EXPERIMENT_TITLE: GSM4802001: G477_S1_Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For Hi-C, libraries were generated from 5 million cultured glioblastoma cell lines and disassociated mouse embryonic tissue as described in (Rao et al., 2014) with minor modifications. Briefly, in situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnII) within intact permeabilized nuclei, (3) filling in, biotinylating the resulting 5′-overhangs and ligating the blunt ends, (4) shearing the DNA, (5) pulling down the biotinylated ligation junctions with streptavidin beads, (6) library amplification and (7) analyzing these fragments using paired end sequencing. As quality control (QC) steps, we checked for efficient sonication with an agarose DNA gel and for appropriate size selection using the Agilent Bioanalyzer on final amplified libraries. For the final QC, we performed superficial sequencing on the Illumina Hiseq 2500 (~30M reads/sample) to assess quality of the libraries using percent of reads passing filter, percent of chimeric reads, and percent of forward-reverse pairs.  125bp paired-end sequencing was performed on the Illumina HiSeq 4000.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Histone H3.3 glycine 34 to arginine/valine (H3.3G34R/V) mutations occur in deadly hemispheric high-grade gliomas. These tumors show exquisite regional and temporal specificity, suggesting a developmental context permissive to the effects of G34R/V mutations. Here we present the molecular landscape of G34R/V gliomas (n = 83) and show that ~50% bear activating mutations in PDGFRA, with strong selection pressure for PDGFRAMUT clones at recurrence. We show that G34R/V tumors arise in interneuron progenitors of the foetal ventral forebrain, expressing GSX2 and the DLX family of homeobox transcription factors, where terminal neuronal differentiation is impaired through aberrant G34R/V-mediated H3K27me3. Frequent co-occurrence of G34R/V & PDGFRAMUT is facilitated in this interneuron lineage-of-origin as PDGFRA forms an aberrant chromatin loop with the adjacent GSX2, hijacking its active chromatin conformation. At the single-cell level, G34R/V tumors entirely lack oligodendroglial transcriptional programs prominent in other glioma entities, and instead harbour dual neuronal and astroglial compartments. CRISPR-removal of H3.3G34R/V does not impact tumorigenicity suggesting this mutation becomes dispensable, while PDGFRAMUT are potently oncogenic regardless of G34 mutation. Collectively, our results suggest that G34R/V gliomas arise in foetal interneuron progenitors unable to terminally differentiate, enabling co-option of PDGFRA through inappropriate expression and activating mutations to promote gliogenesis and oncogenicity. Reliance on PDGFRA for oncogenesis may be of therapeutic opportunity in G34R/V glioma. Overall design: ChIP-seq, Hi-C and RNA-seq were performed on CRISPR-edited and parental G34R/V glioma-derived cell lines and neural progenitor cells (NPCs) derived from in-utero electroporated mice.
SAMPLE_TITLE: G477_S1_Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "patient-derived glioma cell line"}, {"TAG": "tissue", "VALUE": "patient-derived glioma cell line"}, {"TAG": "genotype", "VALUE": "H3 WT"}, {"TAG": "cell line name", "VALUE": "G477"}, {"TAG": "clone name", "VALUE": "-"}, {"TAG": "passage", "VALUE": "-"}, {"TAG": "media", "VALUE": "stem"}, {"TAG": "library type", "VALUE": "Hi-C"}]
Pool_Member_@attributes_sample_title: G477_S1_Hi-C
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