{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001002770"],"host":["EGA"],"description":["EGA study EGAS00001002770"],"dataset_title":["DSRCT RNAseq"],"repository":["EGA"],"category":["restricted"],"name_synonyms":["Non-Polyadenylated RNA, ribonucleic acid, Acid, desmoplastic small-round-cell tumor, RNA, Ribonucleic, ribose nucleic acid, yeast nucleic acid, Ribonukleinsaeure, Non Polyadenylated RNA, Gene Products, ribonucleic acids, pentosenucleic acids, Non-Polyadenylated, Ribonucleic acids, RNS, Ribonucleic Acid, desmoplastic small-round-cell tumour, Non Polyadenylated, RNA Gene Products."],"description_synonyms":["Experimental Designs, Ribonucleic, Research Technique, Problem Formulations, Materials, RNA Sequence Determination, Adjustments, WIT-2, Sequence Determination, RNA Sequence, Design, Error Sources, positive regulation by symbiont of host non-apoptotic programmed cell death, protein, Tumor, Principal Component Analyses, Technic, igf2, CD334, HiSeq 2000, EWS-WT1, Techniques, diseases, Immunogold-Silver Techniques, Method, Immunogold-Silver Technique, IGFII, Line, pathogenesis, diseases and disorders, JTK2, EWSR1, Analysis, Polymerase Chain, protein aggregate, Non Polyadenylated, RNA Gene Products, ChIA-PET, Experimental Design, Group, Chromatin Immunoprecipitation Sequencing Chip, human disease, Chromatin Immuno precipitation Sequencing, Gene Expressions, Man (Taxonomy), stimulation by symbiont of host programmed cell death, Igf-II, Analyses, Determination, ChIP, Matched Group, Chromatin Immuno Precipitation Paired End Tag, Tissue, XFGFR-4a, Designs, Matched, Inverse Polymerase Chain Reaction, Groups, CG3606, desmoplastic small-round-cell tumour, experimental design, Sequence Determinations, fgfr-4, SURGICAL AND MEDICAL PROCEDURES, Chromatin Immunoprecipitation Paired-End Tag, Immunogold-Silver Technic, Reporting, Reaction, ATAC-Seq, Chromatin Immunoprecipitation Sequencing-Chips, Immunolabeling Technique, Research Techniques, Homo sapiens disease, Malignancies, Pen19, TL, P19, Immunogold Technics, Data Reporting, CD200, Tumors, fgfr-4c, Diagnostic Findings, High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, SIGNS SYMPTOMS, Ewsh, Anchored Polymerase Chain Reaction, Research Technic, ribose nucleic acid, Research Methodology, anon-Pen19, DESC, Modern, Cross Linking and Immunoprecipitation Followed by Deep Sequencing, ribonucleic acids, Immunogold Technique, Research Proposals, Validation Studies, p19, Procedure, Fgfr-4, ChIP-PET, results, Research Proposal, pp9974, Determinations, Small-Cell Tumor, Immunogold, Immunogold Techniques, Experimental, Benign, Immunolabeling Technic, Ribonukleinsaeure, XFGFR-4, Desmoplastic Small-Cell, TKF, Diseases, Immunolabeling Technics, modulation by symbiont of host system process, pentosenucleic acids, Genetic Materials, Technics, Ribonucleic acids, simple tissue, Problem Formulation, Igf-2, Problem, Genetic Material, PCR, Lines, IGF-II, Acid, bK984G1.4, Nested Polymerase Chain Reaction, nephroblastoma, Benign Neoplasms, Immunogold Silver Techniques, Desmoplastic Small Cell Tumor, INSDC_feature:gene, ChIP Exonuclease, RNIGF2, human, polymerase chain reaction, Malignant Neoplasms, AL033362, Formulations, disease, Principal Component, PP1446, Patient, Material, activation by symbiont of host programmed cell death, DmelCG3606, Cistron, WT1, wt1, PP9974, other neoplasm, ChIP-Exonuclease, Clinical Finding, Data Adjustments, other disease, Immunogold-Silver, ChIP-Chip, human being, Chromatin Immuno-precipitation, AWT1, regulation by symbiont of host system process, Neoplasms, Mpr, Matched Groups, Benign Neoplasm, number, Gene, CLIP-Seq, Scoring Method, Polymerase Chain Reactions, GUD, Assay for Transposase-Accessible Chromatin Using Sequencing, Inverse, protein-containing complex, Malignant, presence, WAGR, Symptoms and Signs, Human, Intervention or Procedure, Small-Cell Tumors, Adjustment, Inverse PCR, Homo sapiens, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, insigf, Scoring Methods, Sources, Chromatin Immunoprecipitation Sequencing-Chip, Gene Products, C11orf43, disease or disorder, SARFH, Finding, Sarfh, Technique, Man, Immunogold Silver Technics, MRC, Methodology, xwt1, XWT1a, anatomical systems, XWT1b, Genetic, Scoring, Malignancy, fgfr4, Research, xWT1, interventionDescription, Proposals, Chromatin Immunoprecipitation Paired End Tag, Cross-Linking and Immunoprecipitation Followed by Deep Sequencing, Interventional, causes, pen19, igf-2, Expressions, Sequencing, Research Strategy, non-neoplastic, Non-Polyadenylated RNA, Neoplasias, desmoplastic small-round-cell tumor, M6pr, RNA Sequence Analyses, OX-2, Clients, causality, Error Source, RNA Sequencing, disorder, Expression, Anchored PCR, wt-1, Strategies, Cancer, Sequence Analyses, HITS-CLIP, Intervention Strategies, RNA, activation by organism of non-apoptotic programmed cell death in other organism, Malignant Neoplasm, hemolysin activity, Immunogold Technic, MRC OX-2 antigen, Males, RNA Sequence Determinations, protein complex, Desmoplastic Small-Cell Tumor, Proteins, disorders, Cell Lines, ChIP Sequencing, Immunohistocytochemistry, Formulation, RNS, medical condition, BcDNA:GM09207, Cistrons, xfgfr4, Client, Cell, AU018891, ChIP-Exo, Research Strategies, count in organism, Signs and Symptoms, Peg2, MT, native protein, yeast nucleic acid, Protein, Desmoplastic Small-Cell Tumors, Neoplasm, condition, TFIID, rare (European definition), High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, Caz, Proposal, Methods, Immunolabeling, XeWT1, Intervention, ribonucleic acid, Anchored, Immunocytochemistry, Reactions, Nested, distinct, Desmoplastic, Desmoplastic Small Round-Cell Tumor, Source, Non Polyadenylated RNA, Non-Polyadenylated, Research Designs, cas, Chromatin Immunoprecipitation, WT33, Chromatin Immuno-precipitation Sequencing, Cancers, Research Technics, Ribonucleic Acid, MOX2, ChIP-Seq, Assay for Transposase Accessible Chromatin Using Sequencing, MOX1, Ews, EWS, Protein Gene Products, Gene Proteins, Data Adjustment, Error, Data, RNA Sequence Analysis, Modern Man, Chromatin Immuno-Precipitation Paired-End Tag, Immunogold-Silver Technics, Immunolabeling Techniques, Nested PCR, NPHS4, desmoplastic small-round-cell tumour., Strategy, Neoplasia, Intrinsic"],"additional_accession":[]},"is_claimable":false,"name":"DSRCT RNA genomic sequencing","description":"Purpose: To further understand the molecular pathogenesis of desmoplastic small round cell tumor (DSRCT), a rare but often fatal malignancy occurring primarily in young males, we used next-generation RNA sequencing to investigate the gene expression profiles intrinsic to this disease.Experimental Design: RNA from DSRCT tumor samples were obtained from the Cooperative Human Tissue Network biorepository. RNA sequencing was completed using the Illumina HiSeq 2000 system. Presence of the EWSR1-WT1 fusion was verified using both RNA-sequencing and PCR. Validation studies, including WT1 ChIP-seq, RNA sequencing, and EWS-WT1 knockdown experiments, were performed on an established DSRCT cell line, JN-DSRCT-1. Protein expression of clinically relevant genes determined by RNA sequencing was confirmed using immunohistochemistry. A panel of immune signature genes was also evaluated to identify possible immune therapeutic targets.  Results: We analyzed the RNA from 14 tumor samples, of which two were confirmed negative for the diagnostic EWSR1-WT1 translocation. Principal component analysis of the sequencing data indicated that fusion-negative and fusion-positive tumors are transcriptionally distinct entities.  Overlapping the significant ChIP-seq peaks with genes found to be highly expressed in the RNA sequencing data revealed that IGF2 and FGFR4 were both highly expressed, and targets of the EWS-WT1 fusion gene. This finding has potential clinical relevance for targeted therapeutic intervention. In addition, we identified the immune checkpoints CD200 and CD276 as potentially targetable genes whose expression is independent of the EWS-WT1 fusion gene in vitro.Conclusions: Despite the transcriptional complexity of this disease, we were able to identify IGF2, FGFR4, CD200, and CD276 as potential therapeutic targets for patients suffering from DSRCT.","dates":{"updated":"2020-09-15 09:32:00"},"accession":"EGAS00001002770","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001003980","EGAC00001000851"]}}