A Genetic Interaction Analysis Identifies Novel Cancer Driver Modifiers and a Combination Therapy

Abstract

A large number of cancer drivers have been identified through tumor sequencing efforts but how they interact and the degree to which they can substitute for each other has not been systematically explored. To comprehensively investigate how cancer drivers genetically interact, I searched for modifiers of EGFR dependency by performing CRISPR, shRNA and expression screens in a non-small cell lung cancer model. I elucidated a broad spectrum of TSGs and OGs that can genetically modify proliferation and survival of cancer cells when EGFR signaling is altered. I found that mutation of PBRM1, a subunit of the SWI/SNF complex, attenuates the effects of EGFR inhibition in part by sustaining AKT signaling. I also found that mutation of Capicua (CIC), a transcriptional repressor, suppresses the effects of EGFR inhibition by partially restoring the EGFR-promoted gene expression program including the sustained expression of Ets transcription factors like ETV1. Together, my data provide strong support for the hypothesis that many cancer drivers can substitute for each other in certain contexts and broadens our understanding of EGFR regulation. I further applied this strategy of searching for cancer driver modifiers to another cancer disease model to test its generality. Bromodomain and extraterminal domain inhibitors (BETis) show efficacy on NUT midline carcinoma (NMC). However, not all NMC patients respond, and responders eventually develop resistance and relapse. Using CRISPR and ORF expression screens, I systematically examined the ability of cancer drivers to mediate resistance of NMC to BETis and uncovered six general classes/pathways mediating resistance. Among these, I found that RRAS2 attenuated the effect of JQ1 in part by sustaining ERK pathway function during BRD4 inhibition. Furthermore, overexpression of Krüppel-like factor 4 (KLF4), mediated BETi resistance in NMC cells through restoration of the E2F and MYC gene expression program. Finally, I found that expression of cyclin D1 or an oncogenic cyclin D3 mutant or RB1 loss protected NMC cells from BETi-induced cell cycle arrest. Consistent with these findings, cyclin-dependent kinase 4/6 inhibitors showed synergistic effects with BETis on NMC in vitro as well as in vivo, thereby establishing a potential two-drug therapy for NMC.