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Series GSE129765 Query DataSets for GSE129765
Status Public on Jun 29, 2020
Title Reciprocal gene editing defines targetable mutant H3.3 oncohistone effectors in pediatric glioma
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary High-grade pediatric gliomas often contain histone H3.3 mutations, but open questions remain about oncogenic mechanisms. To address this gap, we performed ‘reciprocal gene editing’ using CRISPR-Cas9 to introduce H3.3 mutations (K27M, G34R) into H3.3-wildtype brain and glioma cells, while in parallel reverting pre-existing K27M mutations in glioma cells back to wildtype. Analyses of our reciprocally-edited cells indicate that H3.3 mutation leads to specific transcriptomic and epigenetic events, and associated cell biological changes including in xenograft assays. We used these data and the reciprocally-edited cells to screen selected drugs and identify specific putative treatments that are mutant H3.3-specific. Overall, reciprocal gene editing provides new insights into mutant H3.3 oncogenic mechanisms and more broadly may prove useful for studying other cancer-associated mutations.
Overall design We used CRISPR-Cas9 gene editing of H3F3A to precisely revert preexisting K27M mutations to WT in patient-derived glioma cells to identify consistently functionally important effectors. Two replicates of H3K27me3 and two replicates of H3.3 ChIP-Seq were performed in each of the following cell lines: Line XIII, Line XIII WT, Line XVII, Line XVII WT.
Contributor(s) Klein R, Knoepfler P
Citation(s) 32647372
Submission date Apr 12, 2019
Last update date Jul 20, 2020
Contact name Paul Knoepfler
Organization name University of California Davis
Department Cell Biology and Human Anatomy
Street address 2425 Stockton Blvd, Room 633
City Sacramento
State/province CA
ZIP/Postal code 95817
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (20)
GSM3721804 Line 13 H3.3 rep1
GSM3721805 Line 13 H3.3 rep2
GSM3721806 Line 13 WT H3.3 rep1
BioProject PRJNA532652
SRA SRP192471

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE129765_RAW.tar 51.3 Mb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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