Using Genome-Wide CRISPR/Cas9 Screens to Identify Novel Therapeutic Targets in Small Cell Lung Cancer

Abstract

Small Cell Lung Cancer (SCLC) is a highly aggressive and metastatic form of lung cancer and is one of the most lethal sold tumor malignancies. The classical subtype of SCLC is noted for its neuroendocrine differentiation features. Standard treatment options have not improved in decades and SCLC tumors develop near universal rates of resistance to chemotherapy. This project aimed to elucidate novel therapies to SCLC using genome-wide CRISPR/Cas9 inactivation screens of genetically simplified murine small cell lines developed in our lab. These screens identified genes and pathways in which their functional depletion causes decreased viability in SCLC cells. A number of these identified vulnerabilities are targeted by small molecules, which include known SCLC-specific vulnerabilities like CHEK1 and BCL2L1. Here we show novel SCLC vulnerabilities, specifically focusing on NEDD8 and the neddylation pathway. Perturbation of this pathway causes SCLC death in vitro. Additionally, the SCLC patient derived xenografts models LX108 and RU280 show strong sensitivity to the neddylation inhibitor MLN4924 in vivo. Neddylation inhibition causes reduced expression levels of the neuroendocrine proteins INSM1, ASCL1, and POU3F2 and FOXA2. Genetic perturbation of neddylation pathway members or treatment with MLN4924 leads to a downregulation of the neuroendocrine signature in SCLC cells. A genome-wide CRISPR/Cas9 suppressor screen identified the mTOR and NF-κB pathways as potential mechanisms of resistance to the effects of neddylation inhibition in SCLC. This work identifies neddylation as a novel potential therapeutic target for the treatment of SCLC.