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  • Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells.

Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells.

eLife (2022-12-09)
Karin Purshouse, Elias T Friman, Shelagh Boyle, Pooran Singh Dewari, Vivien Grant, Alhafidz Hamdan, Gillian M Morrison, Paul M Brennan, Sjoerd V Beentjes, Steven M Pollard, Wendy A Bickmore
摘要

Extrachromosomal DNA (ecDNA) are frequently observed in human cancers and are responsible for high levels of oncogene expression. In glioblastoma (GBM), ecDNA copy number correlates with poor prognosis. It is hypothesized that their copy number, size, and chromatin accessibility facilitate clustering of ecDNA and colocalization with transcriptional hubs, and that this underpins their elevated transcriptional activity. Here, we use super-resolution imaging and quantitative image analysis to evaluate GBM stem cells harbouring distinct ecDNA species (EGFR, CDK4, PDGFRA). We find no evidence that ecDNA routinely cluster with one another or closely interact with transcriptional hubs. Cells with EGFR-containing ecDNA have increased EGFR transcriptional output, but transcription per gene copy is similar in ecDNA compared to the endogenous chromosomal locus. These data suggest that it is the increased copy number of oncogene-harbouring ecDNA that primarily drives high levels of oncogene transcription, rather than specific interactions of ecDNA with each other or with high concentrations of the transcriptional machinery.

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Sigma-Aldrich
Accutase® 溶液, sterile-filtered, suitable for cell culture
Roche
重组DNase I,无RNase, from bovine pancreas, expressed in Pichia pastoris
Roche
抗-地高辛, from sheep
Sigma-Aldrich
诺考达唑制备液, 5 mg/mL, DMSO solution