In vivo functional screens reveal KEAP1 loss as a driver of chemoresistance in small cell lung cancer

Abstract

Among the most chemosensitive of all cancer types, small cell lung cancer (SCLC) exhibits dismal clinical outcomes owing to rapid transition to chemoresistance. Elucidating the genetic underpinnings of chemoresistance has been challenging owing to limitations with cellular models. Patient derived xenograft (PDX) models mimic patient responses to chemotherapy, raising potential to use such models for high throughput identification of chemoresistance driver genes. We apply cDNA overexpression, CRISPR knockout screens, and CRISPR activation screens to chemosensitive PDX models of SCLC. cDNA overexpression screens highlight MYC, MYCN and MYCL overexpression as promoting survival in the context of chemotherapy treatment. CRISPR deletion screens identify KEAP1 loss as driving chemoresistance. Deletion of KEAP1 switched a chemosensitive PDX model of SCLC to become chemoresistant and resulted in sensitivity to inhibition of glutamine metabolism. Data from the IMpower133 clinical trial revealed ~6% of extensive stage SCLC patients exhibit KEAP1 genetic alterations, with activation of a KEAP1/NRF2 transcriptional signature associated with reduced SCLC patient survival in the chemotherapy arm. While roles for the KEAP1/NRF2 pathway have been previously overlooked in SCLC, our genetic screens revealed KEAP1 loss as a driver of chemoresistance and we demonstrate functional importance for this pathway in human SCLC. Finally, a CRISPR activation screen revealed multiple new candidate drivers of resistance to chemotherapy in SCLC.