Dissecting DNA-mismatch-repair-driven mutational processes in human cells

Abstract

Mismatch repair (MMR) is an essential DNA repair pathway that preserves genome stability by correcting replication errors and other DNA lesions. MMR deficiency (MMRd) leads to increased mutation rates and microsatellite instability, and contributes to tumorigenesis in multiple cancer types, yet the full spectrum of mutational patterns caused by MMRd remains incompletely defined. Here, using CRISPR-Cas9 knockouts in human isogenic cell lines, we systematically profile mutations arising in MMR-deficient cells. We observe a marked increase in mutation burden and the appearance of established MMRd-associated mutational signatures. Unexpectedly, we also detect signatures SBS57 and DBS14 and connect them to germline single-nucleotide polymorphisms that co-occur with MMR-driven indels. In addition, we provide experimental genomic evidence supporting a role of MMR in preventing mutations underlying the widespread SBS1 signature, and we link MMR deficiency to the indel signature ID12, which currently lacks a known aetiology. Finally, comparing in vitro MMRd profiles from rapidly dividing cells without exogenous mutagen exposure to in vivo tumour genomes that reflect lifelong mutation accumulation reveals pronounced differences in signature composition, underscoring the context dependence of MMR-linked mutagenesis. Together, our results broaden the known mutational footprint of MMR deficiency and illuminate previously uncharacterised mechanisms relevant to cancer development.