Open AccessA systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage
Author(s) -
Xueqing Zou,
Gene Ching Chiek Koh,
Arjun Scott Nanda,
Andrea Degasperi,
Katie Urgo,
Theodoros I. Roumeliotis,
Chukwuma A. Agu,
Cherif Badja,
Sophie Momen,
Jamie Young,
Tauanne Dias Amarante,
Lucy E. Side,
Glen Brice,
Vanesa PérezAlonso,
Daniel Rueda,
Céline Gomez,
Wendy Bushell,
Robert G. Harris,
Jyoti Choudhary,
Josef Jiricny,
William C Skarne
Publication year - 2021
Publication title -
nature cancer
Language(s) - English
Resource type - Journals
ISSN - 2662-1347
DOI - 10.1038/s43018-021-00200-0
Subject(s) - biology , dna mismatch repair , genetics , msh6 , msh2 , dna repair , dna damage , crispr , gene , computational biology , dna
Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. We generated isogenic CRISPR-Cas9 knockouts (Δ) 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. Δ OGG1, Δ UNG, Δ EXO1, Δ RNF168, Δ MLH1, Δ MSH2, Δ MSH6, Δ PMS1, and Δ PMS2 produced marked mutational signatures indicative of being critical mitigators of endogenous DNA modifications. Detailed analyses revealed mutational mechanistic insights, including how 8-oxo-dG 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), differential misincorporation by replicative polymerases (T>C and C>T transitions), and we propose a 'reverse template slippage' model for T>A transversions. Δ MLH1, Δ MSH6, and Δ MSH2 signatures were similar to each other but distinct from Δ PMS2 . Finally, we developed a classifier, MMRDetect, where application to 7,695 WGS cancers showed enhanced detection of MMR-deficient tumors, with implications for responsiveness to immunotherapies.