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

Mismatch repair (MMR) is a crucial DNA repair pathway that maintains genomic integrity by correcting replication errors and various forms of DNA damage. MMR deficiency (MMRd) leads to increased mutation rates, microsatellite instability, and contributes to tumorigenesis in multiple cancer types. Using a CRISPR-Cas9-mediated knockout assay in human isogenic cell lines, we characterised mutational profiles in MMR-deficient cells. Our findings revealed expected increases in mutation burden and the emergence of known MMR-associated mutational signatures. Notably, we identified a previously unconnected process, SBS57, and linked it to germline single-nucleotide polymorphisms and MMR-driven indels in MMRd cells, establishing its association with tensor signature TS27. Comparative analyses of in vitro MMRd profiles and in vivo tumour data uncovered key differences in mutational signatures, highlighting the biological context dependence of MMR-associated mutations. Furthermore, we provide direct experimental evidence that MMR plays a role in repairing 5-methylcytosine deamination, a repair process previously inferred from tumour sequencing data. These findings offer novel insights into MMR deficiency, shedding light on previously uncharacterised mutational mechanisms and their implications in cancer.