The interaction between cytosine methylation and processes of DNA replication and repair shape the mutational landscape of cancer genomes

Nucleic Acids Research
Rebecca C PoulosJason W H Wong

Abstract

Methylated cytosines (5mCs) are frequently mutated in the genome. However, no studies have yet comprehensively analysed mutation-methylation associations across cancer types. Here we analyse 916 cancer genomes, together with tissue type-specific methylation and replication timing data. We describe a strong mutation-methylation association across colorectal cancer subtypes, most interestingly in samples with microsatellite instability (MSI) or Polymerase epsilon (POLE) exonuclease domain mutations. By analysing genomic regions with differential mismatch repair (MMR) efficiency, we suggest a possible role for MMR in the correction of 5mC deamination events, potentially accounting for the high rate of 5mC mutation accumulation in MSI tumours. Additionally, we propose that mutant POLE asserts a mutator phenotype specifically at 5mCs, and we find coding mutation hotspots in POLE-mutant cancers at highly-methylated CpGs in the tumour-suppressor genes APC and TP53. Finally, using multivariable regression models, we demonstrate that different cancers exhibit distinct mutation-methylation associations, with DNA repair influencing such associations in certain cancer genomes. Taken together, we find differential associations with methylat...Continue Reading

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Datasets Mentioned

BETA
GSM983645
GSE34399
GSE67941

Methods Mentioned

BETA
deamination
WGBS

Software Mentioned

BEDtools
R
convert2bed
Strelka
lmtest
ROCR
Roadmap Epigenomics Atlas
UCSC genome browser

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