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10.1126/science.1208347
103,786,089
The release of adenosine triphosphate through autophagy can promote antitumor immune responses.
10.1038/nrd.2017.22
This article demonstrates that autophagy is strictly required for mouse cancer cells that succumb to some chemotherapeutics to release danger signals and hence alert the immune system of a threatening situation.
10.1073/pnas.1319661110
20,639,486
Significance We show that the selective overactivation of autophagy can cause cell death with unique morphological features distinct from apoptosis or necrosis. This unique type of autophagic cell death, termed “autosis,” occurs not only in vitro but also in vivo in cerebral hypoxia–ischemia. Moreover, autosis is inhib...
10.1038/nrd.2017.22
This is the first description of the mechanisms and pathophysiological relevance of autosis, which is an instance of autophagic cell death that also relies on the plasma membrane Na + /K + -ATPase and hence can be inhibited by cardiac glycosides.
10.1126/science.aaa2628
62,273,155
Too hungry to eat, too hungry not to eat Pancreatic beta cells, the source of insulin in response to food, employ an unusual mechanism to adapt to nutrient depletion. Goginashvili et al. found that starvation of beta cells induced selective degradation of newly formed insulin granules through their fusion with lysosome...
10.1038/nrd.2017.22
This article provides compelling evidence in support of the concept that insulin granules are degraded by autophagy in pancreatic β -cells as a mechanism that negatively regulates insulin secretion under fasting conditions.
10.1126/science.1227026
82,817,874
Axing Autophagy When intracellular pathogens like Legionella pneumophila take up residence in mammalian host cells, they must combat the efforts of the host cell to attack them. Autophagy is a process by which cells digest their own constituents, often involved in response to starvation or pathogen attack. Choy et al. ...
10.1038/nrd.2017.22
This paper identifies a protein from L. pneumophila that operates as a virulence factor by inhibiting autophagy in host cells upon LC3 deconjugation.
10.1073/pnas.1218674109
104,176,786
Autophagy, a cytoplasmic catabolic process, plays a critical role in defense against intracellular infection. In turn, evasion or inhibition of autophagy has emerged as an important virulence factor for intracellular pathogens. However, Anaplasma phagocytophilum , the obligatory intracellular bacterium that causes huma...
10.1038/nrd.2017.22
This study provides robust evidence in support of the notion that A. phagocytophilum actively promotes BECN1-dependent autophagic responses in host cells to acquire nutrients for growth.
10.1126/science.1218395
17,842,716
Starvation and Autophagy Starvation stimulates withdrawal from the cell cycle, as well as stimulating autophagy. Are these two events connected? Lee et al. (p. 225 ) show a direct and nutrient-sensitive interaction between the tumor suppressor p53 and the essential autophagy gene Atg7. Further, in the absence of Atg7, ...
10.1038/nrd.2017.22
This study characterizes one of the autophagy-independent functions of ATG7, namely, the regulation of p53 activity in the course of metabolic stress.
10.1101/gad.1021202
79,774,617
To address the role of N- myc in neurogenesis and in nervous system tumors, it was conditionally disrupted in neuronal progenitor cells (NPCs) with a nestin-Cre transgene. Null mice display ataxia, behavioral abnormalities, and tremors that correlate with a twofold decrease in brain mass that disproportionately affects...
10.1038/nrm1703
References 17–19 analyse the effect of Myc knockouts in mammalian organ systems.
10.4049/jimmunol.0902447
19,259,187
Abstract Basophils are recognized as immune modulators through their ability to produce IL-4, a key cytokine required for Th2 immunity. It has also recently been reported that basophils are transiently recruited into the draining lymph node (LN) after allergen immunization and that the recruited basophils promote the d...
10.1038/nri2735
References 29, 30, 36 and 38 report that basophils are T H 2 cell-inducing APCs in some but not all in vivo T H 2-associated models.
10.1084/jem.20081499
17,812,391
Intestinal epithelial cells (IECs) produce thymic stromal lymphopoietin (TSLP); however, the in vivo influence of TSLP–TSLP receptor (TSLPR) interactions on immunity and inflammation in the intestine remains unclear. We show that TSLP–TSLPR interactions are critical for immunity to the intestinal pathogen Trichuris. Mo...
10.1038/nri2735
References 78 and 79 report that TSLP is important for T H 2-type responses to T. muris but not other helminth infections.
10.1084/jem.20051615
123,747,001
Type 2 immunity, which involves coordinated regulation of innate and adaptive immune responses, can protect against helminth parasite infection, but may lead to allergy and asthma after inappropriate activation. We demonstrate that il25−/− mice display inefficient Nippostrongylus brasiliensis expulsion and delayed cyto...
10.1038/nri2735
References 82–84 describe IL-25-responsive NBNT cells that can produce T H 2-associated cytokines, especially IL-5 and IL-13. These cells may be crucial during many T H 2-type responses in vivo . However, whether all these cells are the same population requires further study.
10.1073/pnas.0906988106
58,615,056
Expression of T1ST2, the IL-33R, by Th2 cells requires GATA3. Resting Th2 cells express little GATA3, which is increased by IL-33 and a STAT5 activator, in turn increasing T1ST2 from its low-level expression on resting Th2 cells. Th2 cells that have upregulated T1ST2 produce IL-13, but not IL-4, in response to IL-33 pl...
10.1038/nri2735
This paper reports that IL-33 can induce IL-13 production by T H 2 cells in a TCR-independent manner.
10.1182/blood.v92.5.1549
81,924,315
Abstract Epstein-Barr virus (EBV) causes potentially lethal immunoblastic lymphoma in up to 25% of children receiving bone marrow transplants from unrelated or HLA-mismatched donors. Because this complication appears to stem from a deficiency of EBV-specific cytotoxic T cells, we assessed the safety and efficacy of don...
10.1038/nrc1167
This paper describes the generation and clinical use of lymphocyte cultures for ACT therapy of patients with metastatic cancer.
10.1084/jem.188.2.277
61,147,799
Many tumor-associated antigens are nonmutated, poorly immunogenic tissue differentiation antigens. Their weak immunogenicity may be due to “self”-tolerance. To induce autoreactive T cells, we studied immune responses to gp100/pmel 17, an antigen naturally expressed by both normal melanocytes and melanoma cells. Althoug...
10.1038/nrc1167
Demonstration in an animal model that immune manipulation can result in efficacious tumour treatments mediated through unmutated melanocyte-differentiation antigens.
10.1126/science.3489291
20,704,856
The adoptive transfer of tumor-infiltrating lymphocytes (TIL) expanded in interleukin-2 (IL-2) to mice bearing micrometastases from various types of tumors showed that TIL are 50 to 100 times more effective in their therapeutic potency than are lymphokine-activated killer (LAK) cells. Therefore the use of TIL was explo...
10.1038/nrc1167
This seminal paper describes the use of TILs, together with cyclophosphamide conditioning, to treat advanced tumours in mice.
10.1073/pnas.242600099
82,841,357
Adoptive T cell therapy, involving the ex vivo selection and expansion of antigen-specific T cell clones, provides a means of augmenting antigen-specific immunity without the in vivo constraints that can accompany vaccine-based strategies. A phase I study was performed to evaluate the safety, in vivo persistence, and e...
10.1038/nrc1167
An excellent example of the failure of highly avid T-cell clones to induce objective clinical responses in patients with metastatic solid tumours. T-cell function, transport and persistence were monitored.
10.1002/eji.1830230216
123,053,459
Abstract CD3 antibodies are proven immunosuppressants capable of reversing transplant rejection episodes. Their general application has been limited both by their immunogenicity and, in particular, by the “first‐dose” cytokine‐release syndrome experienced by patients after the initial administration of antibody. We hav...
10.1038/nri1837
References 70 and 71 are excellent early examples of the use of rational design to overcome the limitations of an existing antibody therapeutic.
10.1073/pnas.0508123103
4,804,630
Antibody-dependent cell-mediated cytotoxicity, a key effector function for the clinical efficacy of monoclonal antibodies, is mediated primarily through a set of closely related Fcγ receptors with both activating and inhibitory activities. By using computational design algorithms and high-throughput screening, we have ...
10.1038/nri1837
This paper describes a broadly applicable Fc-region engineering strategy that was used to create variants of several approved therapeutic antibodies, resulting in increases in the potency of effector function by more than 100-fold.
10.1073/pnas.0606247103
122,558,574
Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E. coli NikR, t...
10.1038/nrmicro1717
This study described the structure of the NikR–operator DNA complex and illustrated the mechanism of activation of NikR by nickel ions.
10.1126/science.277.5324.383
122,669,405
Cell divisions that produce progeny differing in their patterns of gene expression are key to the development of multicellular organisms. In the budding yeast Saccharomyces cerevisiae , mother cells but not daughter cells can switch mating type because they selectively express the HO endonuclease gene. This asymmetry i...
10.1038/nrm3918
This is the first demonstration of mRNA localization in yeast.
10.1126/science.280.5363.585
41,743,405
Fluorescence in situ hybridization (FISH) and digital imaging microscopy were modified to allow detection of single RNA molecules. Oligodeoxynucleotide probes were synthesized with five fluorochromes per molecule, and the light emitted by a single probe was calibrated. Points of light in exhaustively deconvolved images...
10.1038/nrm3918
This is the first demonstration of single-molecule FISH in cells.
10.1101/gad.190413.112
80,581,564
Directed cell motility is at the basis of biological phenomena such as development, wound healing, and metastasis. It has been shown that substrate attachments mediate motility by coupling the cell's cytoskeleton with force generation. However, it has been unclear how the persistence of cell directionality is facilitat...
10.1038/nrm3918
Forced mRNA localization at focal adhesions demonstrates how altered mRNA localization affects cell motility.
10.1002/cne.21189
39,966,874
Abstract The mRNA for Arc (activity‐regulated cytoskeletal protein) is delivered into dendrites and localizes selectively at active synapses. Here we use a green fluorescent protein‐based labeling system and confocal microscopy to define the transport kinetics of exogenously expressed mRNA from chimaeric Arc constructs...
10.1038/nrm3918
This paper reports Arc mRNA transporting in dendrites and quantifies multiple aspects of transport.
10.1126/science.1195691
81,357,195
Sequences within messenger RNAs target them to sites in the bacterial cell where the resulting proteins function.
10.1038/nrm3918
This paper demonstrated for the first time that mRNAs in bacteria can localize to specific subcellular sites.
10.1523/jneurosci.16-24-07812.1996
81,798,683
Sorting of RNAs to specific subcellular loci occurs in diverse settings from fly oocytes to mammalian neurons. Using the membrane-permeable nucleic acid stain SYTO 14, we directly visualized the translocation of endogenous RNA in living cells. Labeled RNA was distributed nonrandomly as discrete granules in neuronal pro...
10.1038/nrm3918
Live imaging and tracking of RNA material in neurons reveals oscillatory behaviour and altered movement in response to stimulation.
10.1126/science.1250212
41,741,358
Transcripts Visualized in Situ Despite advances, current methods for single-cell sequencing are unable to resolve transcript location within the cell, so Lee et al. (p. 1360 , published online 27 February) developed a method of fluorescent in situ RNA sequencing (FISSEQ) that works in vivo to show messenger RNA localiz...
10.1038/nrm3918
This is the first demonstration of in situ RNA sequencing, which allows localization analysis of multiple RNA species in cells at the single-molecule level.
10.1242/dev.02212
60,471,897
The Hedgehog morphogen is a major developmental regulator that acts at short and long range to direct cell fate decisions in invertebrate and vertebrate tissues. Hedgehog is the only known metazoan protein to possess a covalently linked cholesterol moiety. Although the role of the cholesterol group of Hedgehog remains ...
10.1038/nrm2414
Shows that cholesterol modification of Hh is required for its long-range signalling activity and for its incorporation into high molecular weight multimers in vivo
10.1101/gad.1185804
107,193,428
Hedgehog (Hh) signaling plays a major role in multiple aspects of embryonic development. A key issue in Hh signaling is to elucidate the molecular mechanism by which a Hh protein morphogen gradient is formed despite its membrane association. In this study, we used a combination of genetic, cellular, and biochemical app...
10.1038/nrm2414
Shows that lipid modification of Sonic Hh is necessary for incorporation into high molecular weight multimeric complexes and that incorporation into these complexes promotes Hh signalling activity.
10.1073/pnas.0602852103
38,591,313
Sterol synthesis is required for Sonic hedgehog (Shh) signal transduction. Errors in Shh signal transduction play important roles in the formation of human tumors, including medulloblastoma (MB). It is not clear which products of sterol synthesis are necessary for Shh signal transduction or how they act. Here we show t...
10.1038/nrm2414
Reports that both Hh signalling and proliferation in a medulloblastoma cell line require cholesterol biosynthesis.
10.1126/science.1139740
103,976,391
Primary cilia are essential for transduction of the Hedgehog (Hh) signal in mammals. We investigated the role of primary cilia in regulation of Patched1 (Ptc1), the receptor for Sonic Hedgehog (Shh). Ptc1 localized to cilia and inhibited Smoothened (Smo) by preventing its accumulation within cilia. When Shh bound to Pt...
10.1038/nrm2414
Shows that Patched localizes to primary cilia and prevents the accumulation of Smoothened. Addition of Sonic Hh removes Patched from the cilium and allows Smoothened accumulation.
10.1177/1403494811399956
62,244,914
Danish registers contain information on many important health and social issues. Because all Danish citizens have a unique personal identification number, linkage at the individual level between these nationwide registers and other data sources is possible and feasible. In this paper we briefly introduce selected Danis...
10.1038/nrg3208
An overview of Danish health and socio-economic registries and research possibilities as an example of extensive population-wide registration.
10.1093/bioinformatics/btq126
41,539,286
Abstract Motivation: Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans (PheWAS) for disease–gene associations. We propose a novel method to scan phenomic data for genetic associations using International Classification of Disease...
10.1038/nrg3208
A demonstration of how EHR data linked with DNA data can be used in a reversal of the normal GWAS approach to search for disease phenotypes associated with SNPs.
10.1126/science.1183439
20,849,904
Homing in on Hotspots The clustering of recombination in the genome, around locations known as hotspots, is associated with specific DNA motifs. Now, using a variety of techniques, three studies implicate a chromatin-modifying protein, the histone-methyltransferase PRDM9, as a major factor involved in human hotspots (s...
10.1038/nrg3573
This paper establishes the role of PRDM9 by using a mouse genetic approach, by showing the major contribution of PRDM9 in crossover localization in humans and by using analysis of the DNA-binding specificity of PRDM9 in vitro
10.1126/science.1182363
62,023,222
Homing in on Hotspots The clustering of recombination in the genome, around locations known as hotspots, is associated with specific DNA motifs. Now, using a variety of techniques, three studies implicate a chromatin-modifying protein, the histone-methyltransferase PRDM9, as a major factor involved in human hotspots (s...
10.1038/nrg3573
The motif previously identified by these authors in 2008 has a pattern of evolution that is consistent with the motif being actively involved in the initiation of meiotic recombination, and PRDM9 is predicted to recognize this motif.
10.1126/science.1195774
29,278,216
Recombination between the sex chromosomes during sperm formation is controlled by a splicing isoform of the SPO11 protein.
10.1038/nrg3573
This study uncovers specific genetic control and structural properties of the PAR region.
10.1242/jcs.115.8.1611
125,329,003
During mouse meiosis, the early prophase RAD51/DMC1 recombination protein sites, which are associated with the chromosome cores and which serve as markers for ongoing DNA-DNA interactions, are in ten-fold excess of the eventual reciprocal recombinant events. Most, if not all, of these early interactions are eliminated ...
10.1038/nrg3573
This is a major report of the dynamics and localization of proteins during meiotic prophase. The laboratories of T. Ashley, M. Hulten, C. Heyting and others have also done similar studies.
10.1126/science.1152422
41,744,205
The genome-wide recombination rate varies between individuals, but the mechanism controlling this variation in humans has remained elusive. A genome-wide search identified sequence variants in the 4p16.3 region correlated with recombination rate in both males and females. These variants are located in the RNF212 gene, ...
10.1038/nrg3573
This study analyses high-resolution, sex-specific human genetic maps, which allows the identification of polymorphisms in the RNF212 gene that are associated with variation in genome-wide crossover rate.
10.1038/ncomms11987
110,276,165
Abstract Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, from a paediatric patient with a rare undifferentiated sarcoma. Here, we confirm th...
10.1038/nrd.2016.244
This study demonstrated the power of integrating chemogenomic screening with genetic methods (such as RNAi and CRISPR–Cas9) to identify new therapeutic targets for a rare type of sarcoma.
10.1073/pnas.1311846111
82,785,476
Significance The treatment of cancer is highly reliant on drug combinations. Next-generation, targeted therapeutics are demonstrating interesting single-agent activities in clinical trials; however, the discovery of companion drugs through iterative clinical trial-and-error is not a tenable mechanism to prioritize clin...
10.1038/nrd.2016.244
This study identified new therapeutically relevant anticancer drug combinations using chemogenomic screening.
10.1128/jvi.02953-15
104,002,946
ABSTRACT While the recent success of adeno-associated virus (AAV)-mediated gene therapy in clinical trials is promising, challenges still face the widespread applicability of recombinant AAV(rAAV). A major goal is to enhance the transduction efficiency of vectors in order to achieve therapeutic levels of gene expressio...
10.1038/nrd.2016.244
This proof-of-concept study highlighted opportunities for the synergistic combination of small molecules with alternative modalities (gene therapy in this case) that can be facilitated by chemogenomics.
10.1126/science.290.5500.2312
58,564,505
The TATA-binding protein (TBP) is believed to function as a key component of the general transcription machinery. We tested the role of TBP during the onset of embryonic transcription by antisense oligonucleotide–mediated turnover of maternal TBP messenger RNA. Embryos without detectable TBP initiated gastrulation but ...
10.1038/nrg2847
Showed that TRF2 is highly expressed in X. laevis oocytes and embryos and that knock down of TRF2 stops embryos from developing past the mid-blastula stage. This provided early evidence that non-prototypical core promoter recognition factors function in embryogenesis.
10.1073/pnas.2036440100
102,650,213
TATA-box-binding protein (TBP) is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex. Two proteins with high homology to TBP have been found: TBP-related factor 1 (TRF1), described only in Drosophila melanogaster , and TR...
10.1038/nrg2847
Identified TRF3 in the human, mouse and frog genomes, and that TRF3 protein is expressed in many human and mouse tissues and cell lines. The identification of TRF3 set the stage for many other studies of this protein and its function in development.
10.1101/gad.869101
16,748,205
Alternate forms of the general transcription machinery have been described in several tissues or cell types. However, the role of tissue-specific TBP-associated factors (TAF II s) and other tissue-specific transcription components in regulating differential gene expression during development was not clear. Here we show...
10.1038/nrg2847
Showed that the protein encoded by the Drosophila cannonball gene is a homologue of TAF5. Cannonball is expressed in Drosophila testes where it controls expression of a series of genes in spermatocytes. After these studies were published additional testes-specific TAFs were discovered that also function in spermatogene...
10.1126/science.1061935
79,455,197
Transcription factor TFIID, composed of TBP and TAF II subunits, is a central component of the RNA polymerase II machinery. Here, we report that the tissue-selective TAF II 105 subunit of TFIID is essential for proper development and function of the mouse ovary. Female mice lacking TAF II 105 are viable but infertile b...
10.1038/nrg2847
Showed that knock out of Taf4b in mice is required for development of the ovary. Taf4b is expressed in granulosa cells and is necessary for expression of ovarian-specific genes during folliculogenesis.
10.1101/gad.1583407
67,315,971
Transcriptional mechanisms that govern cellular differentiation typically include sequence-specific DNA-binding proteins and chromatin-modifying activities. These regulatory factors are assumed necessary and sufficient to drive both divergent programs of proliferation and terminal differentiation. By contrast, potentia...
10.1038/nrg2847
Showed that an unprecedented exchange of core promoter recognition machinery occurs when myoblasts differentiate into myotubes. Specifically, multiple subunits of TFIID decrease, whereas levels of TAF3 remained constant. TAF3 binds TRF3 in myotubes and the two factors associate with the core promoter of the myogenin ge...
10.1101/gad.1608807
62,624,404
The 100 copies of tandemly arrayed Drosophila linker (H1) and core (H2A/B and H3/H4) histone gene cluster are coordinately regulated during the cell cycle. However, the molecular mechanisms that must allow differential transcription of linker versus core histones prevalent during development remain elusive. Here, we us...
10.1038/nrg2847
Showed that TRF2 directs the transcription of histone H1 genes, but not adjacent core histone genes, in the Drosophila histone gene cluster. TRF2 binds the promoter of the TATA-less histone H1 gene, whereas TBP binds the promoters of the core histone genes. Genome-wide studies revealed that TRF2 widely binds TATA-less ...
10.1073/pnas.90.13.5954
18,801,821
The product of the p53 gene suppresses cell growth and plays a critical role in suppressing development of human tumors. p53 protein binds DNA, activates transcription, and can be phosphorylated at N- and C-terminal sites. Previously, wild-type p53 was shown to be hyperphosphorylated compared to mutant p53 during p53-m...
10.1038/nrc1455
One of the first reports to show that post-translational modification of mutant p53 differs from wild-type p53.
10.1126/science.1091362
20,806,066
Although Mdm2-mediated ubiquitination is essential for both degradation and nuclear export of p53, the molecular basis for the differential effects of Mdm2 remains unknown. Here we show that low levels of Mdm2 activity induce monoubiquitination and nuclear export of p53, whereas high levels promote p53's polyubiquitina...
10.1038/nrc1455
Indicates that the level of MDM2 activity determines whether p53 will be exported or degraded in the nucleus.
10.1101/gad.12.17.2658
16,848,784
In this study we elucidated the role of nonactive JNK in regulating p53 stability. The amount of p53–JNK complex was inversely correlated with p53 level. A peptide corresponding to the JNK binding site on p53 efficiently blocked ubiquitination of p53. Similarly, p53 lacking the JNK binding site exhibits a longer half-l...
10.1038/nrc1455
One of the first reports illustrating a function for JNK in the regulation of p53.
10.1242/jcs.111.12.1613
20,729,563
Direct knowledge of Ca2+ patterns in vertebrate development is largely restricted to early stages, in which they control fertilization, ooplasmic segregation and cleavage. To explore new roles of Ca2+ in vertebrate development, we injected the Ca2+ indicator aequorin into zebrafish eggs and imaged Ca2+ throughout the f...
10.1038/nrm1149
A report describing various visualized Ca 2+ signals that are generated by developing zebrafish embryos from the cleavage to segmentation periods.
10.1242/jcs.113.19.3519
104,360,832
Through the injection of f-aequorin (a calcium-sensitive bioluminescent reporter) into the dorsal micromeres of 8-cell stage Xenopus laevis embryos, and the use of a Photon Imaging Microscope, distinct patterns of calcium signalling were visualised during the gastrulation period. We present results to show that localis...
10.1038/nrm1149
This paper describes the visualization of distinct patterns of Ca 2+ signalling that are generated during neural induction in intact Xenopus embryos.
10.1073/pnas.96.1.157
16,753,676
Oscillations of cytosolic free calcium levels have been shown to influence gene regulation and cell differentiation in a variety of model systems. Intercellular calcium waves thus present a plausible mechanism for coordinating cellular processes during embryogenesis. Herein we report use of aequorin and a photon imagin...
10.1038/nrm1149
This article describes the visualization of various Ca 2+ signals that occur during gastrulation in zebrafish.
10.1126/science.282.5392.1281
83,243,373
The ectodomains of numerous proteins are released from cells by proteolysis to yield soluble intercellular regulators. The responsible protease, tumor necrosis factor-α converting enzyme (TACE), has been identified only in the case when tumor necrosis factor-α (TNFα) is released. Analyses of cells lacking this metallop...
10.1038/nrm2120
An excellent example of linking an enzyme, ADAM17, to several substrates, including TGFα, through the analysis of Adam17 -knockout mice and cell-based assays in cells lacking ADAM17, derived from these mice.
10.1073/pnas.0305862101
102,594,091
By proteolytic modification of low abundant signaling proteins and membrane receptors, proteases exert potent posttranslational control over cell behavior at the postsecretion level. Hence, substrate discovery is indispensable for understanding the biological role of proteases in vivo . Indeed, matrix metalloproteinase...
10.1038/nrm2120
A key paper describing the use of isotope mass tags and liquid-chromatography-based mass-spectrometric identification of cleaved products of native substrates in the cellular context.
10.1126/science.8493554
100,837,056
A method is described here for identifying good protease substrates among approximately 10 7 possible sequences. A library of fusion proteins was constructed containing an amino-terminal domain used to bind to an affinity support, followed by a randomized protease substrate sequence and the carboxyl-terminal domain of ...
10.1038/nrm2120
A classic paper on the development of phage display to screen for protease-cleavage sites.
10.1083/jcb.200307137
41,715,118
All ligands of the epidermal growth factor receptor (EGFR), which has important roles in development and disease, are released from the membrane by proteases. In several instances, ectodomain release is critical for activation of EGFR ligands, highlighting the importance of identifying EGFR ligand sheddases. Here, we u...
10.1038/nrm2120
Mouse embryonic fibroblasts from different Adam -knockout mice were used in cell-based assays to identify which ADAM is required for processing of individual epidermal-growth-factor-receptor ligands.
10.1073/pnas.0402353101
62,565,810
Standardized, comprehensive platforms for the discovery of protease substrates have been extremely difficult to create. Screens for protease specificity are now frequently based on the cleavage patterns of peptide substrates, which contain small recognition motifs that are required for the cleavage of the scissile bond...
10.1038/nrm2120
Describes the successful application of DIGE to identify substrates for granzyme A and B.
10.1111/j.1471-4159.2006.04067.x
82,750,229
Abstract Prohormone convertase (PC) 1/3 and 2 are involved in the generation of neuropeptides from their precursors. A quantitative peptidomic approach was used to explore the role PC2 plays in the processing of hypothalamic peptides. In this approach, extracts from mice lacking PC2 activity and from wild‐type litterma...
10.1038/nrm2120
Peptidomic analysis of protease-knockout and wild-type mice focusing on neuropeptide products that result from prohormone convertase-2 activity.
10.1126/science.1132341
62,565,445
Although BACE1 (beta-site amyloid precursor protein–cleaving enzyme 1) is essential for the generation of amyloid-b peptide in Alzheimer's disease, its physiological function is unclear. We found that very high levels of BACE1 were expressed at time points when peripheral nerves become myelinated. Deficiency of BACE1 r...
10.1038/nrm2120
Expression analysis revealed high amounts of BACE in peripheral nerves during myelination, and BACE-deficient mice were found to display hypomyelination and defects in processing of neuregulin, an ErbB-ligand that is crucial for myelination.
10.1101/gad.12.16.2598
18,606,337
The human single-stranded DNA-binding replication A protein (RPA) is involved in various DNA-processing events. By comparing the affinity of hRPA for artificial DNA hairpin structures with 3′- or 5′-protruding single-stranded arms, we found that hRPA binds ssDNA with a defined polarity; a strong ssDNA interaction domai...
10.1038/nrm.2016.177
Describes how RPA binds to single-stranded DNA with a defined polarity and contributes to the control of XPF–ERCC1 and XPG at sites of DNA damage.
10.1126/science.aad5634
62,580,740
A key player in cancer prevention Obstacles that block DNA replication can lead to chromosomal abnormalities and ultimately cancer. Fanconi anemia, for example, is caused by defects in the repair of DNA interstrand cross-links. The Fan1 nuclease was originally identified as a protein essential for this cross-link repai...
10.1038/nrm.2016.177
Shows that recruitment of FAN1 to ubiquitylated FANCD2 through its UBZ motif is crucial during replication inhibition, but is dispensable for ICL repair. A FAN1 variant from high-risk pancreatic cancer is not recruited to ubiquitylated FANCD2.
10.1101/gad.193516.112
81,293,858
To efficiently duplicate their genomic content, cells must overcome DNA lesions that interfere with processive DNA replication. These lesions may be removed and repaired, rather than just tolerated, to allow continuity of DNA replication on an undamaged DNA template. However, it is unclear how this is achieved at a mol...
10.1038/nrm.2016.177
References 95–97 describe how the translocase ZRANB3 is an ATP-dependent SSE that is recruited to ubiquitylated PCNA.
10.1101/gad.1304305
61,283,461
The replication checkpoint kinase Cds1 preserves genome integrity by stabilizing stalled replication forks. Cds1 targets substrates through its FHA domain. The Cds1 FHA domain interacts with Mus81, a subunit of the Mus81-Eme1 structure-specific endonuclease. We report here that Mus81 and Rhp51 are required for generati...
10.1038/nrm.2016.177
Provides evidence of the potentially deleterious effects of Mus81 during replication, especially when not controlled by Cds1.
10.1101/gad.1105003
122,558,292
Growth factor withdrawal results in the termination of factor-dependent transcription. One transcript that declines rapidly following growth factor deprivation of hematopoietic cells is the serine/threonine kinase pim-2 . When constitutively expressed, Pim-2 conferred long-term resistance to a variety of apoptotic stim...
10.1038/nrc2986
This paper is the first study to describe two novel roles for Pim kinases in mediating cell survival: PIM2-specific regulation of 4E-BP1 and the phosphorylation of BAD by PIM2, which was later observed to be shared with the other family members.
10.1128/mcb.24.13.6104-6115.2004
20,516,636
ABSTRACT The Pim family of proto-oncogenes encodes a distinct class of serine/threonine kinases consisting of PIM1, PIM2, and PIM3. Although the Pim genes are evolutionarily highly conserved, the contribution of PIM proteins to mammalian development is unclear. PIM1-deficient mice were previously described but showed o...
10.1038/nrc2986
This study describes the phenotype of Pim2 −/− and Pim3 −/− mice, as well as that of the Pim1 −/− Pim2 −/− Pim3 −/− mouse, and finds that Pim kinases are not required for crucial developmental processes.
10.1083/jcb.200607020
59,526,435
This study demonstrates that the eukaryotic translation initiation factor eIF4E is a critical node in an RNA regulon that impacts nearly every stage of cell cycle progression. Specifically, eIF4E coordinately promotes the messenger RNA (mRNA) export of several genes involved in the cell cycle. A common feature of these...
10.1038/nrc2986
This paper characterizes a novel function for EIF4E in regulating nuclear export of mRNA transcripts, based on the recognition of a structural motif in the UTR sequences, and resulting in higher levels of protein translation.
10.1182/blood-2008-10-184515
109,096,883
Abstract The deregulation of translation markedly contributes to the malignant phenotype in cancers, and the assembly of the translation initiating complex eIF4F is the limiting step of this process. The mammalian Target of Rapamycin Complex 1 (mTORC1) is thought to positively regulate eIF4F assembly and subsequent onc...
10.1038/nrc2986
This paper shows that PIM2-dependent regulation of cap-dependent translation was crucial for rapamycin-insensitive deregulation of oncogenic protein synthesis in AML blast cells, and implicates the regulation of protein translation as a relevant therapeutic target.
10.1083/jcb.153.4.865
83,420,976
We have performed a biochemical and double-stranded RNA-mediated interference (RNAi) analysis of the role of two chromosomal passenger proteins, inner centromere protein (INCENP) and aurora B kinase, in cultured cells of Drosophila melanogaster. INCENP and aurora B function is tightly interlinked. The two proteins bind...
10.1038/nrm3474
Uses for the first time RNAi to probe the function of the CPC in vivo
10.1126/science.1194498
81,110,639
Location, Location, Location Cell division is orchestrated by a complex signaling pathway that ensures the correct segregation of newly replicated chromosomes to the two daughter cells. The pathway is controlled in part by restricting the activity of critical regulators to specific subcellular locations. For example, t...
10.1038/nrm3474
Describes, together with references 20 and 21, the post-translational modifications of histones that define the inner centromere and that are responsible for the targeting of the CPC to centromeres.
10.1083/jcb.200207117
109,222,218
The Aurora B kinase complex is a critical regulator of chromosome segregation and cytokinesis. In Caenorhabditis elegans, AIR-2 (Aurora B) function requires ICP-1 (Incenp) and BIR-1 (Survivin). In various systems, Aurora B binds to orthologues of these proteins. Through genetic analysis, we have identified a new subuni...
10.1038/nrm3474
The first description of a fourth member of the CPC.
10.1126/science.1217180
59,313,837
To Cut or Not to Cut During animal cell division, the final separation of daughter cells requires ESCRT-III (endosomal sorting complex required for transport III), the core membrane scission machinery. Carlton et al. (p. 220 , published online 15 March; see the Perspective by Petronczki and Uhlmann ) report that ESCRT-...
10.1038/nrm3474
References 67 and 68 show that the CPC is involved in the control of abscission by regulating the activity of ESCRT-III proteins.
10.1126/science.1167000
62,029,436
Successful cell division requires that chromosomes attach to opposite poles of the mitotic spindle (bi-orientation). Aurora B kinase regulates chromosome-spindle attachments by phosphorylating kinetochore substrates that bind microtubules. Centromere tension stabilizes bi-oriented attachments, but how physical forces a...
10.1038/nrm3474
Demonstrates, using FRET sensors, distance-dependent Aurora B phosphorylation of kinetochore substrates and proposes that this can have a role in detecting tension and regulating microtubule attachments.
10.1083/jcb.200403084
17,611,188
Mitotic kinases of the Polo and Aurora families are key regulators of chromosome segregation and cytokinesis. Here, we have investigated the role of MKlp1 and MKlp2, two vertebrate mitotic kinesins essential for cytokinesis, in the spatial regulation of the Aurora B kinase. Previously, we have demonstrated that MKlp2 r...
10.1038/nrm3474
Mklp2 mediates targeting of the CPC to the central spindle.
10.1083/jcb.201008138
40,444,302
The chromosomal passenger complex (CPC) and centralspindlin are conserved cytokinesis regulators that localize to the spindle midzone, which forms between the separating chromosomes. Previous work placed the CPC and centralspindlin in a linear pathway that governs midzone formation. Using Caenorhabditis elegans embryos...
10.1038/nrm3474
Important analysis of the role of the CPC in the regulation of cytokinesis.
10.1073/pnas.0737381100
20,333,123
Synthetic hydrogels have been molecularly engineered to mimic the invasive characteristics of native provisional extracellular matrices: a combination of integrin-binding sites and substrates for matrix metalloproteinases (MMP) was required to render the networks degradable and invasive by cells via cell-secreted MMPs....
10.1038/nrm1858
Pioneering demonstration of how synthetic extracellular matrices can be tuned to control many facets of cell behaviour in tissue remodelling, using approaches that are accessible to the general cell-biology laboratory.
10.1101/gad.242002
20,610,271
Branching morphogenesis in the mammalian lung and Drosophila trachea relies on the precise localization of secreted modulators of epithelial growth to select branch sites and direct branch elongation, but the intercellular signals that control blood vessel branching have not been previously identified. We found that VE...
10.1038/nrm1858
This paper showed that heparin-binding VEGF isoforms were necessary for endothelial branching, using transgenic mice that expressed only either matrix-interacting or non-interacting VEGF isoforms.
10.1073/pnas.86.3.933
80,283,657
Regeneration of the dermis does not occur spontaneously in the adult mammal. The epidermis is regenerated spontaneously provided there is a dermal substrate over which it can migrate. Certain highly porous, crosslinked collagen-glycosaminoglycan copolymers have induced partial morphogenesis of skin when seeded with der...
10.1038/nrm1858
Pioneering demonstration of design principles that are applied to the development of synthetic scaffolds for tissue regeneration.
10.1128/mcb.23.8.2953-2968.2003
107,166,789
ABSTRACT The heat shock response, which is accompanied by a rapid and robust upregulation of heat shock proteins (Hsps), is a highly conserved protection mechanism against protein-damaging stress. Hsp induction is mainly regulated at transcriptional level by stress-inducible heat shock factor 1 (HSF1). Upon activation,...
10.1038/nrm1200
The phosphorylation of a specific serine residue of HSF1 precedes sumoylation, thereby providing an excellent example for the interplay between two types of post-translational modification in regulating the activity of a substrate.
10.1083/jcb.200110109
59,505,955
RanGAP1 was the first documented substrate for conjugation with the ubiquitin-like protein SUMO-1. However, the functional significance of this conjugation has not been fully clarified. We sought to examine RanGAP1 behavior during mitosis. We found that RanGAP1 associates with mitotic spindles and that it is particular...
10.1038/nrm1200
Shows that sumoylation is required, not only for the interphasic targeting of the nuclear import factor RanGAP1 to the nuclear pores, but also for RanGAP1 targeting to kinetochores and mitotic spindles during mitosis, where it co-localizes with RanBP2.
10.1091/mbc.6.7.793
28,271,163
The MIF2 gene of Saccharomyces cerevisiae has been implicated in mitosis. Here we provide genetic evidence that MIF2 encodes a centromere protein. Specifically, we found that mutations in MIF2 stabilize dicentric minichromosomes and confer high instability (i.e., a synthetic acentric phenotype) to chromosomes that bear...
10.1038/nrm1200
The demonstration that overexpression of yeast SUMO (Smt3) suppresses the phenotype of a temperature-sensitive mutation in Mif-2, the homologue of the mammalian centromere protein, CENP-C. Although unknown at the time, this is the first example of a genetic interaction between sumoylation and chromosome dynamics.
10.1093/genetics/158.1.95
19,158,371
Abstract In a search for regulatory genes affecting the targeting of the condensin complex to chromatin in Saccharomyces cerevisiae, we identified a member of the adenovirus protease family, SMT4. SMT4 overexpression suppresses the temperature-sensitive conditional lethal phenotype of smc2-6, but not smc2-8 or smc4-1. ...
10.1038/nrm1200
This paper, similar to reference 95 above, shows genetic interactions between sumoylation (notably by Smt4/Ulp2 and Siz1/PIAS) and the control of chromosome condensation in budding yeast.
10.1101/gad.877901
100,831,426
The conserved heterochromatic location of centromeres in higher eukaryotes suggests that intrinsic properties of heterochromatin are important for chromosome inheritance. Based on this hypothesis, mutations in Drosophila melanogaster that alter heterochromatin-induced gene silencing were tested for effects on chromosom...
10.1038/nrm1200
This work demonstrates that in flies, as in yeast, sumoylation might be important for chromosome structure, as mutation of the Drosophila PIAS homologue Suvar2-10/Zimp leads to defects in chromosome condensation and mitosis.
10.1084/jem.20082173
83,561,277
Macrophages (Mϕ) are prominent components of solid tumors and exhibit distinct phenotypes in different microenvironments. We have recently found that tumors can alter the normal developmental process of Mϕ to trigger transient activation of monocytes in peritumoral stroma. We showed that a fraction of monocytes/Mϕ in p...
10.1038/nri3175
This study demonstrated that CD68 + monocytes in the peritumoural stroma of patients with hepatocellular carcinoma express PDL1, induce T cell anergy, promote tumour progression and are associated with poor survival.
10.1182/blood-2010-12-325753
20,466,138
Abstract We recently demonstrated that human BM cells can be treated in vitro with defined growth factors to induce the rapid generation of myeloid-derived suppressor cells (MDSCs), hereafter defined as BM-MDSCs. Indeed, combination of G-CSF + GM-CSF led to the development of a heterogeneous mixture of immature myeloid...
10.1038/nri3175
A relationship between human MDSCs and immature promyelocytes is identified in this study. More importantly, the levels of these cells in the blood are shown to be inversely correlated with the response to chemotherapy in patients with breast or colon cancer.
10.1084/jem.20101956
104,439,000
Tumor-promoted constraints negatively affect cytotoxic T lymphocyte (CTL) trafficking to the tumor core and, as a result, inhibit tumor killing. The production of reactive nitrogen species (RNS) within the tumor microenvironment has been reported in mouse and human cancers. We describe a novel RNS-dependent posttransla...
10.1038/nri3175
References 99, 101 and 102 illustrate the complex negative influence on T cells of peroxynitrite, which is produced in the tumour environment or in tumour-draining lymph nodes by either myeloid or tumour cells.
10.1084/jem.20100587
19,195,944
Myeloid-derived suppressor cells (MDSCs) are a major component of the immune-suppressive network described in cancer and many other pathological conditions. We demonstrate that although MDSCs from peripheral lymphoid organs and the tumor site share similar phenotype and morphology, these cells display profound function...
10.1038/nri3175
This study demonstrated that MDSCs in the tumour microenvironment rapidly differentiate into TAMs and that this effect is mediated by hypoxia.
10.1182/blood-2009-04-217620
26,940,872
Abstract Alternatively activated (M2) macrophages play critical roles in diverse chronic diseases, including parasite infections, cancer, and allergic responses. However, little is known about the acquisition and maintenance of their phenotype. We report that M2-macrophage marker genes are epigenetically regulated by r...
10.1038/nri3175
This study demonstrates that M2 macrophage polarization is partially regulated epigenetically by chromatin or histone remodelling through an IL-4- and STAT6-dependent mechanism.
10.1126/science.1218469
103,733,531
Choosing the Right Path RNA molecules are synthesized in the cell nucleus, yet many have to be moved to the cytoplasm to be processed and/or to effect their function. Different classes of RNA are transported from the nucleus by different transport systems. Messenger RNAs (mRNAs) and uridine-rich small nuclear RNAs (U s...
10.1038/nrm3742
First identification of a specific function for the non-shuttling hnRNP C-type proteins in RNA export.
10.1073/pnas.0802287105
84,375,652
In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2–8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN...
10.1038/nrm3742
Shows that both human and fruitfly SMN–GEMIN2 heterodimers are sufficient for mediating Sm core assembly in vitro
10.1073/pnas.0508947102
41,652,108
Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by loss of spinal motor neurons. The gene encoding the survival of motor neurons (SMN) protein is mutated in >95% of SMA cases. SMN is the central component of a large oligomeric complex, including Gemins2–7, that is necessary and sufficient ...
10.1038/nrm3742
Assays individual Gemins, as well as a panel of SMN missense mutants for ability to carry out Sm core assembly, showing that certain SMA-causing alleles are functional, whereas others are not.
10.1073/pnas.0902020106
39,179,488
Pre-mRNA splicing is a crucial step in eukaryotic gene expression and is carried out by a highly complex ribonucleoprotein assembly, the spliceosome. Many fundamental aspects of spliceosomal function, including the identity of catalytic domains, remain unknown. We show that a base-paired complex of U6 and U2 small nucl...
10.1038/nrm3742
Together with reference 122, demonstrates that protein-free U6/U2 snRNA constructs can recognize 5′ splice site and branch point sequence to carry out the first and second steps of splicing.
10.1101/gad.1563807
29,277,511
Histone deacetylases (HDACs) tighten chromatin structure and repress gene expression through the removal of acetyl groups from histone tails. The class I HDACs, HDAC1 and HDAC2, are expressed ubiquitously, but their potential roles in tissue-specific gene expression and organogenesis have not been defined. To explore t...
10.1038/nrg2485
Reports the first conditional knockout of a class I HDAC.
10.1073/pnas.0706487104
41,270,371
Previous findings have suggested that class IIa histone deacetylases (HDACs) (HDAC4, -5, -7, and -9) are inactive on acetylated substrates, thus differing from class I and IIb enzymes. Here, we present evidence supporting this view and demonstrate that class IIa HDACs are very inefficient enzymes on standard substrates...
10.1038/nrg2485
Describes the mechanism for the loss of enzymatic activity in class IIa HDACs.
10.1126/science.272.5260.408
125,150,432
Trapoxin 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 microseq...
10.1038/nrg2485
A seminal paper describing the cloning of the first mammalian HDAC.
10.1634/theoncologist.12-10-1247
20,746,210
Learning Objectives After completing this course, the reader will be able to: Add vorinostat to the armamentarium of drugs for CTCL.Identify the mechanism of action of vorinostat.Identify goals of therapy of CTCL.Identify active CTCL therapies.Identify CTCL response criteria. Access and take the CME test online and rec...
10.1038/nrg2485
This study highlights the first US Food and Drug Administration (FDA) approval of an HDAC inhibitor.
10.1101/gad.14.7.830
133,917,653
Yeast Los1p, the homolog of human exportin-t, mediates nuclear export of tRNA. Using fluorescence in situ hybridization, we could show that the export of some intronless tRNA species is not detectably affected by the disruption of LOS1 . To find other factors that facilitate tRNA export, we performed a suppressor scree...
10.1038/nrm2255
Reports that tRNA aminoacylation and eEF1α are required for efficient nuclear tRNA export in yeast.
10.1101/gad.1158803
41,626,429
MicroRNAs (miRNAs) are initially expressed as long transcripts that are processed in the nucleus to yield ∼65-nucleotide (nt) RNA hairpin intermediates, termed pre-miRNAs, that are exported to the cytoplasm for additional processing to yield mature, ∼22-nt miRNAs. Here, we demonstrate that human pre-miRNA nuclear expor...
10.1038/nrm2255
References 39–41 report the identification of exportin-5 as the miRNA export receptor.
10.1101/gad.892401
109,157,007
Following transcription and processing, eukaryotic mRNAs are exported from the nucleus to the cytoplasm for translation. Here we present evidence that mRNAs are targeted for nuclear export cotranscriptionally. Combined mutations in the Saccharomyces cerevisiae hnRNP Npl3 and TATA-binding protein (TBP) block mRNA export...
10.1038/nrm2255
Presents evidence that mRNA export factors can be recruited to gene loci.
10.1073/pnas.82.24.8527
18,572,945
It is assumed that the genome of a higher eukaryotic organism is organized into a number of distinct three-dimensional (3-D) structures, each characteristic for a given differentiated state. These discrete 3-D structures are envisioned to develop in a hierarchical and largely irreversible manner from an omnipotent 3-D ...
10.1038/nrm2255
A pioneering paper that anticipated current concepts about the functional connection between nuclear gene positioning, gene expression and mRNA export.
10.1128/mcb.21.10.3405-3415.2001
61,610,149
ABSTRACT Nuclear export of ribosomes requires a subset of nucleoporins and the Ran system, but specific transport factors have not been identified. Using a large subunit reporter (Rpl25p-eGFP), we have isolated several temperature-sensitive ribosomal export ( rix ) mutants. One of these corresponds to the ribosomal pro...
10.1038/nrm2255
References 146 and 147 identify Nmd3 as an adaptor for Crm1–RanGTP-mediated 60S subunit export.
10.1126/science.1138659
83,017,798
We tested the hypothesis that de novo copy number variation (CNV) is associated with autism spectrum disorders (ASDs). We performed comparative genomic hybridization (CGH) on the genomic DNA of patients and unaffected subjects to detect copy number variants not present in their respective parents. Candidate genomic reg...
10.1038/nrg2958
The first study to report CNVs in a common complex neuropsychiatric disease.