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

Published version
Peer-reviewed

Type

Article

Change log

Authors

Zou, Xueqing 
Koh, Gene Ching Chiek 
Urgo, Katie 

Abstract

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. ΔOGG1, ΔUNG, ΔEXO1, ΔRNF168, ΔMLH1, ΔMSH2, ΔMSH6, ΔPMS1, and ΔPMS2 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. ΔMLH1, ΔMSH6, and ΔMSH2 signatures were similar to each other but distinct from ΔPMS2. 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.

Description

Keywords

CRISPR-Cas9 systems, Genomic instability, cancer, cancer genomics, Brain Neoplasms, Clustered Regularly Interspaced Short Palindromic Repeats, Colorectal Neoplasms, DNA Damage, Humans, Induced Pluripotent Stem Cells, Mutation, Neoplastic Syndromes, Hereditary

Journal Title

Nat Cancer

Conference Name

Journal ISSN

2662-1347
2662-1347

Volume Title

2

Publisher

Springer Science and Business Media LLC
Sponsorship
Cancer Research UK (23916)
Medical Research Council (MR/R015724/1)
Cancer Research UK (23433)
National Institute for Health and Care Research (IS-BRC-1215-20014)