A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage.
Document Type
Article
Publication Date
6-1-2021
Publication Title
Nat Cancer
Keywords
JGM
JAX Source
Nat Cancer 2021 Jun; 2(6):643-657
Volume
2
Issue
6
First Page
643
Last Page
657
ISSN
2662-1347
PMID
34164627
DOI
https://doi.org/10.1038/s43018-021-00200-0
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.
Recommended Citation
Zou X,
Koh G,
Nanda A,
Degasperi A,
Urgo K,
Roumeliotis T,
Agu C,
Badja C,
Momen S,
Young J,
Amarante T,
Side L,
Brice G,
Perez-Alonso V,
Rueda D,
Gomez C,
Bushell W,
Harris R,
Choudhary J,
Jiricny J,
Skarnes W,
Nik-Zainal S.
A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. Nat Cancer 2021 Jun; 2(6):643-657