Cargando…

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

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 clusterin...

Descripción completa

Detalles Bibliográficos
Autores principales: Purshouse, Karin, Friman, Elias T, Boyle, Shelagh, Dewari, Pooran Singh, Grant, Vivien, Hamdan, Alhafidz, Morrison, Gillian M, Brennan, Paul M, Beentjes, Sjoerd V, Pollard, Steven M, Bickmore, Wendy A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9728993/
https://www.ncbi.nlm.nih.gov/pubmed/36476408
http://dx.doi.org/10.7554/eLife.80207
_version_ 1784845393629020160
author Purshouse, Karin
Friman, Elias T
Boyle, Shelagh
Dewari, Pooran Singh
Grant, Vivien
Hamdan, Alhafidz
Morrison, Gillian M
Brennan, Paul M
Beentjes, Sjoerd V
Pollard, Steven M
Bickmore, Wendy A
author_facet Purshouse, Karin
Friman, Elias T
Boyle, Shelagh
Dewari, Pooran Singh
Grant, Vivien
Hamdan, Alhafidz
Morrison, Gillian M
Brennan, Paul M
Beentjes, Sjoerd V
Pollard, Steven M
Bickmore, Wendy A
author_sort Purshouse, Karin
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9728993
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher eLife Sciences Publications, Ltd
record_format MEDLINE/PubMed
spelling pubmed-97289932022-12-08 Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells Purshouse, Karin Friman, Elias T Boyle, Shelagh Dewari, Pooran Singh Grant, Vivien Hamdan, Alhafidz Morrison, Gillian M Brennan, Paul M Beentjes, Sjoerd V Pollard, Steven M Bickmore, Wendy A eLife Chromosomes and Gene Expression 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. eLife Sciences Publications, Ltd 2022-12-07 /pmc/articles/PMC9728993/ /pubmed/36476408 http://dx.doi.org/10.7554/eLife.80207 Text en © 2022, Purshouse et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Chromosomes and Gene Expression
Purshouse, Karin
Friman, Elias T
Boyle, Shelagh
Dewari, Pooran Singh
Grant, Vivien
Hamdan, Alhafidz
Morrison, Gillian M
Brennan, Paul M
Beentjes, Sjoerd V
Pollard, Steven M
Bickmore, Wendy A
Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells
title Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells
title_full Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells
title_fullStr Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells
title_full_unstemmed Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells
title_short Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells
title_sort oncogene expression from extrachromosomal dna is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9728993/
https://www.ncbi.nlm.nih.gov/pubmed/36476408
http://dx.doi.org/10.7554/eLife.80207
work_keys_str_mv AT purshousekarin oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT frimaneliast oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT boyleshelagh oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT dewaripooransingh oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT grantvivien oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT hamdanalhafidz oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT morrisongillianm oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT brennanpaulm oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT beentjessjoerdv oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT pollardstevenm oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells
AT bickmorewendya oncogeneexpressionfromextrachromosomaldnaisdrivenbycopynumberamplificationanddoesnotrequirespatialclusteringinglioblastomastemcells