Discovery of Candidate DNA Methylation Cancer Driver Genes.

TitleDiscovery of Candidate DNA Methylation Cancer Driver Genes.
Publication TypeJournal Article
Year of Publication2021
AuthorsPan H, Renaud L, Chaligne R, Bloehdorn J, Tausch E, Mertens D, Fink AMaria, Fischer K, Zhang C, Betel D, Gnirke A, Imielinski M, Moreaux J, Hallek M, Meissner A, Stilgenbauer S, Wu CJ, Elemento O, Landau DA
JournalCancer Discov
Volume11
Issue9
Pagination2266-2281
Date Published2021 Sep
ISSN2159-8290
Abstract

Epigenetic alterations, such as promoter hypermethylation, may drive cancer through tumor suppressor gene inactivation. However, we have limited ability to differentiate driver DNA methylation (DNAme) changes from passenger events. We developed DNAme driver inference-MethSig-accounting for the varying stochastic hypermethylation rate across the genome and between samples. We applied MethSig to bisulfite sequencing data of chronic lymphocytic leukemia (CLL), multiple myeloma, ductal carcinoma , glioblastoma, and to methylation array data across 18 tumor types in TCGA. MethSig resulted in well-calibrated quantile-quantile plots and reproducible inference of likely DNAme drivers with increased sensitivity/specificity compared with benchmarked methods. CRISPR/Cas9 knockout of selected candidate CLL DNAme drivers provided a fitness advantage with and without therapeutic intervention. Notably, DNAme driver risk score was closely associated with adverse outcome in independent CLL cohorts. Collectively, MethSig represents a novel inference framework for DNAme driver discovery to chart the role of aberrant DNAme in cancer. SIGNIFICANCE: MethSig provides a novel statistical framework for the analysis of DNA methylation changes in cancer, to specifically identify candidate DNA methylation driver genes of cancer progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness..

DOI10.1158/2159-8290.CD-20-1334
Alternate JournalCancer Discov
PubMed ID33972312
PubMed Central IDPMC8419066
Grant ListDP2 CA239065 / CA / NCI NIH HHS / United States
R01 CA229902 / CA / NCI NIH HHS / United States
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Marcin Imielinski, M.D., Ph.D.

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