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 used combinatorial CRISPRi screening to comprehensively map genetic interactions required for survival during normal human cell homeostasis across all core DDR genes. We captured known interactions and discovered myriad new connections, which are available in an online resource. We defined the molecular mechanism for two of the strongest interactions: First, we found that WDR48 works with USP1 to restrain PCNA degradation in FEN1/LIG1-deficient cells. Second, we found that SMARCAL1 and FANCM directly unwind TA-rich DNA cruciforms, preventing catastrophic chromosome breakage by the ERCC1-ERCC4 complex. Our data yield fundamental insights into genome maintenance, provide a springboard for mechanistic investigations into new connections between DDR factors, and pinpoint synthetic vulnerabilities that could be exploited in cancer therapy.

DNA损伤应答（DNA damage response, DDR）是一套多维度的通路网络，负责维持基因组稳定性。阐明这些通路间的协同互作机制仍是当前研究的难点。本研究采用组合型CRISPR干扰（CRISPR interference, CRISPRi）筛选技术，全面绘制了人类正常细胞稳态下维持存活所需的全部核心DDR基因间的遗传互作图谱。我们不仅复现了已知的遗传互作网络，还发现了大量全新的关联，相关数据已通过在线资源公开。我们解析了其中两组最强互作的分子机制：其一，WDR48与USP1协同作用，可在FEN1/LIG1缺陷细胞中抑制PCNA的降解；其二，SMARCAL1与FANCM可直接解旋富含TA序列的DNA十字结构，从而避免ERCC1-ERCC4复合物介导的灾难性染色体断裂。本研究的数据为基因组维持机制研究提供了基础性见解，为探究DDR因子间全新关联的分子机制搭建了重要研究平台，并精准定位了可用于癌症治疗的合成致死靶点。