EXPERIMENT_TITLE: GSM8267140: Group 3 Medulloblastoma - UPN1355; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Primary patient tumor tissue was formalin fixed and paraffin embedded according to clinical histopathology standard. Hi-C data was generated using the Arima-HiC kit, according to the manufacturer protocols. Briefly, whole genome DNA was extracted from FFPE sample and crosslinked in 2% formaldehyde. Crosslinked chromatin was digested using restriction enzyme mix for 30 min at 37C followed by 20 min at 62C.  5'-overhangs were then filled with biotinylated nucleotide (buffer/enzyme B 45 min at 25C) before the DNA fragments were  proximally ligated using buffer/enzyme C mix at 15 min at 25C. Purified ligated DNA was fragmented using Biorupter Plus (Diagenode) for goal size 400-600 bp. Biotin enrichment is then performed prior to adapter ligation. Libraries were prepared using the Illumina TruSeq adapter kit according to manufacturer specifications.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Medulloblastoma is the most common malignant brain tumor of childhood. The highest-risk tumors are driven by recurrent Myc amplifications (Myc-MB) and experience poorer outcomes despite intensive multimodal therapy. The Myc transcription factor defines core regulatory circuitry for these tumors and acts to broadly amplify downstream pro-survival transcriptional programs. Therapeutic targeting of Myc directly has proven elusive, but inhibiting transcriptional cofactors may present an indirect means of drugging the oncogenic transcriptional circuitry sustaining Myc-MB. Independent CRISPR-Cas9 screens were pooled to identify conserved dependencies in Myc-MB. We performed chromatin conformation capture (Hi-C) from primary patient Myc-MB samples to map enhancer-promoter interactions. We then treated in vitro and xenograft models with the dual CDK9/7 inhibitor zotiraciclib to evaluate effect on Myc-driven programs and tumor growth. Eight CRISPR-Cas9 screens performed across three independent labs identify CDK9 as a conserved dependency in Myc-MB. Myc-MB cells are susceptible to CDK9 inhibition, which is synergistic with concurrent inhibition of CDK7. The dual CDK9/7 inhibitor zotiraciclib disrupts enhancer-promoter activity in Myc-MB and downregulates Myc-driven transcriptional programs, exerting potent anti-tumor effect. Overall design: Formalin fixed, paraffin embedded primary patient tumor samples were subjected to DNA extraction for chromatin conformation sequencing (Hi-C).
SAMPLE_TITLE: Group 3 Medulloblastoma - UPN1355
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Medulloblastoma"}, {"TAG": "tissue", "VALUE": "Medulloblastoma"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Group 3 Medulloblastoma - UPN1355
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