Resistance mechanisms to autophagy-modulating therapies

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Project Summary Although targeted therapy and immune checkpoint inhibitors have made a major impact on survival for some patients with advanced cancer, the majority of patients do not respond to standard of care treatments. Abundant evidence indicates autophagy is induced by chemotherapy and targeted therapy, and also limits the efficacy of immunotherapy. Clinical trials testing autophagy inhibitor combinations show encouraging preliminary results with increased response rates when compared to standard of care approaches. New autophagy inhibitors are entering clinical trials. Preclinical studies and the available clinical data indicate that tumors can overcome autophagy modulating therapies producing resistance. There is a critical unmet need to understand mechanisms of resistance to autophagy-modulating therapy. Using melanoma as a model we have discovered that extensive lipid raft induction is induced by autophagy modulating therapy. This is especially pronounced with lysosomal autophagy inhibition, which induces the expression of key proteins (LDLR, SR-B1, and UGCG) in the cholesterol and sphingolipid salvage pathways (CSSP). At least one of these enzymes, UGCG, can be targeted with an FDA approved therapy eliglustat and preliminary results indicate combined autophagy inhibition and UGCG inhibition produces synergistic antitumor activity in vivo. This proposal will test the hypothesis that the increased expression of CSSP and subsequent lipid raft formation induced by autophagy-modulating therapy promotes cell survival, and may be a key druggable vulnerability that can be targeted to improve therapeutic outcomes in cancer. To test this hypothesis, we will leverage the longstanding collaboration between Dr. Amaravadi (oncologist, autophagy expert) and Dr. Speicher (systems biology expert). We also recruited Dr. Meenhard Herlyn, a melanoma expert who has developed a humanized mouse model and bank of patient-derived xenografts, as well as Dr. Phyllis Ginotty, a biostatistician who has worked closely with this team for years. In Aim 1 we will define the mechanism by which autophagy modulation regulates the cholesterol and sphingolipid scavenging pathways (CSSP). We will determine the effects of chemical or genetic manipulation inhibition of key CSSP genes in lipid-depleted and precisely reconstituted media on tumor cell survival. In Aim 2 we will determine the role of UGCG as a driver of resistance across melanoma therapy combinations in in vivo models. We will utilize a panel of patient-derived xenograft (PDX) models generated from BRAF mutant and NRAS mutant melanoma patients to determine if targeting UGCG results in decreased lipid raft assembly, that overcomes resistance to clinically relevant therapies. Impact: These studies will determine how two key resistance mechanisms to cancer therapies, autophagy and altered lipid metabolism, intersect. Our results should uncover new therapeutic vulnerabilities in melanoma as well as other cancers and should identify new therapeutic combinations incorporating CSSP inhibitors to be tested in future clinical trials, which could significantly improve outcomes for cancer patients.