappa B beta following stimulation suggests that the phosphorylation does not necessarily constitute the signal-induced event which targets the molecule for proteolysis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "association", "start": 315, "end": 326}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 193, "end": 208}, {"role": "Theme2", "text": "p65", "start": 336, "end": 339}]}, {"trigger": {"text": "association", "start": 315, "end": 326}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 213, "end": 227}, {"role": "Theme2", "text": "p65", "start": 336, "end": 339}]}, {"trigger": {"text": "association", "start": 315, "end": 326}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 193, "end": 208}, {"role": "Theme2", "text": "c-Rel", "start": 343, "end": 348}]}, {"trigger": {"text": "association", "start": 315, "end": 326}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 213, "end": 227}, {"role": "Theme2", "text": "c-Rel", "start": 343, "end": 348}]}, {"trigger": {"text": "associated", "start": 700, "end": 710}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 653, "end": 668}, {"role": "Theme2", "text": "p65", "start": 716, "end": 719}]}, {"trigger": {"text": "associated", "start": 700, "end": 710}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 673, "end": 687}, {"role": "Theme2", "text": "p65", "start": 716, "end": 719}]}], "localization": [{"trigger": {"text": "slow migrating forms", "start": 995, "end": 1015}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 1019, "end": 1033}]}], "negative regulation": [{"trigger": {"text": "absence", "start": 984, "end": 991}, "arguments": [{"role": "Theme", "text": "slow migrating forms", "start": 995, "end": 1015}]}], "phosphorylation": [{"trigger": {"text": "phosphorylated", "start": 917, "end": 931}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 867, "end": 882}]}, {"trigger": {"text": "phosphorylated", "start": 917, "end": 931}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 884, "end": 898}]}, {"trigger": {"text": "phosphorylation", "start": 1074, "end": 1089}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 1019, "end": 1033}]}], "positive regulation": [{"trigger": {"text": "in response to", "start": 756, "end": 770}, "arguments": [{"role": "Theme", "text": "degraded", "start": 747, "end": 755}, {"role": "Cause", "text": "TNF alpha", "start": 771, "end": 780}]}, {"trigger": {"text": "targets", "start": 1153, "end": 1160}, "arguments": [{"role": "Theme", "text": "proteolysis", "start": 1178, "end": 1189}]}], "protein catabolism": [{"trigger": {"text": "proteolytically degraded", "start": 527, "end": 551}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 491, "end": 506}]}, {"trigger": {"text": "proteolytically degraded", "start": 527, "end": 551}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 508, "end": 522}]}, {"trigger": {"text": "degraded", "start": 747, "end": 755}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 729, "end": 743}]}, {"trigger": {"text": "proteolysis", "start": 1178, "end": 1189}, "arguments": [{"role": "Theme", "text": "I kappa B beta", "start": 1019, "end": 1033}]}]}}, "schema": []}
{"input": "NF-kappa B/Rel family members regulating the ICAM-1 promoter in monocytic THP-1 cells. \nA kappa B-site was identified in the promoter of the intercellular adhesion molecule-1 (ICAM-1) gene, which is involved in regulation of ICAM-1 expression by tumor necrosis factor alpha (TNF-alpha) and glucocorticoids. We now report on the transcription factors which bind and transactivate this enhancer sequence. In vitro, the ICAM-1 kappa B site appeared to bind RelA and c-Rel homodimers as well as heterodimers with NF-kappa B1, but weakly NF-kappa B1 homodimers. In addition, both RelA and c-Rel, but not NF-kappa B1, were shown to transactivate an ICAM-1 kappa B-reporter construct. In monocytic THP-1 cells TNF-alpha induced two nuclear complexes which in vitro bound to the ICAM-1 kappa B site. Using antibodies in an electrophoretic mobility supershift assay, one of these complexes was shown to contain NF-kappa B1 and RelA, and to bind with higher affinity to the consensus kappa B site in the HIV long terminal repeat. The second complex contained RelA, and exhibited higher affinity towards the ICAM-1 kappa B than to the HIV kappa B site. The glucocorticoid receptor was shown to repress activity of both the RelA homodimer and the NF-kappa B1/RelA heterodimer. We argue that in vivo RelA homodimers are likely to play a dominant role in TNF-alpha-induced ICAM-1 transcription in monocytic cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 449, "end": 453}, "arguments": [{"role": "Theme", "text": "RelA", "start": 454, "end": 458}]}, {"trigger": {"text": "bind", "start": 449, "end": 453}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 463, "end": 468}]}, {"trigger": {"text": "bind", "start": 449, "end": 453}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 509, "end": 520}]}, {"trigger": {"text": "bind", "start": 449, "end": 453}, "arguments": [{"role": "Theme", "text": "NF-kappa B1", "start": 533, "end": 544}]}], "gene expression": [{"trigger": {"text": "expression", "start": 232, "end": 242}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 225, "end": 231}]}], "negative regulation": [{"trigger": {"text": "repress", "start": 1183, "end": 1190}, "arguments": [{"role": "Cause", "text": "glucocorticoid receptor", "start": 1146, "end": 1169}, {"role": "Theme", "text": "RelA", "start": 1212, "end": 1216}]}, {"trigger": {"text": "repress", "start": 1183, "end": 1190}, "arguments": [{"role": "Cause", "text": "glucocorticoid receptor", "start": 1146, "end": 1169}, {"role": "Theme", "text": "NF-kappa B1", "start": 1235, "end": 1246}]}, {"trigger": {"text": "repress", "start": 1183, "end": 1190}, "arguments": [{"role": "Cause", "text": "glucocorticoid receptor", "start": 1146, "end": 1169}, {"role": "Theme", "text": "RelA", "start": 1247, "end": 1251}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1351, "end": 1358}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 1341, "end": 1350}, {"role": "Theme", "text": "transcription", "start": 1366, "end": 1379}]}], "regulation": [{"trigger": {"text": "regulating", "start": 30, "end": 40}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 45, "end": 51}, {"role": "Site", "text": "promoter", "start": 52, "end": 60}]}, {"trigger": {"text": "involved", "start": 199, "end": 207}, "arguments": [{"role": "CSite", "text": "kappa B-site", "start": 90, "end": 102}, {"role": "Cause", "text": "intercellular adhesion molecule-1", "start": 141, "end": 174}, {"role": "Theme", "text": "regulation", "start": 211, "end": 221}]}, {"trigger": {"text": "regulation", "start": 211, "end": 221}, "arguments": [{"role": "Theme", "text": "expression", "start": 232, "end": 242}, {"role": "Cause", "text": "TNF-alpha", "start": 275, "end": 284}]}, {"trigger": {"text": "regulation", "start": 211, "end": 221}, "arguments": [{"role": "Theme", "text": "expression", "start": 232, "end": 242}]}, {"trigger": {"text": "role", "start": 1333, "end": 1337}, "arguments": [{"role": "Cause", "text": "RelA", "start": 1287, "end": 1291}, {"role": "Theme", "text": "induced", "start": 1351, "end": 1358}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1366, "end": 1379}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1359, "end": 1365}]}]}}, "schema": []}
{"input": "LPS tolerance in monocytes/macrophages: three 3' cytosins are required in the DNA binding motif for detection of upregulated NF-kappa B p50 homodimers. \nWhen monocytes are stimulated with LPS (lipopolysaccharide) repeatedly then the initially high expression of the TNF (tumor necrosis factor) gene is only very low, i.e. the cells are tolerant to LPS. Tolerant cells still express the CD14 receptor and they can still be activated to mobilize NF-kappa B into nucleus. Analysis of the binding proteins employing the -605 motif of the human TNF promoter (GGGGCTGTCCC) revealed that in tolerant cells of the human monocytic cell line Mono Mac 6 there is a predominance of p50p50 of NF-kappa B. We now show that a mutant motif that exchanges the terminal 3' C for a G fails to bind the p50 homodimer that is upregulated in LPS toler ant human Mono Mac 6 cells. The same is true for nuclear extracts taken from the murine P388D1 macrophage cell line when tested with the -516 motif of the murine TNF promoter (GGGGGCTTTCCC). Here the wild type motif gives efficient binding of p50p50 that again is upregulated in tolerant cells whereas a mutant with a 3' G shows hardly any binding of p50p50. Conversely, the murine kappa light chain enhancer motif (GGGGACTTTCCG) does not efficiently bind the nuclear p50p50 from tolerant murine P388 macrophages. Binding is, however, readily detected when the 3' G is replaced by a C. These data show that the detection of upregulated p50 homodimers in LPS tolerant cells is dependent on subtle differences in the sequence of the DNA binding motif. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 485, "end": 492}, "arguments": [{"role": "Theme", "text": "p50", "start": 670, "end": 673}]}, {"trigger": {"text": "binding", "start": 485, "end": 492}, "arguments": [{"role": "Theme", "text": "p50", "start": 673, "end": 676}]}, {"trigger": {"text": "bind", "start": 774, "end": 778}, "arguments": [{"role": "Theme", "text": "p50", "start": 783, "end": 786}]}, {"trigger": {"text": "is true", "start": 867, "end": 874}, "arguments": [{"role": "Theme", "text": "p50", "start": 783, "end": 786}]}, {"trigger": {"text": "binding", "start": 1062, "end": 1069}, "arguments": [{"role": "Theme", "text": "p50", "start": 1073, "end": 1076}]}, {"trigger": {"text": "binding", "start": 1062, "end": 1069}, "arguments": [{"role": "Theme", "text": "p50", "start": 1076, "end": 1079}]}, {"trigger": {"text": "binding", "start": 1170, "end": 1177}, "arguments": [{"role": "Theme", "text": "p50", "start": 1181, "end": 1184}]}, {"trigger": {"text": "binding", "start": 1170, "end": 1177}, "arguments": [{"role": "Theme", "text": "p50", "start": 1184, "end": 1187}]}, {"trigger": {"text": "bind", "start": 1281, "end": 1285}, "arguments": [{"role": "Theme", "text": "kappa light chain", "start": 1212, "end": 1229}, {"role": "Site", "text": "GGGGACTTTCCG", "start": 1246, "end": 1258}, {"role": "Theme2", "text": "p50", "start": 1298, "end": 1301}]}, {"trigger": {"text": "bind", "start": 1281, "end": 1285}, "arguments": [{"role": "Theme", "text": "kappa light chain", "start": 1212, "end": 1229}, {"role": "Site", "text": "GGGGACTTTCCG", "start": 1246, "end": 1258}, {"role": "Theme2", "text": "p50", "start": 1301, "end": 1304}]}], "gene expression": [{"trigger": {"text": "expression", "start": 248, "end": 258}, "arguments": [{"role": "Theme", "text": "TNF", "start": 266, "end": 269}]}, {"trigger": {"text": "express", "start": 374, "end": 381}, "arguments": [{"role": "Theme", "text": "CD14 receptor", "start": 386, "end": 399}]}], "negative regulation": [{"trigger": {"text": "low", "start": 312, "end": 315}, "arguments": [{"role": "Theme", "text": "expression", "start": 248, "end": 258}]}, {"trigger": {"text": "detected", "start": 1373, "end": 1381}, "arguments": [{"role": "Theme", "text": "bind", "start": 1281, "end": 1285}]}], "positive regulation": [{"trigger": {"text": "upregulated", "start": 113, "end": 124}, "arguments": [{"role": "Theme", "text": "p50", "start": 136, "end": 139}]}, {"trigger": {"text": "upregulated", "start": 805, "end": 816}, "arguments": [{"role": "Theme", "text": "p50", "start": 783, "end": 786}]}, {"trigger": {"text": "upregulated", "start": 1094, "end": 1105}, "arguments": [{"role": "Theme", "text": "p50", "start": 1073, "end": 1076}]}, {"trigger": {"text": "upregulated", "start": 1094, "end": 1105}, "arguments": [{"role": "Theme", "text": "p50", "start": 1076, "end": 1079}]}, {"trigger": {"text": "upregulated", "start": 1454, "end": 1465}, "arguments": [{"role": "Theme", "text": "p50", "start": 1466, "end": 1469}]}], "regulation": [{"trigger": {"text": "dependent", "start": 1506, "end": 1515}, "arguments": [{"role": "Theme", "text": "upregulated", "start": 1454, "end": 1465}]}]}}, "schema": []}
{"input": "Temporal control of IgH gene expression in developing B cells by the 3' locus control region. \nThe suggested roles of the downstream 3' regions acting as a Locus Control Region (LCR), have allowed comparisons to be made between the regulation of the IgH locus with other model systems whose gene expression is governed by LCR activity. Here we summarize the importance of the IgH 3'LCR and its putative functional role in IgH gene expression and compare it with the 5'LCR regulatory region of the human beta-globin locus. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 29, "end": 39}, "arguments": [{"role": "Theme", "text": "IgH", "start": 20, "end": 23}]}, {"trigger": {"text": "expression", "start": 431, "end": 441}, "arguments": [{"role": "Theme", "text": "IgH", "start": 422, "end": 425}]}], "regulation": [{"trigger": {"text": "control", "start": 9, "end": 16}, "arguments": [{"role": "Theme", "text": "expression", "start": 29, "end": 39}]}, {"trigger": {"text": "regulation", "start": 232, "end": 242}, "arguments": [{"role": "Theme", "text": "IgH", "start": 250, "end": 253}]}, {"trigger": {"text": "functional role", "start": 403, "end": 418}, "arguments": [{"role": "Theme", "text": "expression", "start": 431, "end": 441}]}]}}, "schema": []}
{"input": "Expression of transcription factor genes after influenza A virus infection. \nInfection of human monocytes with influenza A virus induces a broad range of proinflammatory cytokines and mononuclear cell attracting chemokines before the infected cells undergo apoptosis. The underlying mechanisms by which the corresponding genes are transcriptionally initiated after virus infection are still poorly understood. Activation of NF-kappa B seems to play an important role in the regulation of many proinflammatory cytokine genes, but cannot be the only mechanism, since several cytokine genes lack respective binding sites in their promoter regions. Therefore, we additionally investigated other transcription factors of possible importance such as CREB, CTF, OTF-1, and OTF-2. To explore long-term regulatory mechanisms, we investigated the induction of transcription factors on the gene expression level which may be important to substitute for metabolized transcription factor proteins after their activation. We identified a cell-type-specific differential response: CREB, CTF, OTF-1, OFT-2, and NF-kappa B genes were strongly induced 1 to 4 hours after influenza A virus infection in the monocytic cell line Mono Mac 6, while in freshly prepared human monocytes no significant changes were detected. In infected monocytes, which die by apoptosis, the expression of CREB, CTF, and OTF-2 was rather suppressed 8 hours after infection. In conclusion, the long-term regulation of transcription factor gene expression in non-proliferating cells seems to be of minor importance after influenza infection since in apoptosisprone cells an immediate availability of transcription factor proteins is required. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1351, "end": 1361}, "arguments": [{"role": "Theme", "text": "CTF", "start": 1371, "end": 1374}]}, {"trigger": {"text": "expression", "start": 1351, "end": 1361}, "arguments": [{"role": "Theme", "text": "OTF-2", "start": 1380, "end": 1385}]}], "negative regulation": [{"trigger": {"text": "suppressed", "start": 1397, "end": 1407}, "arguments": [{"role": "Theme", "text": "expression", "start": 1351, "end": 1361}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1126, "end": 1133}, "arguments": [{"role": "Theme", "text": "CTF", "start": 1072, "end": 1075}]}, {"trigger": {"text": "induced", "start": 1126, "end": 1133}, "arguments": [{"role": "Theme", "text": "OTF-1", "start": 1077, "end": 1082}]}, {"trigger": {"text": "induced", "start": 1126, "end": 1133}, "arguments": [{"role": "Theme", "text": "OFT-2", "start": 1084, "end": 1089}]}, {"trigger": {"text": "changes", "start": 1277, "end": 1284}, "arguments": [{"role": "Theme", "text": "CTF", "start": 1072, "end": 1075}]}, {"trigger": {"text": "changes", "start": 1277, "end": 1284}, "arguments": [{"role": "Theme", "text": "OTF-1", "start": 1077, "end": 1082}]}, {"trigger": {"text": "changes", "start": 1277, "end": 1284}, "arguments": [{"role": "Theme", "text": "OFT-2", "start": 1084, "end": 1089}]}], "regulation": [{"trigger": {"text": "importance", "start": 725, "end": 735}, "arguments": [{"role": "Theme", "text": "CTF", "start": 750, "end": 753}]}, {"trigger": {"text": "importance", "start": 725, "end": 735}, "arguments": [{"role": "Theme", "text": "OTF-1", "start": 755, "end": 760}]}, {"trigger": {"text": "importance", "start": 725, "end": 735}, "arguments": [{"role": "Theme", "text": "OTF-2", "start": 766, "end": 771}]}]}}, "schema": []}
{"input": "[Molecular-biologic aspects of interaction between nervous and immune systems] \nThe problem of the neuro-immuno interactions on the level of the protein trans-factors, stimulating interleukin-2 (IL-2) gene expression was discussed. The physico-chemical and functional parameters of the low molecular nuclear proteins (SP and BP- 14, 18, 19 kDs) isolated from splenic and brain cells of immunized rats were studied. The binding of these proteins to the regulatory region of IL-2 gene in vitro and stimulation of the IL-2mRNA synthesis in splenic T-lymphocytes culture in normal conditions were shown. The protective effect of SP and BP on the IL-2mRNA synthesis in stressful conditions and by the T-cells treatment with the CsA was demonstrated. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "gene expression", "start": 201, "end": 216}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 195, "end": 199}]}], "negative regulation": [{"trigger": {"text": "protective effect", "start": 604, "end": 621}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 651, "end": 660}]}], "positive regulation": [{"trigger": {"text": "stimulation", "start": 496, "end": 507}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 524, "end": 533}]}], "regulation": [{"trigger": {"text": "stimulating", "start": 168, "end": 179}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 201, "end": 216}]}], "transcription": [{"trigger": {"text": "synthesis", "start": 524, "end": 533}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 515, "end": 519}]}, {"trigger": {"text": "synthesis", "start": 651, "end": 660}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 642, "end": 646}]}]}}, "schema": []}
{"input": "Induction of interleukin-12 p40 transcript by CD40 ligation via activation of nuclear factor-kappaB. \nInterleukin-12 is produced in response to infection with bacteria or parasites or to bacterial constituents such as LPS in monocytes/macrophages and dendritic cells, and also generated by the interaction between activated T cells and antigen-presenting cells via CD40-CD40 ligand (CD40L). So far, transcriptional analyses of p40 have been carried out only using bacterial constituents such as LPS as stimuli. In the present study, we have characterized the transcriptional induction of p40 by CD40 ligation in a human B lymphoblastoid cell line, Daudi, and a human acute monocytic leukemia cell line, THP-1. These cells, stimulated by an agonistic monoclonal antibody against CD40 or by transfection with a CD40L expression vector, secreted p40 and showed enhanced p40 mRNA expression. Sequence analysis of the p40 promoter region identified two potential nuclear factor (NF)-kappaB binding sites conserved between mouse and human. Electrophoretic mobility shift assay revealed that the potential NF-kappaB binding sequence which is located around 120 bp upstream of the transcription initiation site in murine and human p40 genes formed an NF-kappaB complex with nuclear extract from Daudi cells stimulated by CD40 ligation. Moreover, transfection of Daudi cells with the polymerized NF-kappaB binding sequence ligated to a thymidine kinase/chloramphenicol acetyltransferase (CAT) reporter plasmid greatly induced CAT activity, but transfection with the polymerized mutated NF-kappaB binding sequence did not. These results suggest that the NF-kappaB binding site located around 120 bp upstream of the transcription initiation site in murine and human p40 promoter regions could be important for the p40 induction by CD40 ligation via activation of NF-kappaB. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "ligation", "start": 51, "end": 59}, "arguments": [{"role": "Theme", "text": "CD40", "start": 46, "end": 50}]}, {"trigger": {"text": "-", "start": 369, "end": 370}, "arguments": [{"role": "Theme", "text": "CD40", "start": 365, "end": 369}, {"role": "Theme2", "text": "CD40L", "start": 383, "end": 388}]}, {"trigger": {"text": "ligation", "start": 600, "end": 608}, "arguments": [{"role": "Theme", "text": "CD40", "start": 595, "end": 599}]}, {"trigger": {"text": "ligation", "start": 1318, "end": 1326}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1313, "end": 1317}]}, {"trigger": {"text": "ligation", "start": 1825, "end": 1833}, "arguments": [{"role": "Theme", "text": "CD40", "start": 1820, "end": 1824}]}], "localization": [{"trigger": {"text": "secreted", "start": 834, "end": 842}, "arguments": [{"role": "Theme", "text": "p40", "start": 843, "end": 846}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "transcript", "start": 32, "end": 42}]}, {"trigger": {"text": "as stimuli", "start": 499, "end": 509}, "arguments": [{"role": "Theme", "text": "transcriptional", "start": 399, "end": 414}]}, {"trigger": {"text": "transcriptional induction", "start": 559, "end": 584}, "arguments": [{"role": "Theme", "text": "p40", "start": 588, "end": 591}, {"role": "Cause", "text": "ligation", "start": 600, "end": 608}]}, {"trigger": {"text": "transcriptional induction", "start": 559, "end": 584}, "arguments": [{"role": "Theme", "text": "CD40", "start": 595, "end": 599}, {"role": "Cause", "text": "ligation", "start": 600, "end": 608}]}, {"trigger": {"text": "enhanced", "start": 858, "end": 866}, "arguments": [{"role": "Theme", "text": "expression", "start": 876, "end": 886}]}, {"trigger": {"text": "induced", "start": 1509, "end": 1516}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1517, "end": 1520}]}, {"trigger": {"text": "important", "start": 1785, "end": 1794}, "arguments": [{"role": "Theme", "text": "induction", "start": 1807, "end": 1816}]}, {"trigger": {"text": "induction", "start": 1807, "end": 1816}, "arguments": [{"role": "Theme", "text": "p40", "start": 1803, "end": 1806}]}], "transcription": [{"trigger": {"text": "transcript", "start": 32, "end": 42}, "arguments": [{"role": "Theme", "text": "p40", "start": 28, "end": 31}]}, {"trigger": {"text": "transcriptional", "start": 399, "end": 414}, "arguments": [{"role": "Theme", "text": "p40", "start": 427, "end": 430}]}, {"trigger": {"text": "expression", "start": 876, "end": 886}, "arguments": [{"role": "Theme", "text": "p40", "start": 867, "end": 870}]}]}}, "schema": []}
{"input": "Oxidants, transcription factors, and intestinal inflammation. \nIt is now well appreciated that chronic gut inflammation is characterized by enhanced production of reactive metabolites of oxygen and nitrogen. Some of these oxidants are known to modulate the expression of a variety of genes that are involved in the immune and inflammatory responses. For example, certain oxidants are known to activate the nuclear transcription factor kappa B, which regulates the expression of a variety of different adhesion molecules, cytokines, and enzymes. Oxidants are also known to activate another transcription factor, activator protein-1. This transcription factor is composed of products from the fos and jun proto-oncogene family and is believed to be important in regulating cell growth and proliferation. Finally, oxidants are believed to promote intestinal epithelial cell apoptosis, and the B-cell lymphoma/leukemia-2 gene product is believed to inhibit this phenomenon in an antioxidant-dependent manner. Taken together, these observations suggest that nontoxic concentrations of reactive metabolites of oxygen and nitrogen play an important role in regulating the expression of genes involved in the inflammatory response and in modulating apoptosis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "products", "start": 673, "end": 681}, "arguments": [{"role": "Theme", "text": "fos", "start": 691, "end": 694}]}, {"trigger": {"text": "products", "start": 673, "end": 681}, "arguments": [{"role": "Theme", "text": "jun", "start": 699, "end": 702}]}]}}, "schema": []}
{"input": "Differential induction of DNA-binding activities following CD19 cross-linking in human B lineage cells. \nThe B cell-specific cell surface molecule CD19 is expressed at all stages of B cell development, including normal plasma cells, and mediates signal transduction via interaction with cytoplasmic effector proteins. Cross-linking CD19 on early human B lineage cells induces the formation of a CD19/Vav/phosphatidylinositol-3 kinase complex, tyrosine phosphorylation of CD19 and Vav, and activation of the Ras pathway. To further explore the ramifications of CD19 signaling, the current study examined whether phosphorylation of Elk-1, activation of activator protein-1 (AP-1), or activation of nuclear factor-kappaB (NF-kappaB) transcription factors occurred following CD19 cross-linking. The cells used were the BLIN-1 pre-B cell line expressing low levels of cell surface mu heavy chain associated with surrogate light chain and the 1E8 immature B cell line expressing cell surface mu/kappa. Lysates from CD19 cross-linked 1E8 cells induced robust phosphorylation of an Elk-1 fusion protein in vitro, whereas no phosphorylation of Elk-1 fusion protein occurred using lysates from CD19 cross-linked BLIN-1 cells. An electrophoretic mobility shift assay employing AP-1 and NF-kappaB consensus oligonucleotides was used to demonstrate that AP-1 -binding activity increased, while constitutive NF-kappaB-binding activity was not enhanced, following 2 h of CD19 cross-linking in 1E8 cells. Supershift experiments revealed that JunD and c-Fos proteins mediated anti-CD19 induced AP-1-binding activity in 1E8 cells. In contrast, CD19 cross-linking in BLIN-1 cells resulted in the induction of NF-kappaB, but had no apparent effect on AP-1-binding activity. These data suggest that CD19-mediated signal transduction activates different transcription factors at juxtaposed stages of B cell development that may culminate in the activation or suppression of distinct sets of genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 64, "end": 77}, "arguments": [{"role": "Theme", "text": "CD19", "start": 59, "end": 63}]}, {"trigger": {"text": "interaction", "start": 270, "end": 281}, "arguments": [{"role": "Theme", "text": "CD19", "start": 147, "end": 151}]}, {"trigger": {"text": "Cross-linking", "start": 318, "end": 331}, "arguments": [{"role": "Theme", "text": "CD19", "start": 332, "end": 336}]}, {"trigger": {"text": "complex", "start": 434, "end": 441}, "arguments": [{"role": "Theme", "text": "CD19", "start": 395, "end": 399}]}, {"trigger": {"text": "cross-linking", "start": 776, "end": 789}, "arguments": [{"role": "Theme", "text": "CD19", "start": 771, "end": 775}]}, {"trigger": {"text": "cross-linked", "start": 1014, "end": 1026}, "arguments": [{"role": "Theme", "text": "CD19", "start": 1009, "end": 1013}]}, {"trigger": {"text": "cross-linked", "start": 1189, "end": 1201}, "arguments": [{"role": "Theme", "text": "CD19", "start": 1184, "end": 1188}]}, {"trigger": {"text": "cross-linking", "start": 1461, "end": 1474}, "arguments": [{"role": "Theme", "text": "CD19", "start": 1456, "end": 1460}]}, {"trigger": {"text": "cross-linking", "start": 1631, "end": 1644}, "arguments": [{"role": "Theme", "text": "CD19", "start": 1626, "end": 1630}]}], "gene expression": [{"trigger": {"text": "expressed", "start": 155, "end": 164}, "arguments": [{"role": "Theme", "text": "CD19", "start": 147, "end": 151}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 452, "end": 467}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 443, "end": 451}, {"role": "Theme", "text": "CD19", "start": 471, "end": 475}]}, {"trigger": {"text": "phosphorylation", "start": 611, "end": 626}, "arguments": [{"role": "Theme", "text": "Elk-1", "start": 630, "end": 635}]}, {"trigger": {"text": "phosphorylation", "start": 1052, "end": 1067}, "arguments": [{"role": "Theme", "text": "Elk-1", "start": 1074, "end": 1079}]}, {"trigger": {"text": "phosphorylation", "start": 1116, "end": 1131}, "arguments": [{"role": "Theme", "text": "Elk-1", "start": 1135, "end": 1140}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 368, "end": 375}, "arguments": [{"role": "Cause", "text": "Cross-linking", "start": 318, "end": 331}, {"role": "Theme", "text": "complex", "start": 434, "end": 441}]}, {"trigger": {"text": "induces", "start": 368, "end": 375}, "arguments": [{"role": "Cause", "text": "Cross-linking", "start": 318, "end": 331}, {"role": "Theme", "text": "phosphorylation", "start": 452, "end": 467}]}, {"trigger": {"text": "following", "start": 761, "end": 770}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 611, "end": 626}, {"role": "Cause", "text": "cross-linking", "start": 776, "end": 789}]}, {"trigger": {"text": "induced", "start": 1037, "end": 1044}, "arguments": [{"role": "Cause", "text": "cross-linked", "start": 1014, "end": 1026}, {"role": "Theme", "text": "phosphorylation", "start": 1052, "end": 1067}]}, {"trigger": {"text": "occurred", "start": 1156, "end": 1164}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1116, "end": 1131}, {"role": "Cause", "text": "cross-linked", "start": 1189, "end": 1201}]}]}}, "schema": []}
{"input": "Human immunodeficiency virus type 1 long terminal repeat quasispecies differ in basal transcription and nuclear factor recruitment in human glial cells and lymphocytes. \nThe generation of genomic diversity during the course of infection has the potential to affect all aspects of HIV-1 replication, including expression of the proviral genome. To gain a better understanding of the impact of long terminal repeat (LTR) sequence diversity on LTR-directed gene expression in cells of the central nervous system (CNS) and immune system, we amplified and cloned LTRs from proviral DNA in HIV-1-infected peripheral blood. Sequence analysis of nineteen LTRs cloned from 2 adult and 3 pediatric patients revealed an average of 33 nucleotide changes (with respect to the sequence of the LAI LTR) within the 455-bp U3 region. Transient expression analyses in cells of neuroglial and lymphocytic origin demonstrated that some of these LTRs had activities which varied significantly from the LAI LTR in U-373 MG cells (an astrocytoma cell line) as well as in Jurkat cells (a CD4-positive lymphocyte cell line). While LTRs which demonstrated the highest activities in U-373 MG cells also yielded high activities in Jurkat cells, the LTRs were generally more active in Jurkat cells when compared to the LAI LTR. Differences in LTR sequence also resulted in differences in transcription factor recruitment to cis-acting sites within the U3 region of the LTR, as demonstrated by electrophoretic mobility shift assays. In particular, naturally occurring sequence variation impacted transcription factor binding to an activating transcription factor/cAMP response element binding (ATF/CREB) binding site (located between the LEF-1 and distal NF-kappaB transcription factor binding sites) that we identified in previous studies of the HIV-1 LTR. These findings suggest that LTR sequence changes can significantly affect basal LTR function and transcription factor recruitment, which may, in turn, alter the course of viral replication in cells of CNS and immune system origin. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Inhibition of nuclear factor kappaB activation attenuates apoptosis resistance in lymphoid cells. \nDeath-inducing ligands (DILs) such as tumor necrosis factor alpha (TNFalpha) or the cytotoxic drug doxorubicin have been shown to activate a nuclear factor kappaB (NFkappaB)-dependent program that may rescue cells from apoptosis induction. We demonstrate here that TRAIL (TNF-related apoptosis-inducing ligand), a recently identified DIL, also activates NFkappaB in lymphoid cell lines in a kinetic similar to TNFalpha. NFkappaB activity is independent from FADD, caspases, and apoptosis induction. To study the influence of NFkappaB activity on apoptosis mediated by TRAIL, CD95, TNFalpha, or doxorubicin, NFkappaB activation was inhibited using the proteasome inhibitor N-acetyl-L-leucinyl-L-leucinyl-L-norleucinal or transient overexpression of mutant IkappaBalpha. Sensitivity for induction of apoptosis was markedly increased by these treatments in apoptosis sensitive cell lines. Moreover, both in cell lines and in primary leukemia cells that are resistant towards induction of apoptosis by DILs and doxorubicin, antagonization of NFkappaB activity partially restored apoptosis sensitivity. These data suggest that inhibition of NFkappaB activation may provide a molecular approach to increase apoptosis sensitivity in anticancer treatment. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "overexpression", "start": 829, "end": 843}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 854, "end": 866}]}], "positive regulation": [{"trigger": {"text": "overexpression", "start": 829, "end": 843}, "arguments": [{"role": "Theme", "text": "overexpression", "start": 829, "end": 843}]}]}}, "schema": []}
{"input": "The human toll signaling pathway: divergence of nuclear factor kappaB and JNK/SAPK activation upstream of tumor necrosis factor receptor-associated factor 6 (TRAF6). \nThe human homologue of Drosophila Toll (hToll) is a recently cloned receptor of the interleukin 1 receptor (IL-1R) superfamily, and has been implicated in the activation of adaptive immunity. Signaling by hToll is shown to occur through sequential recruitment of the adapter molecule MyD88 and the IL-1R-associated kinase. Tumor necrosis factor receptor-activated factor 6 (TRAF6) and the nuclear factor kappaB (NF-kappaB)-inducing kinase (NIK) are both involved in subsequent steps of NF-kappaB activation. Conversely, a dominant negative version of TRAF6 failed to block hToll-induced activation of stress-activated protein kinase/c-Jun NH2-terminal kinases, thus suggesting an early divergence of the two pathways. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recruitment", "start": 415, "end": 426}, "arguments": [{"role": "Theme", "text": "MyD88", "start": 451, "end": 456}]}]}}, "schema": []}
{"input": "Coactivation by OCA-B: definition of critical regions and synergism with general cofactors. \nMolecular dissection of the B-cell-specific transcription coactivator OCA-B has revealed distinct regions important, respectively, for recruitment to immunoglobulin promoters through interaction with octamer-bound Oct-1 and for subsequent coactivator function. Further analysis of general coactivator requirements showed that selective removal of PC4 from the essential USA fraction severely impairs Oct-1 and OCA-B function in a cell-free system reconstituted with partially purified factors. Full activity can be restored by the combined action of recombinant PC4 and the PC4-depleted USA fraction, thus suggesting a joint requirement for PC4 and another, USA-derived component(s) for optimal function of Oct-1/OCA-B in the reconstituted system. Indeed, USA-derived PC2 was found to act synergistically with PC4 in reproducing the function of intact USA in the assay system. Consistent with the requirement for PC4 in the reconstituted system, OCA-B was found to interact directly with PC4. Surprisingly, however, removal of PC4 from the unfractionated nuclear extract has no detrimental effect on OCA-B/Oct-1-dependent transcription. These results lead to a general model for the synergistic function of activation domains in Oct-1 and OCA-B (mediated by the combined action of the multiple USA components) and, further, suggest a functional redundancy in general coactivators. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recruitment", "start": 228, "end": 239}, "arguments": [{"role": "Theme", "text": "OCA-B", "start": 163, "end": 168}]}, {"trigger": {"text": "interaction", "start": 276, "end": 287}, "arguments": [{"role": "Theme", "text": "OCA-B", "start": 163, "end": 168}, {"role": "Theme2", "text": "Oct-1", "start": 307, "end": 312}]}, {"trigger": {"text": "interact", "start": 1058, "end": 1066}, "arguments": [{"role": "Theme", "text": "OCA-B", "start": 1039, "end": 1044}, {"role": "Theme2", "text": "PC4", "start": 1081, "end": 1084}]}], "negative regulation": [{"trigger": {"text": "removal", "start": 429, "end": 436}, "arguments": [{"role": "Theme", "text": "PC4", "start": 440, "end": 443}]}, {"trigger": {"text": "impairs", "start": 485, "end": 492}, "arguments": [{"role": "Cause", "text": "removal", "start": 429, "end": 436}, {"role": "Theme", "text": "Oct-1", "start": 493, "end": 498}]}, {"trigger": {"text": "impairs", "start": 485, "end": 492}, "arguments": [{"role": "Cause", "text": "removal", "start": 429, "end": 436}, {"role": "Theme", "text": "OCA-B", "start": 503, "end": 508}]}, {"trigger": {"text": "depleted", "start": 671, "end": 679}, "arguments": [{"role": "Theme", "text": "PC4", "start": 667, "end": 670}]}, {"trigger": {"text": "removal", "start": 1109, "end": 1116}, "arguments": [{"role": "Theme", "text": "PC4", "start": 1120, "end": 1123}]}], "positive regulation": [{"trigger": {"text": "through", "start": 268, "end": 275}, "arguments": [{"role": "Theme", "text": "recruitment", "start": 228, "end": 239}, {"role": "Cause", "text": "interaction", "start": 276, "end": 287}]}, {"trigger": {"text": "restored", "start": 608, "end": 616}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 493, "end": 498}, {"role": "Cause", "text": "PC4", "start": 655, "end": 658}]}, {"trigger": {"text": "restored", "start": 608, "end": 616}, "arguments": [{"role": "Theme", "text": "OCA-B", "start": 503, "end": 508}, {"role": "Cause", "text": "PC4", "start": 655, "end": 658}]}, {"trigger": {"text": "restored", "start": 608, "end": 616}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 493, "end": 498}, {"role": "Cause", "text": "depleted", "start": 671, "end": 679}]}, {"trigger": {"text": "joint requirement", "start": 712, "end": 729}, "arguments": [{"role": "Cause", "text": "PC4", "start": 734, "end": 737}, {"role": "Theme", "text": "Oct-1", "start": 800, "end": 805}]}, {"trigger": {"text": "joint requirement", "start": 712, "end": 729}, "arguments": [{"role": "Cause", "text": "PC4", "start": 734, "end": 737}, {"role": "Theme", "text": "OCA-B", "start": 806, "end": 811}]}]}}, "schema": []}
{"input": "Limited proteolysis for assaying ligand binding affinities of nuclear receptors. \nThe binding of natural or synthetic ligands to nuclear receptors is the triggering event leading to gene transcription activation or repression. Ligand binding to the ligand binding domain of these receptors induces conformational changes that are evidenced by an increased resistance of this domain to proteases. In vitro labeled receptors were incubated with various synthetic or natural agonists or antagonists and submitted to trypsin digestion. Proteolysis products were separated by SDS-PAGE and quantified. The amount of trypsin-resistant fragments was proportional to receptor occupancy by the ligand, and allowed the determination of dissociation constants (kDa). Using the wild-type or mutated human retinoic acid receptor alpha as a model, kDa values determined by classical competition binding assays using tritiated ligands are in agreement with those measured by the proteolytic assay. This method was successfully extended to human retinoic X receptor alpha, glucocorticoid receptor, and progesterone receptor, thus providing a basis for a new, faster assay to determine simultaneously the affinity and conformation of receptors when bound to a given ligand. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Mycobacterium tuberculosis mannose-capped lipoarabinomannan can induce NF-kappaB-dependent activation of human immunodeficiency virus type 1 long terminal repeat in T cells. \nTuberculosis has emerged as an epidemic, extended by the large number of individuals infected with human immunodeficiency virus type 1 (HIV-1). The major goal of this study was to determine whether the mycobacterial cell wall component mannose-capped lipoarabinomannan (ManLAM) of Mycobacterium tuberculosis (M. tuberculosis) could activate transcription of HIV-1 in T cells with the use of an in vitro cell culture system. These experiments are of prime importance considering that CD4-expressing T lymphocytes represent the major virus reservoir in the peripheral blood of infected individuals. Using the 1G5 cell line harbouring the luciferase reporter gene under the control of the HIV-1 LTR, it was first found that culture protein filtrates (CFP) from M. tuberculosis or purified ManLAM could activate HIV-1 LTR-dependent gene expression unlike similarly prepared CFP extracts devoid of ManLAM. The implication of protein tyrosine kinase(s), protein kinase A and/or protein kinase C was highlighted by the abrogation of the ManLAM-mediated activation of HIV-1 LTR-driven gene expression using herbimycin A and H7. It was also determined, using electrophoresis mobility shift assays, that M. tuberculosis ManLAM led to the nuclear translocation of the transcription factor NF-kappaB. M. tuberculosis ManLAM resulted in clear induction of the luciferase gene placed under the control of the wild-type, but not the kappaB-mutated, HIV-1 LTR region. Finally, the ManLAM-mediated activation of HIV-1 LTR transcription was found to be independent of the autocrine or paracrine action of endogenous TNF-alpha. The results suggest that M. tuberculosis can upregulate HIV-1 expression in T cells and could thus have the potential to influence the pathogenesis of HIV-1 infection. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expressing", "start": 662, "end": 672}, "arguments": [{"role": "Theme", "text": "CD4", "start": 658, "end": 661}]}]}}, "schema": []}
{"input": "Oxidative stress suppresses transcription factor activities in stimulated lymphocytes. \nEffects of oxidative stress on stimulation-dependent signal transduction, leading to IL-2 expression, were studied. Purified quiescent human blood T lymphocytes were subjected to: (i) acute exposure to hydrogen peroxide; (ii) chronic exposure to hydrogen peroxide; and (iii) acute exposure to ionizing radiation. The cells were then stimulated for 6 h. DNA-binding activities (determined by the electrophoretic mobility shift assay) of three transcription factors: NFkappaB, AP-1 and NFAT, were abolished in the lymphocytes by all three modes of oxidative stress. The lymphocytes exhibited lipid peroxidation only upon exposure to the lowest level of hydrogen peroxide used (20 microM). All three modes of oxidative stress induced catalase activity in the lymphocytes. The only exception was hydrogen peroxide at 20 microM, which did not induce catalase activity. We conclude that: (i) suppression of specific transcription factor functions can potentially serve as a marker of exposure to oxidative stress and its effects on human lymphocytes; (ii) lipid peroxidation is only detectable in human lymphocytes upon exposure to weak oxidative stress which does not induce catalase activity; (iii) therefore, transcription factor DNA-binding activities are more sensitive to oxidative stress than lipid peroxidation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 178, "end": 188}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 173, "end": 177}]}], "positive regulation": [{"trigger": {"text": "leading", "start": 162, "end": 169}, "arguments": [{"role": "Theme", "text": "expression", "start": 178, "end": 188}]}]}}, "schema": []}
{"input": "Thrombopoietin supports in vitro erythroid differentiation via its specific receptor c-Mpl in a human leukemia cell line. \nThrombopoietin (TPO) acts on megakaryopoiesis and erythropoiesis in vitro and in vivo. We isolated a novel subline, UT-7/GMT, from the human leukemia cell line UT-7/GM (N. Komatsu, et al., Blood, 89: 4021-4033, 1997). A small population of UT-7/GM cells positively stained for hemoglobin (Hb) after a 7-day exposure to TPO. More than 50% of TPO-treated UT-7/GMT cells positively stained for Hb. Using UT-7/GMT cells, we examined how TPO promotes hemoglobinization. TPO induced tyrosine phosphorylation of the TPO receptor but not the erythropoietin (EPO) receptor. There was no competition between TPO and EPO for binding to EPO receptor. These findings suggest that TPO has a direct effect on hemoglobinization via a specific receptor on UT-7/GMT cells. Isoelectric focusing demonstrated that TPO induced fetal and adult Hb synthesis, whereas EPO induced embryonic, fetal, and adult Hb synthesis. Thus, our data suggest that TPO has a distinct action on erythropoiesis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "its specific receptor", "start": 63, "end": 84}, "arguments": [{"role": "Theme", "text": "Thrombopoietin", "start": 0, "end": 14}, {"role": "Theme2", "text": "c-Mpl", "start": 85, "end": 90}]}, {"trigger": {"text": "binding", "start": 737, "end": 744}, "arguments": [{"role": "Theme", "text": "TPO", "start": 721, "end": 724}, {"role": "Theme2", "text": "EPO receptor", "start": 748, "end": 760}]}, {"trigger": {"text": "binding", "start": 737, "end": 744}, "arguments": [{"role": "Theme", "text": "EPO", "start": 729, "end": 732}, {"role": "Theme2", "text": "EPO receptor", "start": 748, "end": 760}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 609, "end": 624}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 600, "end": 608}, {"role": "Theme", "text": "TPO receptor", "start": 632, "end": 644}]}, {"trigger": {"text": "phosphorylation", "start": 609, "end": 624}, "arguments": [{"role": "Site", "text": "tyrosine", "start": 600, "end": 608}, {"role": "Theme", "text": "erythropoietin (EPO) receptor", "start": 657, "end": 686}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 592, "end": 599}, "arguments": [{"role": "Cause", "text": "TPO", "start": 588, "end": 591}, {"role": "Theme", "text": "phosphorylation", "start": 609, "end": 624}]}]}}, "schema": []}
{"input": "Redox signals and NF-kappaB activation in T cells. \nAccumulating data from a number of laboratories have recently indicated that the response of transcription factor NF-kappaB to alterations in the redox homeostasis of cells may play an important role in modulating immune function. The activation of NF-kappaB has been recognized to regulate a number of genes necessary for normal T cell responses including IL-2, IL-6, IL-8, and several T cell surface receptors. Diminished NF-kappaB activity has been shown to occur in T cells with aging, suggesting that impaired activation of NF-kappaB might occur during cellular senescence. In addition, aberrancies in NF-kappaB activity have been implicated in the immunopathogenesis of diseases involving immune or inflammatory processes such as atherosclerosis and HIV-1 infection. The role of H2O2 and other reactive oxygen species (ROS) as an integratory secondary messenger for divergent T cell signals has been complicated by the fact that various T cell lines and peripheral blood T cells differ markedly in the levels of NF-kappaB activation induced by oxidant stress. Additionally, proposed pathways of NF-kappaB activation have been based on indirect evidence provided by experiments which used antioxidants to inhibit active NF-kappaB formation. Further, complete activation of T cells requires at least two signals, one that stimulates an increase in intracellular calcium and one that stimulates enzymatic processes including kinases. Similarly, substantial evidence indicates that full activation of NF-kappaB requires dual signals. The ability of H2O2 or other ROS to induce T cell signals and functional responses by these two mechanisms is reviewed and the specific response of NF-kappaB to redox changes in T cells is examined. Data are also presented to suggest that the redox regulation in NF-kappaB activation may be relevant to immune-related diseases and to aging. ", "output": {"json_structures": {"regulation": [{"trigger": {"text": "regulate", "start": 334, "end": 342}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 409, "end": 413}]}, {"trigger": {"text": "regulate", "start": 334, "end": 342}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 415, "end": 419}]}, {"trigger": {"text": "regulate", "start": 334, "end": 342}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 421, "end": 425}]}]}}, "schema": []}
{"input": "Fibrinogen activates NF-kappa B transcription factors in mononuclear phagocytes. \nAdhesion to extracellular matrices is known to modulate leukocyte activation, although the mechanisms are not fully understood. Mononuclear phagocytes are exposed to fibrinous provisional matrix throughout migration into inflammatory foci, so this study was undertaken to determine whether fibrinogen triggers activation of NF-kappa B transcription factors. U937 cells differentiated with PMA in nonadherent culture were shown to express two fibrinogen-binding integrins, predominately CD11b/CD18, and to a lesser extent, CD11c/CD18. Cells stimulated with fibrinogen (10-100 microg/ml)/Mn2+ (50 microM) for 2 h were examined by electrophoretic mobility shift assay. NF-kappa B activation, minimal in unstimulated cells, was substantially up-regulated by fibrinogen. Fibrinogen also caused activation of AP-1, but not SP1 or cAMP response element-binding protein (CREB) factors. Blocking mAbs against CD18 and CD11b abrogated fibrinogen-induced NF-kappa B activation. To determine the effects on transcriptional regulation, U937 cells were transfected with a plasmid containing the HIV-1 enhancer (bearing two NF-kappa B sites) coupled to a chloramphenicol acetyltransferase (CAT) reporter. Cells were subsequently stimulated with 1) PMA for 24 h, inducing CAT activity by 2.6-fold, 2) fibrinogen/Mn2+ for 2 h, inducing CAT activity by 3.2-fold, or 3) costimulation with fibrinogen and PMA, inducing 5.7-fold the CAT activity induced by PMA alone. We conclude that contact with fibrinogen-derived proteins may contribute to mononuclear phagocyte activation by signaling through CD11b/CD18, resulting in selective activation of transcriptional regulatory factors, including NF-kappa B. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Blocking", "start": 960, "end": 968}, "arguments": [{"role": "Theme", "text": "CD18", "start": 982, "end": 986}]}, {"trigger": {"text": "Blocking", "start": 960, "end": 968}, "arguments": [{"role": "Theme", "text": "CD11b", "start": 991, "end": 996}]}], "gene expression": [{"trigger": {"text": "express", "start": 512, "end": 519}, "arguments": [{"role": "Theme", "text": "CD11b", "start": 568, "end": 573}]}, {"trigger": {"text": "express", "start": 512, "end": 519}, "arguments": [{"role": "Theme", "text": "CD18", "start": 574, "end": 578}]}, {"trigger": {"text": "express", "start": 512, "end": 519}, "arguments": [{"role": "Theme", "text": "CD11c", "start": 604, "end": 609}]}, {"trigger": {"text": "express", "start": 512, "end": 519}, "arguments": [{"role": "Theme", "text": "CD18", "start": 610, "end": 614}]}], "positive regulation": [{"trigger": {"text": "caused", "start": 864, "end": 870}, "arguments": [{"role": "Theme", "text": "activation", "start": 871, "end": 881}]}, {"trigger": {"text": "activation", "start": 871, "end": 881}, "arguments": [{"role": "Theme", "text": "SP1", "start": 899, "end": 902}]}, {"trigger": {"text": "inducing", "start": 1329, "end": 1337}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1338, "end": 1341}]}, {"trigger": {"text": "inducing", "start": 1392, "end": 1400}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1401, "end": 1404}]}, {"trigger": {"text": "inducing", "start": 1472, "end": 1480}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1494, "end": 1497}]}, {"trigger": {"text": "induced", "start": 1507, "end": 1514}, "arguments": [{"role": "Theme", "text": "CAT", "start": 1494, "end": 1497}]}]}}, "schema": []}
{"input": "Ex vivo activation of tumor-draining lymph node T cells reverses defects in signal transduction molecules. \nThe adoptive transfer of tumor-draining lymph node (LN) T cells activated ex vivo with anti-CD3 and interleukin 2 (IL-2) mediates the regression of the poorly immunogenic murine melanoma D5. The efficacy of the activated LN cells is augmented when the sensitizing tumor is a genetically modified variant (designated D5G6) that secretes granulocyte/macrophage-colony-stimulating factor. In contrast to anti-CD3/IL-2-activated LN cells, adoptive transfer of freshly isolated tumor-draining LN T cells has no therapeutic activity. To determine whether the acquisition of antitumor function during ex vivo activation is associated with modifications in signal transduction capacity, the protein tyrosine kinases p56lck and p59fyn and proteins of the NF-kappaB family were analyzed in tumor-draining LN T cells. The levels of p56lck and p59fyn were lower in tumor-draining than in normal LN T cells and production of tyrosine-phosphorylated substrates was markedly depressed following anti-CD3 stimulation. After 5-day anti-CD3/IL-2 activation, levels of p56lck and p59fyn and protein tyrosine kinase activity increased. Interestingly, the levels of p56lck, p59fyn, and tyrosine kinase activity were higher in activated T cells derived from LN that drained D5G6 than they were in those from D5 tumors. In contrast, the cytoplasmic levels of c-Rel and Rel A were normal in freshly isolated tumor-draining LN, as was nuclear kappaB DNA-binding activity induced by anti-CD3 mAb or phorbol myristate acetate. Stimulation of activated LN cells with D5 tumor cells induced the nuclear translocation of NF-kappaB. These findings indicate that the recovery of proteins mediating signal transduction through the T cell receptor/CD3 complex in LN T cells activated ex vivo was associated with the acquisition of antitumor function. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "analyzed", "start": 876, "end": 884}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 816, "end": 822}]}, {"trigger": {"text": "analyzed", "start": 876, "end": 884}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 827, "end": 833}]}, {"trigger": {"text": "levels", "start": 919, "end": 925}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 929, "end": 935}]}, {"trigger": {"text": "levels", "start": 919, "end": 925}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 940, "end": 946}]}, {"trigger": {"text": "levels", "start": 1148, "end": 1154}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 1158, "end": 1164}]}, {"trigger": {"text": "levels", "start": 1148, "end": 1154}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 1169, "end": 1175}]}, {"trigger": {"text": "levels", "start": 1243, "end": 1249}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 1253, "end": 1259}]}, {"trigger": {"text": "levels", "start": 1243, "end": 1249}, "arguments": [{"role": "Theme", "text": "p59fyn", "start": 1261, "end": 1267}]}, {"trigger": {"text": "levels", "start": 1434, "end": 1440}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1444, "end": 1449}]}, {"trigger": {"text": "levels", "start": 1434, "end": 1440}, "arguments": [{"role": "Theme", "text": "Rel A", "start": 1454, "end": 1459}]}], "localization": [{"trigger": {"text": "secretes", "start": 435, "end": 443}, "arguments": [{"role": "Theme", "text": "granulocyte/macrophage-colony-stimulating factor", "start": 444, "end": 492}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 1213, "end": 1222}, "arguments": [{"role": "Theme", "text": "levels", "start": 1148, "end": 1154}]}, {"trigger": {"text": "higher", "start": 1303, "end": 1309}, "arguments": [{"role": "Theme", "text": "levels", "start": 1243, "end": 1249}]}]}}, "schema": []}
{"input": "Targeted disruption of the MyD88 gene results in loss of IL-1- and IL-18-mediated function. \nMyD88, originally isolated as a myeloid differentiation primary response gene, is shown to act as an adaptor in interleukin-1 (IL-1) signaling by interacting with both the IL-1 receptor complex and IL-1 receptor-associated kinase (IRAK). Mice generated by gene targeting to lack MyD88 have defects in T cell proliferation as well as induction of acute phase proteins and cytokines in response to IL-1. Increases in interferon-gamma production and natural killer cell activity in response to IL-18 are abrogated. In vivo Th1 response is also impaired. Furthermore, IL-18-induced activation of NF-kappaB and c-Jun N-terminal kinase (JNK) is blocked in MyD88-/- Th1-developing cells. Taken together, these results demonstrate that MyD88 is a critical component in the signaling cascade that is mediated by IL-1 receptor as well as IL-18 receptor. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interacting", "start": 239, "end": 250}, "arguments": [{"role": "Theme", "text": "MyD88", "start": 93, "end": 98}]}]}}, "schema": []}
{"input": "Epstein-Barr virus-transforming protein latent infection membrane protein 1 activates transcription factor NF-kappaB through a pathway that includes the NF-kappaB-inducing kinase and the IkappaB kinases IKKalpha and IKKbeta. \nThe Epstein-Barr virus oncoprotein latent infection membrane protein 1 (LMP1) is a constitutively aggregated pseudo-tumor necrosis factor receptor (TNFR) that activates transcription factor NF-kappaB through two sites in its C-terminal cytoplasmic domain. One site is similar to activated TNFRII in associating with TNFR-associated factors TRAF1 and TRAF2, and the second site is similar to TNFRI in associating with the TNFRI death domain interacting protein TRADD. TNFRI has been recently shown to activate NF-kappaB through association with TRADD, RIP, and TRAF2; activation of the NF-kappaB-inducing kinase (NIK); activation of the IkappaB alpha kinases (IKKalpha and IKKbeta); and phosphorylation of IkappaB alpha. IkappaB alpha phosphorylation on Ser-32 and Ser-36 is followed by its degradation and NF-kappaB activation. In this report, we show that NF-kappaB activation by LMP1 or by each of its effector sites is mediated by a pathway that includes NIK, IKKalpha, and IKKbeta. Dominant negative mutants of NIK, IKKalpha, or IKKbeta substantially inhibited NF-kappaB activation by LMP1 or by each of its effector sites. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "aggregated", "start": 324, "end": 334}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 298, "end": 302}]}, {"trigger": {"text": "associating", "start": 525, "end": 536}, "arguments": [{"role": "Theme", "text": "TRAF1", "start": 566, "end": 571}]}, {"trigger": {"text": "associating", "start": 525, "end": 536}, "arguments": [{"role": "Theme", "text": "TRAF2", "start": 576, "end": 581}]}, {"trigger": {"text": "associating", "start": 626, "end": 637}, "arguments": [{"role": "Theme", "text": "TNFRI", "start": 617, "end": 622}, {"role": "Theme2", "text": "TRADD", "start": 686, "end": 691}]}, {"trigger": {"text": "associating", "start": 626, "end": 637}, "arguments": [{"role": "Theme", "text": "TRADD", "start": 686, "end": 691}]}, {"trigger": {"text": "interacting", "start": 666, "end": 677}, "arguments": [{"role": "Theme", "text": "TNFRI", "start": 647, "end": 652}, {"role": "Site", "text": "death domain", "start": 653, "end": 665}, {"role": "Theme2", "text": "TRADD", "start": 686, "end": 691}]}, {"trigger": {"text": "association", "start": 753, "end": 764}, "arguments": [{"role": "Theme", "text": "TNFRI", "start": 693, "end": 698}, {"role": "Theme2", "text": "TRADD", "start": 770, "end": 775}]}, {"trigger": {"text": "association", "start": 753, "end": 764}, "arguments": [{"role": "Theme", "text": "TNFRI", "start": 693, "end": 698}, {"role": "Theme2", "text": "RIP", "start": 777, "end": 780}]}, {"trigger": {"text": "association", "start": 753, "end": 764}, "arguments": [{"role": "Theme", "text": "TNFRI", "start": 693, "end": 698}, {"role": "Theme2", "text": "TRAF2", "start": 786, "end": 791}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 912, "end": 927}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 931, "end": 944}]}, {"trigger": {"text": "phosphorylation", "start": 960, "end": 975}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 946, "end": 959}, {"role": "Site", "text": "Ser-32", "start": 979, "end": 985}]}, {"trigger": {"text": "phosphorylation", "start": 960, "end": 975}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 946, "end": 959}, {"role": "Site", "text": "Ser-36", "start": 990, "end": 996}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 505, "end": 514}, "arguments": [{"role": "Theme", "text": "TNFRII", "start": 515, "end": 521}]}, {"trigger": {"text": "activation", "start": 793, "end": 803}, "arguments": [{"role": "Theme", "text": "NIK", "start": 838, "end": 841}]}, {"trigger": {"text": "activation", "start": 844, "end": 854}, "arguments": [{"role": "Theme", "text": "IKKalpha", "start": 885, "end": 893}]}, {"trigger": {"text": "activation", "start": 844, "end": 854}, "arguments": [{"role": "Theme", "text": "IKKbeta", "start": 898, "end": 905}]}, {"trigger": {"text": "followed", "start": 1000, "end": 1008}, "arguments": [{"role": "Cause", "text": "phosphorylation", "start": 960, "end": 975}, {"role": "Theme", "text": "degradation", "start": 1016, "end": 1027}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 1016, "end": 1027}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 946, "end": 959}]}]}}, "schema": []}
{"input": "Dimethyldithiocarbamate inhibits in vitro activation of primary human CD4+ T lymphocytes. \nDithiocarbamates (DTC), a diverse group of industrial and therapeutic chemicals, have been reported to inhibit, enhance or have no effect on the immune system. These apparent inconsistencies reflect the complexity of the DTCs biological activities and are probably due in part to differences in dose, route of exposure, animal species used and/or specific compound tested. The studies described herein were undertaken to investigate the immunotoxicity of one member of this family, dimethyldithiocarbamate (DMDTC). We demonstrate that 0.1-0.5 microM DMDTC inhibits TNF-alpha-induced activation of NF-kappaB in primary human CD4+ T cells. This inhibition is not accompanied by a loss in viability, and DMDTC-treated T cells retain other active signaling pathways throughout the exposure duration. The inhibition of NF-kappaB is apparently permanent as DMDTC-treated T cells did not regain normal TNF-alpha activation, even after 72 h in culture. DMDTC does not appear to alter NF-kappaB directly as pre-incubation of nuclear extracts with DMDTC does not diminish binding activity of this protein. We further demonstrate that 0.1-0.5 microM DMDTC inhibits intracellular IL-2 production and decreases surface expression of CD25 (the alpha subunit of the IL-2 receptor) in T cells stimulated with phorbol ester. These data demonstrate that DMDTC is a potent immunosuppressive compound in vitro. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 1264, "end": 1274}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1259, "end": 1263}]}, {"trigger": {"text": "expression", "start": 1297, "end": 1307}, "arguments": [{"role": "Theme", "text": "CD25", "start": 1311, "end": 1315}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 1236, "end": 1244}, "arguments": [{"role": "Theme", "text": "production", "start": 1264, "end": 1274}]}, {"trigger": {"text": "decreases", "start": 1279, "end": 1288}, "arguments": [{"role": "Theme", "text": "expression", "start": 1297, "end": 1307}]}], "positive regulation": [{"trigger": {"text": "regain", "start": 972, "end": 978}, "arguments": [{"role": "Theme", "text": "activation", "start": 996, "end": 1006}]}, {"trigger": {"text": "activation", "start": 996, "end": 1006}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 986, "end": 995}]}]}}, "schema": []}
{"input": "The small GTP-binding protein Rho potentiates AP-1 transcription in T cells. \nThe Rho family of small GTP-binding proteins is involved in the regulation of cytoskeletal structure, gene transcription, specific cell fate development, and transformation. We demonstrate in this report that overexpression of an activated form of Rho enhances AP-1 activity in Jurkat T cells in the presence of phorbol myristate acetate (PMA), but activated Rho (V14Rho) has little or no effect on NFAT, Oct-1, and NF-kappaB enhancer element activities under similar conditions. Overexpression of a V14Rho construct incapable of membrane localization (CAAX deleted) abolishes PMA-induced AP-1 transcriptional activation. The effect of Rho on AP-1 is independent of the mitogen-activated protein kinase pathway, as a dominant-negative MEK and a MEK inhibitor (PD98059) did not affect Rho-induced AP-1 activity. V14Rho binds strongly to protein kinase Calpha (PKCalpha) in vivo; however, deletion of the CAAX site on V14Rho severely diminished this association. Evidence for a role for PKCalpha as an effector of Rho was obtained by the observation that coexpression of the N-terminal domain of PKCalpha blocked the effects of activated Rho plus PMA on AP-1 transcriptional activity. These data suggest that Rho potentiates AP-1 transcription during T-cell activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 896, "end": 901}, "arguments": [{"role": "Theme", "text": "PKCalpha", "start": 937, "end": 945}]}], "gene expression": [{"trigger": {"text": "coexpression", "start": 1131, "end": 1143}, "arguments": [{"role": "Theme", "text": "PKCalpha", "start": 1172, "end": 1180}]}], "negative regulation": [{"trigger": {"text": "diminished", "start": 1010, "end": 1020}, "arguments": [{"role": "Theme", "text": "binds", "start": 896, "end": 901}]}], "regulation": [{"trigger": {"text": "effect", "start": 467, "end": 473}, "arguments": [{"role": "Theme", "text": "Oct-1", "start": 483, "end": 488}]}]}}, "schema": []}
{"input": "Human T-cell leukemia virus type 1 Tax induction of NF-kappaB involves activation of the IkappaB kinase alpha (IKKalpha) and IKKbeta cellular kinases. \nTax corresponds to a 40-kDa transforming protein from the pathogenic retrovirus human T-cell leukemia virus type 1 (HTLV-1) that activates nuclear expression of the NF-kappaB/Rel family of transcription factors by an unknown mechanism. Tax expression promotes N-terminal phosphorylation and degradation of IkappaB alpha, a principal cytoplasmic inhibitor of NF-kappaB. Our studies now demonstrate that HTLV-1 Tax activates the recently identified cellular kinases IkappaB kinase alpha (IKKalpha) and IKKbeta, which normally phosphorylate IkappaB alpha on both of its N-terminal regulatory serines in response to tumor necrosis factor alpha (TNF-alpha) and interleukin-1 (IL-1) stimulation. In contrast, a mutant of Tax termed M22, which does not induce NF-kappaB, fails to activate either IKKalpha or IKKbeta. Furthermore, endogenous IKK enzymatic activity was significantly elevated in HTLV-1-infected and Tax-expressing T-cell lines. Transfection of kinase-deficient mutants of IKKalpha and IKKbeta into either human Jurkat T or 293 cells also inhibits NF-kappaB-dependent reporter gene expression induced by Tax. Similarly, a kinase-deficient mutant of NIK (NF-kappaB-inducing kinase), which represents an upstream kinase in the TNF-alpha and IL-1 signaling pathways leading to IKKalpha and IKKbeta activation, blocks Tax induction of NF-kappaB. However, plasma membrane-proximal elements in these proinflammatory cytokine pathways are apparently not involved since dominant negative mutants of the TRAF2 and TRAF6 adaptors, which effectively block signaling through the cytoplasmic tails of the TNF-alpha and IL-1 receptors, respectively, do not inhibit Tax induction of NF-kappaB. Together, these studies demonstrate that HTLV-1 Tax exploits a distal part of the proinflammatory cytokine signaling cascade leading to induction of NF-kappaB. The pathological alteration of this cytokine pathway leading to NF-kappaB activation by Tax may play a central role in HTLV-1-mediated transformation of human T cells, clinically manifested as the adult T-cell leukemia. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 392, "end": 402}, "arguments": [{"role": "Theme", "text": "Tax", "start": 388, "end": 391}]}, {"trigger": {"text": "expressing", "start": 1063, "end": 1073}, "arguments": [{"role": "Theme", "text": "Tax", "start": 1059, "end": 1062}]}, {"trigger": {"text": "Transfection", "start": 1088, "end": 1100}, "arguments": [{"role": "Theme", "text": "IKKalpha", "start": 1132, "end": 1140}]}, {"trigger": {"text": "Transfection", "start": 1088, "end": 1100}, "arguments": [{"role": "Theme", "text": "IKKbeta", "start": 1145, "end": 1152}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 423, "end": 438}, "arguments": [{"role": "Site", "text": "N-terminal", "start": 412, "end": 422}, {"role": "Theme", "text": "IkappaB alpha", "start": 458, "end": 471}]}, {"trigger": {"text": "phosphorylate", "start": 676, "end": 689}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 690, "end": 703}, {"role": "Site", "text": "N-terminal regulatory serines", "start": 719, "end": 748}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 71, "end": 81}, "arguments": [{"role": "Theme", "text": "IKKalpha", "start": 111, "end": 119}]}, {"trigger": {"text": "activation", "start": 71, "end": 81}, "arguments": [{"role": "Theme", "text": "IKKbeta", "start": 125, "end": 132}]}, {"trigger": {"text": "promotes", "start": 403, "end": 411}, "arguments": [{"role": "Cause", "text": "expression", "start": 392, "end": 402}, {"role": "Theme", "text": "phosphorylation", "start": 423, "end": 438}]}, {"trigger": {"text": "promotes", "start": 403, "end": 411}, "arguments": [{"role": "Cause", "text": "expression", "start": 392, "end": 402}, {"role": "Theme", "text": "degradation", "start": 443, "end": 454}]}, {"trigger": {"text": "activates", "start": 565, "end": 574}, "arguments": [{"role": "Cause", "text": "Tax", "start": 561, "end": 564}, {"role": "Theme", "text": "IKKalpha", "start": 638, "end": 646}]}, {"trigger": {"text": "activates", "start": 565, "end": 574}, "arguments": [{"role": "Cause", "text": "Tax", "start": 561, "end": 564}, {"role": "Theme", "text": "IKKbeta", "start": 652, "end": 659}]}, {"trigger": {"text": "phosphorylate", "start": 676, "end": 689}, "arguments": [{"role": "Cause", "text": "IKKalpha", "start": 638, "end": 646}, {"role": "Theme", "text": "phosphorylate", "start": 676, "end": 689}]}, {"trigger": {"text": "response", "start": 752, "end": 760}, "arguments": [{"role": "Theme", "text": "phosphorylate", "start": 676, "end": 689}]}, {"trigger": {"text": "activate", "start": 925, "end": 933}, "arguments": [{"role": "Cause", "text": "Tax", "start": 867, "end": 870}, {"role": "Theme", "text": "IKKalpha", "start": 941, "end": 949}]}, {"trigger": {"text": "activate", "start": 925, "end": 933}, "arguments": [{"role": "Cause", "text": "Tax", "start": 867, "end": 870}, {"role": "Theme", "text": "IKKbeta", "start": 953, "end": 960}]}, {"trigger": {"text": "Transfection", "start": 1088, "end": 1100}, "arguments": [{"role": "Theme", "text": "Transfection", "start": 1088, "end": 1100}]}, {"trigger": {"text": "leading", "start": 1422, "end": 1429}, "arguments": [{"role": "Theme", "text": "activation", "start": 1454, "end": 1464}]}, {"trigger": {"text": "activation", "start": 1454, "end": 1464}, "arguments": [{"role": "Theme", "text": "IKKalpha", "start": 1433, "end": 1441}]}, {"trigger": {"text": "activation", "start": 1454, "end": 1464}, "arguments": [{"role": "Theme", "text": "IKKbeta", "start": 1446, "end": 1453}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 443, "end": 454}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 458, "end": 471}]}]}}, "schema": []}
{"input": "A CD28-associated signaling pathway leading to cytokine gene transcription and T cell proliferation without TCR engagement. \nStimulation of resting human T cells with the CD28-specific mAb BW 828 induces proliferation and cytokine synthesis without further requirement for TCR coengagement. This observation prompted us to postulate that signal 2 (costimulatory signal) alone without signal 1 (TCR signal) can activate T cells. To test whether this putative function of CD28 is mediated via a particular signaling pathway, we compared early signaling events initiated in resting T cells by the stimulatory mAb BW 828 with signals triggered by the nonstimulating CD28 mAb 9.3. Stimulation of T cells with BW 828 induced an increase in intracellular Ca2+, but did not lead to detectable activation of the protein kinases p56(lck) and c-Raf-1. This pathway resulted in the induction of the transcription factors NF-kappa B, NF-AT, and proteins binding to the CD28 response element of the IL-2 promoter. On the other hand, stimulation of T cells with mAb 9.3 increased the level of intracellular Ca2+ and triggered the activation of p56(lck) and c-Raf-1, but was unable to induce the binding of transcription factors to the IL-2 promoter. In contrast to the differential signaling of BW 828 and 9.3 in resting T cells, the two mAbs exhibited a similar pattern of early signaling events in activated T cells and Jurkat cells (p56(lck) activation, association of phosphatidylinositol 3-kinase with CD28), indicating that the signaling capacity of CD28 changes with activation. These data support the view that stimulation through CD28 can induce some effector functions in T cells and suggest that this capacity is associated with a particular pattern of early signaling events. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1180, "end": 1187}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1220, "end": 1224}, {"role": "Site", "text": "promoter", "start": 1225, "end": 1233}]}], "positive regulation": [{"trigger": {"text": "mediated", "start": 478, "end": 486}, "arguments": [{"role": "Theme", "text": "CD28", "start": 470, "end": 474}]}, {"trigger": {"text": "not lead to detectable activation", "start": 762, "end": 795}, "arguments": [{"role": "Theme", "text": "p56(lck)", "start": 819, "end": 827}]}, {"trigger": {"text": "not lead to detectable activation", "start": 762, "end": 795}, "arguments": [{"role": "Theme", "text": "c-Raf-1", "start": 832, "end": 839}]}, {"trigger": {"text": "triggered the activation", "start": 1101, "end": 1125}, "arguments": [{"role": "Theme", "text": "p56(lck)", "start": 1129, "end": 1137}]}, {"trigger": {"text": "triggered the activation", "start": 1101, "end": 1125}, "arguments": [{"role": "Theme", "text": "c-Raf-1", "start": 1142, "end": 1149}]}, {"trigger": {"text": "unable to induce", "start": 1159, "end": 1175}, "arguments": [{"role": "Theme", "text": "binding", "start": 1180, "end": 1187}]}, {"trigger": {"text": "exhibited", "start": 1328, "end": 1337}, "arguments": [{"role": "Cause", "text": "BW 828", "start": 1280, "end": 1286}, {"role": "Theme", "text": "activation", "start": 1430, "end": 1440}]}, {"trigger": {"text": "exhibited", "start": 1328, "end": 1337}, "arguments": [{"role": "Cause", "text": "9.3", "start": 1291, "end": 1294}, {"role": "Theme", "text": "activation", "start": 1430, "end": 1440}]}, {"trigger": {"text": "activation", "start": 1430, "end": 1440}, "arguments": [{"role": "Theme", "text": "p56(lck)", "start": 1421, "end": 1429}]}, {"trigger": {"text": "stimulation", "start": 1604, "end": 1615}, "arguments": [{"role": "Theme", "text": "CD28", "start": 1624, "end": 1628}]}]}}, "schema": []}
{"input": "Cyclosporin A-resistant transactivation of the IL-2 promoter requires activity of okadaic acid-sensitive serine/threonine phosphatases. \nExpression of the IL-2 gene requires activation of T cells through stimulation of the TCR and costimulation through accessory receptors. We have found recently that okadaic acid-sensitive Ser/Thr phosphatases are involved in a cyclosporin A-insensitive pathway that selectively transmits costimulatory signals. In this study, we analyzed whether activities of these phosphatases are necessary for the expression of the IL-2 gene. In both activated peripheral blood T lymphocytes and activated tumorigenic T cell lines, IL-2 gene expression was blocked at the transcriptional level by okadaic acid. The transcription factors active at the IL-2 promoter were differentially influenced: upon down-modulation of okadaic acid-sensitive phosphatases, transactivation by octamer, NF-kappa B, and NF of activated T cells proteins was abrogated, while transactivation by AP-1 proteins was even enhanced. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "at", "start": 768, "end": 770}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 775, "end": 779}, {"role": "Site", "text": "promoter", "start": 780, "end": 788}]}], "gene expression": [{"trigger": {"text": "Expression", "start": 137, "end": 147}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 155, "end": 159}]}, {"trigger": {"text": "expression", "start": 538, "end": 548}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 556, "end": 560}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 681, "end": 688}, "arguments": [{"role": "Theme", "text": "at the transcriptional level", "start": 689, "end": 717}]}, {"trigger": {"text": "abrogated", "start": 963, "end": 972}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 882, "end": 897}]}], "positive regulation": [{"trigger": {"text": "transactivation", "start": 24, "end": 39}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 47, "end": 51}, {"role": "Site", "text": "promoter", "start": 52, "end": 60}]}, {"trigger": {"text": "requires", "start": 61, "end": 69}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 24, "end": 39}]}, {"trigger": {"text": "requires", "start": 165, "end": 173}, "arguments": [{"role": "Theme", "text": "Expression", "start": 137, "end": 147}]}, {"trigger": {"text": "necessary", "start": 520, "end": 529}, "arguments": [{"role": "Theme", "text": "expression", "start": 538, "end": 548}]}, {"trigger": {"text": "transactivation", "start": 882, "end": 897}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 775, "end": 779}, {"role": "Site", "text": "promoter", "start": 780, "end": 788}]}, {"trigger": {"text": "transactivation", "start": 980, "end": 995}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 775, "end": 779}, {"role": "Site", "text": "promoter", "start": 780, "end": 788}]}, {"trigger": {"text": "enhanced", "start": 1022, "end": 1030}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 980, "end": 995}]}], "regulation": [{"trigger": {"text": "resistant", "start": 14, "end": 23}, "arguments": [{"role": "Theme", "text": "transactivation", "start": 24, "end": 39}]}], "transcription": [{"trigger": {"text": "at the transcriptional level", "start": 689, "end": 717}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 656, "end": 660}]}]}}, "schema": []}
{"input": "Inducible nitric oxide: an autoregulatory feedback inhibitor of vascular inflammation. \nInducible nitric oxide (iNO) is produced at sites of vascular inflammation by resident and nonresident vascular wall cells, but its role in the inflammatory process is not known. In this study, we show that a novel function of iNO is to terminate inflammatory processes. We find that iNO produced by murine macrophage-like cells, RAW264.7, can inhibit cytokine-induced endothelial cell activation in a separated and mixed endothelial-RAW264.7 coculture system. Both iNO production and endothelial VCAM-1 expression were induced simultaneously with bacterial LPS and murine-specific IFN-gamma. Inhibition of iNO synthase (iNOS) activity with N omega-monomethyl-L-arginine in endothelial-RAW264.7 cocultures, stimulated with murine-specific IFN-gamma and LPS, decreased iNO production by 86%, augmented VCAM-1 and iNOS expression in endothelial and RAW264.7 cells, respectively, and increased monocyte adhesion to the endothelial cell surface. Transient transfection studies using various VCAM-1 promoter constructs demonstrated that inhibitory effects of iNO on VCAM-1 gene transcription were mediated, in part, by inhibitory effects of iNO on kappa B cis-acting elements. Immunofluorescence studies using an Ab to the RelA (p65) subunit of nuclear factor-kappa B revealed that iNO inhibited the activation of nuclear factor-kappa B. These studies indicate that iNO attenuates iNOS expression in macrophages and inhibits monocyte adhesion to endothelial cells, and suggest that endogenously derived iNO may be an important autoregulatory inhibitor of vascular inflammation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 592, "end": 602}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 585, "end": 591}]}, {"trigger": {"text": "expression", "start": 905, "end": 915}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 889, "end": 895}]}, {"trigger": {"text": "expression", "start": 905, "end": 915}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 900, "end": 904}]}, {"trigger": {"text": "expression", "start": 1469, "end": 1479}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 1464, "end": 1468}]}], "negative regulation": [{"trigger": {"text": "Inhibition", "start": 681, "end": 691}, "arguments": [{"role": "Theme", "text": "iNOS", "start": 709, "end": 713}]}, {"trigger": {"text": "inhibitory effects", "start": 1120, "end": 1138}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1161, "end": 1174}]}, {"trigger": {"text": "attenuates", "start": 1453, "end": 1463}, "arguments": [{"role": "Theme", "text": "expression", "start": 1469, "end": 1479}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 608, "end": 615}, "arguments": [{"role": "Theme", "text": "expression", "start": 592, "end": 602}, {"role": "Cause", "text": "IFN-gamma", "start": 670, "end": 679}]}, {"trigger": {"text": "induced", "start": 608, "end": 615}, "arguments": [{"role": "Theme", "text": "expression", "start": 592, "end": 602}]}, {"trigger": {"text": "augmented", "start": 879, "end": 888}, "arguments": [{"role": "Cause", "text": "Inhibition", "start": 681, "end": 691}, {"role": "Theme", "text": "expression", "start": 905, "end": 915}]}, {"trigger": {"text": "mediated", "start": 1180, "end": 1188}, "arguments": [{"role": "Theme", "text": "inhibitory effects", "start": 1120, "end": 1138}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1161, "end": 1174}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1149, "end": 1155}]}]}}, "schema": []}
{"input": "Inhibition of HIV-1 replication by combination of a novel inhibitor of TNF-alpha with AZT. \nThe small molecule S9a was derived from an established tumor necrosis factor-alpha (TNF-alpha) inhibitor (Canventol) by replacement of the isopropylidine group with a phenyl ring. S9a at 10 to 100 nM inhibited HIV production as potently as 3'-azido-3'-deoxythymidine (AZT), an inhibitor of viral reverse transcriptase. Furthermore, S9a and AZT in combination, at noncytoxic concentrations strongly inhibited HIV-1 replication that was more than additive and substantially prolonged the appearance of virus both in acutely infected CD4+ lymphocytes (SupT) in culture and in peripheral blood mononuclear cells (PBMCs) infected with a primary HIV-1 isolate. S9a inhibited TNF-alpha promoter-driven reporter gene activity. It was proposed that the mechanism of antiviral action of S9a was on the host cell, by blocking TNF-alpha transcription via a Tat-induced tar-independent loop, which decreases downstream NF-kappaB activation of HIV-1 long terminal repeat (LTR). S9a was superior to the first generation compound Canventol, which was superior to the natural compound sarcophytol A, demonstrating that further structure-based enhancement of potency of these compounds is feasible. This study suggests a therapeutic approach against AIDS by application of two drugs, one against a cellular and the other a viral target, which may provide an approach to the problem of frequent emergence of resistant variants to combinations of drugs that target only HIV genes. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "inhibitor", "start": 58, "end": 67}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 71, "end": 80}]}, {"trigger": {"text": "blocking", "start": 898, "end": 906}, "arguments": [{"role": "Theme", "text": "transcription", "start": 917, "end": 930}]}], "positive regulation": [{"trigger": {"text": "via", "start": 931, "end": 934}, "arguments": [{"role": "Theme", "text": "transcription", "start": 917, "end": 930}, {"role": "Cause", "text": "induced", "start": 941, "end": 948}]}, {"trigger": {"text": "induced", "start": 941, "end": 948}, "arguments": [{"role": "Theme", "text": "blocking", "start": 898, "end": 906}, {"role": "Cause", "text": "Tat", "start": 937, "end": 940}]}], "transcription": [{"trigger": {"text": "transcription", "start": 917, "end": 930}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 907, "end": 916}]}]}}, "schema": []}
{"input": "Retinoic acid inhibits CD40 + interleukin-4-mediated IgE production in vitro. \nTo elucidate the role of retinoic acid (RA) in anti-CD40 + interleukin-4 (IL-4)-mediated B-cell activation, the effect of 10(-12) to 10(-6) mol/L RA was studied in anti-CD40 (1 microgram/mL) + IL-4 (5 ng/mL)-mediated proliferation and Ig synthesis by human peripheral blood mononuclear cells (PBMC) and B cells in healthy donors. Anti-CD40 + IL-4-mediated proliferation of PBMC and B cells was inhibited by RA in a dose-dependent manner, with maximal inhibition of 62% +/- 5% in PBMC and 55% +/- 4.4% in B cells by all-trans RA, and 58% +/- 6.7% and 51% +/- 4.7%, respectively by 13-cis RA. IgE synthesis was even more markedly inhibited by RA starting at concentrations of >10(-14) mol/L for B cells and >10(-10) mol/L for PBMC. Maximal inhibition of IgE production for B cells was at 10(-8) mol/L for all-trans RA (94% +/- 1.8%) and 96% +/- 3.2% for 13-cis RA. Low concentrations of RA inhibiting IgE synthesis (10(-10) mol/L) affected neither B-cell proliferation nor the production of IgA, IgG, and IgM. Elucidation of the mechanism involved in this inhibition of IgE production shows that epsilon germline transcription is decreased by RA, whereas production of interferon-gamma (IFN-gamma) was not enhanced in the presence of RA. To differentiate whether the RA effect was mediated by RA receptors alpha, beta, and gamma, the expression of the retinoic acid receptors (RAR) was examined by reverse transcriptase-polymerase chain reaction (RT-PCR). The data show that unstimulated human peripheral B cells express mRNA of the RA receptor alpha, beta, and gamma. Using retinoids with different receptor binding specificity (CD336, CD437, CD2019, CD367), dose-dependent inhibition of IgE synthesis was shown by all four derivates, but was most marked by an RA binding the alpha receptor with high specificity. Taken together, this study shows that RA inhibits IgE production of anti-CD40 + IL-4-stimulated B cells in vitro. Copyright 1998 by The American Society of Hematology. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 1232, "end": 1242}, "arguments": [{"role": "Theme", "text": "IFN-gamma", "start": 1264, "end": 1273}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 1283, "end": 1291}, "arguments": [{"role": "Theme", "text": "production", "start": 1232, "end": 1242}]}], "transcription": [{"trigger": {"text": "express", "start": 1590, "end": 1597}, "arguments": [{"role": "Theme", "text": "RA receptor alpha", "start": 1610, "end": 1627}]}, {"trigger": {"text": "express", "start": 1590, "end": 1597}, "arguments": [{"role": "Theme", "text": "beta", "start": 1629, "end": 1633}]}, {"trigger": {"text": "express", "start": 1590, "end": 1597}, "arguments": [{"role": "Theme", "text": "gamma", "start": 1639, "end": 1644}]}]}}, "schema": []}
{"input": "Nuclear factor-kappaB induction in CD45RO+ and CD45RA+ T cell subsets during aging. \nAn increase in the ratio of memory to naive T cells has been postulated to underlie immune hyporesponsiveness accompanying aging. Our analyses of the induction of nuclear factor-kappaB (NFkappaB) in activated memory (CD45RO+) and naive (CD45RA+) T cell subsets from young and elderly donors has demonstrated that, regardless of donor age, memory T cells are not significantly altered in their responsiveness to TNF-alpha-mediated induction of NFkappaB. Although treatment with TNF-alpha induced nuclear localization of NFkappaB in both memory and naive T cell subsets, irrespective of the age of the donor, the levels of induced NFkappaB were significantly lower in both subsets of T cells obtained from the elderly, when compared to those in young. Examination of IkappaB alpha regulation revealed that TNF-alpha-mediated degradation of IkappaB alpha in both memory and naive T cells from the elderly was severely impaired, thus contributing to the lowered induction of the observed NFkappaB. In addition, this age-related decrease in induction of nuclear NFkappaB correlated with decrease in intracellular IL-2 receptor expression and anti-CD3-induced proliferation of both memory and naive T cells subsets. Taken together, our results suggest that the age-related hyporesponsiveness cannot be attributed to a skewing of the T cell population towards a memory phenotype in the elderly. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "impaired", "start": 1000, "end": 1008}, "arguments": [{"role": "Theme", "text": "degradation", "start": 908, "end": 919}]}], "positive regulation": [{"trigger": {"text": "mediated", "start": 899, "end": 907}, "arguments": [{"role": "Cause", "text": "TNF-alpha", "start": 889, "end": 898}, {"role": "Theme", "text": "degradation", "start": 908, "end": 919}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 908, "end": 919}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 923, "end": 936}]}], "regulation": [{"trigger": {"text": "regulation", "start": 864, "end": 874}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 850, "end": 863}]}]}}, "schema": []}
{"input": "Activation of E2F-mediated transcription by human T-cell leukemia virus type I Tax protein in a p16(INK4A)-negative T-cell line. \nThe human T-cell leukemia virus type I (HTLV-I) is a causative agent of adult T-cell leukemia. Although the exact mechanism by which HTLV-I contributes to leukemogenesis is still unclear, the Tax protein is thought to play a major role in this process. This 40-kDa polypeptide is able to interact with the tumor suppressor p16(INK4A). Consequently, Tax can activate the signaling pathway that lead to the release of E2F that in turn induces expression of factors required for cell cycle progression. In this paper, we demonstrate that Tax can also activate E2F-mediated transcription independently of p16(INK4A). Indeed, when Tax is coexpressed with the E2F-1 transcription factor in CEM T-cells, which lack expression of p16(INK4A), it strongly potentiates the E2F-dependent activation of a reporter construct driven by a promoter containing E2F binding sites. This stimulation is abrogated by mutations affecting the E2F-binding sites. In addition, Tax also stimulates the transcription of the E2F-1 gene itself. Using Tax mutants that fail to activate either ATF- or NF-kappaB-dependent promoters and different 5' truncation mutants of the E2F-1 promoter, we show that the Tax-dependent transcriptional control of the E2F1 gene involves, at least in part, the ATF binding site located in the E2F-1 promoter. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 418, "end": 426}, "arguments": [{"role": "Theme", "text": "Tax", "start": 322, "end": 325}, {"role": "Theme2", "text": "INK4A", "start": 457, "end": 462}]}], "gene expression": [{"trigger": {"text": "negative", "start": 107, "end": 115}, "arguments": [{"role": "Theme", "text": "INK4A", "start": 100, "end": 105}]}, {"trigger": {"text": "coexpressed", "start": 763, "end": 774}, "arguments": [{"role": "Theme", "text": "Tax", "start": 756, "end": 759}]}], "positive regulation": [{"trigger": {"text": "stimulates", "start": 1090, "end": 1100}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1081, "end": 1084}, {"role": "Theme", "text": "transcription", "start": 1105, "end": 1118}]}, {"trigger": {"text": "activate", "start": 1176, "end": 1184}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1151, "end": 1154}, {"role": "Theme", "text": "E2F-1", "start": 1273, "end": 1278}, {"role": "Site", "text": "promoter", "start": 1279, "end": 1287}]}], "regulation": [{"trigger": {"text": "transcriptional control", "start": 1320, "end": 1343}, "arguments": [{"role": "Cause", "text": "Tax", "start": 1306, "end": 1309}, {"role": "Theme", "text": "E2F1", "start": 1351, "end": 1355}]}], "transcription": [{"trigger": {"text": "transcription", "start": 1105, "end": 1118}, "arguments": [{"role": "Theme", "text": "E2F-1", "start": 1126, "end": 1131}]}]}}, "schema": []}
{"input": "Glucocorticoid-induced apoptosis and regulation of NF-kappaB activity in human leukemic T cells. \nGlucocorticoid-induced apoptosis was investigated in glucocorticoid-sensitive 6TG1.1 and resistant ICR27TK.3 human leukemic T cells. Following glucocorticoid treatment of 6TG1.1 cells, chromatin fragmentation was observed after a delay of 24 h. Fragmentation was not observed in ICR27TK.3 cells containing mutant glucocorticoid receptors (L753F) that are activation-deficient but retain the ability to repress AP-1 activity. Nor was fragmentation observed after treatment with RU38486, indicating that repression of AP-1 activity is not involved. As described in other systems, fragmentation required ongoing protein synthesis. However, inhibition of protein synthesis with cycloheximide anytime during the first 18 h of steroid treatment was as effective in blocking chromatin fragmentation as inhibition for the entire period, suggesting that synthesis of a component with a rapid turnover rate is required. Dexamethasone treatment completely blocked 12-O-tetradecanoylphorbol 13-acetate induction of nuclear factor-kappaB (NF-kappaB) activity and elicited an increase in the amount of immunoreactive IkappaB alpha in sensitive 6TG1.1 cells but not in resistant ICR27TK.3 cells. In addition, mild detergent treatment of cell extracts indicated that a substantial amount of cytoplasmic NF-kappaB is complexed with IkappaB alpha or some other inhibitory factor. These results suggest that induction of a labile inhibitory factor such as IkappaB alpha may contribute to glucocorticoid-induced apoptosis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "complexed", "start": 1398, "end": 1407}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 1413, "end": 1426}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 1160, "end": 1168}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 1201, "end": 1214}]}, {"trigger": {"text": "induction", "start": 1487, "end": 1496}, "arguments": [{"role": "Theme", "text": "IkappaB alpha", "start": 1535, "end": 1548}]}]}}, "schema": []}
{"input": "Peripheral T lymphocytes from women with breast cancer exhibit abnormal protein expression of several signaling molecules. \nWe examined signaling molecules of peripheral blood T lymphocytes obtained from women with breast cancer. In 6 of 14 patients, T lymphocytes displayed an impaired ability to translocate NFeB p65 (Rel-A) following activation by anti-CD3 and IL-2. This observation was made despite normal cytoplasmic levels of the Rel-A protein. We also detected abnormally low levels of the signaling molecules T-cell receptor (TCR)-zeta, ZAP-70 and p56lck in 4 of 14 breast cancer patients, i.e., defects in T-cell signaling molecules. T lymphocytes from 6 of the 14 patients also exhibited an increased expression of the dual specificity phosphatase, map kinase phosphatase-1 (MKP-1). MKP-1 inactivates MAP kinase and therefore may interfere with the activation of c-jun and c-fos. Abnormalities of I or more signaling molecules were found in 9 of 14 patients; however, only 3 patients had T cells that exhibited all 5 defects. Our data have implications for the detection of potentially dysfunctional T cells in patients with cancer. For example, the analysis of only 1 signaling molecule may allow patients with significant defects in T-cell signaling to go unnoticed. Finally, despite impaired Rel-A translocation, T cells were capable of transcribing IL-2. Impairments in the translocation of Rel-B and c-Rel further suggest that the NFKB family members Rel-A, Rel-B and c-Rel are not required for the transcription of IL-2 in the peripheral T lymphocytes of patients with breast cancer. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "levels", "start": 423, "end": 429}, "arguments": [{"role": "Theme", "text": "Rel-A", "start": 437, "end": 442}]}, {"trigger": {"text": "expression", "start": 712, "end": 722}, "arguments": [{"role": "Theme", "text": "MKP-1", "start": 786, "end": 791}]}], "localization": [{"trigger": {"text": "translocate", "start": 298, "end": 309}, "arguments": [{"role": "Theme", "text": "Rel-A", "start": 320, "end": 325}]}, {"trigger": {"text": "translocation", "start": 1312, "end": 1325}, "arguments": [{"role": "Theme", "text": "Rel-A", "start": 1306, "end": 1311}]}, {"trigger": {"text": "translocation", "start": 1389, "end": 1402}, "arguments": [{"role": "Theme", "text": "Rel-B", "start": 1406, "end": 1411}]}, {"trigger": {"text": "translocation", "start": 1389, "end": 1402}, "arguments": [{"role": "Theme", "text": "c-Rel", "start": 1416, "end": 1421}]}], "negative regulation": [{"trigger": {"text": "impaired", "start": 278, "end": 286}, "arguments": [{"role": "Theme", "text": "translocate", "start": 298, "end": 309}]}, {"trigger": {"text": "impaired", "start": 278, "end": 286}, "arguments": [{"role": "Theme", "text": "following", "start": 327, "end": 336}]}, {"trigger": {"text": "abnormally low levels", "start": 469, "end": 490}, "arguments": [{"role": "Theme", "text": "T-cell receptor (TCR)-zeta", "start": 518, "end": 544}]}, {"trigger": {"text": "abnormally low levels", "start": 469, "end": 490}, "arguments": [{"role": "Theme", "text": "ZAP-70", "start": 546, "end": 552}]}, {"trigger": {"text": "abnormally low levels", "start": 469, "end": 490}, "arguments": [{"role": "Theme", "text": "p56lck", "start": 557, "end": 563}]}, {"trigger": {"text": "interfere", "start": 841, "end": 850}, "arguments": [{"role": "Theme", "text": "activation", "start": 860, "end": 870}]}, {"trigger": {"text": "despite", "start": 1289, "end": 1296}, "arguments": [{"role": "Cause", "text": "impaired", "start": 1297, "end": 1305}, {"role": "Theme", "text": "transcribing", "start": 1351, "end": 1363}]}, {"trigger": {"text": "impaired", "start": 1297, "end": 1305}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1312, "end": 1325}]}, {"trigger": {"text": "Impairments", "start": 1370, "end": 1381}, "arguments": [{"role": "Theme", "text": "translocation", "start": 1389, "end": 1402}]}], "positive regulation": [{"trigger": {"text": "following", "start": 327, "end": 336}, "arguments": [{"role": "Theme", "text": "translocate", "start": 298, "end": 309}]}, {"trigger": {"text": "increased", "start": 702, "end": 711}, "arguments": [{"role": "Theme", "text": "expression", "start": 712, "end": 722}]}, {"trigger": {"text": "activation", "start": 860, "end": 870}, "arguments": [{"role": "Theme", "text": "c-jun", "start": 874, "end": 879}]}, {"trigger": {"text": "activation", "start": 860, "end": 870}, "arguments": [{"role": "Theme", "text": "c-fos", "start": 884, "end": 889}]}], "regulation": [{"trigger": {"text": "required", "start": 1498, "end": 1506}, "arguments": [{"role": "Cause", "text": "Rel-A", "start": 1467, "end": 1472}, {"role": "Theme", "text": "transcription", "start": 1515, "end": 1528}]}, {"trigger": {"text": "required", "start": 1498, "end": 1506}, "arguments": [{"role": "Cause", "text": "Rel-B", "start": 1474, "end": 1479}, {"role": "Theme", "text": "transcription", "start": 1515, "end": 1528}]}, {"trigger": {"text": "required", "start": 1498, "end": 1506}, "arguments": [{"role": "Cause", "text": "c-Rel", "start": 1484, "end": 1489}, {"role": "Theme", "text": "transcription", "start": 1515, "end": 1528}]}], "transcription": [{"trigger": {"text": "transcribing", "start": 1351, "end": 1363}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1364, "end": 1368}]}, {"trigger": {"text": "transcription", "start": 1515, "end": 1528}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1532, "end": 1536}]}]}}, "schema": []}
{"input": "Transcription of a minimal promoter from the NF-IL6 gene is regulated by CREB/ATF and SP1 proteins in U937 promonocytic cells. \nNF-IL6 is an important transcriptional regulator of genes induced in activated monocytes/macrophages, and NF-IL6 is the only CCAAT/enhancer-binding protein (C/EBP) family member whose steady-state mRNA levels increase upon activation of monocytes (1). We show that increased transcription of the NF-IL6 gene is responsible, at least in part, for induction of NF-IL6 mRNA following activation of U937 promonocytic cells. We have identified a 104-bp minimal promoter region of the NF-IL6 gene that is sufficient for basal and activation-dependent induction of transcription in U937 cells. This region contains binding sites for the cAMP response element-binding protein/activation transcription factor (CREB/ATF) and Sp1 families of transcription factors. Each site is functionally important and contributes independently to transcription of the NF-IL6 gene in U937 cells. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "increase", "start": 337, "end": 345}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 234, "end": 240}]}, {"trigger": {"text": "increased", "start": 393, "end": 402}, "arguments": [{"role": "Theme", "text": "transcription", "start": 403, "end": 416}]}, {"trigger": {"text": "responsible", "start": 439, "end": 450}, "arguments": [{"role": "Cause", "text": "increased", "start": 393, "end": 402}, {"role": "Theme", "text": "induction", "start": 474, "end": 483}]}, {"trigger": {"text": "induction", "start": 474, "end": 483}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 487, "end": 493}]}, {"trigger": {"text": "sufficient", "start": 627, "end": 637}, "arguments": [{"role": "CSite", "text": "104-bp minimal promoter region", "start": 569, "end": 599}, {"role": "Cause", "text": "NF-IL6", "start": 607, "end": 613}, {"role": "Theme", "text": "induction", "start": 673, "end": 682}]}, {"trigger": {"text": "induction", "start": 673, "end": 682}, "arguments": [{"role": "Theme", "text": "transcription", "start": 686, "end": 699}]}], "transcription": [{"trigger": {"text": "transcription", "start": 403, "end": 416}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 424, "end": 430}]}, {"trigger": {"text": "transcription", "start": 686, "end": 699}, "arguments": [{"role": "Theme", "text": "NF-IL6", "start": 607, "end": 613}]}]}}, "schema": []}
{"input": "CD30 is a CD40-inducible molecule that negatively regulates CD40-mediated immunoglobulin class switching in non-antigen-selected human B cells. \nWe used our monoclonal model of germinal center maturation, CL-01 B cells, to investigate the role of CD30 in human B cell differentiation. CL-01 cells are IgM+ IgD+ CD30+ and switch to IgG, IgA, and IgE when exposed to CD40L and IL-4. Switching is hampered by CD30 coengagement, possibly through interference with the CD40-mediated NF-kappaB-dependent transcriptional activation of downstream C(H) genes. The physiological relevance of this phenomenon is emphasized by similar CD30-mediated effects in naive B cells. Expression of CD30 by these cells is induced by CD40L but is inhibited by B cell receptor coengagement and/or exposure to IL-6 and IL-12. Our data suggest that CD30 critically regulates the CD40-mediated differentiation of non-antigen-selected human B cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "coengagement", "start": 411, "end": 423}, "arguments": [{"role": "Theme", "text": "CD30", "start": 406, "end": 410}]}], "gene expression": [{"trigger": {"text": "+", "start": 315, "end": 316}, "arguments": [{"role": "Theme", "text": "CD30", "start": 311, "end": 315}]}, {"trigger": {"text": "Expression", "start": 663, "end": 673}, "arguments": [{"role": "Theme", "text": "CD30", "start": 677, "end": 681}]}], "negative regulation": [{"trigger": {"text": "switch", "start": 321, "end": 327}, "arguments": [{"role": "Theme", "text": "+", "start": 315, "end": 316}]}, {"trigger": {"text": "inhibited", "start": 724, "end": 733}, "arguments": [{"role": "Theme", "text": "is induced", "start": 697, "end": 707}]}], "positive regulation": [{"trigger": {"text": "inducible", "start": 15, "end": 24}, "arguments": [{"role": "Theme", "text": "CD30", "start": 0, "end": 4}, {"role": "Cause", "text": "CD40", "start": 10, "end": 14}]}, {"trigger": {"text": "is induced", "start": 697, "end": 707}, "arguments": [{"role": "Theme", "text": "Expression", "start": 663, "end": 673}, {"role": "Cause", "text": "CD40L", "start": 711, "end": 716}]}]}}, "schema": []}
{"input": "Induction of Mn SOD in human monocytes without inflammatory cytokine production by a mutant endotoxin. \nEndotoxin selectively induces monocyte Mn superoxide dismutase (SOD) without affecting levels of Cu,Zn SOD, catalase, or glutathione peroxidase. However, little is known about the structure-activity relationship and the mechanism by which endotoxin induces Mn SOD. In this study we demonstrated that a mutant Escherichia coli endotoxin lacking myristoyl fatty acid at the 3' R-3-hydroxymyristate position of the lipid A moiety retained its full capacity to coagulate Limulus amoebocyte lysate compared with the wild-type E. coli endotoxin and markedly stimulated the activation of human monocyte nuclear factor-kappaB and the induction of Mn SOD mRNA and enzyme activity. However, in contrast to the wild-type endotoxin, it failed to induce significant production of tumor necrosis factor-alpha and macrophage inflammatory protein-1alpha by monocytes and did not induce the phosphorylation and nuclear translocation of mitogen-activated protein kinase. These results suggest that 1) lipid A myristoyl fatty acid, although it is important for the induction of inflammatory cytokine production by human monocytes, is not necessary for the induction of Mn SOD, 2) endotoxin-mediated induction of Mn SOD and inflammatory cytokines are regulated, at least in part, through different signal transduction pathways, and 3) failure of the mutant endotoxin to induce tumor necrosis factor-alpha production is, at least in part, due to its inability to activate mitogen-activated protein kinase. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 857, "end": 867}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 871, "end": 898}]}, {"trigger": {"text": "production", "start": 857, "end": 867}, "arguments": [{"role": "Theme", "text": "macrophage inflammatory protein-1alpha", "start": 903, "end": 941}]}, {"trigger": {"text": "production", "start": 1489, "end": 1499}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 1461, "end": 1488}]}], "positive regulation": [{"trigger": {"text": "Induction", "start": 0, "end": 9}, "arguments": [{"role": "Theme", "text": "Mn SOD", "start": 13, "end": 19}]}, {"trigger": {"text": "induces", "start": 126, "end": 133}, "arguments": [{"role": "Theme", "text": "Mn superoxide dismutase", "start": 143, "end": 166}]}, {"trigger": {"text": "induces", "start": 353, "end": 360}, "arguments": [{"role": "Theme", "text": "Mn SOD", "start": 361, "end": 367}]}, {"trigger": {"text": "stimulated", "start": 656, "end": 666}, "arguments": [{"role": "Theme", "text": "induction", "start": 730, "end": 739}]}, {"trigger": {"text": "induce", "start": 838, "end": 844}, "arguments": [{"role": "Theme", "text": "production", "start": 857, "end": 867}]}, {"trigger": {"text": "necessary", "start": 1223, "end": 1232}, "arguments": [{"role": "Theme", "text": "induction", "start": 1241, "end": 1250}]}, {"trigger": {"text": "induction", "start": 1241, "end": 1250}, "arguments": [{"role": "Theme", "text": "Mn SOD", "start": 1254, "end": 1260}]}, {"trigger": {"text": "induction", "start": 1284, "end": 1293}, "arguments": [{"role": "Theme", "text": "Mn SOD", "start": 1297, "end": 1303}]}, {"trigger": {"text": "induce", "start": 1454, "end": 1460}, "arguments": [{"role": "Theme", "text": "production", "start": 1489, "end": 1499}]}, {"trigger": {"text": "due", "start": 1522, "end": 1525}, "arguments": [{"role": "Theme", "text": "induce", "start": 1454, "end": 1460}]}], "regulation": [{"trigger": {"text": "affecting", "start": 181, "end": 190}, "arguments": [{"role": "Theme", "text": "Cu,Zn SOD", "start": 201, "end": 210}]}, {"trigger": {"text": "affecting", "start": 181, "end": 190}, "arguments": [{"role": "Theme", "text": "catalase", "start": 212, "end": 220}]}, {"trigger": {"text": "regulated", "start": 1335, "end": 1344}, "arguments": [{"role": "Theme", "text": "induction", "start": 1284, "end": 1293}]}], "transcription": [{"trigger": {"text": "induction", "start": 730, "end": 739}, "arguments": [{"role": "Theme", "text": "Mn SOD", "start": 743, "end": 749}]}]}}, "schema": []}
{"input": "An allosteric drug, o,o'-bismyristoyl thiamine disulfide, suppresses HIV-1 replication through prevention of nuclear translocation of both HIV-1 Tat and NF-kappa B. \nThe efficacy of o,o'-bismyristoyl thiamine disulfide (BMT) was examined in detail against HIV-1 laboratory isolates (HTLV-IIIB, JRFL, and MN), primary isolates (KMT and KMO), and simian immunodeficiency virus (SIVmac251) in vitro. BMT inhibited the replication of HIV-1 in both laboratory and primary isolates in vitro. In addition, BMT exhibited antiviral activity against SIVmac251. Minimizing energy studies of BMT structure reveal that a trans-disulfide of thiamine (holo drug) disulfide (TDS, protodrug) is allosterically transited to the reactive twisted disulfide of BMT (allo drug) by o,o'-bismyristoyl esterification of TDS. BMT inhibits nuclear translocation of both HIV-1 transactivator (TAT) and the cellular transcriptional nuclear factor-KB (NF-kappa B), resulting in the suppression of HIV-1 replication. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "translocation", "start": 117, "end": 130}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 109, "end": 116}, {"role": "Theme", "text": "Tat", "start": 145, "end": 148}]}, {"trigger": {"text": "translocation", "start": 821, "end": 834}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 813, "end": 820}, {"role": "Theme", "text": "TAT", "start": 865, "end": 868}]}], "negative regulation": [{"trigger": {"text": "prevention", "start": 95, "end": 105}, "arguments": [{"role": "Theme", "text": "translocation", "start": 117, "end": 130}]}, {"trigger": {"text": "inhibits", "start": 804, "end": 812}, "arguments": [{"role": "Theme", "text": "translocation", "start": 821, "end": 834}]}]}}, "schema": []}
{"input": "Retinoid X receptor and c-cerbA/thyroid hormone receptor regulate erythroid cell growth and differentiation. \nNuclear receptors are important regulators of erythroid cell development. Here we investigated the impact of retinoid X receptor (RXR), retinoic acid receptor (RAR), and of the c-erbA/thyroid hormone (T3) receptor (c-erbA/TR) on growth and differentiation of erythroid cells using an in vitro culture system of stem cell factor-dependent erythroid progenitors. RXR, RAR, and c-erbA/TR-specific ligands were found to induce erythroid-specific gene expression and to accelerate erythroid differentiation in culture, with T3 being most effective. Furthermore, while ligand-activated c-erbA/TR accelerated differentiation, unliganded c-erbA/TR effectively blocked differentiation and supported sustained progenitor growth in culture. Thus, c-erbA/TR appears to act as a binary switch affecting erythroid cell fate: unliganded c-erbA/TR supports growth while ligand-activated c-erbA/TR induces differentiation. Additionally, to determine the impact of RXR for erythroid cell development, dominant interfering mutant RXRs, lacking the transcriptional activator functions AF-1 and AF-2, or AF-2 only, or the entire DNA-binding domain, were introduced into erythroid progenitor cells via recombinant retrovirus vectors and analyzed for RXR-specific effects. It was found that expression of wild-type RXR and of the RXR mutants devoid of AF-1 and/or AF-2 supported a transient outgrowth of erythroid cells. In marked contrast, expression of the dominant interfering deltaDNA-binding domain RXR, containing a deletion of the entire DNA-binding domain, was incompatible with erythroid cell growth in vitro, suggesting a pivotal role of RXR for erythroid cell development. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Phosphatidylinositides bind to plasma membrane CD14 and can prevent monocyte activation by bacterial lipopolysaccharide. \nAlthough bacterial lipopolysaccharides (LPS) and several other microbial agonists can bind to mCD14 (membrane CD14), a cell-surface receptor found principally on monocytes and neutrophils, host-derived mCD14 ligands are poorly defined. We report here that phosphatidylinositol (PtdIns), phosphatidylinositol-4-phosphate, and other phosphatidylinositides can bind to mCD14. Phosphatidylserine (PS), another anionic glycerophospholipid, binds to mCD14 with lower apparent affinity than does PtdIns. LPS-binding protein, a lipid transfer protein found in serum, facilitates both PS- and PtdIns-mCD14 binding. PtdIns binding to mCD14 can be blocked by anti-CD14 monoclonal antibodies that inhibit LPS-mCD14 binding, and PtdIns can inhibit both LPS-mCD14 binding and LPS-induced responses in monocytes. Serum-equilibrated PtdIns also binds to mCD14-expressing cells, raising the possibility that endogenous PtdIns may modulate cellular responses to LPS and other mCD14 ligands in vivo. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 23, "end": 27}, "arguments": [{"role": "Theme", "text": "CD14", "start": 47, "end": 51}]}, {"trigger": {"text": "bind", "start": 208, "end": 212}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 216, "end": 221}]}, {"trigger": {"text": "bind", "start": 480, "end": 484}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 488, "end": 493}]}, {"trigger": {"text": "binds", "start": 557, "end": 562}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 566, "end": 571}]}, {"trigger": {"text": "binding", "start": 719, "end": 726}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 713, "end": 718}]}, {"trigger": {"text": "binding", "start": 735, "end": 742}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 746, "end": 751}]}, {"trigger": {"text": "binding", "start": 825, "end": 832}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 819, "end": 824}]}, {"trigger": {"text": "binding", "start": 872, "end": 879}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 866, "end": 871}]}], "gene expression": [{"trigger": {"text": "expressing", "start": 966, "end": 976}, "arguments": [{"role": "Theme", "text": "mCD14", "start": 960, "end": 965}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 759, "end": 766}, "arguments": [{"role": "Theme", "text": "binding", "start": 735, "end": 742}, {"role": "Cause", "text": "inhibit", "start": 807, "end": 814}]}, {"trigger": {"text": "inhibit", "start": 807, "end": 814}, "arguments": [{"role": "Theme", "text": "binding", "start": 825, "end": 832}]}, {"trigger": {"text": "inhibit", "start": 849, "end": 856}, "arguments": [{"role": "Theme", "text": "binding", "start": 872, "end": 879}]}], "positive regulation": [{"trigger": {"text": "facilitates", "start": 681, "end": 692}, "arguments": [{"role": "Theme", "text": "binding", "start": 719, "end": 726}]}]}}, "schema": []}
{"input": "Low CD3+CD28-induced interleukin-2 production correlates with decreased reactive oxygen intermediate formation in neonatal T cells. \nThe capacity of neonatal T cells to secrete interleukin-2 (IL-2) has been reported to be variable. We analysed IL-2 production in purified neonatal and adult T cells using polyclonal activator phorbol ester + calcium ionophore (PDBu + iono) or receptor-mediated anti-CD3/anti-CD3+ anti-CD28 stimulation. PDBu + iono induced equally high IL-2 levels in both groups and, when stimulated with plate-bound anti-CD3 monoclonal antibody (mAb), the IL-2 secretion by neonatal cells was undetectable and adult cells produced low amounts of IL-2 (mean 331 +/- 86 pg/ml). The addition of anti-CD28 mAb to anti-CD3-stimulated cells markedly increased IL-2 production in both cell types, but levels of IL-2 in neonatal T cells remained clearly lower than those of adult T cells (respective mean values: 385 +/- 109 pg/ml and 4494 +/- 1199 pg/ml). As NF-kappa B is a critical transcription factor in the control of IL-2 expression, we next analysed its nuclear translocation in neonatal and adult T cells using the electrophoretic mobility shift assay and, because induction of reactive oxygen intermediates (ROI) is required for the activation of NF-kappa B, we also analysed levels of intracellular ROI in these cells using the ROI-reactive fluorochrome DCFH-DA and flow cytometry. In neonatal T cells NF-kappa B activation and ROI formation after anti-CD3 stimulation were low compared with adult T cells and, although addition of anti-CD28 mAb increased induction of NF-kappa B and ROI formation, levels similar to those of adults were not achieved. After PDBu + iono stimulation, the cells showed similar ROI formation and IL-2 secretion. Our results suggest that reduced IL-2 production by neonatal T cells is specific for anti-CD3 and anti-CD3+ anti-CD28-mediated stimulation and that these activators cannot effectively activate the ROI-NF-kappa B signalling pathway in neonatal T cells. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 35, "end": 45}, "arguments": [{"role": "Theme", "text": "interleukin-2", "start": 21, "end": 34}]}, {"trigger": {"text": "production", "start": 249, "end": 259}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 244, "end": 248}]}, {"trigger": {"text": "produced", "start": 641, "end": 649}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 665, "end": 669}]}, {"trigger": {"text": "production", "start": 778, "end": 788}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 773, "end": 777}]}, {"trigger": {"text": "expression", "start": 1040, "end": 1050}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1035, "end": 1039}]}, {"trigger": {"text": "production", "start": 1802, "end": 1812}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1797, "end": 1801}]}], "localization": [{"trigger": {"text": "secrete", "start": 169, "end": 176}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 192, "end": 196}]}, {"trigger": {"text": "secretion", "start": 580, "end": 589}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 575, "end": 579}]}, {"trigger": {"text": "secretion", "start": 1753, "end": 1762}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1748, "end": 1752}]}], "negative regulation": [{"trigger": {"text": "was undetectable", "start": 608, "end": 624}, "arguments": [{"role": "Theme", "text": "secretion", "start": 580, "end": 589}]}, {"trigger": {"text": "low amounts", "start": 650, "end": 661}, "arguments": [{"role": "Theme", "text": "produced", "start": 641, "end": 649}]}, {"trigger": {"text": "reduced", "start": 1789, "end": 1796}, "arguments": [{"role": "Theme", "text": "production", "start": 1802, "end": 1812}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 13, "end": 20}, "arguments": [{"role": "Cause", "text": "CD28", "start": 8, "end": 12}, {"role": "Theme", "text": "production", "start": 35, "end": 45}]}, {"trigger": {"text": "induced", "start": 449, "end": 456}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 470, "end": 474}]}, {"trigger": {"text": "increased", "start": 763, "end": 772}, "arguments": [{"role": "Theme", "text": "production", "start": 778, "end": 788}]}], "regulation": [{"trigger": {"text": "using", "start": 299, "end": 304}, "arguments": [{"role": "Theme", "text": "production", "start": 249, "end": 259}]}, {"trigger": {"text": "control", "start": 1024, "end": 1031}, "arguments": [{"role": "Theme", "text": "expression", "start": 1040, "end": 1050}]}, {"trigger": {"text": "specific", "start": 1836, "end": 1844}, "arguments": [{"role": "Theme", "text": "reduced", "start": 1789, "end": 1796}]}]}}, "schema": []}
{"input": "Activated platelets induce monocyte chemotactic protein-1 secretion and surface expression of intercellular adhesion molecule-1 on endothelial cells [see comments] \nBACKGROUND: Platelet/endothelium interaction plays an important role in the pathophysiology of inflammation and atherosclerosis. The role of platelets for monocyte chemotactic protein-1 (MCP-1) secretion and surface expression of intercellular adhesion molecule-1 (ICAM-1) on endothelial cells has been assessed. METHODS AND RESULTS: Monolayers of human umbilical vein endothelial cells were incubated with nonstimulated or ADP-activated platelets for 6 hours, and secretion of MCP-1 and surface expression of ICAM-1 were determined by ELISA and flow cytometry, respectively. In the presence of ADP-activated platelets, both MCP-1 secretion and ICAM-1 surface expression were significantly increased compared with nonstimulated platelets (P<0.02). Activation of the transcription factor nuclear factor-kappaB (NF-kappaB) determined by electrophoretic mobility shift assay and kappaB-dependent transcriptional activity was enhanced in the presence of activated platelets. In addition, ADP-activated platelets induced MCP-1 and ICAM-1 promoter-dependent transcription. Liposomal transfection of a double-stranded kappaB phosphorothioate oligonucleotide, but not of the mutated form, inhibited MCP-1 secretion and surface expression of ICAM-1 on activated endothelium (P<0.05). CONCLUSIONS: The present study indicates that activated platelets modulate chemotactic (MCP-1) and adhesive (ICAM-1) properties of endothelial cells via an NF-kappaB-dependent mechanism. Platelet-induced activation of the NF-kappaB system might contribute to early inflammatory events in atherogenesis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 80, "end": 90}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 94, "end": 127}]}, {"trigger": {"text": "expression", "start": 381, "end": 391}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 430, "end": 436}]}], "localization": [{"trigger": {"text": "secretion", "start": 58, "end": 67}, "arguments": [{"role": "Theme", "text": "monocyte chemotactic protein-1", "start": 27, "end": 57}]}, {"trigger": {"text": "secretion", "start": 359, "end": 368}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 352, "end": 357}]}, {"trigger": {"text": "secretion", "start": 630, "end": 639}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 643, "end": 648}]}, {"trigger": {"text": "expression", "start": 661, "end": 671}, "arguments": [{"role": "AtLoc", "text": "surface", "start": 653, "end": 660}, {"role": "Theme", "text": "ICAM-1", "start": 675, "end": 681}]}, {"trigger": {"text": "secretion", "start": 796, "end": 805}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 790, "end": 795}]}, {"trigger": {"text": "expression", "start": 825, "end": 835}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 810, "end": 816}, {"role": "AtLoc", "text": "surface", "start": 817, "end": 824}]}, {"trigger": {"text": "secretion", "start": 1362, "end": 1371}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 1356, "end": 1361}]}, {"trigger": {"text": "expression", "start": 1384, "end": 1394}, "arguments": [{"role": "AtLoc", "text": "surface", "start": 1376, "end": 1383}, {"role": "Theme", "text": "ICAM-1", "start": 1398, "end": 1404}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1346, "end": 1355}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1362, "end": 1371}]}, {"trigger": {"text": "inhibited", "start": 1346, "end": 1355}, "arguments": [{"role": "Theme", "text": "expression", "start": 1384, "end": 1394}]}], "positive regulation": [{"trigger": {"text": "induce", "start": 20, "end": 26}, "arguments": [{"role": "Theme", "text": "secretion", "start": 58, "end": 67}]}, {"trigger": {"text": "induce", "start": 20, "end": 26}, "arguments": [{"role": "Theme", "text": "expression", "start": 80, "end": 90}]}, {"trigger": {"text": "increased", "start": 855, "end": 864}, "arguments": [{"role": "Theme", "text": "secretion", "start": 796, "end": 805}]}, {"trigger": {"text": "increased", "start": 855, "end": 864}, "arguments": [{"role": "Theme", "text": "expression", "start": 825, "end": 835}]}, {"trigger": {"text": "modulate", "start": 1506, "end": 1514}, "arguments": [{"role": "Theme", "text": "MCP-1", "start": 1528, "end": 1533}]}, {"trigger": {"text": "modulate", "start": 1506, "end": 1514}, "arguments": [{"role": "Theme", "text": "ICAM-1", "start": 1549, "end": 1555}]}], "regulation": [{"trigger": {"text": "role", "start": 298, "end": 302}, "arguments": [{"role": "Theme", "text": "secretion", "start": 359, "end": 368}]}, {"trigger": {"text": "role", "start": 298, "end": 302}, "arguments": [{"role": "Theme", "text": "expression", "start": 381, "end": 391}]}, {"trigger": {"text": "dependent", "start": 1606, "end": 1615}, "arguments": [{"role": "Theme", "text": "modulate", "start": 1506, "end": 1514}]}]}}, "schema": []}
{"input": "Altered DNA-binding specificity mutants of EKLF and Sp1 show that EKLF is an activator of the beta-globin locus control region in vivo. \nThe locus control region of the beta-globin cluster contains five DNase I hypersensitive sites (5'HS1-5) required for locus activation. 5'HS3 contains six G-rich motifs that are essential for its activity. Members of a protein family, characterized by three zinc fingers highly homologous to those found in transcription factor Sp1, interact with these motifs. Because point mutagenesis cannot distinguish between family members, it is not known which protein activates 5'HS3. We show that the function of such closely related proteins can be distinguished in vivo by matching point mutations in 5'HS3 with amino acid changes in the zinc fingers of Sp1 and EKLF. Testing their activity in transgenic mice shows that EKLF is a direct activator of 5'HS3. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding specificity", "start": 12, "end": 31}, "arguments": [{"role": "Theme", "text": "EKLF", "start": 43, "end": 47}]}, {"trigger": {"text": "binding specificity", "start": 12, "end": 31}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 52, "end": 55}]}, {"trigger": {"text": "interact", "start": 470, "end": 478}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 465, "end": 468}]}], "positive regulation": [{"trigger": {"text": "required", "start": 242, "end": 250}, "arguments": [{"role": "Theme", "text": "activation", "start": 261, "end": 271}]}, {"trigger": {"text": "activation", "start": 261, "end": 271}, "arguments": [{"role": "Theme", "text": "beta-globin", "start": 169, "end": 180}]}, {"trigger": {"text": "essential", "start": 315, "end": 324}, "arguments": [{"role": "Theme", "text": "activation", "start": 261, "end": 271}]}]}}, "schema": []}
{"input": "Activation of distinct transcription factors in neutrophils by bacterial LPS, interferon-gamma, and GM-CSF and the necessity to overcome the action of endogenous proteases. \nHuman neutrophils can be induced to actively transcribe a number of early-response genes, in particular those encoding cytokines, chemokines, and the high-affinity surface receptor for IgG, FcgammaRI. Although little is known to date about the regulation of gene transcription in neutrophils, several indications point to a role for distinct transcription factors, such as members of the NF-kappaB and STAT families. In this study, we investigated whether these transcription factors become activated under stimulatory conditions which are known to induce gene transcription in neutrophils. Unexpectedly, we found that conventional procedures employed to prepare cellular extracts cause the release of proteolytic activities that are normally stored in intracellular granules, resulting in the degradation of various NF-kappaB/Rel and STAT proteins. To circumvent this problem, we developed an alternative procedure which allowed us to show that in neutrophils, LPS and TNFalpha induce a NF-kappaB DNA-binding activity which essentially consists of p50/RelA dimers, and that IFNgamma promotes the binding of STAT1 homodimers to the IFNgamma response region of the FcgammaRI promoter. Moreover, we report that neutrophil stimulation with GM-CSF results in the formation of a STAT5-containing DNA-binding activity. Collectively, the current findings open new perspectives about mechanisms that are likely to regulate gene transcription in neutrophils. In addition, the procedure described herein could prove useful in other cell types that express high levels of endogenous proteases. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1176, "end": 1183}, "arguments": [{"role": "Theme", "text": "p50", "start": 1223, "end": 1226}]}, {"trigger": {"text": "binding", "start": 1176, "end": 1183}, "arguments": [{"role": "Theme", "text": "RelA", "start": 1227, "end": 1231}]}, {"trigger": {"text": "binding", "start": 1271, "end": 1278}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 1282, "end": 1287}]}], "positive regulation": [{"trigger": {"text": "Activation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "GM-CSF", "start": 100, "end": 106}]}, {"trigger": {"text": "Activation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "interferon-gamma", "start": 78, "end": 94}]}, {"trigger": {"text": "induced", "start": 199, "end": 206}, "arguments": [{"role": "Theme", "text": "transcribe", "start": 219, "end": 229}]}, {"trigger": {"text": "promotes", "start": 1258, "end": 1266}, "arguments": [{"role": "Cause", "text": "IFNgamma", "start": 1249, "end": 1257}, {"role": "Theme", "text": "binding", "start": 1271, "end": 1278}]}], "transcription": [{"trigger": {"text": "transcribe", "start": 219, "end": 229}, "arguments": [{"role": "Theme", "text": "FcgammaRI", "start": 364, "end": 373}]}]}}, "schema": []}
{"input": "Transcription factor activation in lymphokine activated killer cells and lymphocytes from patients receiving IL-2 immunotherapy. \nAdministration of the cytokine interleukin-2 (IL-2) can result in therapeutic benefits for individuals with renal cell carcinoma and melanoma. Here we report an analysis of the transcription factor families AP-1, Sp1, NF-kappaB, and signal transducers and activators of transcription (STAT) in cancer patients' lymphocytes before and after IL-2 immunotherapy, as assessed by a gel-shift assay. An in vitro surrogate of IL-2 immunotherapy is the incubation of fresh peripheral blood mononuclear cells (PBMC) from healthy individuals in IL-2 for several days, resulting in the production of lymphokine-activated killer (LAK) activity in these cultures. One purpose of this study was to describe the profile of transcription factor activation in these different populations, and assess whether the patterns observed correlated with functional differences in these cells. Prior to in vivo IL-2 administration, the typical binding pattern of transcription factors in PBMC from patients resembled that seen in fresh PBMC from healthy individuals. Over a 3-week course of IL-2 therapy, in most patients the binding patterns of AP-1 , Sp1, and NF-kappaB proteins changed to resemble those seen in PBMC activated by IL-2 in vitro. However, the cells obtained from IL-2-treated patients did not have low-level constitutive expression of STAT binding factors as did LAK cells. When these patient cells were further stimulated by IL-2 in vitro, additional differences in STAT induction patterns were noted. These data provide further information on the molecular events occurring in immune cells generated through in vivo and in vitro administration of IL-2, and further document that there is not a precise congruence between PBMC activated in vivo and in vitro by IL-2. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 1230, "end": 1237}, "arguments": [{"role": "Theme", "text": "Sp1", "start": 1257, "end": 1260}]}], "positive regulation": [{"trigger": {"text": "changed", "start": 1285, "end": 1292}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1195, "end": 1199}, {"role": "Theme", "text": "binding", "start": 1230, "end": 1237}]}]}}, "schema": []}
{"input": "A critical role of the p75 tumor necrosis factor receptor (p75TNF-R) in organ inflammation independent of TNF, lymphotoxin alpha, or the p55TNF-R. \nDespite overwhelming evidence that enhanced production of the p75 tumor necrosis factor receptor (p75TNF-R) accompanies development of specific human inflammatory pathologies such as multi-organ failure during sepsis, inflammatory liver disease, pancreatitis, respiratory distress syndrome, or AIDS, the function of this receptor remains poorly defined in vivo. We show here that at levels relevant to human disease, production of the human p75TNF-R in transgenic mice results in a severe inflammatory syndrome involving mainly the pancreas, liver, kidney, and lung, and characterized by constitutively increased NF-kappaB activity in the peripheral blood mononuclear cell compartment. This process is shown to evolve independently of the presence of TNF, lymphotoxin alpha, or the p55TNF-R, although coexpression of a human TNF transgene accelerated pathology. These results establish an independent role for enhanced p75TNF-R production in the pathogenesis of inflammatory disease and implicate the direct involvement of this receptor in a wide range of human inflammatory pathologies. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 192, "end": 202}, "arguments": [{"role": "Theme", "text": "p75TNF-R", "start": 246, "end": 254}]}, {"trigger": {"text": "production", "start": 565, "end": 575}, "arguments": [{"role": "Theme", "text": "p75TNF-R", "start": 589, "end": 597}]}, {"trigger": {"text": "production", "start": 1076, "end": 1086}, "arguments": [{"role": "Theme", "text": "p75TNF-R", "start": 1067, "end": 1075}]}], "positive regulation": [{"trigger": {"text": "enhanced", "start": 183, "end": 191}, "arguments": [{"role": "Theme", "text": "production", "start": 192, "end": 202}]}, {"trigger": {"text": "enhanced", "start": 1058, "end": 1066}, "arguments": [{"role": "Theme", "text": "production", "start": 1076, "end": 1086}]}], "regulation": [{"trigger": {"text": "evolve independently", "start": 859, "end": 879}, "arguments": [{"role": "Theme", "text": "production", "start": 565, "end": 575}, {"role": "Cause", "text": "lymphotoxin alpha", "start": 904, "end": 921}]}, {"trigger": {"text": "evolve independently", "start": 859, "end": 879}, "arguments": [{"role": "Theme", "text": "production", "start": 565, "end": 575}, {"role": "Cause", "text": "p55TNF-R", "start": 930, "end": 938}]}, {"trigger": {"text": "evolve independently", "start": 859, "end": 879}, "arguments": [{"role": "Theme", "text": "production", "start": 565, "end": 575}]}]}}, "schema": []}
{"input": "Potent inhibition of HIV type 1 replication by an antiinflammatory alkaloid, cepharanthine, in chronically infected monocytic cells. \nCepharanthine is a biscoclaurine alkaloid isolated from Stephania cepharantha Hayata and has been shown to have antiinflammatory, antiallergic, and immunomodulatory activities in vivo. As several inflammatory cytokines and oxidative stresses are involved in the pathogenesis of HIV-1 infection, we investigated the inhibitory effects of cepharanthine on tumor necrosis factor alpha (TNF-alpha)- and phorbol 12-myristate 13-acetate (PMA)-induced HIV-1 replication in chronically infected cell lines. Two chronically HIV-1-infected cell lines, U1 (monocytic) and ACH-2 (T lymphocytic), were stimulated with TNF-alpha or PMA and cultured in the presence of various concentrations of the compound. HIV-1 replication was determined by p24 antigen level. The inhibitory effects of cepharanthine on HIV-1 long terminal repeat (LTR)-driven gene expression and nuclear factor kappaB (NF-kappaB) activation were also examined. Cepharanthine dose dependently inhibited HIV-1 replication in TNF-alpha- and PMA-stimulated U1 cells but not in ACH-2 cells. Its 50% effective and cytotoxic concentrations were 0.016 and 2.2 microg/ml in PMA-stimulated U1 cells, respectively. Cepharanthine was found to suppress HIV-1 LTR-driven gene expression through the inhibition of NF-kappaB activation. These results indicate that cepharanthine is a highly potent inhibitor of HIV-1 replication in a chronically infected monocytic cell line. Since biscoclaurine alkaloids, containing cepharanthine as a major component, are widely used for the treatment of patients with various inflammatory diseases in Japan, cepharanthine should be further pursued for its chemotherapeutic potential in HIV-1-infected patients. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Prostaglandin E2 Up-regulates HIV-1 long terminal repeat-driven gene activity in T cells via NF-kappaB-dependent and -independent signaling pathways. \nReplication of human immunodeficiency virus type-1 (HIV-1) is highly dependent on the state of activation of the infected cells and is modulated by interactions between viral and host cellular factors. Prostaglandin E2 (PGE2), a pleiotropic immunomodulatory molecule, is observed at elevated levels during HIV-1 infection as well as during the course of other pathogenic infections. In 1G5, a Jurkat-derived T cell line stably transfected with a luciferase gene driven by HIV-1 long terminal repeat (LTR), we found that PGE2 markedly enhanced HIV-1 LTR-mediated reporter gene activity. Experiments have been conducted to identify second messengers involved in this PGE2-dependent up-regulating effect on the regulatory element of HIV-1. In this study, we present evidence indicating that signal transduction pathways induced by PGE2 necessitate the participation of cyclic AMP, protein kinase A, and Ca2+. Experiments conducted with different HIV-1 LTR-based vectors suggested that PGE2-mediated activation effect on HIV-1 transcription was transduced via both NF-kappaB-dependent and -independent signaling pathways. The involvement of NF-kappaB in the PGE2-dependent activating effect on HIV-1 transcription was further confirmed using a kappaB-regulated luciferase encoding vector and by electrophoretic mobility shift assays. Results from Northern blot and flow cytometric analyses, as well as the use of a selective antagonist indicated that PGE2 modulation of HIV-1 LTR-driven reporter gene activity in studied T lymphoid cells is transduced via the EP4 receptor subtype. These results suggest that secretion of PGE2 by macrophages in response to infection or inflammatory activators could induce signaling events resulting in activation of proviral DNA present into T cells latently infected with HIV-1. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Fcgamma receptor-mediated mitogen-activated protein kinase activation in monocytes is independent of Ras. \nReceptors for the Fc portion of immunoglobulin molecules (FcR) present on leukocyte cell membranes mediate a large number of cellular responses that are very important in host defense, including phagocytosis, cell cytotoxicity, production and secretion of inflammatory mediators, and modulation of the immune response. Cross-linking of FcR with immune complexes leads, first to activation of protein-tyrosine kinases. The molecular events that follow and that transduce signals from these receptors to the nucleus are still poorly defined. We have investigated the signal transduction pathway from Fc receptors that leads to gene activation and production of cytokines in monocytes. Cross-linking of FcR, on the THP-1 monocytic cell line, by immune complexes resulted in both activation of the transcription factor NF-kappaB and interleukin 1 production. These responses were completely blocked by tyrosine kinase inhibitors. In contrast, expression of dominant negative mutants of Ras and Raf-1, in these cells, did not have any effect on FcR-mediated nuclear factor activation, suggesting that the mitogen-activated protein kinase (MAPK) signaling pathway was not used by these receptors. However, MAPK activation was easily detected by in vitro kinase assays, after FcR cross-linking with immune complexes. Using the specific MAPK/extracellular signal-regulated kinase kinase (MAPK kinase) inhibitor PD98059, we found that MAPK activation is necessary for FcR-dependent activation of the nuclear factor NF-kappaB. These results strongly suggest that the signaling pathway from Fc receptors leading to expression of different genes important to leukocyte biology, initiates with tyrosine kinases and requires MAPK activation; but in contrast to other tyrosine kinase receptors, FcR-mediated MAPK activation does not involve Ras and Raf. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1046, "end": 1056}, "arguments": [{"role": "Theme", "text": "Raf-1", "start": 1097, "end": 1102}]}]}}, "schema": []}
{"input": "Differential RNA display identifies novel genes associated with decreased vitamin D receptor expression. \nTo characterize further the function of the intracellular vitamin D receptor (VDR), we have developed stable transfectant variants of a vitamin D-responsive cell line (U937) which express either decreased or increased numbers of VDR. In this study we have analyzed changes in gene expression associated with this variable VDR expression. Initial experiments indicated that a 50% decrease in VDR levels was associated with a 2-fold increase in cell proliferation and a similar rise in c-myc mRNA expression. Further studies were carried out using differential RNA display (DD). Sequence analysis of DD products revealed two cDNAs with identity to known gene products: the catalytic sub-unit of DNA-protein kinase (DNA-PK(CS)), and the peroxisomal enzyme 17beta-hydroxysteroid dehydrogenase type IV (17beta-HSD IV). Northern analysis confirmed that expression of both mRNAs was reduced in cells with decreased numbers of VDR. Down-regulation of 17beta-HSD IV mRNA expression was associated with enhanced estradiol inactivation by U937 cells, suggesting a link between estrogenic pathways and cell proliferation. Further Northern analyses indicated that there was no significant change in 17beta-HSD IV or DNA-PK(CS) mRNA levels following treatment with 1,25(OH)2D3, although expression of both genes varied with changes in cell proliferation. These data suggest that, in addition to its established role as a hormone-dependent trans-activator, VDR may influence gene expression by ligand-independent mechanisms. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 93, "end": 103}, "arguments": [{"role": "Theme", "text": "vitamin D receptor", "start": 74, "end": 92}]}, {"trigger": {"text": "express", "start": 286, "end": 293}, "arguments": [{"role": "Theme", "text": "VDR", "start": 335, "end": 338}]}, {"trigger": {"text": "expression", "start": 432, "end": 442}, "arguments": [{"role": "Theme", "text": "VDR", "start": 428, "end": 431}]}, {"trigger": {"text": "expression", "start": 1379, "end": 1389}, "arguments": [{"role": "Theme", "text": "17beta-HSD IV", "start": 1292, "end": 1305}]}, {"trigger": {"text": "expression", "start": 1379, "end": 1389}, "arguments": [{"role": "Theme", "text": "DNA-PK(CS)", "start": 1309, "end": 1319}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 64, "end": 73}, "arguments": [{"role": "Theme", "text": "expression", "start": 93, "end": 103}]}, {"trigger": {"text": "numbers", "start": 324, "end": 331}, "arguments": [{"role": "Theme", "text": "express", "start": 286, "end": 293}]}, {"trigger": {"text": "decrease", "start": 485, "end": 493}, "arguments": [{"role": "Theme", "text": "VDR", "start": 497, "end": 500}]}, {"trigger": {"text": "reduced", "start": 982, "end": 989}, "arguments": [{"role": "Theme", "text": "expression", "start": 953, "end": 963}, {"role": "Cause", "text": "decreased numbers", "start": 1004, "end": 1021}]}, {"trigger": {"text": "decreased numbers", "start": 1004, "end": 1021}, "arguments": [{"role": "Theme", "text": "VDR", "start": 1025, "end": 1028}]}, {"trigger": {"text": "Down-regulation", "start": 1030, "end": 1045}, "arguments": [{"role": "Theme", "text": "expression", "start": 1068, "end": 1078}]}], "positive regulation": [{"trigger": {"text": "increased numbers", "start": 314, "end": 331}, "arguments": [{"role": "Theme", "text": "express", "start": 286, "end": 293}]}, {"trigger": {"text": "rise", "start": 582, "end": 586}, "arguments": [{"role": "Theme", "text": "expression", "start": 601, "end": 611}]}], "regulation": [{"trigger": {"text": "change", "start": 1282, "end": 1288}, "arguments": [{"role": "Theme", "text": "17beta-HSD IV", "start": 1292, "end": 1305}]}, {"trigger": {"text": "change", "start": 1282, "end": 1288}, "arguments": [{"role": "Theme", "text": "DNA-PK(CS)", "start": 1309, "end": 1319}]}], "transcription": [{"trigger": {"text": "expression", "start": 601, "end": 611}, "arguments": [{"role": "Theme", "text": "c-myc", "start": 590, "end": 595}]}, {"trigger": {"text": "expression", "start": 953, "end": 963}, "arguments": [{"role": "Theme", "text": "DNA-PK(CS)", "start": 819, "end": 829}]}, {"trigger": {"text": "expression", "start": 953, "end": 963}, "arguments": [{"role": "Theme", "text": "17beta-HSD IV", "start": 904, "end": 917}]}, {"trigger": {"text": "expression", "start": 1068, "end": 1078}, "arguments": [{"role": "Theme", "text": "17beta-HSD IV", "start": 1049, "end": 1062}]}]}}, "schema": []}
{"input": "Downstream activation of a TATA-less promoter by Oct-2, Bob1, and NF-kappaB directs expression of the homing receptor BLR1 to mature B cells. \nThe chemokine receptor, BLR1, is a major regulator of the microenvironmental homing of B cells in lymphoid organs. In vitro studies identify three essential elements of the TATA-less blr1 core promoter that confer cell type- and differentiation-specific expression in the B cells of both humans and mice, a functional promoter region (-36 with respect to the transcription start site), a NF-kappaB motif (+44), and a noncanonical octamer motif (+157). The importance of these sites was confirmed by in vivo studies in gene-targeted mice deficient of either Oct-2, Bob1, or both NF-kappaB subunits p50 and p52. In all of these animals, the expression of BLR1 was reduced or absent. In mice deficient only of p52/NF-kappaB, BLR1 expression was unaffected. Thus our data demonstrate that BLR1 is a target gene for Oct-2, Bob1, and members of the NF-kappaB/Rel family and provides a link to the impaired B cell functions in mice deficient for these factors. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 84, "end": 94}, "arguments": [{"role": "Theme", "text": "BLR1", "start": 118, "end": 122}]}, {"trigger": {"text": "expression", "start": 397, "end": 407}, "arguments": [{"role": "Theme", "text": "blr1", "start": 326, "end": 330}]}, {"trigger": {"text": "expression", "start": 782, "end": 792}, "arguments": [{"role": "Theme", "text": "BLR1", "start": 796, "end": 800}]}, {"trigger": {"text": "expression", "start": 870, "end": 880}, "arguments": [{"role": "Theme", "text": "BLR1", "start": 865, "end": 869}]}, {"trigger": {"text": "deficient", "start": 1068, "end": 1077}, "arguments": [{"role": "Theme", "text": "Oct-2", "start": 954, "end": 959}]}, {"trigger": {"text": "deficient", "start": 1068, "end": 1077}, "arguments": [{"role": "Theme", "text": "Bob1", "start": 961, "end": 965}]}], "negative regulation": [{"trigger": {"text": "reduced", "start": 805, "end": 812}, "arguments": [{"role": "Theme", "text": "expression", "start": 782, "end": 792}]}], "positive regulation": [{"trigger": {"text": "directs", "start": 76, "end": 83}, "arguments": [{"role": "Theme", "text": "expression", "start": 84, "end": 94}]}, {"trigger": {"text": "confer", "start": 350, "end": 356}, "arguments": [{"role": "Theme", "text": "expression", "start": 397, "end": 407}]}], "regulation": [{"trigger": {"text": "unaffected", "start": 885, "end": 895}, "arguments": [{"role": "Theme", "text": "expression", "start": 870, "end": 880}]}, {"trigger": {"text": "target", "start": 938, "end": 944}, "arguments": [{"role": "Theme", "text": "BLR1", "start": 928, "end": 932}, {"role": "Cause", "text": "Oct-2", "start": 954, "end": 959}]}, {"trigger": {"text": "target", "start": 938, "end": 944}, "arguments": [{"role": "Theme", "text": "BLR1", "start": 928, "end": 932}, {"role": "Cause", "text": "Bob1", "start": 961, "end": 965}]}, {"trigger": {"text": "target", "start": 938, "end": 944}, "arguments": [{"role": "Theme", "text": "BLR1", "start": 928, "end": 932}]}]}}, "schema": []}
{"input": "Interaction of sickle erythrocytes with endothelial cells in the presence of endothelial cell conditioned medium induces oxidant stress leading to transendothelial migration of monocytes. \nThe abnormal adherence of sickle red blood cells (SS RBC) to endothelial cells has been thought to contribute to vascular occlusion, a major cause of morbidity in sickle cell disease (SCD). We determined whether the interaction of SS RBC with cultured endothelial cells induced cellular oxidant stress that would culminate in expression of cell adhesion molecules (CAMs) involved in the adhesion and diapedesis of monocytes and the adherence of SS reticulocytes. We showed that the interaction of SS RBC at 2% concentration in the presence of multimers of von Willebrand factor (vWf), derived from endothelial cell-derived conditioned medium (E-CM) with cultured human umbilical vein endothelial cells (HUVEC), resulted in a fivefold increased formation of thiobarbituric acid-reactive substances (TBARS) and activation of the transcription factor NF-kB, both indicators of cellular oxidant stress. Normal RBC show none of these phenomena. The oxidant stress-induced signaling resulted in an increased surface expression of a subset of CAMs, ICAM-1, E-selectin, and VCAM-1 in HUVEC. The addition of oxygen radical scavenger enzymes (catalase, superoxide dismutase) and antioxidant (probucol) inhibited these events. Additionally, preincubation of HUVEC with a synthetic peptide Arg-Gly-Asp (RGD) that prevents vWf-mediated adhesion of SS RBC reduced the surface expression of VCAM-1 and NF-kB activation. Furthermore, SS RBC-induced oxidant stress resulted in a twofold increase in the transendothelial migration of both monocyte-like HL-60 cells and human peripheral blood monocytes, and approximately a sixfold increase in platelet-endothelial cell adhesion molecule-1 (PECAM-1) phosphorylation, each of which was blocked by protein kinase C inhibitor and antioxidants. These results suggest that the adherence/contact of SS RBC to endothelial cells in large vessel can generate enhanced oxidant stress leading to increased adhesion and diapedesis of monocytes, as well as heightened adherence of SS reticulocytes, indicating that injury/activation of endothelium can contribute to vaso-occlusion in SCD. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "multimers", "start": 732, "end": 741}, "arguments": [{"role": "Theme", "text": "vWf", "start": 768, "end": 771}]}], "gene expression": [{"trigger": {"text": "expression", "start": 1551, "end": 1561}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1565, "end": 1571}]}], "localization": [{"trigger": {"text": "expression", "start": 1199, "end": 1209}, "arguments": [{"role": "AtLoc", "text": "surface", "start": 1191, "end": 1198}, {"role": "Theme", "text": "ICAM-1", "start": 1231, "end": 1237}]}, {"trigger": {"text": "expression", "start": 1199, "end": 1209}, "arguments": [{"role": "AtLoc", "text": "surface", "start": 1191, "end": 1198}, {"role": "Theme", "text": "E-selectin", "start": 1239, "end": 1249}]}, {"trigger": {"text": "expression", "start": 1199, "end": 1209}, "arguments": [{"role": "AtLoc", "text": "surface", "start": 1191, "end": 1198}, {"role": "Theme", "text": "VCAM-1", "start": 1255, "end": 1261}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1381, "end": 1390}, "arguments": [{"role": "Theme", "text": "resulted in an increased", "start": 1166, "end": 1190}, {"role": "Cause", "text": "catalase", "start": 1322, "end": 1330}]}, {"trigger": {"text": "inhibited", "start": 1381, "end": 1390}, "arguments": [{"role": "Theme", "text": "resulted in an increased", "start": 1166, "end": 1190}, {"role": "Cause", "text": "superoxide dismutase", "start": 1332, "end": 1352}]}, {"trigger": {"text": "inhibited", "start": 1381, "end": 1390}, "arguments": [{"role": "Theme", "text": "resulted in an increased", "start": 1166, "end": 1190}]}, {"trigger": {"text": "reduced", "start": 1531, "end": 1538}, "arguments": [{"role": "Theme", "text": "expression", "start": 1551, "end": 1561}]}, {"trigger": {"text": "blocked", "start": 1905, "end": 1912}, "arguments": [{"role": "Theme", "text": "increase", "start": 1802, "end": 1810}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 1870, "end": 1885}, "arguments": [{"role": "Theme", "text": "PECAM-1", "start": 1861, "end": 1868}]}], "positive regulation": [{"trigger": {"text": "resulted in an increased", "start": 1166, "end": 1190}, "arguments": [{"role": "Theme", "text": "expression", "start": 1199, "end": 1209}]}, {"trigger": {"text": "increase", "start": 1802, "end": 1810}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1870, "end": 1885}]}]}}, "schema": []}
{"input": "Tobacco smoke induces coordinate activation of HSF and inhibition of NFkappaB in human monocytes: effects on TNFalpha release. \nTobacco smoke (TS) exposure is a major risk factor for human disease, and macrophages of healthy smokers have a depressed capacity to release cytokines, including tumor necrosis factor (TNF)alpha. TS induces the synthesis of heat shock (HS)/stress proteins (HSP), and, in particular, of Hsp70. We determined whether Hsp70 induction by TS was mediated by the activation of the HS transcription factor, HSF. HSF activation has been shown to inhibit NFkappaB. Thus, we also determined the effects of TS on NFkappaB. U937 cells and human peripheral blood monocytes were exposed to TS, binding activities of the respective transcription factors were analyzed, and Hsp70 expression and TNFalpha release were determined in parallel. TS activated HSF, which was associated with Hsp70 overexpression and inhibition of NFkappaB binding activity and TNFalpha release. The altered cytokine profile observed in smokers may relate to an HSF/Hsp70-mediated inhibition of NFkappaB activity. Copyright 1998 Academic Press. ", "output": {"json_structures": {"localization": [{"trigger": {"text": "release", "start": 118, "end": 125}, "arguments": [{"role": "Theme", "text": "TNFalpha", "start": 109, "end": 117}]}, {"trigger": {"text": "release", "start": 817, "end": 824}, "arguments": [{"role": "Theme", "text": "TNFalpha", "start": 808, "end": 816}]}, {"trigger": {"text": "release", "start": 976, "end": 983}, "arguments": [{"role": "Theme", "text": "TNFalpha", "start": 967, "end": 975}]}], "regulation": [{"trigger": {"text": "effects", "start": 98, "end": 105}, "arguments": [{"role": "Theme", "text": "release", "start": 118, "end": 125}]}]}}, "schema": []}
{"input": "Transcriptional regulation of the beta-casein gene by cytokines: cross-talk between STAT5 and other signaling molecules. \nThe beta-casein promoter has been widely used to monitor the activation of STAT (signal transducer and activator of transcription)5 since STAT5 was originally found as a mediator of PRL-inducible beta-casein expression. However, not only is expression of the beta-casein gene regulated by STAT5 but it is also affected by other molecules such as glucocorticoid and Ras. In this report, we describe the transcriptional regulation of the beta-casein gene by cytokines in T cells. We have found that the beta-casein gene is expressed in a cytotoxic T cell line, CTLL-2, in response to interleukin-2 (IL-2), which activates STAT5. While IL-4 does not activate STAT5, it induces expression of STAT5-regulated genes in CTLL-2, i.e. beta-casein, a cytokine-inducible SH2-containing protein (CIS), and oncostatin M (OSM), suggesting that STAT6 activated by IL-4 substitutes for the function of STAT5 in T cells. IL-2-induced beta-casein expression was enhanced by dexamethasone, and this synergistic effect of Dexamethasone requires the sequence between -155 and -193 in the beta-casein promoter. Coincidentally, a deletion of this region enhanced the IL-2-induced expression of beta-casein. Expression of an active form of Ras, Ras(G12V), suppressed the IL-2-induced beta-casein and OSM gene expression, and the negative effect of Ras is mediated by the region between -105 and -193 in the beta-casein promoter. In apparent contradiction, expression of a dominant negative form of Ras, RasN17, also inhibited IL-2-induced activation of the promoter containing the minimal beta-casein STAT5 element as well as the promoters of CIS and OSM. In addition, Ras(G12V) complemented signaling by an erythropoietin receptor mutant defective in Ras activation and augmented the activation of the beta-casein promoter by the mutant erythropoietin receptor signaling, suggesting a possible role of Ras in Stat5-mediated gene expression. These results collectively reveal a complex interaction of STAT5 with other signaling pathways and illustrate that regulation of gene expression requires integration of opposing signals. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 330, "end": 340}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 318, "end": 329}]}, {"trigger": {"text": "expression", "start": 363, "end": 373}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 381, "end": 392}]}, {"trigger": {"text": "expressed", "start": 643, "end": 652}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 623, "end": 634}]}, {"trigger": {"text": "expression", "start": 796, "end": 806}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 848, "end": 859}]}, {"trigger": {"text": "expression", "start": 796, "end": 806}, "arguments": [{"role": "Theme", "text": "CIS", "start": 906, "end": 909}]}, {"trigger": {"text": "expression", "start": 796, "end": 806}, "arguments": [{"role": "Theme", "text": "OSM", "start": 930, "end": 933}]}, {"trigger": {"text": "expression", "start": 1051, "end": 1061}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 1039, "end": 1050}]}, {"trigger": {"text": "expression", "start": 1279, "end": 1289}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 1293, "end": 1304}]}, {"trigger": {"text": "Expression", "start": 1306, "end": 1316}, "arguments": [{"role": "Theme", "text": "Ras(G12V)", "start": 1343, "end": 1352}]}, {"trigger": {"text": "expression", "start": 1407, "end": 1417}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 1382, "end": 1393}]}, {"trigger": {"text": "expression", "start": 1407, "end": 1417}, "arguments": [{"role": "Theme", "text": "OSM", "start": 1398, "end": 1401}]}], "negative regulation": [{"trigger": {"text": "deletion", "start": 1229, "end": 1237}, "arguments": [{"role": "Site", "text": "sequence between -155 and -193", "start": 1151, "end": 1181}, {"role": "Theme", "text": "beta-casein", "start": 1189, "end": 1200}]}, {"trigger": {"text": "suppressed", "start": 1354, "end": 1364}, "arguments": [{"role": "Cause", "text": "Expression", "start": 1306, "end": 1316}, {"role": "Theme", "text": "induced", "start": 1374, "end": 1381}]}, {"trigger": {"text": "inhibited", "start": 1614, "end": 1623}, "arguments": [{"role": "Cause", "text": "RasN17", "start": 1601, "end": 1607}, {"role": "Theme", "text": "activation", "start": 1637, "end": 1647}]}], "positive regulation": [{"trigger": {"text": "activation", "start": 183, "end": 193}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 126, "end": 137}, {"role": "Site", "text": "promoter", "start": 138, "end": 146}, {"role": "Cause", "text": "STAT (signal transducer and activator of transcription)5", "start": 197, "end": 253}]}, {"trigger": {"text": "mediator", "start": 292, "end": 300}, "arguments": [{"role": "Cause", "text": "STAT5", "start": 260, "end": 265}, {"role": "Theme", "text": "inducible", "start": 308, "end": 317}]}, {"trigger": {"text": "inducible", "start": 308, "end": 317}, "arguments": [{"role": "Cause", "text": "PRL", "start": 304, "end": 307}, {"role": "Theme", "text": "expression", "start": 330, "end": 340}]}, {"trigger": {"text": "in response", "start": 689, "end": 700}, "arguments": [{"role": "Theme", "text": "expressed", "start": 643, "end": 652}, {"role": "Cause", "text": "IL-2", "start": 719, "end": 723}]}, {"trigger": {"text": "activates", "start": 732, "end": 741}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 719, "end": 723}, {"role": "Theme", "text": "STAT5", "start": 742, "end": 747}]}, {"trigger": {"text": "activate", "start": 769, "end": 777}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 755, "end": 759}, {"role": "Theme", "text": "STAT5", "start": 778, "end": 783}]}, {"trigger": {"text": "induces", "start": 788, "end": 795}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 755, "end": 759}, {"role": "Theme", "text": "expression", "start": 796, "end": 806}]}, {"trigger": {"text": "activated", "start": 958, "end": 967}, "arguments": [{"role": "Theme", "text": "STAT6", "start": 952, "end": 957}, {"role": "Cause", "text": "IL-4", "start": 971, "end": 975}]}, {"trigger": {"text": "induced", "start": 1031, "end": 1038}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1026, "end": 1030}, {"role": "Theme", "text": "expression", "start": 1051, "end": 1061}]}, {"trigger": {"text": "enhanced", "start": 1066, "end": 1074}, "arguments": [{"role": "Theme", "text": "induced", "start": 1031, "end": 1038}]}, {"trigger": {"text": "enhanced", "start": 1253, "end": 1261}, "arguments": [{"role": "Cause", "text": "deletion", "start": 1229, "end": 1237}, {"role": "Theme", "text": "induced", "start": 1271, "end": 1278}]}, {"trigger": {"text": "induced", "start": 1271, "end": 1278}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1266, "end": 1270}, {"role": "Theme", "text": "expression", "start": 1279, "end": 1289}]}, {"trigger": {"text": "induced", "start": 1374, "end": 1381}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1369, "end": 1373}, {"role": "Theme", "text": "expression", "start": 1407, "end": 1417}]}, {"trigger": {"text": "mediated", "start": 1453, "end": 1461}, "arguments": [{"role": "Theme", "text": "suppressed", "start": 1354, "end": 1364}, {"role": "CSite", "text": "region between -105 and -193", "start": 1469, "end": 1497}, {"role": "Cause", "text": "beta-casein", "start": 1505, "end": 1516}]}, {"trigger": {"text": "activation", "start": 1637, "end": 1647}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1624, "end": 1628}, {"role": "Theme", "text": "CIS", "start": 1741, "end": 1744}]}, {"trigger": {"text": "activation", "start": 1637, "end": 1647}, "arguments": [{"role": "Cause", "text": "IL-2", "start": 1624, "end": 1628}, {"role": "Theme", "text": "OSM", "start": 1749, "end": 1752}]}, {"trigger": {"text": "augmented", "start": 1869, "end": 1878}, "arguments": [{"role": "Cause", "text": "Ras(G12V)", "start": 1767, "end": 1776}, {"role": "Theme", "text": "activation", "start": 1883, "end": 1893}]}, {"trigger": {"text": "activation", "start": 1883, "end": 1893}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 1901, "end": 1912}, {"role": "Site", "text": "promoter", "start": 1913, "end": 1921}, {"role": "Cause", "text": "signaling", "start": 1960, "end": 1969}]}], "regulation": [{"trigger": {"text": "Transcriptional regulation", "start": 0, "end": 26}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 34, "end": 45}]}, {"trigger": {"text": "regulated", "start": 398, "end": 407}, "arguments": [{"role": "Theme", "text": "expression", "start": 363, "end": 373}, {"role": "Cause", "text": "STAT5", "start": 411, "end": 416}]}, {"trigger": {"text": "affected", "start": 432, "end": 440}, "arguments": [{"role": "Theme", "text": "expression", "start": 363, "end": 373}]}, {"trigger": {"text": "transcriptional regulation", "start": 524, "end": 550}, "arguments": [{"role": "Theme", "text": "beta-casein", "start": 558, "end": 569}]}, {"trigger": {"text": "regulated", "start": 816, "end": 825}, "arguments": [{"role": "Cause", "text": "STAT5", "start": 810, "end": 815}, {"role": "Theme", "text": "beta-casein", "start": 848, "end": 859}]}, {"trigger": {"text": "regulated", "start": 816, "end": 825}, "arguments": [{"role": "Cause", "text": "STAT5", "start": 810, "end": 815}, {"role": "Theme", "text": "CIS", "start": 906, "end": 909}]}, {"trigger": {"text": "regulated", "start": 816, "end": 825}, "arguments": [{"role": "Cause", "text": "STAT5", "start": 810, "end": 815}, {"role": "Theme", "text": "OSM", "start": 930, "end": 933}]}, {"trigger": {"text": "signaling", "start": 1960, "end": 1969}, "arguments": [{"role": "Theme", "text": "erythropoietin receptor", "start": 1936, "end": 1959}]}]}}, "schema": []}
{"input": "Transcription factor NF-kappaB regulation of renal fibrosis during ureteral obstruction. \nIrrespective of the etiology, many kidney diseases result in inflammation and fibrosis of the tubulointerstitium, with the subsequent loss of renal function. To initiate any disease process or for any disease process to progress, there must be changes in the transcription of genes within the affected tissue. The nuclear factor-kappa B (NF-kappaB) family of transcription factors regulates genes involved in inflammation, cell proliferation, and cell differentiation. This review discusses the NF-kappaB transcription factor family in general and the association of NF-kappaB activation with cellular/molecular events of renal inflammation and fibrosis. ", "output": {"json_structures": {}}, "schema": []}
{"input": "TAL1 and LIM-only proteins synergistically induce retinaldehyde dehydrogenase 2 expression in T-cell acute lymphoblastic leukemia by acting as cofactors for GATA3. \nPreviously, we have shown that TAL1 and the LIM-only protein gene (LMO) are regularly coactivated in T-cell acute lymphoblastic leukemia (T-ALL). This observation is likely to relate to the findings that TAL1 and LMO are highly synergistic in T-cell tumorigenesis in double-transgenic mice. To understand the molecular mechanisms of functional synergy between TAL1 and LMO in tumorigenesis and transcriptional regulation, we tried to identify downstream target genes regulated by TAL1 and LMO by a subtractive PCR method. One of the isolated genes, that for retinaldehyde dehydrogenase 2 (RALDH2), was regularly expressed in most of the T-ALL cell lines that coexpressed TAL1 and LMO. Exogenously transfected TAL1 and LMO, but not either alone, induced RALDH2 expression in a T-ALL cell line, HPB-ALL, not expressing endogeneous TAL1 or LMO. The RALDH2 transcripts in T-ALL were, however, mostly initiated within the second intron. Promoter analysis revealed that a GATA site in a cryptic promoter in the second intron was essential and sufficient for the TAL1- and LMO-dependent transcriptional activation, and GATA3 binds to this site. In addition, forced expression of GATA3 potentiated the induction of RALDH2 by TAL1 and LMO, and these three factors formed a complex in vivo. Furthermore, a TAL1 mutant not binding to DNA also activated the transcription of RALDH2 in the presence of LMO and GATA3. Collectively, we have identified the RALDH2 gene as a first example of direct transcriptional target genes regulated by TAL1 and LMO in T-ALL. In this case, TAL1 and LMO act as cofactors for GATA3 to activate the transcription of RALDH2. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 1283, "end": 1288}, "arguments": [{"role": "Theme", "text": "GATA3", "start": 1277, "end": 1282}]}, {"trigger": {"text": "formed a complex", "start": 1420, "end": 1436}, "arguments": [{"role": "Theme", "text": "GATA3", "start": 1337, "end": 1342}, {"role": "Theme2", "text": "TAL1", "start": 1382, "end": 1386}]}, {"trigger": {"text": "binding", "start": 1477, "end": 1484}, "arguments": [{"role": "Theme", "text": "TAL1", "start": 1461, "end": 1465}]}], "gene expression": [{"trigger": {"text": "expression", "start": 80, "end": 90}, "arguments": [{"role": "Theme", "text": "retinaldehyde dehydrogenase 2", "start": 50, "end": 79}]}, {"trigger": {"text": "expressed", "start": 777, "end": 786}, "arguments": [{"role": "Theme", "text": "RALDH2", "start": 754, "end": 760}]}, {"trigger": {"text": "coexpressed", "start": 824, "end": 835}, "arguments": [{"role": "Theme", "text": "TAL1", "start": 836, "end": 840}]}, {"trigger": {"text": "transfected", "start": 862, "end": 873}, "arguments": [{"role": "Theme", "text": "TAL1", "start": 874, "end": 878}]}, {"trigger": {"text": "expression", "start": 925, "end": 935}, "arguments": [{"role": "Theme", "text": "RALDH2", "start": 918, "end": 924}]}, {"trigger": {"text": "expressing", "start": 971, "end": 981}, "arguments": [{"role": "Theme", "text": "TAL1", "start": 994, "end": 998}]}, {"trigger": {"text": "expression", "start": 1323, "end": 1333}, "arguments": [{"role": "Theme", "text": "GATA3", "start": 1337, "end": 1342}]}], "positive regulation": [{"trigger": {"text": "induce", "start": 43, "end": 49}, "arguments": [{"role": "Theme", "text": "expression", "start": 80, "end": 90}]}, {"trigger": {"text": "coactivated", "start": 251, "end": 262}, "arguments": [{"role": "Theme", "text": "TAL1", "start": 196, "end": 200}]}, {"trigger": {"text": "transfected", "start": 862, "end": 873}, "arguments": [{"role": "Theme", "text": "transfected", "start": 862, "end": 873}]}, {"trigger": {"text": "induced", "start": 910, "end": 917}, "arguments": [{"role": "Cause", "text": "transfected", "start": 862, "end": 873}, {"role": "Theme", "text": "expression", "start": 925, "end": 935}]}, {"trigger": {"text": "induced", "start": 910, "end": 917}, "arguments": [{"role": "Theme", "text": "expression", "start": 925, "end": 935}]}, {"trigger": {"text": "forced", "start": 1316, "end": 1322}, "arguments": [{"role": "Theme", "text": "expression", "start": 1323, "end": 1333}]}, {"trigger": {"text": "potentiated", "start": 1343, "end": 1354}, "arguments": [{"role": "Cause", "text": "forced", "start": 1316, "end": 1322}, {"role": "Theme", "text": "induction", "start": 1359, "end": 1368}]}, {"trigger": {"text": "induction", "start": 1359, "end": 1368}, "arguments": [{"role": "Theme", "text": "RALDH2", "start": 1372, "end": 1378}, {"role": "Cause", "text": "TAL1", "start": 1382, "end": 1386}]}, {"trigger": {"text": "activated", "start": 1497, "end": 1506}, "arguments": [{"role": "Cause", "text": "TAL1", "start": 1461, "end": 1465}, {"role": "Theme", "text": "transcription", "start": 1511, "end": 1524}]}, {"trigger": {"text": "in the presence of", "start": 1535, "end": 1553}, "arguments": [{"role": "Theme", "text": "activated", "start": 1497, "end": 1506}, {"role": "Cause", "text": "GATA3", "start": 1562, "end": 1567}]}, {"trigger": {"text": "activate", "start": 1769, "end": 1777}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1782, "end": 1795}]}], "regulation": [{"trigger": {"text": "regulated", "start": 1676, "end": 1685}, "arguments": [{"role": "Theme", "text": "RALDH2", "start": 1606, "end": 1612}, {"role": "Cause", "text": "TAL1", "start": 1689, "end": 1693}]}], "transcription": [{"trigger": {"text": "initiated", "start": 1061, "end": 1070}, "arguments": [{"role": "Theme", "text": "RALDH2", "start": 1011, "end": 1017}]}, {"trigger": {"text": "transcription", "start": 1511, "end": 1524}, "arguments": [{"role": "Theme", "text": "RALDH2", "start": 1528, "end": 1534}]}, {"trigger": {"text": "transcription", "start": 1782, "end": 1795}, "arguments": [{"role": "Theme", "text": "RALDH2", "start": 1799, "end": 1805}]}]}}, "schema": []}
{"input": "Granulocyte colony-stimulating factor activates a 72-kDa isoform of STAT3 in human neutrophils. \nGranulocyte colony-stimulating factor (G-CSF) signaling involves activation of STATs, proteins that serve the dual function of signal transduction and activation of transcription. We previously demonstrated that G-CSF activated a distinct Stat3-like protein in immature and mature normal myeloid cells, StatG. StatG in normal immature human myeloid cells, i.e. adult CD34+ bone marrow cells, was composed of Stat3beta. This investigation was undertaken to determine the composition of StatG in mature normal human myeloid cells, i.e. polymorphonuclear neutrophilic granulocytes (PMN). These studies revealed that the major protein in extracts of PMN activated by G-CSF to bind the high-affinity serum-inducible element (hSIE) is a 72-kDa protein that cross-reacts with Stat3 monoclonal antibody, which we have designated Stat3gamma. Stat3gamma is derived from Stat3alpha by limited proteolysis and lacks the carboxyl-terminal portion of Stat3alpha. Because this region of Stat3alpha is involved in transcriptional activation, our findings suggest the possibility that Stat3gamma may be transcriptionally inactive and may compete with Stat3alpha for Stat3 binding sites in these terminally differentiated myeloid cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-reacts", "start": 848, "end": 860}, "arguments": [{"role": "Theme", "text": "Stat3gamma", "start": 918, "end": 928}]}, {"trigger": {"text": "binding", "start": 1252, "end": 1259}, "arguments": [{"role": "Theme", "text": "Stat3gamma", "start": 1165, "end": 1175}]}, {"trigger": {"text": "binding", "start": 1252, "end": 1259}, "arguments": [{"role": "Theme", "text": "Stat3alpha", "start": 1231, "end": 1241}]}], "negative regulation": [{"trigger": {"text": "compete", "start": 1218, "end": 1225}, "arguments": [{"role": "Theme", "text": "Stat3alpha", "start": 1231, "end": 1241}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 315, "end": 324}, "arguments": [{"role": "Cause", "text": "G-CSF", "start": 309, "end": 314}, {"role": "Theme", "text": "StatG", "start": 400, "end": 405}]}, {"trigger": {"text": "derived", "start": 944, "end": 951}, "arguments": [{"role": "Theme", "text": "Stat3gamma", "start": 930, "end": 940}, {"role": "Cause", "text": "proteolysis", "start": 979, "end": 990}]}], "protein catabolism": [{"trigger": {"text": "proteolysis", "start": 979, "end": 990}, "arguments": [{"role": "Theme", "text": "Stat3alpha", "start": 957, "end": 967}]}]}}, "schema": []}
{"input": "Differential effects of protein kinase C inhibitors on fibronectin-induced interleukin-beta gene transcription, protein synthesis and secretion in human monocytic cells. \nHuman monocytic cells express interleukin-1beta (IL-1beta) when stimulated with the extracellular matrix glycoprotein, fibronectin (FN). Protein kinase C (PKC) activation is considered important for this process; however, the metabolic steps at which PKC acts upon to mediate the FN-induced IL-1beta response remain unclear. We performed an analysis of the mechanisms by which two PKC inhibitors, Calphostin C and Staurosporine, prevent the FN-induced IL-1beta response. Both inhibitors blocked the secretion of IL-1beta protein into the media of peripheral blood mononuclear cells exposed to FN. Immunoprecipitation analysis revealed that under these circumstances, Calphostin C inhibited the production of IL-1beta protein, whereas Staurosporine allowed protein production, but inhibited its secretion. To determine the mechanisms responsible for these differences, we turned to human U937 promonocytic cells. U937 cells transfected with the human full-length IL-1beta promoter connected to a luciferase reporter gene were submitted to transcription assays, Northern blotting, and DNA electrophoresis mobility gel shift assays. These studies revealed that Calphostin C inhibited the nuclear translocation of the transcription factor activator protein-1 (AP-1) which is considered necessary for FN induction of IL-1beta gene transcription, and prevented the transcription of the IL-1beta gene. In contrast, Staurosporine alone induced AP-1 translocation and stimulation of the gene. Overall, our data indicate that Calphostin C prevents the transcription of the IL-1beta gene thereby inhibiting protein synthesis. Based on the high specificity of this compound for PKC, we conclude that PKC is necessary for FN-induced IL-1beta protein production. In contrast, Staurosporine prevented secretion of IL-1beta by unknown mechanisms. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "express", "start": 193, "end": 200}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 220, "end": 228}]}, {"trigger": {"text": "production", "start": 865, "end": 875}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 879, "end": 887}]}, {"trigger": {"text": "production", "start": 935, "end": 945}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 879, "end": 887}]}, {"trigger": {"text": "synthesis", "start": 1775, "end": 1784}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1734, "end": 1742}]}, {"trigger": {"text": "production", "start": 1908, "end": 1918}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1891, "end": 1899}]}], "localization": [{"trigger": {"text": "secretion", "start": 134, "end": 143}, "arguments": [{"role": "Theme", "text": "interleukin-beta", "start": 75, "end": 91}]}, {"trigger": {"text": "secretion", "start": 670, "end": 679}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 683, "end": 691}]}, {"trigger": {"text": "secretion", "start": 965, "end": 974}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 879, "end": 887}]}, {"trigger": {"text": "secretion", "start": 1957, "end": 1966}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1970, "end": 1978}]}], "negative regulation": [{"trigger": {"text": "prevent", "start": 600, "end": 607}, "arguments": [{"role": "Theme", "text": "induced", "start": 615, "end": 622}]}, {"trigger": {"text": "blocked", "start": 658, "end": 665}, "arguments": [{"role": "Theme", "text": "into", "start": 700, "end": 704}]}, {"trigger": {"text": "inhibited", "start": 851, "end": 860}, "arguments": [{"role": "Theme", "text": "production", "start": 865, "end": 875}]}, {"trigger": {"text": "allowed", "start": 919, "end": 926}, "arguments": [{"role": "Theme", "text": "production", "start": 935, "end": 945}]}, {"trigger": {"text": "inhibited", "start": 951, "end": 960}, "arguments": [{"role": "Theme", "text": "secretion", "start": 965, "end": 974}]}, {"trigger": {"text": "prevented", "start": 1516, "end": 1525}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1530, "end": 1543}]}, {"trigger": {"text": "prevents", "start": 1700, "end": 1708}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1713, "end": 1726}]}, {"trigger": {"text": "inhibiting", "start": 1756, "end": 1766}, "arguments": [{"role": "Cause", "text": "prevents", "start": 1700, "end": 1708}, {"role": "Theme", "text": "synthesis", "start": 1775, "end": 1784}]}, {"trigger": {"text": "prevented", "start": 1947, "end": 1956}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1957, "end": 1966}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 67, "end": 74}, "arguments": [{"role": "Cause", "text": "fibronectin", "start": 55, "end": 66}, {"role": "Theme", "text": "secretion", "start": 134, "end": 143}]}, {"trigger": {"text": "induced", "start": 67, "end": 74}, "arguments": [{"role": "Cause", "text": "fibronectin", "start": 55, "end": 66}, {"role": "Theme", "text": "transcription", "start": 97, "end": 110}]}, {"trigger": {"text": "when", "start": 230, "end": 234}, "arguments": [{"role": "Theme", "text": "express", "start": 193, "end": 200}]}, {"trigger": {"text": "important", "start": 356, "end": 365}, "arguments": [{"role": "Theme", "text": "when", "start": 230, "end": 234}]}, {"trigger": {"text": "acts upon to mediate", "start": 426, "end": 446}, "arguments": [{"role": "Theme", "text": "induced", "start": 454, "end": 461}]}, {"trigger": {"text": "induced", "start": 454, "end": 461}, "arguments": [{"role": "Cause", "text": "FN", "start": 451, "end": 453}, {"role": "Theme", "text": "IL-1beta", "start": 462, "end": 470}]}, {"trigger": {"text": "induced", "start": 615, "end": 622}, "arguments": [{"role": "Cause", "text": "FN", "start": 612, "end": 614}, {"role": "Theme", "text": "IL-1beta", "start": 623, "end": 631}]}, {"trigger": {"text": "into", "start": 700, "end": 704}, "arguments": [{"role": "Theme", "text": "secretion", "start": 670, "end": 679}]}, {"trigger": {"text": "necessary", "start": 1453, "end": 1462}, "arguments": [{"role": "Theme", "text": "induction", "start": 1470, "end": 1479}]}, {"trigger": {"text": "induction", "start": 1470, "end": 1479}, "arguments": [{"role": "Cause", "text": "FN", "start": 1467, "end": 1469}, {"role": "Theme", "text": "transcription", "start": 1497, "end": 1510}]}, {"trigger": {"text": "induced", "start": 1599, "end": 1606}, "arguments": [{"role": "Theme", "text": "stimulation", "start": 1630, "end": 1641}]}, {"trigger": {"text": "stimulation", "start": 1630, "end": 1641}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1551, "end": 1559}]}, {"trigger": {"text": "necessary", "start": 1866, "end": 1875}, "arguments": [{"role": "Theme", "text": "induced", "start": 1883, "end": 1890}]}, {"trigger": {"text": "induced", "start": 1883, "end": 1890}, "arguments": [{"role": "Cause", "text": "FN", "start": 1880, "end": 1882}, {"role": "Theme", "text": "production", "start": 1908, "end": 1918}]}], "regulation": [{"trigger": {"text": "effects", "start": 13, "end": 20}, "arguments": [{"role": "Theme", "text": "induced", "start": 67, "end": 74}]}], "transcription": [{"trigger": {"text": "transcription", "start": 97, "end": 110}, "arguments": [{"role": "Theme", "text": "interleukin-beta", "start": 75, "end": 91}]}, {"trigger": {"text": "transcription", "start": 1497, "end": 1510}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1483, "end": 1491}]}, {"trigger": {"text": "transcription", "start": 1530, "end": 1543}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1551, "end": 1559}]}, {"trigger": {"text": "transcription", "start": 1713, "end": 1726}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 1734, "end": 1742}]}]}}, "schema": []}
{"input": "Cloning of ARE-containing genes by AU-motif-directed display. \nA procedure suitable for cloning labile mRNAs that contain AU motifs is presented (AU-DD). These motifs are regulatory sequences within the so-called AU-rich elements (AREs) often found in 3' untranslated regions of genes such as cytokines, proto-oncogenes, and transcription factors. AU-DD is an AU-motif-directed differential display that permits the identification of ARE-containing genes differentially expressed after cell activation. It has been applied to peripheral blood monocytes and a T cell clone to isolate 59 cDNA fragments associated to activation. Fourteen percent of isolated fragments belong to already known genes that certainly are cytokines and transduction/transcription factors. The remaining 86% correspond to unknown genes of which 92% have been confirmed to be differentially expressed. These data demonstrate the efficiency of the system and support the notion that numerous genes falling into those categories remain unidentified and that they can be cloned by this method. Copyright 1998 Academic Press. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Signaling pathways mediated by the TNF- and cytokine-receptor families target a common cis-element of the IFN regulatory factor 1 promoter. \nCD40 activation of B cells is strongly influenced by the presence of cytokines. However, the molecular basis for the interplay between these distinct stimuli is not clearly delineated. IFN regulatory factor 1 (IRF-1) is a transcription factor activated by either CD40 or cytokines. We have found that these different sets of signals target a common cis-acting element in the promoter of this gene, the IRF-1 gamma-activated site (GAS). Targeting of the IRF-1 GAS is not confined to activation via CD40 but extends to other stimuli that mimic the CD40 signaling cascade, like TNF-alpha and EBV. In contrast to induction of STATs by cytokines, the IRF-1 GAS-binding complex activated by CD40, TNF-alpha, or EBV contains Rel proteins, specifically p50 and p65. In this system, simultaneous exposure to CD40L together with either IL-4 or IFN-gamma does not lead to the activation of novel Rel/STAT complexes. Given the importance of IRF-1 in a variety of biologic functions from proliferation to apoptosis, our findings support the notion that modulation of IRF-1 levels may be a critical control point in B cell activation. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "contains", "start": 850, "end": 858}, "arguments": [{"role": "Theme", "text": "p50", "start": 886, "end": 889}]}, {"trigger": {"text": "contains", "start": 850, "end": 858}, "arguments": [{"role": "Theme", "text": "p65", "start": 894, "end": 897}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 384, "end": 393}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 351, "end": 356}, {"role": "Cause", "text": "CD40", "start": 404, "end": 408}]}, {"trigger": {"text": "activated", "start": 384, "end": 393}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 351, "end": 356}]}, {"trigger": {"text": "activation", "start": 623, "end": 633}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 351, "end": 356}, {"role": "Cause", "text": "CD40", "start": 638, "end": 642}]}, {"trigger": {"text": "activation", "start": 623, "end": 633}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 351, "end": 356}, {"role": "Cause", "text": "TNF-alpha", "start": 716, "end": 725}]}, {"trigger": {"text": "activation", "start": 623, "end": 633}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 351, "end": 356}]}, {"trigger": {"text": "activated", "start": 813, "end": 822}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 787, "end": 792}, {"role": "Cause", "text": "CD40", "start": 826, "end": 830}]}, {"trigger": {"text": "activated", "start": 813, "end": 822}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 787, "end": 792}, {"role": "Cause", "text": "TNF-alpha", "start": 832, "end": 841}]}, {"trigger": {"text": "activated", "start": 813, "end": 822}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 787, "end": 792}]}], "regulation": [{"trigger": {"text": "target", "start": 71, "end": 77}, "arguments": [{"role": "Theme", "text": "IFN regulatory factor 1", "start": 106, "end": 129}, {"role": "Site", "text": "promoter", "start": 130, "end": 138}]}, {"trigger": {"text": "modulation", "start": 1181, "end": 1191}, "arguments": [{"role": "Theme", "text": "IRF-1", "start": 1195, "end": 1200}]}]}}, "schema": []}
{"input": "Regulation of NF-kappa B, AP-1, NFAT, and STAT1 nuclear import in T lymphocytes by noninvasive delivery of peptide carrying the nuclear localization sequence of NF-kappa B p50. \nActivation of T lymphocytes by Ags or cytokines results in translocation of the transcription factors NF-kappa B, AP-1, NFAT, and STAT from the cytoplasm into the nucleus. The first step in the nuclear import process is recognition of a nuclear localization sequence (NLS) within the karyophilic protein by a cytoplasmic receptor such as the importin (karyopherin)-alpha subunit. The NLSs of NF-kappa B, AP-1, and NFAT differ and the NLS of STAT1 has not yet been identified. Herein we demonstrate that the inducible nuclear import of NF-kappa B, AP-1, NFAT, and STAT1 in Jurkat T lymphocytes is significantly inhibited by a cell-permeable peptide carrying the NLS of the NF-kappa B p50 subunit. NLS peptide-mediated disruption of the nuclear import of these transcription factors results in inhibition of I kappa B alpha and IL-2 gene expression, processes dependent on NF-kappa B or the combination of NF-kappa B, AP-1, and NFAT. Further, we show that inhibitory NLS peptide interacts in vitro with a cytoplasmic NLS receptor complex comprised of the Rch1/importin (karyopherin)-beta heterodimer expressed in Jurkat T cells. Taken together, these data indicate that the inducible nuclear import of NF-kappa B, AP-1, NFAT, and STAT1 in Jurkat T cells can be regulated by NLS peptide delivered noninvasively to the cytoplasm of Jurkat T cells to target members of the importin (karyopherin)-alpha beta NLS receptor complex. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 1014, "end": 1024}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1004, "end": 1008}]}, {"trigger": {"text": "expression", "start": 1014, "end": 1024}, "arguments": [{"role": "Theme", "text": "I kappa B alpha", "start": 984, "end": 999}]}, {"trigger": {"text": "expressed", "start": 1276, "end": 1285}, "arguments": [{"role": "Theme", "text": "Rch1", "start": 1231, "end": 1235}]}], "localization": [{"trigger": {"text": "import", "start": 56, "end": 62}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 42, "end": 47}, {"role": "ToLoc", "text": "nuclear", "start": 48, "end": 55}]}, {"trigger": {"text": "import", "start": 703, "end": 709}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 695, "end": 702}, {"role": "Theme", "text": "STAT1", "start": 741, "end": 746}]}, {"trigger": {"text": "import", "start": 921, "end": 927}, "arguments": [{"role": "Theme", "text": "STAT1", "start": 741, "end": 746}, {"role": "ToLoc", "text": "nuclear", "start": 913, "end": 920}]}, {"trigger": {"text": "import", "start": 1368, "end": 1374}, "arguments": [{"role": "ToLoc", "text": "nuclear", "start": 1360, "end": 1367}, {"role": "Theme", "text": "STAT1", "start": 1406, "end": 1411}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 788, "end": 797}, "arguments": [{"role": "Theme", "text": "import", "start": 703, "end": 709}]}, {"trigger": {"text": "disruption", "start": 895, "end": 905}, "arguments": [{"role": "Theme", "text": "import", "start": 921, "end": 927}]}, {"trigger": {"text": "inhibition", "start": 970, "end": 980}, "arguments": [{"role": "Cause", "text": "disruption", "start": 895, "end": 905}, {"role": "Theme", "text": "expression", "start": 1014, "end": 1024}]}, {"trigger": {"text": "inhibition", "start": 970, "end": 980}, "arguments": [{"role": "Theme", "text": "expression", "start": 1014, "end": 1024}]}], "positive regulation": [{"trigger": {"text": "inducible", "start": 685, "end": 694}, "arguments": [{"role": "Theme", "text": "import", "start": 703, "end": 709}]}, {"trigger": {"text": "inducible", "start": 1350, "end": 1359}, "arguments": [{"role": "Theme", "text": "import", "start": 1368, "end": 1374}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "import", "start": 56, "end": 62}]}, {"trigger": {"text": "dependent", "start": 1036, "end": 1045}, "arguments": [{"role": "Theme", "text": "expression", "start": 1014, "end": 1024}]}, {"trigger": {"text": "regulated", "start": 1437, "end": 1446}, "arguments": [{"role": "Theme", "text": "import", "start": 1368, "end": 1374}]}]}}, "schema": []}
{"input": "Epithelial cell-initiated inflammation plays a crucial role in early tissue damage in amebic infection of human intestine. \nBACKGROUND & AIMS: Entamoeba histolytica infection of the intestine can induce severe gut inflammation. The aims of this study were to assess the role of the host inflammatory response in the tissue damage observed with amebiasis and the role of the intestinal epithelial cell in initiating that response. METHODS: E. histolytica infection was established in human intestinal xenografts in severe combined immunodeficient (SCID-HU-INT) mice. Human intestinal epithelial cell inflammatory responses to amebic infection were inhibited by the intraluminal administration of an antisense oligonucleotide to the human p65 subunit of nuclear factor kappaB, and the role of neutrophils in tissue damage observed with amebiasis was studied by depleting neutrophils from SCID-HU-INT mice. RESULTS: Administration of the antisense oligonucleotide blocked the production of human interleukin 1beta and interleukin 8 by intestinal epithelial cells and inhibited neutrophil influx into the E. histolytica-infected intestinal xenografts. Inhibition of the gut inflammatory response by the antisense oligonucleotide or the depletion of neutrophils from SCID-HU- INT mice blocked the increase in intestinal permeability observed with amebic infection. CONCLUSIONS: Intestinal epithelial cells initiate an inflammatory response with resulting neutrophil-mediated tissue damage in response to E. histolytica infection; this inflammatory cascade can be blocked by inhibiting the transcription of genes regulated by nuclear factor kappaB. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 973, "end": 983}, "arguments": [{"role": "Theme", "text": "interleukin 8", "start": 1015, "end": 1028}]}, {"trigger": {"text": "production", "start": 973, "end": 983}, "arguments": [{"role": "Theme", "text": "interleukin 1beta", "start": 993, "end": 1010}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 961, "end": 968}, "arguments": [{"role": "Theme", "text": "production", "start": 973, "end": 983}]}]}}, "schema": []}
{"input": "In vitro suppression of programmed cell death of B cells by tissue inhibitor of metalloproteinases-1. \nCellular pathways for induction of programmed cell death (PCD) have been identified, but little is known about specific extracellular matrix processes that may affect apoptosis along those pathways. In this study, a series of Burkitt's lymphoma (BL) cell lines were assayed for their expression of tissue inhibitor of metalloproteinases (TIMP)-1. Results indicate that TIMP-1-positive BL lines show resistance to cold-shock-induced apoptosis. Furthermore, recombinant TIMP-1, but not TIMP-2 or a synthetic metalloproteinase inhibitor (BB-94), confers resistance to apoptosis induced by both CD95-dependent and -independent (cold shock, serum deprivation, and gamma-radiation) pathways in TIMP-1-negative BL lines. TIMP-1 suppression of PCD is not due to metalloproteinase inhibition, as reduction and alkylation of the TIMP-1 did not abolish this activity. Retroviral induction of TIMP-1 not only resulted in cell survival but also in continued DNA synthesis for up to 5 d in the absence of serum, while controls underwent apoptosis. This resistance to apoptosis is reversed by anti-TIMP-1 antibodies, demonstrating that secreted TIMP-1 is active in blocking apoptosis. Furthermore, TIMP-1 upregulation induced expression of Bcl-XL but not Bcl-2 as well as decreased NF-kappaB activity as compared with controls. These results demonstrate that TIMP-1 suppresses apoptosis in B cells and suggests a novel activity for TIMP-1 in tissue homeostasis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 387, "end": 397}, "arguments": [{"role": "Theme", "text": "tissue inhibitor of metalloproteinases (TIMP)-1", "start": 401, "end": 448}]}, {"trigger": {"text": "expression", "start": 1314, "end": 1324}, "arguments": [{"role": "Theme", "text": "Bcl-XL", "start": 1328, "end": 1334}]}, {"trigger": {"text": "expression", "start": 1314, "end": 1324}, "arguments": [{"role": "Theme", "text": "Bcl-2", "start": 1343, "end": 1348}]}], "localization": [{"trigger": {"text": "secreted", "start": 1224, "end": 1232}, "arguments": [{"role": "Theme", "text": "TIMP-1", "start": 1233, "end": 1239}]}], "negative regulation": [{"trigger": {"text": "reduction", "start": 890, "end": 899}, "arguments": [{"role": "Theme", "text": "TIMP-1", "start": 922, "end": 928}]}], "positive regulation": [{"trigger": {"text": "induction", "start": 971, "end": 980}, "arguments": [{"role": "Theme", "text": "TIMP-1", "start": 984, "end": 990}]}, {"trigger": {"text": "upregulation", "start": 1293, "end": 1305}, "arguments": [{"role": "Theme", "text": "TIMP-1", "start": 1286, "end": 1292}]}, {"trigger": {"text": "induced", "start": 1306, "end": 1313}, "arguments": [{"role": "Cause", "text": "upregulation", "start": 1293, "end": 1305}, {"role": "Theme", "text": "expression", "start": 1314, "end": 1324}]}]}}, "schema": []}
{"input": "Interleukin-12 expression in B cells by transformation with Epstein-Barr virus. \nAlthough interleukin (IL)-12 was originally purified from an Epstein-Barr (EBV)-transformed B cell line and the high correlation of EBV infection and IL-12 expression has been suggested, no study has reported whether EBV infection is directly linked to IL-12 expression. To address this issue, we have investigated IL-12 expression in B cells during in vitro transformation with EBV. Human peripheral B cells became capable of constitutively producing p40 by in vitro transformation with EBV, coincident with the expression of latent membrane protein 1 (LMP1) of EBV. These B cells expressed p40 and p35 mRNA, and phorbol myristate acetate (PMA) stimulation strongly enhanced p40 and p70 production. Furthermore, transfection with LMP1 expression vector into a human B lymphoma cell line, Daudi, led to p40 production with nuclear factor (NF)-kappaB activation. These results suggest that transformation of primary B cells with EBV induces IL-12 expression potentially through LMP1 expression. Copyright 1998 Academic Press. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "producing", "start": 523, "end": 532}, "arguments": [{"role": "Theme", "text": "p40", "start": 533, "end": 536}]}, {"trigger": {"text": "expression", "start": 594, "end": 604}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 635, "end": 639}]}, {"trigger": {"text": "production", "start": 769, "end": 779}, "arguments": [{"role": "Theme", "text": "p40", "start": 757, "end": 760}]}, {"trigger": {"text": "production", "start": 888, "end": 898}, "arguments": [{"role": "Theme", "text": "p40", "start": 884, "end": 887}]}, {"trigger": {"text": "expression", "start": 1063, "end": 1073}, "arguments": [{"role": "Theme", "text": "LMP1", "start": 1058, "end": 1062}]}], "positive regulation": [{"trigger": {"text": "became capable", "start": 490, "end": 504}, "arguments": [{"role": "Theme", "text": "producing", "start": 523, "end": 532}]}, {"trigger": {"text": "enhanced", "start": 748, "end": 756}, "arguments": [{"role": "Theme", "text": "production", "start": 769, "end": 779}]}, {"trigger": {"text": "led", "start": 877, "end": 880}, "arguments": [{"role": "Theme", "text": "production", "start": 888, "end": 898}]}, {"trigger": {"text": "induces", "start": 1013, "end": 1020}, "arguments": [{"role": "Theme", "text": "expression", "start": 1063, "end": 1073}]}], "transcription": [{"trigger": {"text": "expressed", "start": 663, "end": 672}, "arguments": [{"role": "Theme", "text": "p40", "start": 673, "end": 676}]}, {"trigger": {"text": "expressed", "start": 663, "end": 672}, "arguments": [{"role": "Theme", "text": "p35", "start": 681, "end": 684}]}]}}, "schema": []}
{"input": "Anaphylatoxins C5a and C3a induce nuclear factor kappaB activation in human peripheral blood monocytes. \nThe anaphylatoxins C5a and C3a are involved in the regulation of cytokine production. In this study the capability of C5a and C3a to induce transcription factor activation was examined. C5a and C3a stimulation of human peripheral blood monocytes resulted in nuclear expression of a DNA binding activity with specificity to the kappaB sequence. The p50 and p65 proteins, constituents of the prototypic nuclear factor kappaB, were identified as components of the DNA-protein complexes by anti-peptide antibodies in gel supershift assays. C5a induced kappaB binding activity was detected 15 min after agonist stimulation, peaked at 30-40 min, and remained detectable at 2 h. Binding to kappaB sequence was accompanied by an initial decrease and subsequent increase in the cytoplasmic IkappaBalpha levels, as detected by Western blotting using an anti-IkappaBalpha antibody. Pertussis toxin treatment markedly decreased kappaB binding activities induced by both C5a and C3a, whereas cholera toxin displayed no inhibitory effect. Neither of the two toxins affected kappaB binding activity induced by TNFalpha in the same cells. These results imply a potential role of the anaphylatoxins C5a and C3a in regulating leukocytes gene expression through G protein-coupled transcription factor activation. ", "output": {"json_structures": {"negative regulation": [{"trigger": {"text": "decrease", "start": 834, "end": 842}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 886, "end": 898}]}], "positive regulation": [{"trigger": {"text": "increase", "start": 858, "end": 866}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 886, "end": 898}]}]}}, "schema": []}
{"input": "Tpl-2 induces IL-2 expression in T-cell lines by triggering multiple signaling pathways that activate NFAT and NF-kappaB. \nThe Tpl-2 kinase activates the nuclear factor of activated T cells (NFAT) and induces IL-2 expression in T-cell lines. Here we show that the activation of the IL-2 promoter by Tpl-2 is inhibited by mutant signaling molecules that inhibit the mitogen-activated protein kinase (MAPK) or the calcineurin/NFAT pathways and is promoted by combinations of signaling molecules that activate these pathways. We, therefore, conclude that signals generated by the convergence of the MAPK and the calcineurin/NFAT pathway are necessary and sufficient for the activation of the IL-2 promoter by Tpl-2. The activation of both the IL-2 promoter and an NFAT-driven minimal promoter were shown to depend on signals transduced by Raf1. However, it was only the IL-2 promoter whose activation by Tpl-2 was fully blocked by the dominant negative mutant MEK1S218/222A and the MEK1/MEK2 inhibitor PD098059. Since the activation of NFAT is MAPK-dependent these findings suggested that the activation of MAPK by Tpl-2 is either independent or only partially dependent on MEK1 and MEK2. In addition, they suggested that the activation of the IL-2 promoter is under the control of not only NFAT but also a second factor whose activation is MEK-dependent. Experiments in COS-1 and EL-4 cells confirmed both hypotheses and revealed that the second factor activated by Tpl-2 is NF-kappaB. While the activation of the IL-2 promoter and an NFAT-driven minimal promoter by Tpl-2 was fully blocked by the dominant negative mutant NFAT delta418, it was only partially blocked by the calcineurin inhibitor cyclosporin A suggesting that the Tpl-2-mediated NFAT activation is under the control of a combination of calcineurin-dependent and independent pathways. Both pathways were fully blocked by Bcl-2 or Bcl-X(L). ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 19, "end": 29}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 14, "end": 18}]}, {"trigger": {"text": "expression", "start": 214, "end": 224}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 209, "end": 213}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 308, "end": 317}, "arguments": [{"role": "Theme", "text": "activation", "start": 264, "end": 274}]}, {"trigger": {"text": "blocked", "start": 917, "end": 924}, "arguments": [{"role": "Theme", "text": "activation", "start": 887, "end": 897}]}, {"trigger": {"text": "inhibitor", "start": 989, "end": 998}, "arguments": [{"role": "Theme", "text": "Tpl-2", "start": 901, "end": 906}]}, {"trigger": {"text": "inhibitor", "start": 989, "end": 998}, "arguments": [{"role": "Theme", "text": "MEK1", "start": 979, "end": 983}]}, {"trigger": {"text": "blocked", "start": 1581, "end": 1588}, "arguments": [{"role": "Theme", "text": "activation", "start": 1494, "end": 1504}]}, {"trigger": {"text": "blocked", "start": 1658, "end": 1665}, "arguments": [{"role": "Theme", "text": "activation", "start": 1494, "end": 1504}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 6, "end": 13}, "arguments": [{"role": "Theme", "text": "expression", "start": 19, "end": 29}]}, {"trigger": {"text": "induces", "start": 201, "end": 208}, "arguments": [{"role": "Cause", "text": "Tpl-2", "start": 127, "end": 132}, {"role": "Theme", "text": "expression", "start": 214, "end": 224}]}, {"trigger": {"text": "activation", "start": 264, "end": 274}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 282, "end": 286}, {"role": "Site", "text": "promoter", "start": 287, "end": 295}, {"role": "Cause", "text": "Tpl-2", "start": 299, "end": 304}]}, {"trigger": {"text": "promoted", "start": 445, "end": 453}, "arguments": [{"role": "Theme", "text": "activation", "start": 264, "end": 274}]}, {"trigger": {"text": "necessary and sufficient", "start": 638, "end": 662}, "arguments": [{"role": "Theme", "text": "activation", "start": 671, "end": 681}]}, {"trigger": {"text": "activation", "start": 671, "end": 681}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 689, "end": 693}, {"role": "Site", "text": "promoter", "start": 694, "end": 702}, {"role": "Cause", "text": "Tpl-2", "start": 706, "end": 711}]}, {"trigger": {"text": "activation", "start": 717, "end": 727}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 740, "end": 744}, {"role": "Site", "text": "promoter", "start": 745, "end": 753}]}, {"trigger": {"text": "activation", "start": 887, "end": 897}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 867, "end": 871}, {"role": "Site", "text": "promoter", "start": 872, "end": 880}, {"role": "Cause", "text": "Tpl-2", "start": 901, "end": 906}]}, {"trigger": {"text": "activation", "start": 1223, "end": 1233}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1241, "end": 1245}, {"role": "Site", "text": "promoter", "start": 1246, "end": 1254}]}, {"trigger": {"text": "activation", "start": 1494, "end": 1504}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 1512, "end": 1516}, {"role": "Site", "text": "promoter", "start": 1517, "end": 1525}, {"role": "Cause", "text": "Tpl-2", "start": 1565, "end": 1570}]}], "regulation": [{"trigger": {"text": "depend", "start": 804, "end": 810}, "arguments": [{"role": "Theme", "text": "activation", "start": 717, "end": 727}]}, {"trigger": {"text": "under the control", "start": 1258, "end": 1275}, "arguments": [{"role": "Theme", "text": "activation", "start": 1223, "end": 1233}]}]}}, "schema": []}
{"input": "Activation of human macrophages by mechanical ventilation in vitro. \nPositive-pressure mechanical ventilation supports gas exchange in patients with respiratory failure but is also responsible for significant lung injury. In this study, we have developed an in vitro model in which isolated lung cells can be submitted to a prolonged cyclic pressure-stretching strain resembling that of conventional mechanical ventilation. In this model, cells cultured on a Silastic membrane were elongated up to 7% of their initial diameter, corresponding to a 12% increase in cell surface. The lung macrophage was identified as the main cellular source for critical inflammatory mediators such as tumor necrosis factor-alpha, the chemokines interleukin (IL)-8 and -6, and matrix metalloproteinase-9 in this model system of mechanical ventilation. These mediators were measured in supernatants from ventilated alveolar macrophages, monocyte-derived macrophages, and promonocytic THP-1 cells. Nuclear factor-kappaB was found to be activated in ventilated macrophages. Synergistic proinflammatory effects of mechanical stress and molecules such as bacterial endotoxin were observed, suggesting that mechanical ventilation might be particularly deleterious in preinjured or infected lungs. Dexamethasone prevented IL-8 and tumor necrosis factor-alpha secretion in ventilated macrophages. Mechanical ventilation induced low levels of IL-8 secretion by alveolar type II-like cells. Other lung cell types such as endothelial cells, bronchial cells, and fibroblasts failed to produce IL-8 in response to a prolonged cyclic pressure-stretching load. This model is of particular value for exploring physical stress-induced signaling pathways, as well as for testing the effects of novel ventilatory strategies or adjunctive substances aimed at modulating cell activation induced by mechanical ventilation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "source", "start": 633, "end": 639}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 684, "end": 711}]}, {"trigger": {"text": "source", "start": 633, "end": 639}, "arguments": [{"role": "Theme", "text": "interleukin (IL)-8", "start": 728, "end": 746}]}, {"trigger": {"text": "source", "start": 633, "end": 639}, "arguments": [{"role": "Theme", "text": "-6", "start": 751, "end": 753}]}, {"trigger": {"text": "source", "start": 633, "end": 639}, "arguments": [{"role": "Theme", "text": "matrix metalloproteinase-9", "start": 759, "end": 785}]}, {"trigger": {"text": "produce", "start": 1555, "end": 1562}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1563, "end": 1567}]}], "localization": [{"trigger": {"text": "secretion", "start": 1334, "end": 1343}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1297, "end": 1301}]}, {"trigger": {"text": "secretion", "start": 1334, "end": 1343}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 1306, "end": 1333}]}, {"trigger": {"text": "secretion", "start": 1421, "end": 1430}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1416, "end": 1420}]}], "negative regulation": [{"trigger": {"text": "prevented", "start": 1287, "end": 1296}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1334, "end": 1343}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 1394, "end": 1401}, "arguments": [{"role": "Theme", "text": "secretion", "start": 1421, "end": 1430}]}, {"trigger": {"text": "in response to", "start": 1568, "end": 1582}, "arguments": [{"role": "Theme", "text": "produce", "start": 1555, "end": 1562}]}]}}, "schema": []}
{"input": "Stat6 inhibits human interleukin-4 promoter activity in T cells. \nThe differentiation of naive T-helper (Th) cells into cytokine-secreting effector Th cells requires exposure to multiple signals, including exogenous cytokines. Interleukin-4 (IL-4) plays a major role in this process by promoting the differentiation of IL-4-secreting Th2 cells. In Th2 cells, IL-4 gene expression is tightly controlled at the level of transcription by the coordinated binding of multiple transcription factors to regulatory elements in the proximal promoter region. Nuclear factor of activated T cell (NFAT) family members play a critical role in regulating IL-4 transcription and interact with up to five sequences (termed P0 through P4) in the IL-4 promoter. The molecular mechanisms by which IL-4 induces expression of the IL-4 gene are not known, although the IL-4-activated transcription factor signal transducer and activator of transcription 6 (Stat6) is required for this effect. We report here that Stat6 interacts with three binding sites in the human IL-4 promoter by electrophoretic mobility shift assays. These sites overlap the P1, P2, and P4 NFAT elements. To investigate the role of Stat6 in regulating IL-4 transcription, we used Stat6-deficient Jurkat T cells with different intact IL-4 promoter constructs in cotransfection assays. We show that, whereas a multimerized response element from the germline IgE promoter was highly induced by IL-4 in Stat6-expressing Jurkat cells, the intact human IL-4 promoter was repressed under similar conditions. We conclude that the function of Stat6 is highly dependent on promoter context and that this factor promotes IL-4 gene expression in an indirect manner. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "interact", "start": 664, "end": 672}, "arguments": [{"role": "Site", "text": "sequences (termed P0 through P4)", "start": 689, "end": 721}, {"role": "Theme", "text": "IL-4", "start": 729, "end": 733}]}, {"trigger": {"text": "interacts", "start": 997, "end": 1006}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 991, "end": 996}, {"role": "Theme2", "text": "IL-4", "start": 1045, "end": 1049}, {"role": "Site2", "text": "promoter", "start": 1050, "end": 1058}]}], "gene expression": [{"trigger": {"text": "expression", "start": 791, "end": 801}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 809, "end": 813}]}, {"trigger": {"text": "expressing", "start": 1455, "end": 1465}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 1449, "end": 1454}]}, {"trigger": {"text": "gene expression", "start": 1665, "end": 1680}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1660, "end": 1664}]}], "localization": [{"trigger": {"text": "secreting", "start": 324, "end": 333}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 319, "end": 323}]}], "negative regulation": [{"trigger": {"text": "inhibits", "start": 6, "end": 14}, "arguments": [{"role": "Cause", "text": "Stat6", "start": 0, "end": 5}, {"role": "Theme", "text": "interleukin-4", "start": 21, "end": 34}, {"role": "Site", "text": "promoter", "start": 35, "end": 43}]}, {"trigger": {"text": "repressed", "start": 1515, "end": 1524}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 1441, "end": 1445}, {"role": "Theme", "text": "IL-4", "start": 1497, "end": 1501}, {"role": "Site", "text": "promoter", "start": 1502, "end": 1510}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 783, "end": 790}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 778, "end": 782}, {"role": "Theme", "text": "expression", "start": 791, "end": 801}]}, {"trigger": {"text": "activated", "start": 852, "end": 861}, "arguments": [{"role": "Cause", "text": "IL-4", "start": 847, "end": 851}, {"role": "Theme", "text": "Stat6", "start": 935, "end": 940}]}, {"trigger": {"text": "required", "start": 945, "end": 953}, "arguments": [{"role": "Theme", "text": "induces", "start": 783, "end": 790}, {"role": "Cause", "text": "activated", "start": 852, "end": 861}]}, {"trigger": {"text": "promotes", "start": 1651, "end": 1659}, "arguments": [{"role": "Cause", "text": "Stat6", "start": 1584, "end": 1589}, {"role": "Theme", "text": "gene expression", "start": 1665, "end": 1680}]}], "regulation": [{"trigger": {"text": "controlled", "start": 391, "end": 401}, "arguments": [{"role": "Theme", "text": "at the level of transcription", "start": 402, "end": 431}]}, {"trigger": {"text": "role", "start": 622, "end": 626}, "arguments": [{"role": "Theme", "text": "regulating", "start": 630, "end": 640}]}, {"trigger": {"text": "regulating", "start": 630, "end": 640}, "arguments": [{"role": "Theme", "text": "transcription", "start": 646, "end": 659}]}, {"trigger": {"text": "role", "start": 1174, "end": 1178}, "arguments": [{"role": "Cause", "text": "Stat6", "start": 1182, "end": 1187}, {"role": "Theme", "text": "regulating", "start": 1191, "end": 1201}]}, {"trigger": {"text": "regulating", "start": 1191, "end": 1201}, "arguments": [{"role": "Theme", "text": "transcription", "start": 1207, "end": 1220}]}, {"trigger": {"text": "dependent", "start": 1600, "end": 1609}, "arguments": [{"role": "Theme", "text": "Stat6", "start": 1584, "end": 1589}]}], "transcription": [{"trigger": {"text": "at the level of transcription", "start": 402, "end": 431}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 359, "end": 363}]}, {"trigger": {"text": "transcription", "start": 646, "end": 659}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 641, "end": 645}]}, {"trigger": {"text": "transcription", "start": 1207, "end": 1220}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1202, "end": 1206}]}]}}, "schema": []}
{"input": "Interleukin-10 and transforming growth factor-beta promoter polymorphisms in allergies and asthma. \nInterleukin-10 (IL-10) and transforming growth factor beta (TGF-beta) are inhibitory for B and T cells, IgE production, and mast cell proliferation, and they induce apoptosis in eosinophils. These cytokines are therefore candidate genes which could contribute to the development of asthma or allergies. We investigated the hypothesis that polymorphic nucleotides within the IL-10 and TGF-beta gene promoters would link to the expression of allergies and asthma. DNA taken from families with an asthmatic proband was examined for base exchanges by single-stranded conformational polymorphism (SSCP). We demonstrated the presence of a polymorphism in the promoter region of the IL-10 gene and four in the TGF-beta gene promoters (3 in TGF-beta1 and 1 in TGF-beta2). The IL-10 gene polymorphism was a C-to-A exchange 571 base pairs upstream from the translation start site and was present between consensus binding sequences for Sp1 and elevated total serum. This polymorphism was associated with elevated total serum IgE in subjects heterozygotic or homozygotic for this base exchange (p < 0.009). The base exchange at -509 (from the transcription initiation site) in the TGF-beta promoter also linked to elevated total IgE (p < 0.01). This polymorphism represented a C-to-T base exchange which induced a YY1 consensus sequence and is present in a region of the promoter associated with negative transcription regulation. ", "output": {"json_structures": {}}, "schema": []}
{"input": "The control of lytic replication of Epstein-Barr virus in B lymphocytes (Review). \nUncontrolled replication of a virus, which is harmful to the host is also disadvantageous to the virus. Most viruses cannot compete with the various immune mechanisms and become eliminated in the course of infection. Therefore, only the time between infection and eradication remains for these viruses to proliferate. A few viruses, like the Herpesviruses or the papillomaviruses, however, have developed a sophisticated strategy for persisting lifelong, usually asymptomatically in the host, hiding from the immune system and producing infectious progeny at the same time. This strategy depends on a separation of latency and the lytic replication, either by time due to differentiation-dependent mechanisms or by spatial separation as the result of different host cell types. Both are true for the Epstein-Barr virus (EBV). B cells and epithelial cells have a pivotal role in the life cycle of the virus. The former can become latently infected and are thought to be the virus reservoir in vivo, whereas the latter were shown to be permissive for lytic replication. However, replication of EBV in vivo is controlled primarily by host immune mechanisms selecting for cells that are not permissive for viral replication as the result of a particular set of transcription factors. These factors control the activity of the regulatory immediate-early genes and, in addition, lytic and latent cycle regulatory genes negatively interfere with each other and thus link cellular and viral gene regulatory mechanisms. Disturbance of both the immune surveillance as well as viral gene regulation may result in EBV-associated disease. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Human immunodeficiency virus type-1 transcription: role of the 5'-untranslated leader region (review). \nHuman immunodeficiency virus type-1 (HIV-1) transcription is dependent on the interaction of host-cell transcription factors with cis-regulatory DNA elements within the viral long terminal repeat (LTR). Much attention has focused on the series of sequence elements upstream of the transcriptional initiation site in the U3 region of the LTR including the Sp1 and NF-kappaB binding sites. Recent studies, however, demonstrate that the transcribed 5'-untranslated leader region (5'-UTR) also contains important transcriptional elements. These regulatory elements situated downstream of transcription interact with constitutive and inducible transcription factors, mediate transmission of cellular activation signals, and are important for efficient HIV-1 transcription and replication. The 5'-UTR contains binding sites for the transcription factors AP-1, NF-kappaB, NF-AT, IRF, and Sp1. Mutations in these binding sites can interfere with the viral response to cell activation signals, decrease LTR transcription, and inhibit viral replication. The 5'-UTR also interacts with a specific nucleosome that is rapidly displaced during transcriptional activation of the latent provirus. We propose that the inducible transcription factor binding sites in the 5'-UTR comprise a downstream enhancer domain that can function independent of, or in concert with, the LTR promoter to rapidly increase latent proviral transcription in response to cell activation signals. In this review, we describe the host-cell transcription factors that interact with the 5'-UTR and discuss their role in the transcriptional regulation of HIV-1 gene expression. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Molecular cloning of FKHRL1P2, a member of the developmentally regulated fork head domain transcription factor family. \nHere we report the expression of a fork head domain protein in human T helper cells. We cloned and characterized a fork head cDNA from human T helper cell mRNA using differential display RT-PCR. The cDNA contains a 546-nucleotide (nt) open reading frame (ORF) that codes for the carboxyl-terminal 180 amino acids (aa) of the recently identified fkhrl1 gene. This ORF does not contain the characteristic DNA-binding domain found in members of the forkhead protein family. In-vitro transcription/translation of this cDNA expressed a protein of approximately 20 kDa. We have generated antibodies that specifically immunoprecipitated the in-vitro-translated 20-kDa protein. This antibody also recognizes in human T lymphocytes a 70-kDa protein corresponding in size to that predicted for the fkhrl1 gene product. The mRNA levels for fkhrl1 is elevated in T helper-induced lymphocytes in comparison to PHA-stimulated T lymphocytes. Further characterization of FKHRL1 and its related family members should shed light on the transcriptional mechanisms of this fork head gene subfamily and their role in T helper cell differentiation and regulation of cell growth. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "recognizes", "start": 809, "end": 819}, "arguments": [{"role": "Theme", "text": "fkhrl1", "start": 908, "end": 914}]}], "gene expression": [{"trigger": {"text": "product", "start": 920, "end": 927}, "arguments": [{"role": "Theme", "text": "fkhrl1", "start": 908, "end": 914}]}], "positive regulation": [{"trigger": {"text": "elevated", "start": 959, "end": 967}, "arguments": [{"role": "Theme", "text": "mRNA levels", "start": 933, "end": 944}]}], "regulation": [{"trigger": {"text": "developmentally regulated", "start": 47, "end": 72}, "arguments": [{"role": "Theme", "text": "FKHRL1P2", "start": 21, "end": 29}]}], "transcription": [{"trigger": {"text": "mRNA levels", "start": 933, "end": 944}, "arguments": [{"role": "Theme", "text": "fkhrl1", "start": 949, "end": 955}]}]}}, "schema": []}
{"input": "Activation of the human delta-globin gene promoter in primary adult erythroid cells. \nRestoration of the CCAAT box or insertion of an erythroid Kruppel-like factor (EKLF) binding site in the delta promoter activates its expression in several erythroid cell lines. We extended these studies using a novel primary human adult erythroid cell (hAEC) system to investigate these effects at the late erythroblast stage. Restoration of the CCAAT box at -70 bp, or insertion of an EKLF binding site at -85 bp or -95 bp in the promoter significantly increased delta globin gene expression in hAEC. Our results demonstrate that the altered CCAAT box (CCAAC) and the lack of an EKLF binding site in delta-globin contribute to its low level of expression in the hAEC model as well. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 220, "end": 230}, "arguments": [{"role": "Theme", "text": "delta-globin", "start": 24, "end": 36}]}, {"trigger": {"text": "expression", "start": 569, "end": 579}, "arguments": [{"role": "Theme", "text": "delta globin", "start": 551, "end": 563}]}, {"trigger": {"text": "expression", "start": 732, "end": 742}, "arguments": [{"role": "Theme", "text": "delta-globin", "start": 688, "end": 700}]}], "negative regulation": [{"trigger": {"text": "low level", "start": 719, "end": 728}, "arguments": [{"role": "Theme", "text": "expression", "start": 732, "end": 742}]}], "positive regulation": [{"trigger": {"text": "Activation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "delta-globin", "start": 24, "end": 36}, {"role": "Site", "text": "promoter", "start": 42, "end": 50}]}, {"trigger": {"text": "activates", "start": 206, "end": 215}, "arguments": [{"role": "Theme", "text": "expression", "start": 220, "end": 230}]}, {"trigger": {"text": "increased", "start": 541, "end": 550}, "arguments": [{"role": "Theme", "text": "expression", "start": 569, "end": 579}]}, {"trigger": {"text": "contribute", "start": 701, "end": 711}, "arguments": [{"role": "Theme", "text": "low level", "start": 719, "end": 728}]}]}}, "schema": []}
{"input": "Interactions between the class II transactivator and CREB binding protein increase transcription of major histocompatibility complex class II genes. \nClass II major histocompatibility (class II) genes are regulated in a B-cell-specific and gamma interferon-inducible fashion. The master switch for the expression of these genes is the class II transactivator (CIITA). In this report, we demonstrate that one of the functions of CIITA is to recruit the CREB binding protein (CBP) to class II promoters. Not only functional but also specific binding interactions between CIITA and CBP were demonstrated. Moreover, a dominant negative form of CBP decreased the activity of class II promoters and levels of class II determinants on the surface of cells. Finally, the inhibition of class II gene expression by the glucocorticoid hormone could be attributed to the squelching of CBP by the glucocorticoid receptor. We conclude that CBP, a histone acetyltransferase, plays an important role in the transcription of class II genes. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "Interactions", "start": 0, "end": 12}, "arguments": [{"role": "Theme", "text": "class II transactivator", "start": 25, "end": 48}, {"role": "Theme2", "text": "CREB binding protein", "start": 53, "end": 73}]}, {"trigger": {"text": "recruit", "start": 440, "end": 447}, "arguments": [{"role": "Theme", "text": "CBP", "start": 474, "end": 477}]}, {"trigger": {"text": "binding interactions", "start": 540, "end": 560}, "arguments": [{"role": "Theme", "text": "CIITA", "start": 569, "end": 574}, {"role": "Theme2", "text": "CBP", "start": 579, "end": 582}]}], "negative regulation": [{"trigger": {"text": "squelching", "start": 859, "end": 869}, "arguments": [{"role": "Theme", "text": "CBP", "start": 873, "end": 876}, {"role": "Cause", "text": "glucocorticoid receptor", "start": 884, "end": 907}]}], "positive regulation": [{"trigger": {"text": "functions", "start": 415, "end": 424}, "arguments": [{"role": "Cause", "text": "CIITA", "start": 428, "end": 433}, {"role": "Theme", "text": "recruit", "start": 440, "end": 447}]}]}}, "schema": []}
{"input": "Nuclear factor of activated T cells and AP-1 are insufficient for IL-2 promoter activation: requirement for CD28 up-regulation of RE/AP. \nIL-2 gene transcription in T cells requires both TCR and costimulatory signals. IL-2 promoter activation in Jurkat T cells stimulated with superantigen presented by Raji B cells requires CD28 activation. The addition of rCTLA4Ig, which blocks CD28 binding to its ligand, to the cultures decreased IL-2 promoter activation by >80%. Interestingly, CTLA4Ig did not significantly inhibit the activation of either NF of activated T cells (NFAT) or AP-1 reporters. Therefore, activation of NFAT and AP-1 is insufficient for IL-2 promoter activation. In contrast, an RE/AP reporter was blocked by CTLA4Ig by >90%. Thus, the requirement for CD28 in IL-2 promoter activation appears to be due to RE/AP and not the NFAT or AP-1 sites. In addition, these data suggest that transcriptional activation of RE/AP is not mediated by NFAT, because activation of a NFAT reporter is not affected by the addition of CTLA4Ig. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binding", "start": 386, "end": 393}, "arguments": [{"role": "Theme", "text": "CD28", "start": 381, "end": 385}]}], "negative regulation": [{"trigger": {"text": "blocks", "start": 374, "end": 380}, "arguments": [{"role": "Theme", "text": "binding", "start": 386, "end": 393}]}, {"trigger": {"text": "decreased", "start": 425, "end": 434}, "arguments": [{"role": "Theme", "text": "activation", "start": 449, "end": 459}]}], "positive regulation": [{"trigger": {"text": "insufficient", "start": 49, "end": 61}, "arguments": [{"role": "Theme", "text": "activation", "start": 80, "end": 90}]}, {"trigger": {"text": "activation", "start": 80, "end": 90}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 66, "end": 70}, {"role": "Site", "text": "promoter", "start": 71, "end": 79}]}, {"trigger": {"text": "requirement", "start": 92, "end": 103}, "arguments": [{"role": "Theme", "text": "activation", "start": 80, "end": 90}]}, {"trigger": {"text": "requires", "start": 173, "end": 181}, "arguments": [{"role": "Theme", "text": "transcription", "start": 148, "end": 161}]}, {"trigger": {"text": "activation", "start": 232, "end": 242}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 218, "end": 222}, {"role": "Site", "text": "promoter", "start": 223, "end": 231}]}, {"trigger": {"text": "requires", "start": 316, "end": 324}, "arguments": [{"role": "Theme", "text": "activation", "start": 232, "end": 242}, {"role": "Cause", "text": "activation", "start": 330, "end": 340}]}, {"trigger": {"text": "activation", "start": 330, "end": 340}, "arguments": [{"role": "Theme", "text": "CD28", "start": 325, "end": 329}]}, {"trigger": {"text": "activation", "start": 449, "end": 459}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 435, "end": 439}, {"role": "Site", "text": "promoter", "start": 440, "end": 448}]}, {"trigger": {"text": "insufficient", "start": 639, "end": 651}, "arguments": [{"role": "Theme", "text": "activation", "start": 670, "end": 680}]}, {"trigger": {"text": "activation", "start": 670, "end": 680}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 656, "end": 660}, {"role": "Site", "text": "promoter", "start": 661, "end": 669}]}, {"trigger": {"text": "requirement", "start": 755, "end": 766}, "arguments": [{"role": "Cause", "text": "CD28", "start": 771, "end": 775}, {"role": "Theme", "text": "activation", "start": 793, "end": 803}]}, {"trigger": {"text": "activation", "start": 793, "end": 803}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 779, "end": 783}, {"role": "Site", "text": "promoter", "start": 784, "end": 792}]}], "regulation": [{"trigger": {"text": "due", "start": 818, "end": 821}, "arguments": [{"role": "Theme", "text": "requirement", "start": 755, "end": 766}]}], "transcription": [{"trigger": {"text": "transcription", "start": 148, "end": 161}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 138, "end": 142}]}]}}, "schema": []}
{"input": "Phenylarsine oxide inhibits ex vivo HIV-1 expression. \nPhenylarsine oxide (PAO), which is described as an inhibitor of tyrosine phosphatase activity, inhibits H2O2 release from human peripheral blood mononuclear cells (PBMCs) as measured by electrochemistry. Since human immunodeficiency virus type 1 (HIV-1) replication is known to be favored under oxidative stress conditions, ex vivo experiments using uninfected PBMCs, primary monocytes or a latently infected promonocytic U1 cell line show that HIV-1 replication and reactivation, monitored by p24 antigen measurement, are inhibited by PAO in a time- and concentration-dependent manner. These observations can be linked with the inhibition of NF-kappa B activation when uninfected monocytes are induced by either tumor necrosis factor alpha (TNF-alpha) phorbol 12-myristate 13-acetate (PMA) or lipopolysaccharide (LPS). ", "output": {"json_structures": {}}, "schema": []}
{"input": "Interleukin-10 stabilizes inhibitory kappaB-alpha in human monocytes. \nInterleukin-10 (IL-10) protects animals from lethal endotoxemia. This beneficial effect is mediated, in part, by inhibition of inflammatory cytokine production, including tumor necrosis factor-alpha (TNF-alpha). Evidence suggests that IL-10 may inhibit activation of the transcription factor nuclear factor-kappaB (NF-kappaB) through an unknown mechanism. NF-kappaB activation in response to inflammatory signals is dependent upon degradation of its associated inhibitory peptide, inhibitory kappaB-alpha (IkappaB-alpha). We hypothesized that IL-10 prevents human monocyte NF-kappaB activation and resultant TNF-alpha production by stabilization of IkappaB-alpha. The purpose of this study was to determine the effect of IL-10 on lipopolysaccharide (LPS)-induced human monocyte TNF-alpha production, NF-kappaB activation, and IkappaB-alpha degradation. Monocytes were isolated from human donors. Cells were stimulated with endotoxin (LPS, 100 ng/mL) with and without human IL-10 (10 ng/mL). Following stimulation, TNF-alpha was measured in cell supernatants by ELISA, NF-kappaB activity by electrophoretic mobility shift assay, and IkappaB-alpha levels by Western blot. We observed that after LPS stimulation of human monocytes, TNF-alpha increased to 798+/-67 pg/mL (p < .001 versus control). IL-10 attenuated LPS-stimulated TNF-alpha production (297+/-54; p < .001 versus LPS alone). After LPS stimulation in human monocytes, IkappaB-alpha protein levels decreased, and NF-kappaB DNA binding increased. IL-10 pretreatment prevented LPS-induced decreases in IkappaB-alpha protein levels and attenuated NF-kappaB DNA binding. IL-10 appears to prevent activation of NF-kappaB by preserving IkappaB-alpha protein levels, leading to a reduction in TNF-alpha release. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "associated", "start": 521, "end": 531}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 577, "end": 590}]}], "gene expression": [{"trigger": {"text": "production", "start": 220, "end": 230}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 271, "end": 280}]}, {"trigger": {"text": "production", "start": 689, "end": 699}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 679, "end": 688}]}, {"trigger": {"text": "production", "start": 859, "end": 869}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 849, "end": 858}]}, {"trigger": {"text": "levels", "start": 1217, "end": 1223}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1203, "end": 1216}]}, {"trigger": {"text": "production", "start": 1407, "end": 1417}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1397, "end": 1406}]}], "localization": [{"trigger": {"text": "release", "start": 1826, "end": 1833}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1816, "end": 1825}]}], "negative regulation": [{"trigger": {"text": "inhibition", "start": 184, "end": 194}, "arguments": [{"role": "Theme", "text": "production", "start": 220, "end": 230}]}, {"trigger": {"text": "prevents", "start": 620, "end": 628}, "arguments": [{"role": "Theme", "text": "resultant", "start": 669, "end": 678}, {"role": "Cause", "text": "stabilization", "start": 703, "end": 716}]}, {"trigger": {"text": "attenuated", "start": 1371, "end": 1381}, "arguments": [{"role": "Cause", "text": "IL-10", "start": 1365, "end": 1370}, {"role": "Theme", "text": "stimulated", "start": 1386, "end": 1396}]}, {"trigger": {"text": "decreased", "start": 1528, "end": 1537}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1499, "end": 1512}]}, {"trigger": {"text": "prevented", "start": 1595, "end": 1604}, "arguments": [{"role": "Theme", "text": "decreases", "start": 1617, "end": 1626}]}, {"trigger": {"text": "decreases", "start": 1617, "end": 1626}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 1630, "end": 1643}]}, {"trigger": {"text": "reduction", "start": 1803, "end": 1812}, "arguments": [{"role": "Theme", "text": "release", "start": 1826, "end": 1833}]}], "positive regulation": [{"trigger": {"text": "stabilizes", "start": 15, "end": 25}, "arguments": [{"role": "Cause", "text": "Interleukin-10", "start": 0, "end": 14}, {"role": "Theme", "text": "inhibitory kappaB-alpha", "start": 26, "end": 49}]}, {"trigger": {"text": "resultant", "start": 669, "end": 678}, "arguments": [{"role": "Theme", "text": "production", "start": 689, "end": 699}]}, {"trigger": {"text": "stabilization", "start": 703, "end": 716}, "arguments": [{"role": "Cause", "text": "IL-10", "start": 614, "end": 619}, {"role": "Theme", "text": "IkappaB-alpha", "start": 720, "end": 733}]}, {"trigger": {"text": "induced", "start": 826, "end": 833}, "arguments": [{"role": "Theme", "text": "production", "start": 859, "end": 869}]}, {"trigger": {"text": "induced", "start": 826, "end": 833}, "arguments": [{"role": "Theme", "text": "degradation", "start": 911, "end": 922}]}, {"trigger": {"text": "increased", "start": 1310, "end": 1319}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1300, "end": 1309}]}, {"trigger": {"text": "stimulated", "start": 1386, "end": 1396}, "arguments": [{"role": "Theme", "text": "production", "start": 1407, "end": 1417}]}, {"trigger": {"text": "preserving", "start": 1749, "end": 1759}, "arguments": [{"role": "Cause", "text": "IL-10", "start": 1697, "end": 1702}, {"role": "Theme", "text": "IkappaB-alpha", "start": 1760, "end": 1773}]}], "protein catabolism": [{"trigger": {"text": "degradation", "start": 502, "end": 513}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 577, "end": 590}]}, {"trigger": {"text": "degradation", "start": 911, "end": 922}, "arguments": [{"role": "Theme", "text": "IkappaB-alpha", "start": 897, "end": 910}]}], "regulation": [{"trigger": {"text": "effect", "start": 782, "end": 788}, "arguments": [{"role": "Cause", "text": "IL-10", "start": 792, "end": 797}, {"role": "Theme", "text": "production", "start": 859, "end": 869}]}, {"trigger": {"text": "effect", "start": 782, "end": 788}, "arguments": [{"role": "Cause", "text": "IL-10", "start": 792, "end": 797}, {"role": "Theme", "text": "degradation", "start": 911, "end": 922}]}, {"trigger": {"text": "measured", "start": 1099, "end": 1107}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1085, "end": 1094}]}, {"trigger": {"text": "measured", "start": 1099, "end": 1107}, "arguments": [{"role": "Theme", "text": "levels", "start": 1217, "end": 1223}]}]}}, "schema": []}
{"input": "Regulation of fas-ligand expression during activation-induced cell death in T lymphocytes via nuclear factor kappaB. \nT cell receptor engagement activates transcription factors important for cytokine gene regulation. Additionally, this signaling pathway also leads to activation-induced apoptosis in T lymphocytes that is dependent on FasL transcription and expression. Here we demonstrate that nuclear factor kappaB (NF-kappaB), which is involved in the transcriptional regulation of many cytokine genes expressed in activated lymphocytes, also plays a role in T cell activation-induced FasL expression. Inhibition of NF-kappaB activity in a T cell hybridoma leads to decreased FasL expression and apoptosis upon T cell receptor stimulation. We identified the NF-kappaB site in the FasL promoter that contributes to such regulation. Co-expression of p65 (Rel A) with the FasL promoter enhanced its activity, and co-expression of IkappaB dramatically inhibited the inducible promoter activity. In contrast, the transcription factor AP-1 is not required for activation-induced FasL promoter activity. These results define a role for NF-kappaB in mediating FasL expression during T cell activation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 25, "end": 35}, "arguments": [{"role": "Theme", "text": "fas-ligand", "start": 14, "end": 24}]}, {"trigger": {"text": "expression", "start": 358, "end": 368}, "arguments": [{"role": "Theme", "text": "FasL", "start": 335, "end": 339}]}, {"trigger": {"text": "expression", "start": 593, "end": 603}, "arguments": [{"role": "Theme", "text": "FasL", "start": 588, "end": 592}]}, {"trigger": {"text": "expression", "start": 684, "end": 694}, "arguments": [{"role": "Theme", "text": "FasL", "start": 679, "end": 683}]}, {"trigger": {"text": "Co-expression", "start": 834, "end": 847}, "arguments": [{"role": "Theme", "text": "p65", "start": 851, "end": 854}]}, {"trigger": {"text": "Co-expression", "start": 834, "end": 847}, "arguments": [{"role": "Theme", "text": "FasL", "start": 872, "end": 876}]}, {"trigger": {"text": "expression", "start": 1160, "end": 1170}, "arguments": [{"role": "Theme", "text": "FasL", "start": 1155, "end": 1159}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 669, "end": 678}, "arguments": [{"role": "Theme", "text": "expression", "start": 684, "end": 694}]}, {"trigger": {"text": "inhibited", "start": 951, "end": 960}, "arguments": [{"role": "Theme", "text": "FasL", "start": 872, "end": 876}, {"role": "Site", "text": "promoter", "start": 877, "end": 885}]}], "positive regulation": [{"trigger": {"text": "induced", "start": 580, "end": 587}, "arguments": [{"role": "Theme", "text": "expression", "start": 593, "end": 603}]}, {"trigger": {"text": "leads", "start": 660, "end": 665}, "arguments": [{"role": "Theme", "text": "decreased", "start": 669, "end": 678}]}, {"trigger": {"text": "contributes", "start": 802, "end": 813}, "arguments": [{"role": "Theme", "text": "leads", "start": 660, "end": 665}, {"role": "Cause", "text": "FasL", "start": 783, "end": 787}, {"role": "CSite", "text": "promoter", "start": 788, "end": 796}]}, {"trigger": {"text": "enhanced", "start": 886, "end": 894}, "arguments": [{"role": "Cause", "text": "Co-expression", "start": 834, "end": 847}, {"role": "Theme", "text": "FasL", "start": 872, "end": 876}, {"role": "Site", "text": "promoter", "start": 877, "end": 885}]}, {"trigger": {"text": "inducible", "start": 965, "end": 974}, "arguments": [{"role": "Theme", "text": "FasL", "start": 872, "end": 876}, {"role": "Site", "text": "promoter", "start": 877, "end": 885}]}, {"trigger": {"text": "required", "start": 1044, "end": 1052}, "arguments": [{"role": "Theme", "text": "FasL", "start": 1076, "end": 1080}, {"role": "Site", "text": "promoter", "start": 1081, "end": 1089}]}, {"trigger": {"text": "mediating", "start": 1145, "end": 1154}, "arguments": [{"role": "Theme", "text": "expression", "start": 1160, "end": 1170}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "expression", "start": 25, "end": 35}]}, {"trigger": {"text": "plays a role", "start": 546, "end": 558}, "arguments": [{"role": "Theme", "text": "induced", "start": 580, "end": 587}]}, {"trigger": {"text": "role", "start": 1123, "end": 1127}, "arguments": [{"role": "Theme", "text": "mediating", "start": 1145, "end": 1154}]}], "transcription": [{"trigger": {"text": "transcription", "start": 340, "end": 353}, "arguments": [{"role": "Theme", "text": "FasL", "start": 335, "end": 339}]}]}}, "schema": []}
{"input": "X-rays-induced secretion of cellular factor(s) that enhance(s) HIV-1 promoter transcription in various non-irradiated transfected cell lines. \nVarious cellular stress agents like ionizing radiation exposure could activate human immunodeficiency virus type 1 (HIV- 1) replication or reporter gene expression. In addition, extracellular factor(s) released by X-ray-treated human colonic carcinoma cell line (HT29) might activate the long terminal repeat (LTR) of HIV-1 in non-irradiated HT29 cells. In the present report we show that in various transiently or stably transfected cell lines, X-ray irradiation up-regulates HIV-1 LTR transcription through the kappaB regulatory elements. A factor(s), which is processed by and acts upon a variety of cell types, was detected by addition to non-irradiated cells of either X-ray-treated cells or a conditioned medium taken from irradiated cultures. The magnitude of responsiveness is cell type dependent. In addition, X-ray activation of HIV-1 LTR in transiently or stably transfected cell lines is inhibited by a potent antioxidant drug, pyrrolidine dithiocarbamate and by another drug, known for its role in the trapping of growth factors, suramin. The importance of these observations in the pathophysiology of patients with AIDS-related cancers treated by radiotherapy remains to be established. ", "output": {"json_structures": {}}, "schema": []}
{"input": "Reactivation of Kaposi's sarcoma-associated herpesvirus infection from latency by expression of the ORF 50 transactivator, a homolog of the EBV R protein. \nKaposi's sarcoma (KS)-associated herpesvirus (KSHV), or human herpesvirus 8, is a lymphotropic virus strongly linked to several AIDS-related neoplasms. The primary reservoir of infection consists of latently infected B lymphocytes and possibly other mononuclear cells. Viral reactivation from latency and spread from this lymphoid reservoir is presumably required for development of nonlymphoid tumors like KS. Here we show that deregulated expression of a single viral gene, ORF 50, which encodes a transactivator able to selectively upregulate delayed-early viral genes, suffices to disrupt latency and induce the lytic gene cascade in latently infected B cells. The identification of this gene opens the way to studies of the physiologic mechanisms controlling reactvation of KSHV from latency. Copyright 1998 Academic Press. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 82, "end": 92}, "arguments": [{"role": "Theme", "text": "ORF 50 transactivator", "start": 100, "end": 121}]}, {"trigger": {"text": "expression", "start": 597, "end": 607}, "arguments": [{"role": "Theme", "text": "ORF 50", "start": 632, "end": 638}]}], "regulation": [{"trigger": {"text": "deregulated", "start": 585, "end": 596}, "arguments": [{"role": "Theme", "text": "expression", "start": 597, "end": 607}]}]}}, "schema": []}
{"input": "Human T-cell leukemia virus type 1 tax protein abrogates interleukin-2 dependence in a mouse T-cell line. \nHuman T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia. Tax, the viral protein, is thought to be crucial in the development of the disease, since it transforms healthy T cells in vitro and induces tumors in transgenic animals. We examined the effect of Tax activity on the growth of the interleukin-2 (IL-2)-dependent T-cell line CTLL-2. Stable expression of Tax in CTLL-2 transformed cell growth from being IL-2 dependent to IL-2 independent. Tax stimulated transcription through NF-kappaB and the cyclic AMP-responsive element-like sequence in the HTLV-1 promoter. The finding of Tax mutants segregating these two pathways suggested that the NF-kappaB pathway was essential for IL-2-independent growth of CTLL-2 cells while the CRE pathway was unnecessary. However, both pathways were necessary for another transformation-related activity (colony formation in soft agar) of CTLL-2/Tax. Our results show that Tax has at least two distinct activities on T cells, and suggest that Tax plays a crucial role in IL-2-independent T-cell transformation induced by HTLV-1, in addition to its well-known IL-2-dependent cell transformation. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 489, "end": 499}, "arguments": [{"role": "Theme", "text": "Tax", "start": 503, "end": 506}]}]}}, "schema": []}
{"input": "Regulation of IL-6 synthesis in human peripheral blood mononuclear cells by C3a and C3a(desArg). \nThe anaphylatoxin C3a has been reported to have immunomodulatory effects on a number of different cell types. In this study we investigated the effects of C3a and C3a(desArg) on gene expression and protein secretion of IL-6 in human PBMCs, either alone or in combination with LPS or IL-1beta. C3a or C3a(desArg) alone exhibited no effect on the expression or secretion of IL-6. However, when PBMC were stimulated with LPS or IL-1beta, both C3a and C3a(desArg) were found to enhance IL-6 release by PBMC in a dose-dependent manner. Since C3a has been shown to induce PGE2 production by monocytes, and PGE2 has been shown to influence cytokine production, we investigated the potential role of PGE2 in C3a-mediated enhancement of LPS- and IL-1beta-induced IL-6 production. Indomethacin blocked PGE2 release, but had no influence on the observed effects of C3a, suggesting that the effects of C3a on IL-6 production are independent of PGE2 formation by monocytes. Northern blot analysis showed that C3a as well as C3a(desArg) enhanced LPS-induced mRNA levels for IL-6. Pretreatment of PBMCs with pertussis toxin blocked the functions of C3a and C3a(desArg), indicating that the actions of these two molecules are mediated by a G protein-coupled pathway. Furthermore, we investigated the effects of C3a and C3a(desArg) on induction of NF-kappaB and activating protein-1 binding. Both molecules enhanced LPS-induced NF-kappaB and activating protein-1 binding activity. These results demonstrate the capacity of intact C3a and its circulating des-Arg form to exert immunmodulatory effects in vitro. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "synthesis", "start": 19, "end": 28}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 14, "end": 18}]}, {"trigger": {"text": "gene expression", "start": 276, "end": 291}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 317, "end": 321}]}, {"trigger": {"text": "expression", "start": 443, "end": 453}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 470, "end": 474}]}, {"trigger": {"text": "production", "start": 857, "end": 867}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 852, "end": 856}]}, {"trigger": {"text": "production", "start": 1000, "end": 1010}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 995, "end": 999}]}], "localization": [{"trigger": {"text": "protein secretion", "start": 296, "end": 313}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 317, "end": 321}]}, {"trigger": {"text": "secretion", "start": 457, "end": 466}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 470, "end": 474}]}, {"trigger": {"text": "release", "start": 585, "end": 592}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 580, "end": 584}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 1207, "end": 1214}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 1121, "end": 1129}]}], "positive regulation": [{"trigger": {"text": "when", "start": 485, "end": 489}, "arguments": [{"role": "Theme", "text": "enhance", "start": 572, "end": 579}]}, {"trigger": {"text": "enhance", "start": 572, "end": 579}, "arguments": [{"role": "Cause", "text": "C3a", "start": 538, "end": 541}, {"role": "Theme", "text": "release", "start": 585, "end": 592}]}, {"trigger": {"text": "enhance", "start": 572, "end": 579}, "arguments": [{"role": "Cause", "text": "C3a(desArg)", "start": 546, "end": 557}, {"role": "Theme", "text": "release", "start": 585, "end": 592}]}, {"trigger": {"text": "enhancement", "start": 811, "end": 822}, "arguments": [{"role": "Cause", "text": "C3a", "start": 798, "end": 801}, {"role": "Theme", "text": "production", "start": 857, "end": 867}]}, {"trigger": {"text": "induced", "start": 844, "end": 851}, "arguments": [{"role": "Cause", "text": "IL-1beta", "start": 835, "end": 843}, {"role": "Theme", "text": "production", "start": 857, "end": 867}]}, {"trigger": {"text": "induced", "start": 844, "end": 851}, "arguments": [{"role": "Theme", "text": "production", "start": 857, "end": 867}]}, {"trigger": {"text": "enhanced", "start": 1121, "end": 1129}, "arguments": [{"role": "Cause", "text": "C3a", "start": 1094, "end": 1097}, {"role": "Theme", "text": "induced", "start": 1134, "end": 1141}]}, {"trigger": {"text": "enhanced", "start": 1121, "end": 1129}, "arguments": [{"role": "Cause", "text": "C3a(desArg)", "start": 1109, "end": 1120}, {"role": "Theme", "text": "induced", "start": 1134, "end": 1141}]}, {"trigger": {"text": "induced", "start": 1134, "end": 1141}, "arguments": [{"role": "Theme", "text": "IL-6", "start": 1158, "end": 1162}]}, {"trigger": {"text": "mediated", "start": 1308, "end": 1316}, "arguments": [{"role": "Theme", "text": "enhanced", "start": 1121, "end": 1129}]}], "regulation": [{"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 19, "end": 28}, {"role": "Cause", "text": "C3a", "start": 76, "end": 79}]}, {"trigger": {"text": "Regulation", "start": 0, "end": 10}, "arguments": [{"role": "Theme", "text": "synthesis", "start": 19, "end": 28}, {"role": "Cause", "text": "C3a(desArg)", "start": 84, "end": 95}]}, {"trigger": {"text": "effects", "start": 242, "end": 249}, "arguments": [{"role": "Cause", "text": "C3a", "start": 253, "end": 256}, {"role": "Theme", "text": "gene expression", "start": 276, "end": 291}]}, {"trigger": {"text": "effects", "start": 242, "end": 249}, "arguments": [{"role": "Cause", "text": "C3a", "start": 253, "end": 256}, {"role": "Theme", "text": "protein secretion", "start": 296, "end": 313}]}, {"trigger": {"text": "effects", "start": 242, "end": 249}, "arguments": [{"role": "Cause", "text": "C3a(desArg)", "start": 261, "end": 272}, {"role": "Theme", "text": "gene expression", "start": 276, "end": 291}]}, {"trigger": {"text": "effects", "start": 242, "end": 249}, "arguments": [{"role": "Cause", "text": "C3a(desArg)", "start": 261, "end": 272}, {"role": "Theme", "text": "protein secretion", "start": 296, "end": 313}]}, {"trigger": {"text": "effects", "start": 242, "end": 249}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 276, "end": 291}, {"role": "Cause", "text": "IL-1beta", "start": 381, "end": 389}]}, {"trigger": {"text": "effects", "start": 242, "end": 249}, "arguments": [{"role": "Theme", "text": "protein secretion", "start": 296, "end": 313}, {"role": "Cause", "text": "IL-1beta", "start": 381, "end": 389}]}, {"trigger": {"text": "effect", "start": 429, "end": 435}, "arguments": [{"role": "Cause", "text": "C3a", "start": 391, "end": 394}, {"role": "Theme", "text": "expression", "start": 443, "end": 453}]}, {"trigger": {"text": "effect", "start": 429, "end": 435}, "arguments": [{"role": "Cause", "text": "C3a", "start": 391, "end": 394}, {"role": "Theme", "text": "secretion", "start": 457, "end": 466}]}, {"trigger": {"text": "effect", "start": 429, "end": 435}, "arguments": [{"role": "Cause", "text": "C3a(desArg)", "start": 398, "end": 409}, {"role": "Theme", "text": "expression", "start": 443, "end": 453}]}, {"trigger": {"text": "effect", "start": 429, "end": 435}, "arguments": [{"role": "Cause", "text": "C3a(desArg)", "start": 398, "end": 409}, {"role": "Theme", "text": "secretion", "start": 457, "end": 466}]}, {"trigger": {"text": "role", "start": 782, "end": 786}, "arguments": [{"role": "Theme", "text": "enhancement", "start": 811, "end": 822}]}, {"trigger": {"text": "influence", "start": 915, "end": 924}, "arguments": [{"role": "Theme", "text": "enhancement", "start": 811, "end": 822}]}, {"trigger": {"text": "effects", "start": 977, "end": 984}, "arguments": [{"role": "Cause", "text": "C3a", "start": 988, "end": 991}, {"role": "Theme", "text": "production", "start": 1000, "end": 1010}]}, {"trigger": {"text": "independent", "start": 1015, "end": 1026}, "arguments": [{"role": "Theme", "text": "effects", "start": 977, "end": 984}]}]}}, "schema": []}
{"input": "Differential monocyte adhesion and adhesion molecule expression in venous and arterial endothelial cells. \nWe compared U-937 cell adhesion and adhesion molecule expression in human umbilical venous (HUVECs) and arterial (HUAECs) endothelial cells exposed to tumor necrosis factor (TNF), interleukin-1, and lipopolysaccharide (LPS). TNF and LPS stimulated vascular cell adhesion molecule (VCAM)-1 surface expression and adhesion of U-937 monocyte-like cells to HUVECs but not to HUAECs. Antibody studies demonstrated that in HUVECs at least 75% of the adhesion response is VCAM-1 mediated. Interleukin-1 stimulated U-937 cell adhesion to and VCAM-1 surface expression in both HUVECs and HUAECs. Pyrrolidinedithiocarbamate and the proteasome inhibitor MG-132 blocked TNF- and LPS-stimulated U-937 cell adhesion to HUVECs. These agents also significantly decreased TNF- and LPS-stimulated increases in HUVEC surface VCAM-1. TNF increased VCAM-1 protein and mRNA in HUVECs that was blocked by pyrrolidinedithiocarbamate. However, neither TNF or LPS stimulated VCAM-1 expression in HUAECs. TNF stimulated expression of both intercellular adhesion molecule-1 and E-selectin in HUVECs, but in HUAECs, only intercellular adhesion molecule-1 was increased. Electrophoretic mobility shift assays demonstrated no difference in the pattern of TNF-stimulated nuclear factor-kappaB activation between HUVECs and HUAECs. These studies demonstrate a novel and striking insensitivity of arterial endothelium to the effects of TNF and LPS and indicate a dissociation between the ability of HUAECs to upregulate nuclear factor-kappaB and VCAM-1. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 404, "end": 414}, "arguments": [{"role": "Theme", "text": "vascular cell adhesion molecule (VCAM)-1", "start": 355, "end": 395}]}, {"trigger": {"text": "expression", "start": 656, "end": 666}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 641, "end": 647}]}, {"trigger": {"text": "expression", "start": 1063, "end": 1073}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1056, "end": 1062}]}, {"trigger": {"text": "expression", "start": 1100, "end": 1110}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 1119, "end": 1152}]}, {"trigger": {"text": "expression", "start": 1100, "end": 1110}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 1157, "end": 1167}]}], "negative regulation": [{"trigger": {"text": "decreased", "start": 852, "end": 861}, "arguments": [{"role": "Theme", "text": "increases", "start": 886, "end": 895}]}, {"trigger": {"text": "blocked", "start": 978, "end": 985}, "arguments": [{"role": "Theme", "text": "increased", "start": 925, "end": 934}]}], "positive regulation": [{"trigger": {"text": "stimulated", "start": 344, "end": 354}, "arguments": [{"role": "Theme", "text": "expression", "start": 404, "end": 414}]}, {"trigger": {"text": "stimulated", "start": 603, "end": 613}, "arguments": [{"role": "Theme", "text": "expression", "start": 656, "end": 666}]}, {"trigger": {"text": "increases", "start": 886, "end": 895}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 913, "end": 919}]}, {"trigger": {"text": "increased", "start": 925, "end": 934}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 935, "end": 941}]}, {"trigger": {"text": "stimulated", "start": 1045, "end": 1055}, "arguments": [{"role": "Theme", "text": "expression", "start": 1063, "end": 1073}]}, {"trigger": {"text": "stimulated", "start": 1089, "end": 1099}, "arguments": [{"role": "Theme", "text": "expression", "start": 1100, "end": 1110}]}, {"trigger": {"text": "increased", "start": 1237, "end": 1246}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 1199, "end": 1232}]}, {"trigger": {"text": "upregulate", "start": 1582, "end": 1592}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1619, "end": 1625}]}]}}, "schema": []}
{"input": "Tissue factor expression of human monocytes is suppressed by lysophosphatidylcholine. \nThe expression of tissue factor (TF), the principal initiator of coagulation, is increased during inflammation and atherosclerosis. Both conditions are promoted by lysophosphatidylcholine (lysoPC). We observed in the present study that lysoPC (1 to 10 micromol/L) dose-dependently reduced TF activity in human monocytes, as elicited by lipopolysaccharide (LPS). Lysophosphatidylethanolamine (lysoPE) and other lysophospholipids did not affect LPS-induced TF activity of human monocytes. TF antigen expression as elicited by LPS was also lowered by lysoPC. Phospholipid analyses indicated a selective increase in the lysoPC content of the monocytes after preincubation with the lysophospholipid. LysoPC inhibited the TF activity of Mono Mac-6 cells to a similar extent as in the monocytes. LPS binding to plasma membrane receptors and internalization of LPS into monocytes were not affected by lysoPC. In contrast, LPS-mediated nuclear binding of nuclear factor-kappaB/Rel to a TF-specific kappaB site was inhibited by lysoPC. Induction of TF mRNA expression by LPS tended to be partially reduced by the lysophospholipid. Preincubation with lysoPC increased monocytic cAMP levels. Inhibition of adenylyl cyclase by pretreatment with 2'-deoxy-3'-adenosine monophosphate partially reversed the inhibition of TF activity promoted by lysoPC. In conclusion, lysoPC markedly decreases LPS-mediated TF expression of human monocytes, the effect probably being mediated by both transcriptional and posttranscriptional mechanisms. LysoPC may thus attenuate activation of coagulation during inflammation and atherosclerosis. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 14, "end": 24}, "arguments": [{"role": "Theme", "text": "Tissue factor", "start": 0, "end": 13}]}, {"trigger": {"text": "expression", "start": 91, "end": 101}, "arguments": [{"role": "Theme", "text": "TF", "start": 120, "end": 122}]}, {"trigger": {"text": "expression", "start": 585, "end": 595}, "arguments": [{"role": "Theme", "text": "TF", "start": 574, "end": 576}]}, {"trigger": {"text": "expression", "start": 1481, "end": 1491}, "arguments": [{"role": "Theme", "text": "TF", "start": 1478, "end": 1480}]}], "negative regulation": [{"trigger": {"text": "suppressed", "start": 47, "end": 57}, "arguments": [{"role": "Theme", "text": "expression", "start": 14, "end": 24}]}, {"trigger": {"text": "reduced", "start": 368, "end": 375}, "arguments": [{"role": "Theme", "text": "elicited", "start": 411, "end": 419}]}, {"trigger": {"text": "lowered", "start": 624, "end": 631}, "arguments": [{"role": "Theme", "text": "elicited", "start": 599, "end": 607}]}, {"trigger": {"text": "inhibited", "start": 789, "end": 798}, "arguments": [{"role": "Theme", "text": "TF", "start": 803, "end": 805}]}, {"trigger": {"text": "reduced", "start": 1175, "end": 1182}, "arguments": [{"role": "Theme", "text": "Induction", "start": 1113, "end": 1122}]}, {"trigger": {"text": "reversed", "start": 1365, "end": 1373}, "arguments": [{"role": "Theme", "text": "inhibition", "start": 1378, "end": 1388}]}, {"trigger": {"text": "inhibition", "start": 1378, "end": 1388}, "arguments": [{"role": "Theme", "text": "TF", "start": 1392, "end": 1394}]}, {"trigger": {"text": "decreases", "start": 1455, "end": 1464}, "arguments": [{"role": "Theme", "text": "mediated", "start": 1469, "end": 1477}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 168, "end": 177}, "arguments": [{"role": "Theme", "text": "expression", "start": 91, "end": 101}]}, {"trigger": {"text": "promoted", "start": 239, "end": 247}, "arguments": [{"role": "Theme", "text": "increased", "start": 168, "end": 177}]}, {"trigger": {"text": "elicited", "start": 411, "end": 419}, "arguments": [{"role": "Theme", "text": "TF", "start": 376, "end": 378}]}, {"trigger": {"text": "induced", "start": 534, "end": 541}, "arguments": [{"role": "Theme", "text": "TF", "start": 542, "end": 544}]}, {"trigger": {"text": "elicited", "start": 599, "end": 607}, "arguments": [{"role": "Theme", "text": "expression", "start": 585, "end": 595}]}, {"trigger": {"text": "Induction", "start": 1113, "end": 1122}, "arguments": [{"role": "Theme", "text": "expression", "start": 1134, "end": 1144}]}, {"trigger": {"text": "mediated", "start": 1469, "end": 1477}, "arguments": [{"role": "Theme", "text": "expression", "start": 1481, "end": 1491}]}, {"trigger": {"text": "mediated", "start": 1538, "end": 1546}, "arguments": [{"role": "Theme", "text": "decreases", "start": 1455, "end": 1464}]}], "regulation": [{"trigger": {"text": "affect", "start": 523, "end": 529}, "arguments": [{"role": "Theme", "text": "induced", "start": 534, "end": 541}]}], "transcription": [{"trigger": {"text": "expression", "start": 1134, "end": 1144}, "arguments": [{"role": "Theme", "text": "TF", "start": 1126, "end": 1128}]}]}}, "schema": []}
{"input": "Intranuclear targeted delivery of functional NF-kappaB by 70 kDa heat shock protein. \nThe 70 kDa heat shock protein (Hsp70) is a highly conserved, ubiquitous protein involved in chaperoning proteins to various cellular organelles. Here we show that when added exogenously to cells, Hsp70 is readily imported into both cytoplasmic and nuclear compartments in a cell-type-specific fashion. We exploited this ability of Hsp70 to deliver NF-kappaB, a key transcriptional regulator of inflammatory responses. We demonstrate that a fusion protein composed of a C-terminal Hsp70 peptide and the p50 subunit of NF-kappaB was directed into the nucleus of cells, could bind DNA specifically, and activated Igkappa expression and TNFalpha production. We therefore propose that Hsp70 can be used as a vehicle for intracytoplasmic and intranuclear delivery of proteins or DNA to modulate gene expression and thereby control immune responses. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "bind", "start": 659, "end": 663}, "arguments": [{"role": "Theme", "text": "p50", "start": 588, "end": 591}]}], "gene expression": [{"trigger": {"text": "expression", "start": 704, "end": 714}, "arguments": [{"role": "Theme", "text": "Igkappa", "start": 696, "end": 703}]}, {"trigger": {"text": "production", "start": 728, "end": 738}, "arguments": [{"role": "Theme", "text": "TNFalpha", "start": 719, "end": 727}]}], "localization": [{"trigger": {"text": "directed", "start": 617, "end": 625}, "arguments": [{"role": "Theme", "text": "p50", "start": 588, "end": 591}, {"role": "ToLoc", "text": "nucleus", "start": 635, "end": 642}]}], "positive regulation": [{"trigger": {"text": "activated", "start": 686, "end": 695}, "arguments": [{"role": "Cause", "text": "bind", "start": 659, "end": 663}, {"role": "Theme", "text": "expression", "start": 704, "end": 714}]}, {"trigger": {"text": "activated", "start": 686, "end": 695}, "arguments": [{"role": "Cause", "text": "bind", "start": 659, "end": 663}, {"role": "Theme", "text": "production", "start": 728, "end": 738}]}]}}, "schema": []}
{"input": "CD2 signalling induces phosphorylation of CREB in primary lymphocytes. \nPromoter sequences responsive to cyclic AMP (cAMP) are found in a number of cellular genes, and bind transcription factors of the cAMP response element binding protein (CREB)/activating transcription factor-1 (ATF-1) family. We have used a human T-lymphotropic virus type 1 (HTLV-1) model of cAMP response element (CRE) transcription to investigate the influence of lymphocyte activation on transcription from homologous regions in the viral promoter. We previously demonstrated increased HTLV-1 transcription following CD2 but not CD3 receptor cross-linking. We hypothesized that this increased viral transcription was mediated, in part, through the phosphorylation of CREB. Therefore, we investigated CD2 and CD3 receptor-mediated signalling in primary human peripheral blood mononuclear cells (PBMC). CD2, but not CD3, cross-linking increased cAMP detected by competitive enzyme-linked immunosorbent assay (ELISA) approximately fourfold. CD2 cross-linking concurrently increased phosphorylation of CREB detected by immunoblot assay eightfold. Consistent with post-translational regulation, no change in total level of CREB protein was observed. Phosphorylation of CREB occurred through a herbimycin A and Rp-cAMP- sensitive pathway, suggesting phosphorylation required antecedent activation of both protein tyrosine kinases (PTK) and protein kinase A (PKA). Both CD2 and CD3 cross-linking increased binding of nuclear proteins to a radiolabelled CRE oligonucleotide probe in electrophoretic mobility shift assays suggesting that lymphocyte activation enhances binding independently of phosphorylation of CREB at serine 133. These data indicate specific modulation of the CREB/ATF-1 family of transcription factors by the CD2 signalling pathway and suggest CD2 receptor modulation of CRE-mediated transcription following ligand engagement (e.g. cell-to-cell contact). ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 617, "end": 630}, "arguments": [{"role": "Theme", "text": "CD2", "start": 592, "end": 595}]}, {"trigger": {"text": "cross-linking", "start": 894, "end": 907}, "arguments": [{"role": "Theme", "text": "CD2", "start": 876, "end": 879}]}, {"trigger": {"text": "cross-linking", "start": 1017, "end": 1030}, "arguments": [{"role": "Theme", "text": "CD2", "start": 1013, "end": 1016}]}, {"trigger": {"text": "cross-linking", "start": 1450, "end": 1463}, "arguments": [{"role": "Theme", "text": "CD2", "start": 1438, "end": 1441}]}], "phosphorylation": [{"trigger": {"text": "phosphorylation", "start": 23, "end": 38}, "arguments": [{"role": "Theme", "text": "CREB", "start": 42, "end": 46}]}, {"trigger": {"text": "phosphorylation", "start": 723, "end": 738}, "arguments": [{"role": "Theme", "text": "CREB", "start": 742, "end": 746}]}, {"trigger": {"text": "phosphorylation", "start": 1054, "end": 1069}, "arguments": [{"role": "Theme", "text": "CREB", "start": 1073, "end": 1077}]}, {"trigger": {"text": "Phosphorylation", "start": 1220, "end": 1235}, "arguments": [{"role": "Theme", "text": "CREB", "start": 1239, "end": 1243}]}, {"trigger": {"text": "phosphorylation", "start": 1660, "end": 1675}, "arguments": [{"role": "Theme", "text": "CREB", "start": 1679, "end": 1683}, {"role": "Site", "text": "serine 133", "start": 1687, "end": 1697}]}], "positive regulation": [{"trigger": {"text": "induces", "start": 15, "end": 22}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 23, "end": 38}]}, {"trigger": {"text": "increased", "start": 1044, "end": 1053}, "arguments": [{"role": "Theme", "text": "phosphorylation", "start": 1054, "end": 1069}]}, {"trigger": {"text": "through", "start": 1253, "end": 1260}, "arguments": [{"role": "Theme", "text": "Phosphorylation", "start": 1220, "end": 1235}]}, {"trigger": {"text": "required", "start": 1335, "end": 1343}, "arguments": [{"role": "Theme", "text": "Phosphorylation", "start": 1220, "end": 1235}]}], "regulation": [{"trigger": {"text": "modulation", "start": 1728, "end": 1738}, "arguments": [{"role": "Theme", "text": "CREB", "start": 1746, "end": 1750}, {"role": "Cause", "text": "CD2", "start": 1796, "end": 1799}]}, {"trigger": {"text": "modulation", "start": 1728, "end": 1738}, "arguments": [{"role": "Theme", "text": "ATF-1", "start": 1751, "end": 1756}, {"role": "Cause", "text": "CD2", "start": 1796, "end": 1799}]}]}}, "schema": []}
{"input": "Anoxia/reoxygenation-induced tolerance with respect to polymorphonuclear leukocyte adhesion to cultured endothelial cells. A nuclear factor-kappaB-mediated phenomenon. \nExposing human umbilical vein endothelial cells (HUVECs) to anoxia/reoxygenation (A/R) results in an increase in polymorphonuclear leukocyte (PMN) adhesion to HUVECs. This A/R-induced hyperadhesion is completely prevented by a previous (24 hours earlier) exposure of HUVECs to A/R. This phenomenon has been termed \"A/R tolerance.\" Exposing HUVECs to A/R induces an increase in nuclear factor kappaB (NF-kappaB) in HUVEC nuclei within 4 hours. Interfering with either NF-kappaB activation (proteasome inhibitor) or translocation (double-stranded oligonucleotides containing NF-kappaB binding sequence) prevents the development of A/R tolerance (ie, the increase in A/R-induced PMN adhesion to HUVECs is the same after the first and second A/R challenges). NO production by HUVECs is increased after the second A/R challenge, but not after the first A/R challenge. Inhibition of NO synthase (NOS) during the second A/R challenge prevents the development of A/R tolerance with respect to PMN adhesion. However, while HUVECs contained endothelial NOS protein, no inducible NOS was detected in either tolerant or nontolerant cells. Further studies indicated that inhibition of GTP-cyclohydrolase I (an enzyme involved in de novo synthesis of an important cofactor for NOS activity, tetrahydrobiopterin) prevented the generation of NO in A/R-tolerant cells. Extracellular generation of NO (NO donor) did not effect the hyperadhesion response induced by the initial A/R challenge. A/R also induced an oxidant stress in naive HUVECs, but not in A/R-tolerant HUVECs. Inhibition of NOS during the second A/R insult results in the generation of an oxidant stress similar to that observed after the first A/R challenge. Taken together, the findings of the present study are consistent with a role for NF-kappaB in the development of A/R tolerance (with respect to PMN adhesion), perhaps by transcriptional regulation of GTP-cyclohydrolase. The increased NO production during the second A/R insult reduces PMN adhesion most likely by reducing the intracellular oxidant stress induced by A/R. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "contained", "start": 1190, "end": 1199}, "arguments": [{"role": "Theme", "text": "NOS", "start": 1212, "end": 1215}]}], "negative regulation": [{"trigger": {"text": "Inhibition", "start": 1032, "end": 1042}, "arguments": [{"role": "Theme", "text": "NOS", "start": 1059, "end": 1062}]}, {"trigger": {"text": "inhibition", "start": 1327, "end": 1337}, "arguments": [{"role": "Theme", "text": "GTP-cyclohydrolase I", "start": 1341, "end": 1361}]}, {"trigger": {"text": "Inhibition", "start": 1727, "end": 1737}, "arguments": [{"role": "Theme", "text": "NOS", "start": 1741, "end": 1744}]}], "positive regulation": [{"trigger": {"text": "inducible", "start": 1228, "end": 1237}, "arguments": [{"role": "Theme", "text": "NOS", "start": 1238, "end": 1241}]}], "regulation": [{"trigger": {"text": "transcriptional regulation", "start": 2047, "end": 2073}, "arguments": [{"role": "Theme", "text": "GTP-cyclohydrolase", "start": 2077, "end": 2095}]}]}}, "schema": []}
{"input": "Role of Egr-2 in up-regulation of Fas ligand in normal T cells and aberrant double-negative lpr and gld T cells. \nWe previously identified a Fas ligand regulatory element (FLRE) in the Fas ligand (fasL) promoter that binds Egr family proteins and demonstrated that Egr-3 (PILOT) but not Egr-1 (NGFI-A, Krox-24, Tis-8, and Zif-268) induces transcription of fasL. The aberrant CD4(-)CD8(-) T cells from lpr/lpr and gld/gld mice, which have mutations in the genes encoding Fas and FasL, respectively, have an activated phenotype and constitutively express high levels of fasL mRNA, prompting us to ask what role if any the FLRE and Egr family proteins have in this aberrant expression of fasL. Unstimulated MRL-lpr/lpr and C3H-gld/gld CD4(-)CD8(-) T cells constitutively contained high levels of two proteins that bound to the FLRE. Supershift analysis revealed these proteins to be Egr-1 and Egr-2 (Krox-20); Egr-3 was not detected. Activation of normal lymph node cells resulted in increased expression of Egr-1, -2, and -3. As with egr-3, expression of egr-2 was blocked by cyclosporin A. Although overexpressed Egr-1 was ineffective, overexpressed Egr-2 was as potent as Egr-3 in inducing fasL promoter-dependent reporter constructs in T cell hybridomas and HeLa cells, and both up-regulated endogenous fasL mRNA in HeLa cells. FasL-dependent reporter constructs in MRL-lpr/lpr and C3H-gld/gld CD4(-)CD8(-) T cells were constitutively active, and this activity was largely prevented by mutation of the critical Egr family binding element. Thus, Egr-2, in addition to Egr-3, regulates FasL expression in activated normal T cells, and Egr-2 is likely to play a direct role in aberrant fasL up-regulation in lpr/lpr and gld/gld CD4(-)CD8(-) T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "binds", "start": 217, "end": 222}, "arguments": [{"role": "Theme", "text": "Fas ligand", "start": 185, "end": 195}, {"role": "Site", "text": "promoter", "start": 203, "end": 211}]}], "gene expression": [{"trigger": {"text": "detected", "start": 921, "end": 929}, "arguments": [{"role": "Theme", "text": "Egr-3", "start": 907, "end": 912}]}, {"trigger": {"text": "expression", "start": 991, "end": 1001}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1005, "end": 1010}]}, {"trigger": {"text": "expression", "start": 991, "end": 1001}, "arguments": [{"role": "Theme", "text": "-2", "start": 1012, "end": 1014}]}, {"trigger": {"text": "expression", "start": 991, "end": 1001}, "arguments": [{"role": "Theme", "text": "-3", "start": 1020, "end": 1022}]}, {"trigger": {"text": "expression", "start": 1039, "end": 1049}, "arguments": [{"role": "Theme", "text": "egr-3", "start": 1032, "end": 1037}]}, {"trigger": {"text": "expression", "start": 1039, "end": 1049}, "arguments": [{"role": "Theme", "text": "egr-2", "start": 1053, "end": 1058}]}, {"trigger": {"text": "overexpressed", "start": 1098, "end": 1111}, "arguments": [{"role": "Theme", "text": "Egr-1", "start": 1112, "end": 1117}]}, {"trigger": {"text": "overexpressed", "start": 1135, "end": 1148}, "arguments": [{"role": "Theme", "text": "Egr-2", "start": 1149, "end": 1154}]}, {"trigger": {"text": "expression", "start": 1590, "end": 1600}, "arguments": [{"role": "Theme", "text": "FasL", "start": 1585, "end": 1589}]}], "negative regulation": [{"trigger": {"text": "blocked", "start": 1063, "end": 1070}, "arguments": [{"role": "Theme", "text": "expression", "start": 1039, "end": 1049}]}], "positive regulation": [{"trigger": {"text": "up-regulation", "start": 17, "end": 30}, "arguments": [{"role": "Theme", "text": "Fas ligand", "start": 34, "end": 44}]}, {"trigger": {"text": "induces", "start": 331, "end": 338}, "arguments": [{"role": "Cause", "text": "PILOT", "start": 272, "end": 277}, {"role": "Theme", "text": "transcription", "start": 339, "end": 352}]}, {"trigger": {"text": "induces", "start": 331, "end": 338}, "arguments": [{"role": "Cause", "text": "Egr-1", "start": 287, "end": 292}, {"role": "Theme", "text": "transcription", "start": 339, "end": 352}]}, {"trigger": {"text": "high levels", "start": 553, "end": 564}, "arguments": [{"role": "Theme", "text": "express", "start": 545, "end": 552}]}, {"trigger": {"text": "resulted in increased", "start": 969, "end": 990}, "arguments": [{"role": "Theme", "text": "expression", "start": 991, "end": 1001}]}, {"trigger": {"text": "overexpressed", "start": 1098, "end": 1111}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 1098, "end": 1111}]}, {"trigger": {"text": "overexpressed", "start": 1135, "end": 1148}, "arguments": [{"role": "Theme", "text": "overexpressed", "start": 1135, "end": 1148}]}, {"trigger": {"text": "up-regulated", "start": 1280, "end": 1292}, "arguments": [{"role": "Cause", "text": "Egr-2", "start": 1149, "end": 1154}, {"role": "Theme", "text": "fasL", "start": 1304, "end": 1308}]}, {"trigger": {"text": "up-regulated", "start": 1280, "end": 1292}, "arguments": [{"role": "Cause", "text": "Egr-3", "start": 1172, "end": 1177}, {"role": "Theme", "text": "fasL", "start": 1304, "end": 1308}]}, {"trigger": {"text": "up-regulation", "start": 1689, "end": 1702}, "arguments": [{"role": "Theme", "text": "fasL", "start": 1684, "end": 1688}]}], "regulation": [{"trigger": {"text": "Role", "start": 0, "end": 4}, "arguments": [{"role": "Cause", "text": "Egr-2", "start": 8, "end": 13}, {"role": "Theme", "text": "up-regulation", "start": 17, "end": 30}]}, {"trigger": {"text": "role", "start": 604, "end": 608}, "arguments": [{"role": "Theme", "text": "high levels", "start": 553, "end": 564}]}, {"trigger": {"text": "regulates", "start": 1575, "end": 1584}, "arguments": [{"role": "Cause", "text": "Egr-2", "start": 1546, "end": 1551}, {"role": "Theme", "text": "expression", "start": 1590, "end": 1600}]}, {"trigger": {"text": "regulates", "start": 1575, "end": 1584}, "arguments": [{"role": "Cause", "text": "Egr-3", "start": 1568, "end": 1573}, {"role": "Theme", "text": "expression", "start": 1590, "end": 1600}]}, {"trigger": {"text": "role", "start": 1667, "end": 1671}, "arguments": [{"role": "Theme", "text": "Egr-2", "start": 1634, "end": 1639}]}], "transcription": [{"trigger": {"text": "transcription", "start": 339, "end": 352}, "arguments": [{"role": "Theme", "text": "fasL", "start": 356, "end": 360}]}, {"trigger": {"text": "express", "start": 545, "end": 552}, "arguments": [{"role": "Theme", "text": "fasL", "start": 568, "end": 572}]}]}}, "schema": []}
{"input": "Involvement of mitogen-activated protein kinase pathways in interleukin-8 production by human monocytes and polymorphonuclear cells stimulated with lipopolysaccharide or Mycoplasma fermentans membrane lipoproteins. \nInterleukin-8 (IL-8) is a chemokine that belongs to the alpha-chemokine or CXC subfamily and is produced by a wide variety of human cells, including monocytes and polymorphonuclear cells (PMN). IL-8 is secreted in response to inflammatory stimuli, notably bacterial products such as lipopolysaccharide (LPS), but little is known about the mechanisms by which these agents mediate IL-8 induction. In this report, we show that Mycoplasma fermentans lipid-associated membrane proteins (LAMPf) induce the production of high levels of IL-8 by THP-1 (human monocyte) cells and PMN at the same extent as LPS. It was previously demonstrated that stimulation of monocytic cells with either LPS or LAMPf led to a series of common downstream signaling events, including the activation of protein tyrosine kinase and of mitogen-activated protein kinase cascades. By using PD-98059 and SB203580, two potent and selective inhibitors of MEK1 (a kinase upstream of ERK1/2) and p38, respectively, we have demonstrated that both ERK1/2 and p38 cascades play a key role in the production of IL-8 by monocytes and PMN stimulated with bacterial fractions. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 74, "end": 84}, "arguments": [{"role": "Theme", "text": "interleukin-8", "start": 60, "end": 73}]}, {"trigger": {"text": "produced", "start": 312, "end": 320}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 231, "end": 235}]}, {"trigger": {"text": "production", "start": 717, "end": 727}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 746, "end": 750}]}, {"trigger": {"text": "production", "start": 1274, "end": 1284}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 1288, "end": 1292}]}], "localization": [{"trigger": {"text": "secreted", "start": 418, "end": 426}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 410, "end": 414}]}], "negative regulation": [{"trigger": {"text": "inhibitors", "start": 1124, "end": 1134}, "arguments": [{"role": "Theme", "text": "MEK1", "start": 1138, "end": 1142}]}], "positive regulation": [{"trigger": {"text": "in response to", "start": 427, "end": 441}, "arguments": [{"role": "Theme", "text": "secreted", "start": 418, "end": 426}]}, {"trigger": {"text": "induction", "start": 601, "end": 610}, "arguments": [{"role": "Theme", "text": "IL-8", "start": 596, "end": 600}]}, {"trigger": {"text": "induce", "start": 706, "end": 712}, "arguments": [{"role": "Theme", "text": "production", "start": 717, "end": 727}]}, {"trigger": {"text": "high levels", "start": 731, "end": 742}, "arguments": [{"role": "Theme", "text": "production", "start": 717, "end": 727}]}, {"trigger": {"text": "role", "start": 1262, "end": 1266}, "arguments": [{"role": "Theme", "text": "production", "start": 1274, "end": 1284}]}], "regulation": [{"trigger": {"text": "Involvement", "start": 0, "end": 11}, "arguments": [{"role": "Theme", "text": "production", "start": 74, "end": 84}]}]}}, "schema": []}
{"input": "T cell priming enhances IL-4 gene expression by increasing nuclear factor of activated T cells. \nThe repetitive activation of T cells (priming) enhances the expression of many cytokines, such as IL-4, but not others, such as IL-2. Molecular mechanisms underlying selective expression of cytokines by T cells remain poorly understood. Here we show that priming of CD4 T cells selectively enhances IL-4 expression relative to IL-2 expression by a transcriptional mechanism involving nuclear factor of activated T cells (NFAT) proteins. As detected by in vivo footprinting, priming markedly increases the activation-dependent engagement of the P0 and P1 NFAT-binding elements of the IL-4 promoter. Moreover, each proximal P element is essential for optimal IL-4 promoter activity. Activated primed CD4 T cells contain more NFAT1 and support greater NFAT-directed transcription than unprimed CD4 T cells, while activator protein 1 binding and activator protein 1-mediated transcription by both cell types is similar. Increased expression of wild-type NFAT1 substantially increases IL-4 promoter activity in unprimed CD4 T cells, suggesting NFAT1 may be limiting for IL-4 gene expression in this cell type. Furthermore, a truncated form of NFAT1 acts as a dominant-negative, reducing IL-4 promoter activity in primed CD4 T cells and confirming the importance of endogenous NFAT to increased IL-4 gene expression by effector T cells. NFAT1 appears to be the major NFAT family member responsible for the initial increased expression of IL-4 by primed CD4 T cells. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "engagement", "start": 623, "end": 633}, "arguments": [{"role": "Site", "text": "P0", "start": 641, "end": 643}, {"role": "Theme", "text": "IL-4", "start": 680, "end": 684}]}, {"trigger": {"text": "engagement", "start": 623, "end": 633}, "arguments": [{"role": "Site", "text": "P1 NFAT-binding elements", "start": 648, "end": 672}, {"role": "Theme", "text": "IL-4", "start": 680, "end": 684}]}], "gene expression": [{"trigger": {"text": "expression", "start": 34, "end": 44}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 24, "end": 28}]}, {"trigger": {"text": "expression", "start": 157, "end": 167}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 195, "end": 199}]}, {"trigger": {"text": "expression", "start": 157, "end": 167}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 225, "end": 229}]}, {"trigger": {"text": "expression", "start": 429, "end": 439}, "arguments": [{"role": "Theme", "text": "IL-2", "start": 424, "end": 428}]}, {"trigger": {"text": "contain", "start": 807, "end": 814}, "arguments": [{"role": "Theme", "text": "NFAT1", "start": 820, "end": 825}]}, {"trigger": {"text": "expression", "start": 1023, "end": 1033}, "arguments": [{"role": "Theme", "text": "NFAT1", "start": 1047, "end": 1052}]}, {"trigger": {"text": "gene expression", "start": 1167, "end": 1182}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1077, "end": 1081}]}, {"trigger": {"text": "gene expression", "start": 1391, "end": 1406}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1386, "end": 1390}]}, {"trigger": {"text": "expression", "start": 1515, "end": 1525}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1529, "end": 1533}]}], "negative regulation": [{"trigger": {"text": "limiting", "start": 1149, "end": 1157}, "arguments": [{"role": "Cause", "text": "NFAT1", "start": 1136, "end": 1141}, {"role": "Theme", "text": "gene expression", "start": 1167, "end": 1182}]}, {"trigger": {"text": "reducing", "start": 1270, "end": 1278}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 1279, "end": 1283}, {"role": "Site", "text": "promoter", "start": 1284, "end": 1292}]}], "positive regulation": [{"trigger": {"text": "enhances", "start": 15, "end": 23}, "arguments": [{"role": "Theme", "text": "expression", "start": 34, "end": 44}]}, {"trigger": {"text": "enhances", "start": 144, "end": 152}, "arguments": [{"role": "Theme", "text": "expression", "start": 157, "end": 167}]}, {"trigger": {"text": "increases", "start": 588, "end": 597}, "arguments": [{"role": "Theme", "text": "engagement", "start": 623, "end": 633}]}, {"trigger": {"text": "activation", "start": 602, "end": 612}, "arguments": [{"role": "Theme", "text": "IL-4", "start": 680, "end": 684}, {"role": "Site", "text": "promoter", "start": 685, "end": 693}]}, {"trigger": {"text": "essential", "start": 732, "end": 741}, "arguments": [{"role": "CSite", "text": "P0", "start": 641, "end": 643}, {"role": "Cause", "text": "IL-4", "start": 680, "end": 684}, {"role": "Theme", "text": "IL-4", "start": 754, "end": 758}, {"role": "Site", "text": "promoter", "start": 759, "end": 767}]}, {"trigger": {"text": "essential", "start": 732, "end": 741}, "arguments": [{"role": "CSite", "text": "P1 NFAT-binding elements", "start": 648, "end": 672}, {"role": "Cause", "text": "IL-4", "start": 680, "end": 684}, {"role": "Theme", "text": "IL-4", "start": 754, "end": 758}, {"role": "Site", "text": "promoter", "start": 759, "end": 767}]}, {"trigger": {"text": "more", "start": 815, "end": 819}, "arguments": [{"role": "Theme", "text": "contain", "start": 807, "end": 814}]}, {"trigger": {"text": "increases", "start": 1067, "end": 1076}, "arguments": [{"role": "Cause", "text": "expression", "start": 1023, "end": 1033}, {"role": "Theme", "text": "IL-4", "start": 1077, "end": 1081}, {"role": "Site", "text": "promoter", "start": 1082, "end": 1090}]}, {"trigger": {"text": "increased", "start": 1376, "end": 1385}, "arguments": [{"role": "Theme", "text": "gene expression", "start": 1391, "end": 1406}]}, {"trigger": {"text": "increased", "start": 1505, "end": 1514}, "arguments": [{"role": "Theme", "text": "expression", "start": 1515, "end": 1525}]}], "regulation": [{"trigger": {"text": "dependent", "start": 613, "end": 622}, "arguments": [{"role": "Cause", "text": "activation", "start": 602, "end": 612}, {"role": "Theme", "text": "engagement", "start": 623, "end": 633}]}, {"trigger": {"text": "importance", "start": 1343, "end": 1353}, "arguments": [{"role": "Theme", "text": "increased", "start": 1376, "end": 1385}]}, {"trigger": {"text": "responsible", "start": 1477, "end": 1488}, "arguments": [{"role": "Cause", "text": "NFAT1", "start": 1428, "end": 1433}, {"role": "Theme", "text": "increased", "start": 1505, "end": 1514}]}]}}, "schema": []}
{"input": "Inhibition of NF-kappa B activation in vitro and in vivo: role of 26S proteasome. \nIt is becoming increasingly apparent that NF-kappa B plays a critical role in regulating the inflammatory response. Data obtained from studies in our laboratories demonstrate that the proteasome plays an important role in the inflammatory cascade by regulating the activation of NF-kappa B. Indeed, the availability of selective and orally active proteasome inhibitors should prove useful in delineating the roles of the proteasome and NF-kappa B in other pathophysiological conditions such as cancer and heart disease. ", "output": {"json_structures": {}}, "schema": []}
{"input": "NF-kappaB activation is a critical regulator of human granulocyte apoptosis in vitro. \nDuring beneficial inflammation, potentially tissue-damaging granulocytes undergo apoptosis before being cleared by phagocytes in a non-phlogistic manner. Here we show that the rate of constitutive apoptosis in human neutrophils and eosinophils is greatly accelerated in both a rapid and concentration-dependent manner by the fungal metabolite gliotoxin, but not by its inactive analog methylthiogliotoxin. This induction of apoptosis was abolished by the caspase inhibitor zVAD-fmk, correlated with the inhibition of nuclear factor-kappa B (NF-kappaB), and was mimicked by a cell permeable inhibitory peptide of NF-kappaB, SN-50; other NF-kappaB inhibitors, curcumin and pyrrolidine dithiocarbamate; and the proteasome inhibitor, MG-132. Gliotoxin also augmented dramatically the early (2-6 h) pro-apoptotic effects of tumor necrosis factor-alpha (TNF-alpha) in neutrophils and unmasked the ability of TNF-alpha to induce eosinophil apoptosis. In neutrophils, TNF-alpha caused a gliotoxin-inhibitable activation of an inducible form of NF-kappaB, a response that may underlie the ability of TNF-alpha to delay apoptosis at later times (12-24 h) and limit its early killing effect. Furthermore, cycloheximide displayed a similar capacity to enhance TNF-alpha induced neutrophil apoptosis even at time points when cycloheximide alone had no pro-apoptotic effect, suggesting that NF-kappaB may regulate the production of protein(s) which protect neutrophils from the cytotoxic effects of TNF-alpha. These data shed light on the biochemical and molecular mechanisms regulating human granulocyte apoptosis and, in particular, indicate that the transcription factor NF-kappaB plays a crucial role in regulating the physiological cell death pathway in granulocytes. ", "output": {"json_structures": {"positive regulation": [{"trigger": {"text": "underlie the ability", "start": 1154, "end": 1174}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 1178, "end": 1187}]}]}}, "schema": []}
{"input": "Lactobacilli and vaginal host defense: activation of the human immunodeficiency virus type 1 long terminal repeat, cytokine production, and NF-kappaB. \nLactobacilli, a component of the normal vaginal flora, can activate the human immunodeficiency virus (HIV)-1 long terminal repeat (LTR) in the Jurkat T lymphocyte and THP-1 macrophage cell lines. Activation of the LTR in Jurkat cells was strongly enhanced by vanadate and inhibited by catalase, implicating H2O2. In contrast, activation in THP-1 cells occurred in the absence of vanadate and was unaffected by catalase. The active material partitioned into the phenol layer on hot aqueous phenol extraction. Lactobacilli also increased tumor necrosis factor-alphaand interleukin-1betaproduction and activated NF-kappaB in THP-1 cells and increased tumor necrosis factor-alphaproduction by human monocytes. Human vaginal fluid specimens had comparable properties, which correlated with their bacterial content. These findings suggest the presence in vaginal fluid of agent(s) derived from indigenous bacteria that can activate the HIV-1 LTR, cytokine production, and NF-kappaB in cells of macrophage lineage, with possible influence on vaginal physiology and host defense. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "production", "start": 736, "end": 746}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 688, "end": 715}]}, {"trigger": {"text": "production", "start": 736, "end": 746}, "arguments": [{"role": "Theme", "text": "interleukin-1beta", "start": 719, "end": 736}]}, {"trigger": {"text": "production", "start": 827, "end": 837}, "arguments": [{"role": "Theme", "text": "tumor necrosis factor-alpha", "start": 800, "end": 827}]}], "positive regulation": [{"trigger": {"text": "increased", "start": 678, "end": 687}, "arguments": [{"role": "Theme", "text": "production", "start": 736, "end": 746}]}, {"trigger": {"text": "increased", "start": 790, "end": 799}, "arguments": [{"role": "Theme", "text": "production", "start": 827, "end": 837}]}]}}, "schema": []}
{"input": "High-level replication of human immunodeficiency virus in thymocytes requires NF-kappaB activation through interaction with thymic epithelial cells. \nWe have previously demonstrated that interaction of infected thymocytes with autologous thymic epithelial cells (TEC) is a prerequisite for a high level of human immunodeficiency virus type 1 (HIV-1) replication in thymocytes (M.Rothe, L.Chene, M.Nugeyre, F.Barre-Sinoussi, and N.Israel, J.Virol.72:5852-5861, 1998). We report here that this activation of HIV replication takes place at the transcriptional level through activation of the Rel/NF-kappaB transcription factors. We first demonstrate that an HIV-1 provirus (SF-2 strain) very effectively replicates in thymocytes cocultured with TEC whereas this provirus, with kappaB sites deleted, fails to replicate. We provide evidence that several NF-kappaB complexes are constitutively found in the nuclei of thymocytes either freshly isolated from the thymus or maintained in coculture with autologous or heterologous TEC. The prevalent complex is the heterodimer p50-p65. NF-kappaB activity is tightly correlated with the transcriptional activity of a long terminal repeat (LTR) of HIV-1 transfected in thymocytes. The cotransfection of this LTR with a mutated IkappaBalpha molecule formally demonstrates that LTR transactivation is regulated by members of the Rel/NF-kappaB family in thymocytes. We also showed that tumor necrosis factor (TNF) and to a lesser extent interleukin-1 (IL-1), secreted within the coculture, induce NF-kappaB activity and a correlative LTR transactivation. However IL-7, a crucial factor for thymopoiesis that is secreted mainly by TEC, is a necessary cofactor for NF-kappaB activation elicited by TNF or IL-1. Together, these data indicate that NF-kappaB activation, required for a high level of HIV replication in thymocytes, is regulated in a specific manner in the thymic microenvironment which provides the necessary cytokines: TNF, IL-1, and IL-7. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "cotransfection", "start": 1223, "end": 1237}, "arguments": [{"role": "Theme", "text": "IkappaBalpha", "start": 1265, "end": 1277}]}, {"trigger": {"text": "provides", "start": 1932, "end": 1940}, "arguments": [{"role": "Theme", "text": "IL-7", "start": 1981, "end": 1985}]}], "localization": [{"trigger": {"text": "secreted", "start": 1646, "end": 1654}, "arguments": [{"role": "Theme", "text": "IL-7", "start": 1598, "end": 1602}]}], "positive regulation": [{"trigger": {"text": "cotransfection", "start": 1223, "end": 1237}, "arguments": [{"role": "Theme", "text": "cotransfection", "start": 1223, "end": 1237}]}]}}, "schema": []}
{"input": "Cross-linking of CD44 on rheumatoid synovial cells up-regulates VCAM-1. \nCD44 is a ubiquitous molecule also known as hyaluronic acid or homing receptor. However, the cellular functions and its role in inflammation, for example, rheumatoid synovitis, are currently unknown. In this study, we propose a novel function for CD44. Using synovial cells from rheumatoid arthritis (RA) patients, we demonstrated that CD44 cross-linking and binding to hyaluronan augmented VCAM-1 expression and subsequently VCAM-1-mediated cell adhesion. Briefly, we found that 1) rheumatoid synovial cells highly expressed CD44; 2) cross-linking of CD44 markedly but transiently augmented VCAM-1 expression and its mRNA transcription much more than did IL-1beta and TNF-alpha; 3) hyaluronan, especially when fragmented, also up-regulated VCAM-1; 4) CD44 activated the transcription factor AP-1; and 5) the integrin-dependent adhesive function of RA synovial cells to T cells was also amplified by CD44 cross-linking. These results indicate that the adhesion of RA synovial cells to matrices such as hyaluronic acid through CD44 could up-regulate VCAM-1 expression and VCAM-1-mediated adhesion to T cells, which might in turn cause activation of T cells and synovial cells in RA synovitis. We therefore propose that such cross-talking among distinct adhesion molecules may be involved in the pathogenesis of inflammation, including RA synovitis. ", "output": {"json_structures": {"binding": [{"trigger": {"text": "cross-linking", "start": 414, "end": 427}, "arguments": [{"role": "Theme", "text": "CD44", "start": 409, "end": 413}]}, {"trigger": {"text": "binding", "start": 432, "end": 439}, "arguments": [{"role": "Theme", "text": "CD44", "start": 409, "end": 413}]}, {"trigger": {"text": "cross-linking", "start": 608, "end": 621}, "arguments": [{"role": "Theme", "text": "CD44", "start": 625, "end": 629}]}, {"trigger": {"text": "cross-linking", "start": 978, "end": 991}, "arguments": [{"role": "Theme", "text": "CD44", "start": 973, "end": 977}]}], "gene expression": [{"trigger": {"text": "expression", "start": 471, "end": 481}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 499, "end": 505}]}, {"trigger": {"text": "expressed", "start": 589, "end": 598}, "arguments": [{"role": "Theme", "text": "CD44", "start": 599, "end": 603}]}, {"trigger": {"text": "expression", "start": 672, "end": 682}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 665, "end": 671}]}, {"trigger": {"text": "expression", "start": 672, "end": 682}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 729, "end": 737}]}, {"trigger": {"text": "expression", "start": 1129, "end": 1139}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1122, "end": 1128}]}], "positive regulation": [{"trigger": {"text": "up-regulates", "start": 51, "end": 63}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 64, "end": 70}]}, {"trigger": {"text": "augmented", "start": 454, "end": 463}, "arguments": [{"role": "Cause", "text": "binding", "start": 432, "end": 439}, {"role": "Theme", "text": "expression", "start": 471, "end": 481}]}, {"trigger": {"text": "augmented", "start": 655, "end": 664}, "arguments": [{"role": "Cause", "text": "cross-linking", "start": 608, "end": 621}, {"role": "Theme", "text": "expression", "start": 672, "end": 682}]}, {"trigger": {"text": "augmented", "start": 655, "end": 664}, "arguments": [{"role": "Cause", "text": "cross-linking", "start": 608, "end": 621}, {"role": "Theme", "text": "transcription", "start": 696, "end": 709}]}, {"trigger": {"text": "up-regulated", "start": 801, "end": 813}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 814, "end": 820}]}, {"trigger": {"text": "activated", "start": 830, "end": 839}, "arguments": [{"role": "Cause", "text": "CD44", "start": 825, "end": 829}, {"role": "Theme", "text": "AP-1", "start": 865, "end": 869}]}, {"trigger": {"text": "up-regulate", "start": 1110, "end": 1121}, "arguments": [{"role": "Theme", "text": "expression", "start": 1129, "end": 1139}]}], "transcription": [{"trigger": {"text": "transcription", "start": 696, "end": 709}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 665, "end": 671}]}, {"trigger": {"text": "transcription", "start": 696, "end": 709}, "arguments": [{"role": "Theme", "text": "IL-1beta", "start": 729, "end": 737}]}, {"trigger": {"text": "transcription", "start": 696, "end": 709}, "arguments": [{"role": "Theme", "text": "TNF-alpha", "start": 742, "end": 751}]}]}}, "schema": []}
{"input": "Oleic acid inhibits endothelial activation : A direct vascular antiatherogenic mechanism of a nutritional component in the mediterranean diet. \nBecause oleic acid is implicated in the antiatherogenic effects attributed to the Mediterranean diet, we investigated whether this fatty acid can modulate endothelial activation, ie, the concerted expression of gene products involved in leukocyte recruitment and early atherogenesis. We incubated sodium oleate with human umbilical vein endothelial cells for 0 to 72 hours, followed by coincubation of oleate with human recombinant tumor necrosis factor, interleukin (IL)-1alpha, IL-1beta, IL-4, Escherichia coli lipopolysaccharide (LPS), or phorbol 12-myristate 13-acetate for a further 6 to 24 hours. The endothelial expression of vascular cell adhesion molecule-1 (VCAM-1), E-selectin, and intercellular adhesion molecule-1 was monitored by cell surface enzyme immunoassays or flow cytometry, and steady-state levels of VCAM-1 mRNA were assessed by Northern blot analysis. At 10 to 100 micromol/L for >24 hours, oleate inhibited the expression of all adhesion molecules tested. After a 72-hour incubation with oleate and a further 16-hour incubation with oleate plus 1 microg/mL LPS, VCAM-1 expression was reduced by >40% compared with control. Adhesion of monocytoid U937 cells to LPS-treated endothelial cells was reduced concomitantly. Oleate also produced a quantitatively similar reduction of VCAM-1 mRNA levels on Northern blot analysis and inhibited nuclear factor-kappaB activation on electrophoretic mobility shift assays. Incubation of endothelial cells with oleate for 72 hours decreased the relative proportions of saturated (palmitic and stearic) acids in total cell lipids and increased the proportions of oleate in total cell lipids without significantly changing the relative proportions of polyunsaturated fatty acids. Although less potent than polyunsaturated fatty acids in inhibiting endothelial activation, oleic acid may contribute to the prevention of atherogenesis through selective displacement of saturated fatty acids in cell membrane phospholipids and a consequent modulation of gene expression for molecules involved in monocyte recruitment. ", "output": {"json_structures": {"gene expression": [{"trigger": {"text": "expression", "start": 763, "end": 773}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 812, "end": 818}]}, {"trigger": {"text": "expression", "start": 763, "end": 773}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 821, "end": 831}]}, {"trigger": {"text": "expression", "start": 763, "end": 773}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 837, "end": 870}]}, {"trigger": {"text": "expression", "start": 1080, "end": 1090}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 812, "end": 818}]}, {"trigger": {"text": "expression", "start": 1080, "end": 1090}, "arguments": [{"role": "Theme", "text": "E-selectin", "start": 821, "end": 831}]}, {"trigger": {"text": "expression", "start": 1080, "end": 1090}, "arguments": [{"role": "Theme", "text": "intercellular adhesion molecule-1", "start": 837, "end": 870}]}, {"trigger": {"text": "expression", "start": 1238, "end": 1248}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1231, "end": 1237}]}], "negative regulation": [{"trigger": {"text": "inhibited", "start": 1066, "end": 1075}, "arguments": [{"role": "Theme", "text": "expression", "start": 1080, "end": 1090}]}, {"trigger": {"text": "reduced", "start": 1253, "end": 1260}, "arguments": [{"role": "Theme", "text": "expression", "start": 1238, "end": 1248}]}, {"trigger": {"text": "reduction", "start": 1432, "end": 1441}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 1445, "end": 1451}]}], "transcription": [{"trigger": {"text": "levels", "start": 957, "end": 963}, "arguments": [{"role": "Theme", "text": "VCAM-1", "start": 967, "end": 973}]}]}}, "schema": []}