Resistance mechanisms to autophagy-modulating therapies

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.

Grant Number: 5R01CA266404-05
NIH Institute/Center: NIH
Principal Investigator: RAVI AMARAVADI