Comprehensive interrogation of chemo-genomic interactions between DNA damaging agents and DNA damage repair genes with targeted CRISPR knockout screening
Genetic instability is a hallmark of cancer, often arising from mutations to DNA damage repair and response (DDR) genes. Classical genetic, biochemical and structural approaches have elucidated the foundational mechanisms of DDR pathways and provided a scientific understanding of their involvement in repair of broad classes of DNA-damaging agents (DDAs). However, given the chemical diversity of DDAs and resultant DNA lesions, along with the multitude of interconnected DDR factors, the chemogenomic landscape of DDA–DDR interactions remains incompletely mapped. To this end, we developed a DDR-targeted, CRISPR knockout screening approach and assessed relationships among 353 DNA repair genes and 15 DDAs in LN229 glioma cells. Within this dataset of 5295 DDR-related chemogenomic interactions, we identified many established interactions and discovered novel ones. For example, we observed a specific role of TC-NER in the repair of adducts generated by monofunctional alkylating agents, a role for the FA pathway in addressing methyl lesions, overt differences in DSB repair following treatment with topoisomerase I and II poisons, and repair dependencies associated with imidazotetrazine derivatives temozolomide, mitozolomide, and KL-50. Future directions will continue to investigate the mechanisms of novel chemogenomic interactions that we have uncovered as well as work to identify chemogenomic interactions amenable to clinical translation. Overall design: NOT PROVIDED; REQUESTED