Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors

The ataxia telangiectasia and Rad3-related (ATR) protein kinase is a key regulator of the cellular response to DNA damage. Due to increased amount of replication stress, cancer cells heavily rely on ATR to complete DNA replication and cell cycle progression. Thus, ATR inhibition is an emerging target in cancer therapy, with multiple ATR inhibitors currently undergoing clinical trials. Here, we describe dual genome-wide CRISPR knockout and CRISPR activation screens employed to comprehensively identify genes that regulate the cellular resistance to ATR inhibitors. Specifically, we investigated two different ATR inhibitors, namely VE822 and AZD6738, in both HeLa and MCF10A cells. We identified and validated multiple genes that alter the resistance to ATR inhibitors. Importantly, we show that the mechanisms of resistance employed by these genes are varied, and include restoring DNA replication fork progression, and prevention of ATR inhibitor-induced apoptosis. In particular, we describe a role for MED12-mediated inhibition of the TGFβ signaling pathway in regulating replication fork stability and cellular survival upon ATR inhibition. Our dual genome-wide screen findings pave the way for personalized medicine by identifying potential biomarkers for ATR inhibitor resistance.
Author summary Cancer cells rely on the ATR replication stress response pathway to ensure DNA replication and continued cellular proliferation. As such, inhibitors of the ATR kinase activity represent promising new anti-cancer drugs. However, the tumors’ susceptibility to these drugs can be markedly impacted by their genomic profile. To address this, we employed dual CRISPR knockout and activation genome-wide genetic screens to catalog the genetic determinants of the cellular resistance to multiple ATR inhibitors. We identified several mechanisms which control this resistance, including regulation of apoptosis and stabilization of replication fork stability. Our work lays the foundation for personalized deployment of ATR inhibitors in cancer therapy.