EXPERIMENT_TITLE: GSM7773149: JN-DSRCT1_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Genomic DNA was isolated from x-linked nuclei after Mbo1 restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol. Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif
STUDY_DESCRIPTOR_STUDY_ABSTRACT: EWS fusion oncoproteins underlie the pathogenesis of several human malignancies including Desmoplastic Small Round Cell Tumor (DSRCT), an aggressive mesenchymal tumor driven by fusions between the disordered domain of EWS and the developmental transcription factor WT1. Here we combined chromatin occupancy and long-range interaction profiles to identify EWS-WT1-dependent gene regulation networks and directly controlled target genes. We show that EWS-WT1 operates primarily as a powerful activator of distal regulatory elements and controls an oncogenic gene expression program that characterize primary DSRCTs. Moreover, EWS-WT1 has two isoforms that differ by three amino acids in their DNA binding domain (+/- KTS), as observed for wild type WT1, and we show that each fusion isoform has a specific DNA binding profile that is distinct from its wild type counterparts and requires a functional EWSR1 prion like domain. Remarkably, xenograft experiments using human mesothelial cells, candidate cells of origin of DSRCT, reveal that both isoforms are required to generate viable tumors that resemble DSRCT. Finally, we identify new candidate EWS-WT1 target genes with potential therapeutic implications, including CCND1, whose inhibition by the clinically-approved drug Palbociclib leads to marked tumor burden decrease in DSRCT PDXs in vivo. Taken together, our studies identify gene regulation programs and therapeutic vulnerabilities in DSRCT and provide a mechanistic understanding of the complex isoform-dependent oncogenic activity of EWS-WT1. Overall design: Using in-situ HiC, we characterized the TAD boundary regions and profiled the organization of EWS-WT1 mediated enhancer connectome in DSRCT model cell.
SAMPLE_TITLE: JN-DSRCT1_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "JN-DSRCT1 cells"}, {"TAG": "treatment", "VALUE": "untreated"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: JN-DSRCT1_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: JN-DSRCT1_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DSRCT_R1.fastq.gz", "size": "15785076896", "date": "2023-09-11 19:07:38", "md5": "8c1e3b05767fc491e5bedd3d9bc435c4", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DSRCT_R2.fastq.gz", "size": "15931542011", "date": "2023-09-11 19:06:38", "md5": "2aed7d5fc9c7965a9894e7d6db743164", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR26028053", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26028053/SRR26028053", "size": "14344504181", "date": "2023-09-11 19:09:30", "md5": "b9a1db15f0a2e207faaabdb8e9986f54", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR26028053.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR026/26028/SRR26028053/SRR26028053.lite.1", "size": "11418660789", "date": "2023-09-16 20:10:26", "md5": "119898e6b2b16cfca72d395d6de17d52", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]