Functional interrogation of DNA damage response variants with base editing screens

Mutations in DNA damage response (DDR) genes endanger genome integrity and predispose to cancer and genetic disorders. Here, using CRISPR-dependent cytosine base editing screens, we identify > 2,000 sgRNAs that generate nucleotide variants in 86 DDR genes, resulting in altered cellular fitness upon DNA damage. Among those variants, we discover loss- and gain-of-function mutants in the Tudor domain of the DDR regulator 53BP1 that define a non-canonical surface required for binding the deubiquitinase USP28. Moreover, we characterize variants of the TRAIP ubiquitin ligase that define a domain, whose loss renders cells resistant to topoisomerase I inhibition. Finally, we identify mutations in the ATM kinase with opposing genome stability phenotypes and loss-of-function mutations in the CHK2 kinase previously categorized as variants of uncertain significance for breast cancer. We anticipate that this resource will enable the discovery of additional DDR gene functions and expedite studies of DDR variants in human disease.

Automated summary

Through CRISPR-dependent cytosine base editing screens, this study identified over 2,000 sgRNAs that induce nucleotide variants in DNA damage response (DDR) genes, altering cellular fitness upon DNA damage. The research also discovered critical mutations in DDR regulator 53BP1 and TRAIP ligase, shedding light on their roles in cellular damage response. The findings provide valuable insights into the function of DDR genes and their implications in human diseases.