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

Autor: Zou X; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; MRC Cancer Unit, University of Cambridge, Cambridge, UK.; Wellcome Sanger Institute, Hinxton, UK., Koh GCC; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; MRC Cancer Unit, University of Cambridge, Cambridge, UK.; Wellcome Sanger Institute, Hinxton, UK., Nanda AS; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; MRC Cancer Unit, University of Cambridge, Cambridge, UK., Degasperi A; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; MRC Cancer Unit, University of Cambridge, Cambridge, UK.; Wellcome Sanger Institute, Hinxton, UK., Urgo K; Wellcome Sanger Institute, Hinxton, UK., Roumeliotis TI; The Institute of Cancer Research, Chester Beatty Laboratories, London, UK., Agu CA; Wellcome Sanger Institute, Hinxton, UK., Badja C; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; MRC Cancer Unit, University of Cambridge, Cambridge, UK.; Wellcome Sanger Institute, Hinxton, UK., Momen S; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; MRC Cancer Unit, University of Cambridge, Cambridge, UK., Young J; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK., Amarante TD; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; MRC Cancer Unit, University of Cambridge, Cambridge, UK., Side L; UCL Institute for Women's Health, Great Ormond Street Hospital, London, UK.; Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK., Brice G; Southwest Thames Regional Genetics Service, St George's University of London, London, UK., Perez-Alonso V; Pediatrics Department, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain., Rueda D; Hereditary Cancer Laboratory, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain., Gomez C; Wellcome Sanger Institute, Hinxton, UK., Bushell W; Wellcome Sanger Institute, Hinxton, UK., Harris R; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.; Wellcome Sanger Institute, Hinxton, UK., Choudhary JS; The Institute of Cancer Research, Chester Beatty Laboratories, London, UK., Jiricny J; Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; Institute of Biochemistry, ETH Zurich, Zurich, Switzerland., Skarnes WC; Wellcome Sanger Institute, Hinxton, UK.; William Harvey Research Institute, Queen Mary University of London, London, UK., Nik-Zainal S; Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK. snz@mrc-cu.cam.ac.uk.; MRC Cancer Unit, University of Cambridge, Cambridge, UK. snz@mrc-cu.cam.ac.uk.; Wellcome Sanger Institute, Hinxton, UK. snz@mrc-cu.cam.ac.uk.
Jazyk: angličtina
Zdroj: Nature cancer [Nat Cancer] 2021 Jun; Vol. 2 (6), pp. 643-657. Date of Electronic Publication: 2021 Apr 26.
DOI: 10.1038/s43018-021-00200-0
Abstrakt: 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.
Competing Interests: Competing Interests Statement SNZ holds patents on clinical algorithms of mutational signatures and during the completion of this project, served advisory roles for Astra Zeneca, Artios Pharma Ltd and Scottish Genome Project.
Databáze: MEDLINE
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