Widespread perturbation of ETS factor binding sites in cancer

Sebastian Carrasco Pro, Heather Hook, David Bray, Daniel Berenzy, Devlin Moyer, Meimei Yin, Adam Thomas Labadorf, Ryan Tewhey, Trevor Siggers () and Juan Ignacio Fuxman Bass ()
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Sebastian Carrasco Pro: Boston University
Heather Hook: Boston University
David Bray: Boston University
Daniel Berenzy: The Jackson Laboratory
Devlin Moyer: Boston University
Meimei Yin: Boston University
Adam Thomas Labadorf: Boston University
Ryan Tewhey: The Jackson Laboratory
Trevor Siggers: Boston University
Juan Ignacio Fuxman Bass: Boston University

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Although >90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a transcription factor (TF)-aware burden test based on a model of coherent TF function in promoters. We apply this test to NCVs from the Pan-Cancer Analysis of Whole Genomes cohort and predict 2555 driver NCVs in the promoters of 813 genes across 20 cancer types. These genes are enriched in cancer-related gene ontologies, essential genes, and genes associated with cancer prognosis. We find that 765 candidate driver NCVs alter transcriptional activity, 510 lead to differential binding of TF-cofactor regulatory complexes, and that they primarily impact the binding of ETS factors. Finally, we show that different NCVs within a promoter often affect transcriptional activity through shared mechanisms. Our integrated computational and experimental approach shows that cancer NCVs are widespread and that ETS factors are commonly disrupted.

Date: 2023
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DOI: 10.1038/s41467-023-36535-8

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