Mardiyyah/TAPT_data_V2_split · Datasets at Hugging Face

PMCID stringclasses 24 values	Title stringclasses 24 values	Sentences stringlengths 2 40.7k
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	PDE3A protein expression was investigated with immunohistochemistry in 181 LPS samples, and PDE3A and SLFN12 mRNA expression with RT-qPCR were investigated in 63 LPS samples.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Immunoblotting and cell viability assays were used to study LPS cell lines and their sensitivity to PDE3A modulators.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	We identified 97, 247, and 37 subtype-specific, highly expressed genes in dedifferentiated, myxoid, and pleomorphic LPS subtypes, respectively.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Signaling pathway analysis revealed a highly activated hedgehog signaling pathway in dedifferentiated LPS, phospholipase c mediated cascade and insulin signaling in myxoid LPS, and pathways associated with cell proliferation in pleomorphic LPS.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	We discovered a strong association between high PDE3A expression and myxoid LPS, particularly in high-grade tumors.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Moreover, myxoid LPS samples showed elevated expression levels of SLFN12 mRNA.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	In addition, PDE3A- and SLFN12-coexpressing LPS cell lines SA4 and GOT3 were sensitive to PDE3A modulators.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Our results indicate that PDE3A modulators are promising drugs to treat myxoid LPS.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Further studies are required to develop these drugs for clinical use.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Soft-tissue sarcomas (STSs) are malignancies of mesenchymal origin that comprise approximately 1% of all cancer cases worldwide.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Among the most common STS types are liposarcomas (LPSs), which arise from adipose tissue .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Due to their distinct histology and genetic background, LPSs are divided into the following four subtypes: well-differentiated LPS (WDLPS), low- and high-grade dedifferentiated LPS (DDLPS), myxoid LPS (MLPS), and pleomorphic LPS (PLPS) .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The 5-year overall survival rates range from 21% in high-grade DDLPS to 100% in WDLPS .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Despite varying outcomes, all LPS subtypes are usually treated similarly, with surgery combined with (neo-)adjuvant chemotherapy, radiation, or both.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	First-line chemotherapies used for LPS treatment include doxorubicin, which is frequently combined with ifosfamide .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	A combination of docetaxel and gemcitabine is another treatment option, with survival outcomes that are similar to those resulting from doxorubicin treatment .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Two other chemotherapeutics, eribulin and trabectedin, have been approved to treat unresectable pretreated STS .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Eribulin treatment has shown an increased survival benefit that is greater than that of dacarbazine treatment ; it is somewhat more effective in DDLPS and PLPS than in MLPS .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	In contrast, treatment with trabectedin increases progression-free survival more effectively than dacarbazine treatment, specifically in MLPS .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Histologically divided LPS subtypes have distinct genetic characteristics.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	WDLPS is a low-grade tumor that can differentiate over time into more aggressive DDLPS.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	However, 90% of DDLPS tumors arise de novo.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Most WDLPS/DDLPS tumors have increased MDM2/CDK4 expression, due to an amplification in the chromosome 12q13-15 region .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	MDM2, CDK4/6, and exportin 1 (XPO1) inhibitors are currently undergoing clinical trials for treating WD-/DDLPS .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Like WDLPS and DDLPS tumors, low-grade MLPS tumors can progress to a high-grade phenotype that is characterized by the presence of round tumor cells.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Over 90% of MLPS tumors contain a fusion gene (FUS-DDIT3 or EWSR1-DDIT3) that drives tumorigenesis .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Moreover, MLPS tumors frequently have upregulation of the IGF1R/PI3K/Akt signaling pathway, driven by the fusion protein; targeting these pathway alterations with PI3K and mTOR inhibitors is being investigated .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Highly aggressive PLPS is the rarest LPS subtype and accounts for approximately 5% of all LPSs.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Due to its rarity, collecting large sample series has been challenging and no definite genetic aberrations or specific therapy targets of PLPS have been identified .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	In summary, LPSs are a group of molecularly, histologically, and clinically heterogeneous tumors, and there is an unmet clinical need for targeting LPS subtype-specific highly expressed genes.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Phosphodiesterases (PDEs) constitute a superfamily of enzymes (PDE1–PDE11) whose main function is to regulate the signaling of secondary messengers cAMP and cGMP by hydrolyzing 3′,5′-cyclic nucleotides to their 5′-monophosphate form.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Tissue-specific expression of various PDE isoforms enables cellular function regulation in a cell-type specific manner.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Aberrant expression of PDE isoforms is linked to many diseases .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	PDE3A-targeting compounds have recently been described as inhibiting tumor growth in mice inoculated with PDE3A-expressing cervical cancer HeLa , neuroglioma H4 , and melanoma SK-MEL-3 cells , and in patient-derived gastrointestinal stromal tumor (GIST) xenograft models .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	These compounds act like a molecular glue and form a complex between PDE3A and Schlafen 12 (SLFN12), leading to cell-cycle arrest or cell death .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	While the precise downstream signaling pathways remain unclear, the formed complex stabilizes SLFN12 and its RNase activity, resulting in protein synthesis inhibition .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	We sought to discover novel LPS-subtype-specific oncogenes that could serve as precision medicine targets.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	RNA-Seq transcriptome analysis of LPS patient tissue samples were first compared to transcriptomes of other cancerous and healthy tissue samples, resulting in ranked lists of highly expressed genes in three LPS subtypes and their enrichment in biological signaling pathways.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	PDE3A expression was high in MLPS, and its expression frequency in other STS subtypes and its potential role as a therapy target in LPS were further investigated.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Patients who were diagnosed with LPS from 1987 to 2017 in the Helsinki University Hospital (HUH) were identified.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Clinical data were extracted from the patient registry, and hematoxylin and eosin-stained tissue slides and corresponding formalin-fixed, paraffin-embedded (FFPE) tissue blocks were extracted from the archives of the Department of Pathology.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Histological classifications of tumors were reviewed by Mika Sampo, one of the authors, based on the 2020 WHO classification of soft-tissue tumors .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	A total of 190 patients with primary tumor samples were identified for the retrospective study series.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Two samples were excluded due to missing clinical data (MLPSs), four samples were excluded due to a paucity of tumor tissue, and three samples were excluded due to technical problems in immunohistochemistry (WDLPS, DDLPS, MLPS).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Thus, a total of 181 samples were included in the series.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The median follow-up time for survival in the series was 4.7 years (the range was from 0.3 to 20.3).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	RNA was extracted from 186 LPS FFPE tissue samples, including samples that were excluded from immunohistochemistry (IHC) analysis and two samples for which histology was reviewed but clinical data were not available.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The RNA samples were subjected to RNA sequencing, resulting in sequences from 152 samples.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Of these, 131 transcriptomes passed the quality control analysis and were further investigated for LPS-subtype-specifically overexpressed genes.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Of note, all WDLPS samples (n = 10) were excluded from the analyses, due to low RNA yield from sequencing.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	In addition, a previously collected series of 543 STS samples were investigated by using IHC and tissue microarray (TMA) from the following subtypes: fibrosarcoma, GIST, LPS, leiomyosarcoma, malignant peripheral nerve sheath tumor, myxofibrosarcoma, sarcoma with unspecified histotype, and synovial sarcoma .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	TMA blocks included two to three 1-mm diameter core punches from each tumor sample.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Tissue samples were retrieved from the archives of the Department of Pathology, HUH.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	TMAs were generated with an automated tissue microarrayer (TMA Grand Master, 3DHISTECH Ltd., Budapest, Hungary) in the Biobank Helsinki.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Tissue sections (2 × 10 µm) were collected in 2-mL microfuge tubes (Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 72.693.005, Sarstedt, NRW, Nümbrecht, Germany) and deparaffinized with 160 µL of deparaffinization solution (Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 939018, QIAGEN, NRW, Hilden, Germany).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	If tumor cells were estimated to present >50% of all cells in a tissue section, a representative tumor area was scraped to the tube from the slide.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Samples were mixed by vortexing and, subsequently, centrifuged and incubated at 56 °C for 3 min.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	One hundred and twenty µL of buffer PKD (Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 1034963, QIAGEN) was added, mixed by vortexing, and centrifuged for 13,000× g for 1 min.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Ten µL of proteinase K (Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 19133, QIAGEN) was added to the lower liquid phase of the samples.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	After a 1 h incubation at 56 °C in a tube shaker, samples were centrifuged and RNA was extracted with QIAsymphony RNA Kit (Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 931636, QIAGEN) using a QIAsymphony SP instrument (QIAGEN).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	RNA quality and concentration were measured with a 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	RNA sequencing was conducted, as described earlier .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Shortly after adding 1 µL of ERCC RNA spike-in control (1:1000) to each sample, an RNA sequencing library was prepared with a QuantSeq 3′ mRNA Library kit (Lexogen, Vienna, Austria) following the manufacturer’s instructions, as previously described.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Sequencing was performed with a HiSeq 2500 System (Illumina, San Diego, CA, USA) using a high-throughput mode and v4 chemistry in three batches that included samples from different LPS subtypes.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Sequences were processed with the data analysis pipeline, the BlueBee Genomics platform (BlueBee Holding BV, NB, Rijswijk, The Netherlands), following the manufacturer’s instructions.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Htseq-count files from the Bluebee sequencing process were read into R (version 4.1.2) and matched to clinical data per sample.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Gene annotation was retrieved from AnnotationHub (snapshotDate: 20 October 2021).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Data were imported into a DGEList object by using edgeR package (version 3.36.0).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Genes were further filtered by the filterByExpr function (default parameters) from edgeR. log2 counts per million were calculated with the cpm function (default parameters) from edgeR. Additional sample quality control was performed by excluding samples with a median logcount, with deviation >10% from the median logcount over all samples (21 samples were excluded, resulting in 131 samples for downstream analysis).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The final analysis included RNA sequence data from 53 DDLPS samples, 54 MLPS samples, and 24 PLPS samples.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	QC metrics for the BAM files produced by Bluebee pipeline were additionally calculated by parallel run of RNA-SeQC 2 with summarising results with MultiQC .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Genome annotation file and version used in the QC calculations was Homo_sapiens.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	GRCh38.104.genes.gtf (collapsed to gene level), also available from project Github page.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The sequencing coverage and quality statistics of each sample are presented in Table S1.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Data from the newest version of in silico transcriptomic (IST; ) database (MediSapiens Ltd., Helsinki, Finland) were fetched into R by using Dplyr extension for SQlite.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	We calculated the mean expression for each gene (excluding genes with <6 datapoints) per each healthy anatomical tissue type (n = 95) and per each cancerous tissue type (n = 106).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	For each tissue type (healthy and cancerous), we then chose the top 500 expressing genes.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The final IST reference gene list was calculated by choosing a unique list of genes, in which each gene did not appear in more than one of the healthy-tissue top 500 lists and in more than three of the cancer-tissue top 500 lists.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	This final IST reference list contained a total of 2754 genes and was used as an exclusion list, to eliminate non-LPS-specific genes from the LPS-subtype differential-gene-expression analyses.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	A differential expression test of genes for the LPS subtypes was performed, using the estimateDisp and exactTest functions from edgeR, with default parameters.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Differential-expression genes (DEGs) were defined as genes with a positive logFC > 1.5 (with p value < 0.05) between one subtype and all other subtypes, resulting in three lists of DEGs.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Altogether, we identified 97 DEGs between the DDLPS subtype and the other two subtypes, 247 DEGs between the MLPS subtype and the other two subtypes, and 37 DEGs between the PLPS subtype and the other two subtypes, after using the IST-derived exclusion lists (see above).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Upregulated signaling pathways in the three LPS subtypes were described with all of the identified subtype-specific DEGs, using Enrichr and the NCATS BioPlanet 2019 library .
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The scatter plots and the bar charts with their related genes were visualized via Appyters (https://appyters.maayanlab.cloud/#/).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The pathway search was conducted on 30 June 2023.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	PDE3A and SLFN12 mRNA levels were measured from 63 randomly selected FFPE LPS samples, excluding WDLPS samples.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	RNA extracted from the FFPE block derived from the GIST882 cell line was used as a reference sample for PDE3A and SLFN12 expression levels.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	cDNA was synthesized from RNA with SuperScript™ IV VILO™ Master Mix (Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 11756500, Invitrogen™, Thermo Fisher Scientific, Waltham, MA, USA).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Primers and hybridization probes (Universal ProbeLibrary Set, Human Probes #1–#90, Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 04683633001 Roche, Basel, Switzerland) were designed using ProbeFinder version 2.53 for Human.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	The primers were as follows: PDE3A, F: 5′-AAA GAC AAG CTT GCT ATT CCA AA-3′, R: 5′-GTG GAA GAA ACT CGT CTC AAC A-3′; SLFN12, F: 5′-CTT TGT TCA ACA CGC CAA GA-3′, R: 5′-ATG CAG TGT CCA AGC AGA AA-3′; and YWHAZ, F: 5′-CGT TAC TTG GCT GAG GTT GC-3′, R: 5′-TGC TTG TTG TGA CTG ATC GAC-3′. Real-time qPCR was performed with the LightCycler 480 Probes Master Kit (Cat.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	No. 04887301001, Roche) and the CFX96 Touch Real-Time PCR detection system (Bio-Rad, Hercules, CA, USA), under the following conditions: 95 °C for 10 min; 45 cycles of 95 °C for 30 s, 60°C for 30 s, and 72 °C for 45 s with plate read (amplification); 72 °C for 7 min; 65 °C to 95 °C (increment 0.01 °C s, melt curve).
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	PCR was performed in triplicate for each sample.
PMC10669966	PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma	Relative PDE3A and SLFN12 mRNA expression were calculated using the ΔΔCt method and normalized to YWHAZ expression.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

PDE3A protein expression was investigated with immunohistochemistry in 181 LPS samples, and PDE3A and SLFN12 mRNA expression with RT-qPCR were investigated in 63 LPS samples.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Immunoblotting and cell viability assays were used to study LPS cell lines and their sensitivity to PDE3A modulators.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

We identified 97, 247, and 37 subtype-specific, highly expressed genes in dedifferentiated, myxoid, and pleomorphic LPS subtypes, respectively.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Signaling pathway analysis revealed a highly activated hedgehog signaling pathway in dedifferentiated LPS, phospholipase c mediated cascade and insulin signaling in myxoid LPS, and pathways associated with cell proliferation in pleomorphic LPS.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

We discovered a strong association between high PDE3A expression and myxoid LPS, particularly in high-grade tumors.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Moreover, myxoid LPS samples showed elevated expression levels of SLFN12 mRNA.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

In addition, PDE3A- and SLFN12-coexpressing LPS cell lines SA4 and GOT3 were sensitive to PDE3A modulators.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Our results indicate that PDE3A modulators are promising drugs to treat myxoid LPS.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Further studies are required to develop these drugs for clinical use.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Soft-tissue sarcomas (STSs) are malignancies of mesenchymal origin that comprise approximately 1% of all cancer cases worldwide.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Among the most common STS types are liposarcomas (LPSs), which arise from adipose tissue .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Due to their distinct histology and genetic background, LPSs are divided into the following four subtypes: well-differentiated LPS (WDLPS), low- and high-grade dedifferentiated LPS (DDLPS), myxoid LPS (MLPS), and pleomorphic LPS (PLPS) .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The 5-year overall survival rates range from 21% in high-grade DDLPS to 100% in WDLPS .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Despite varying outcomes, all LPS subtypes are usually treated similarly, with surgery combined with (neo-)adjuvant chemotherapy, radiation, or both.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

First-line chemotherapies used for LPS treatment include doxorubicin, which is frequently combined with ifosfamide .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

A combination of docetaxel and gemcitabine is another treatment option, with survival outcomes that are similar to those resulting from doxorubicin treatment .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Two other chemotherapeutics, eribulin and trabectedin, have been approved to treat unresectable pretreated STS .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Eribulin treatment has shown an increased survival benefit that is greater than that of dacarbazine treatment ; it is somewhat more effective in DDLPS and PLPS than in MLPS .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

In contrast, treatment with trabectedin increases progression-free survival more effectively than dacarbazine treatment, specifically in MLPS .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Histologically divided LPS subtypes have distinct genetic characteristics.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

WDLPS is a low-grade tumor that can differentiate over time into more aggressive DDLPS.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

However, 90% of DDLPS tumors arise de novo.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Most WDLPS/DDLPS tumors have increased MDM2/CDK4 expression, due to an amplification in the chromosome 12q13-15 region .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

MDM2, CDK4/6, and exportin 1 (XPO1) inhibitors are currently undergoing clinical trials for treating WD-/DDLPS .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Like WDLPS and DDLPS tumors, low-grade MLPS tumors can progress to a high-grade phenotype that is characterized by the presence of round tumor cells.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Over 90% of MLPS tumors contain a fusion gene (FUS-DDIT3 or EWSR1-DDIT3) that drives tumorigenesis .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Moreover, MLPS tumors frequently have upregulation of the IGF1R/PI3K/Akt signaling pathway, driven by the fusion protein; targeting these pathway alterations with PI3K and mTOR inhibitors is being investigated .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Highly aggressive PLPS is the rarest LPS subtype and accounts for approximately 5% of all LPSs.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Due to its rarity, collecting large sample series has been challenging and no definite genetic aberrations or specific therapy targets of PLPS have been identified .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

In summary, LPSs are a group of molecularly, histologically, and clinically heterogeneous tumors, and there is an unmet clinical need for targeting LPS subtype-specific highly expressed genes.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Phosphodiesterases (PDEs) constitute a superfamily of enzymes (PDE1–PDE11) whose main function is to regulate the signaling of secondary messengers cAMP and cGMP by hydrolyzing 3′,5′-cyclic nucleotides to their 5′-monophosphate form.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Tissue-specific expression of various PDE isoforms enables cellular function regulation in a cell-type specific manner.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Aberrant expression of PDE isoforms is linked to many diseases .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

PDE3A-targeting compounds have recently been described as inhibiting tumor growth in mice inoculated with PDE3A-expressing cervical cancer HeLa , neuroglioma H4 , and melanoma SK-MEL-3 cells , and in patient-derived gastrointestinal stromal tumor (GIST) xenograft models .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

These compounds act like a molecular glue and form a complex between PDE3A and Schlafen 12 (SLFN12), leading to cell-cycle arrest or cell death .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

While the precise downstream signaling pathways remain unclear, the formed complex stabilizes SLFN12 and its RNase activity, resulting in protein synthesis inhibition .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

We sought to discover novel LPS-subtype-specific oncogenes that could serve as precision medicine targets.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

RNA-Seq transcriptome analysis of LPS patient tissue samples were first compared to transcriptomes of other cancerous and healthy tissue samples, resulting in ranked lists of highly expressed genes in three LPS subtypes and their enrichment in biological signaling pathways.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

PDE3A expression was high in MLPS, and its expression frequency in other STS subtypes and its potential role as a therapy target in LPS were further investigated.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Patients who were diagnosed with LPS from 1987 to 2017 in the Helsinki University Hospital (HUH) were identified.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Clinical data were extracted from the patient registry, and hematoxylin and eosin-stained tissue slides and corresponding formalin-fixed, paraffin-embedded (FFPE) tissue blocks were extracted from the archives of the Department of Pathology.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Histological classifications of tumors were reviewed by Mika Sampo, one of the authors, based on the 2020 WHO classification of soft-tissue tumors .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

A total of 190 patients with primary tumor samples were identified for the retrospective study series.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Two samples were excluded due to missing clinical data (MLPSs), four samples were excluded due to a paucity of tumor tissue, and three samples were excluded due to technical problems in immunohistochemistry (WDLPS, DDLPS, MLPS).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Thus, a total of 181 samples were included in the series.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The median follow-up time for survival in the series was 4.7 years (the range was from 0.3 to 20.3).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

RNA was extracted from 186 LPS FFPE tissue samples, including samples that were excluded from immunohistochemistry (IHC) analysis and two samples for which histology was reviewed but clinical data were not available.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The RNA samples were subjected to RNA sequencing, resulting in sequences from 152 samples.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Of these, 131 transcriptomes passed the quality control analysis and were further investigated for LPS-subtype-specifically overexpressed genes.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Of note, all WDLPS samples (n = 10) were excluded from the analyses, due to low RNA yield from sequencing.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

In addition, a previously collected series of 543 STS samples were investigated by using IHC and tissue microarray (TMA) from the following subtypes: fibrosarcoma, GIST, LPS, leiomyosarcoma, malignant peripheral nerve sheath tumor, myxofibrosarcoma, sarcoma with unspecified histotype, and synovial sarcoma .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

TMA blocks included two to three 1-mm diameter core punches from each tumor sample.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Tissue samples were retrieved from the archives of the Department of Pathology, HUH.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

TMAs were generated with an automated tissue microarrayer (TMA Grand Master, 3DHISTECH Ltd., Budapest, Hungary) in the Biobank Helsinki.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Tissue sections (2 × 10 µm) were collected in 2-mL microfuge tubes (Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 72.693.005, Sarstedt, NRW, Nümbrecht, Germany) and deparaffinized with 160 µL of deparaffinization solution (Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 939018, QIAGEN, NRW, Hilden, Germany).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

If tumor cells were estimated to present >50% of all cells in a tissue section, a representative tumor area was scraped to the tube from the slide.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Samples were mixed by vortexing and, subsequently, centrifuged and incubated at 56 °C for 3 min.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

One hundred and twenty µL of buffer PKD (Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 1034963, QIAGEN) was added, mixed by vortexing, and centrifuged for 13,000× g for 1 min.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Ten µL of proteinase K (Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 19133, QIAGEN) was added to the lower liquid phase of the samples.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

After a 1 h incubation at 56 °C in a tube shaker, samples were centrifuged and RNA was extracted with QIAsymphony RNA Kit (Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 931636, QIAGEN) using a QIAsymphony SP instrument (QIAGEN).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

RNA quality and concentration were measured with a 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

RNA sequencing was conducted, as described earlier .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Shortly after adding 1 µL of ERCC RNA spike-in control (1:1000) to each sample, an RNA sequencing library was prepared with a QuantSeq 3′ mRNA Library kit (Lexogen, Vienna, Austria) following the manufacturer’s instructions, as previously described.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Sequencing was performed with a HiSeq 2500 System (Illumina, San Diego, CA, USA) using a high-throughput mode and v4 chemistry in three batches that included samples from different LPS subtypes.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Sequences were processed with the data analysis pipeline, the BlueBee Genomics platform (BlueBee Holding BV, NB, Rijswijk, The Netherlands), following the manufacturer’s instructions.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Htseq-count files from the Bluebee sequencing process were read into R (version 4.1.2) and matched to clinical data per sample.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Gene annotation was retrieved from AnnotationHub (snapshotDate: 20 October 2021).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Data were imported into a DGEList object by using edgeR package (version 3.36.0).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Genes were further filtered by the filterByExpr function (default parameters) from edgeR. log2 counts per million were calculated with the cpm function (default parameters) from edgeR. Additional sample quality control was performed by excluding samples with a median logcount, with deviation >10% from the median logcount over all samples (21 samples were excluded, resulting in 131 samples for downstream analysis).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The final analysis included RNA sequence data from 53 DDLPS samples, 54 MLPS samples, and 24 PLPS samples.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

QC metrics for the BAM files produced by Bluebee pipeline were additionally calculated by parallel run of RNA-SeQC 2 with summarising results with MultiQC .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Genome annotation file and version used in the QC calculations was Homo_sapiens.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

GRCh38.104.genes.gtf (collapsed to gene level), also available from project Github page.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The sequencing coverage and quality statistics of each sample are presented in Table S1.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Data from the newest version of in silico transcriptomic (IST; ) database (MediSapiens Ltd., Helsinki, Finland) were fetched into R by using Dplyr extension for SQlite.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

We calculated the mean expression for each gene (excluding genes with <6 datapoints) per each healthy anatomical tissue type (n = 95) and per each cancerous tissue type (n = 106).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

For each tissue type (healthy and cancerous), we then chose the top 500 expressing genes.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The final IST reference gene list was calculated by choosing a unique list of genes, in which each gene did not appear in more than one of the healthy-tissue top 500 lists and in more than three of the cancer-tissue top 500 lists.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

This final IST reference list contained a total of 2754 genes and was used as an exclusion list, to eliminate non-LPS-specific genes from the LPS-subtype differential-gene-expression analyses.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

A differential expression test of genes for the LPS subtypes was performed, using the estimateDisp and exactTest functions from edgeR, with default parameters.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Differential-expression genes (DEGs) were defined as genes with a positive logFC > 1.5 (with p value < 0.05) between one subtype and all other subtypes, resulting in three lists of DEGs.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Altogether, we identified 97 DEGs between the DDLPS subtype and the other two subtypes, 247 DEGs between the MLPS subtype and the other two subtypes, and 37 DEGs between the PLPS subtype and the other two subtypes, after using the IST-derived exclusion lists (see above).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Upregulated signaling pathways in the three LPS subtypes were described with all of the identified subtype-specific DEGs, using Enrichr and the NCATS BioPlanet 2019 library .

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The scatter plots and the bar charts with their related genes were visualized via Appyters (https://appyters.maayanlab.cloud/#/).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The pathway search was conducted on 30 June 2023.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

PDE3A and SLFN12 mRNA levels were measured from 63 randomly selected FFPE LPS samples, excluding WDLPS samples.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

RNA extracted from the FFPE block derived from the GIST882 cell line was used as a reference sample for PDE3A and SLFN12 expression levels.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

cDNA was synthesized from RNA with SuperScript™ IV VILO™ Master Mix (Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 11756500, Invitrogen™, Thermo Fisher Scientific, Waltham, MA, USA).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Primers and hybridization probes (Universal ProbeLibrary Set, Human Probes #1–#90, Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 04683633001 Roche, Basel, Switzerland) were designed using ProbeFinder version 2.53 for Human.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

The primers were as follows: PDE3A, F: 5′-AAA GAC AAG CTT GCT ATT CCA AA-3′, R: 5′-GTG GAA GAA ACT CGT CTC AAC A-3′; SLFN12, F: 5′-CTT TGT TCA ACA CGC CAA GA-3′, R: 5′-ATG CAG TGT CCA AGC AGA AA-3′; and YWHAZ, F: 5′-CGT TAC TTG GCT GAG GTT GC-3′, R: 5′-TGC TTG TTG TGA CTG ATC GAC-3′. Real-time qPCR was performed with the LightCycler 480 Probes Master Kit (Cat.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

No. 04887301001, Roche) and the CFX96 Touch Real-Time PCR detection system (Bio-Rad, Hercules, CA, USA), under the following conditions: 95 °C for 10 min; 45 cycles of 95 °C for 30 s, 60°C for 30 s, and 72 °C for 45 s with plate read (amplification); 72 °C for 7 min; 65 °C to 95 °C (increment 0.01 °C s, melt curve).

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

PCR was performed in triplicate for each sample.

PMC10669966

PDE3A Is a Highly Expressed Therapy Target in Myxoid Liposarcoma

Relative PDE3A and SLFN12 mRNA expression were calculated using the ΔΔCt method and normalized to YWHAZ expression.