Comprehensive Interrogation of Synthetic Relationships in the Human DNA Damage Response

The DNA damage response (DDR) is a multi-faceted network of pathways that preserves genome stability. Unraveling the complementary interplay between these pathways remains a challenge. Here, we comprehensively mapped genetic interactions for all core DDR genes using combinatorial CRISPRi screening. We discovered myriad new connections, including interactions between cancer genes and small molecule targets. We focused on two of the strongest interactions: FEN1/LIG1:WDR48 and FANCM:SMARCAL1. First, we found that WDR48 works with USP1 to restrain overactive translesion synthesis in FEN1/LIG1-deficient cells, and that a preclinical inhibitor of USP1 specifically kills FEN1-deficient cells. Second, we found that SMARCAL1 and FANCM suppress DNA double-strand break (DSB) formation at TA-rich repeats in late replicating regions that otherwise escape into mitosis and cause nuclear fragmentation. We present fundamental insights into genome maintenance processes and our dataset provides a springboard for mechanistic investigations into connections between DDR factors and suggests multiple interactions that could be exploited in cancer therapy.