Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens

Yichao Zhao; Daniel Tabet; Diana Rubio Contreras; Linjiang Lao; Arne Nedergaard Kousholt; Jochen Weile; Henrique Melo; Lisa Hoeg; Sumin Feng; Atina G Coté; Zhen-Yuan Lin; Dheva Setiaputra; Jos Jonkers; Anne-Claude Gingras; Fernando Gómez Herreros; Frederick P Roth; Daniel Durocher

doi:10.1016/j.molcel.2023.06.025

Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens

Mol Cell. 2023 Aug 3;83(15):2792-2809.e9. doi: 10.1016/j.molcel.2023.06.025. Epub 2023 Jul 20.

Authors

Yichao Zhao¹, Daniel Tabet¹, Diana Rubio Contreras², Linjiang Lao³, Arne Nedergaard Kousholt⁴, Jochen Weile⁵, Henrique Melo³, Lisa Hoeg³, Sumin Feng³, Atina G Coté³, Zhen-Yuan Lin³, Dheva Setiaputra³, Jos Jonkers⁴, Anne-Claude Gingras¹, Fernando Gómez Herreros², Frederick P Roth⁵, Daniel Durocher⁶

Affiliations

¹ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
² Instituto de Biomedicina de Sevilla (IBiS), Manuel Siurot s/n, 41013 Sevilla, Spain.
³ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada.
⁴ Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
⁵ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada.
⁶ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada. Electronic address: durocher@lunenfeld.ca.

PMID: 37478847
PMCID: PMC10530064 (available on 2024-08-03)
DOI: 10.1016/j.molcel.2023.06.025

Abstract

To maintain genome integrity, cells must accurately duplicate their genome and repair DNA lesions when they occur. To uncover genes that suppress DNA damage in human cells, we undertook flow-cytometry-based CRISPR-Cas9 screens that monitored DNA damage. We identified 160 genes whose mutation caused spontaneous DNA damage, a list enriched in essential genes, highlighting the importance of genomic integrity for cellular fitness. We also identified 227 genes whose mutation caused DNA damage in replication-perturbed cells. Among the genes characterized, we discovered that deoxyribose-phosphate aldolase DERA suppresses DNA damage caused by cytarabine (Ara-C) and that GNB1L, a gene implicated in 22q11.2 syndrome, promotes biogenesis of ATR and related phosphatidylinositol 3-kinase-related kinases (PIKKs). These results implicate defective PIKK biogenesis as a cause of some phenotypes associated with 22q11.2 syndrome. The phenotypic mapping of genes that suppress DNA damage therefore provides a rich resource to probe the cellular pathways that influence genome maintenance.

Keywords: ATR; DNA damage; DNA replication stress; TTT complex; cytarabine; genome stability.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

CRISPR-Cas Systems*
DNA Damage*
DNA Repair
Humans
Mutation
Phenotype

Abstract

Publication types

MeSH terms

Grants and funding