A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage

Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. We generated isogenic CRISPR-Cas9 knockouts ( increment ) of 43 genes in human induced pluripotent stem cells, cultured them in the absence of added DNA damage and performed whole-genome sequencing of 173 subclones. increment OGG1, increment UNG, increment EXO1, increment RNF168, increment MLH1, increment MSH2, increment MSH6, increment PMS1 and increment PMS2 produced marked mutational signatures indicative of them being critical mitigators of endogenous DNA modifications. Detailed analyses revealed mutational mechanistic insights, including how 8-oxo-2 '-deoxyguanosine elimination is sequence context specific while uracil clearance is sequence context independent. Mismatch repair (MMR) deficiency signatures are engendered by oxidative damage (C > A transversions) and differential misincorporation by replicative polymerases (T > C and C > T transitions), and we propose a reverse template slippage model for T > A transversions. increment MLH1, increment MSH6 and increment MSH2 signatures were similar to each other but distinct from increment PMS2. Finally, we developed a classifier, MMRDetect, where application to 7,695 whole-genome-sequenced cancers showed enhanced detection of MMR-deficient tumors, with implications for responsiveness to immunotherapies. Nik-Zainal and colleagues leverage CRISPR-Cas9 and whole-genome sequencing to examine mutational patterns following knockout of 42 human DNA repair genes. They further develop and validate a clinically relevant tool to detect mismatch repair-deficient tumors.

Automated summary

The study investigates the impact of knockout of 42 human DNA repair genes on mutational patterns using CRISPR-Cas9 and whole-genome sequencing. A clinically relevant tool to detect mismatch repair-deficient tumors was developed and validated for enhanced detection of MMR-deficient tumors with implications for immunotherapy responsiveness.