MAP kinase and autophagy pathways cooperate to maintain RAS mutant cancer cell survival

Abstract

Oncogenic mutations in the small GTPase KRAS are frequently found in human cancers, and, currently, there are no effective targeted therapies for these tumors. Using a combinatorial siRNA approach, we analyzed a panel of <i>KRAS</i> mutant colorectal and pancreatic cancer cell lines for their dependency on 28 gene nodes that represent canonical RAS effector pathways and selected stress response pathways. We found that RAF node knockdown best differentiated <i>KRAS</i> mutant and <i>KRAS</i> WT cancer cells, suggesting RAF kinases are key oncoeffectors for <i>KRAS</i> addiction. By analyzing all 376 pairwise combination of these gene nodes, we found that cotargeting the RAF, RAC, and autophagy pathways can improve the capture of <i>KRAS</i> dependency better than targeting RAF alone. In particular, codepletion of the oncoeffector kinases BRAF and CRAF, together with the autophagy E1 ligase ATG7, gives the best therapeutic window between <i>KRAS</i> mutant cells and normal, untransformed cells. Distinct patterns of RAS effector dependency were observed across <i>KRAS</i> mutant cell lines, indicative of heterogeneous utilization of effector and stress response pathways in supporting KRAS addiction. Our findings revealed previously unappreciated complexity in the signaling network downstream of the <i>KRAS</i> oncogene and suggest rational target combinations for more effective therapeutic intervention.