Inhibition of Acetyl-CoA-carboxylase induces endoplasmic reticulum stress and has synergistic effects with anti-cancer therapies

Background: Acetyle-CoA-carboxylase-1 (ACC1) is overexpressed in many cancer types relative to normal tissues and catalyzes the rate limiting step of de novo fatty acid synthesis. In this study, we identified a new downstream effect of ACC inhibition and demonstrate synergy between a small molecule inhibitor of ACC, PF0517515, and clinically used anti-cancer agents. Methods: High throughput cell line (N=300 10 cell lines) and combinatorial drug screens (n=166 FDA-approved drugs) were performed along with in vivo mice xenograft experiments. We analyzed bulk and single cell RNA sequencing, and lipid profiling results of PF0517515 treated cells, and performed western blot analysis of endoplasmic reticulum stress proteins to elucidate cellular effects of ACC inhibition. Results: Single agent PF-05175157 inhibited the growth of several different cancer types, myeloma, ovarian, lung and breast cancer cells resistant to various targeted therapies. PF-05175157 augmented the anti-cancer efficacy of a range of drugs including tyrosine kinase inhibitors and chemotherapy agents. Synergy with doxorubicin and vinorelbine were also demonstrated in mice xenografts. In breast cancer cells, ACC inhibition increased the protein (and mRNA) expression levels of genes involved in endoplasmic reticulum stress and unfolded protein response including a rapid increase in phospho-IRE1 by 6h, and more gradual increase in phospho-EIF2, ATF4, and ATF6 expressions by 24h and 72h. Lipid profiling after 48h exposure to drug showed decrease in many membrane components including c14:0/c16:0 and c16:0/c18:1 that facilitate membrane protein integration. There was an increase in unsaturated long-chain fatty acids and an increase in 4-Hydroxynonenal and 4-Hydroxyhexenal indicating increased lipid peroxidation. Single cell RNA sequencing showed large scale metabolic slowdown with decreased oxidative phosphorylation, amino acid and steroid biosynthesis, glutathione-, carbon-, pyruvate-, and purine-metabolism. Pathways of ferroptosis, reactive oxygen, sphingolipid, steroid hormone and folate biosynthesis were upregulated suggesting response to oxidative stress and compensatory lipid synthesis. Seven-day post-recovery cells compared to pretreatment, continued to show downregulation of proteasome, spliceosome, amino acid synthesis, DNA replication/DNA repair, cell cycle, oxidative phosphorylation, and glycolysis /gluconeogenesis indicating less than full metabolic recovery. Conclusion: PF-05175157 alters cellular lipid composition, induces endoplasmic reticulum stress, and shows broad synergy with various anti-cancer therapies in vitro and in vivo.