Mapping the Genetic Interaction Network of PARP inhibitor Response

Genetic interactions have long informed our understanding of the coordinated proteins and pathways that respond to DNA damage in mammalian cells, but systematic interrogation of the genetic network underlying this system has yet to be achieved. Towards this goal, we measured 147,153 pairwise interactions among genes implicated in PARP inhibitor (PARPi) response with and without exposure to PARPi. By applying an analytical framework we defined differential genetic interactions at scale, identified novel interactions belonging to different interaction categories, and revealed PARP1-trapping as a common mode of sensitization of PARPi across genetic backgrounds. We uncovered the minimally characterized gene, AUNIP, while not essential for genome stability under normal conditions, plays a key role in repairing PARPi induced DNA damage together with FA pathway genes and is antagonized by the BRCA1-A complex. Our work thus establishes a foundation for mapping differential genetic interactions in mammalian cells and provides a comprehensive resource for future studies of DNA repair and PARP inhibitors. Overall design: The GI library of dual-sgRNA expression constructs were cloned and transduced into a well-validated K562 CRISPRi cell line, with or without exposure to niraparib, collecting cells at the beginning of the screen (T0, day of drug treatment) and after ten days of growth (reference or PARPi endpoints). Expression cassettes were isolated and sequenced from each sample to generate counts for each sgRNA pair, from which three metrics of phenotype scores were calculated: reference growth phenotypes (?), growth phenotypes after PARPi exposure (t), and PARPi sensitization phenotypes (?). Genetic interaction scores and differential genetic interactions were derived from those measurements.