ATP citrate lyase fuels lipid storage to support triple negative breast cancer chemoresistance

Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype in which neoadjuvant chemotherapy (NACT) is the backbone of standard of care. Unfortunately, ~45% of patients have residual tumor burden following NACT, which is strongly associated with poor prognoses. Our group previously demonstrated that mitochondrial oxidative phosphorylation is upregulated and is a therapeutic vulnerability of chemo-refractory TNBC. We used metabolomic flux tracing to show a heightened contribution of glucose oxidation to the tricarboxylic acid (TCA) cycle in residual human TNBC cells surviving several conventional chemotherapies. We found significantly elevated abundance of citrate and acetyl-coA (AcCoA) in residual cells. Further, glucose, but not palmitate, glutamine, or acetate, derived heavy carbon was more strongly incorporated into citrate and AcCoA in residual relative to naïve cells. Concomitantly, we observed drastic lipidomic remodeling, largely characterized by elevation of triglycerides, long chain fatty acids, and poly unsaturated fatty acids (PUFAs) in cultured TNBC cells and orthotopic patient-derived xenograft (PDX) tumors following chemotherapy relative to their treatment naïve counterparts. This was accompanied by a significant increase in the number of lipid droplets (LDs) in residual cells. Together, these data suggest glucose oxidation supports fatty acid synthesis (FAS) and storage in chemoresistant TNBC. Our analyses of human TNBC proteomic and transcriptomic data affirmed the significant association of fatty acid metabolism with TNBC chemoresistance, as well as its upregulation in chemotherapy-treated tumors relative to their pre-treated counterparts. Mining those data led us to ATP citrate lyase (ACLY), the rate limiting enzyme for cytosolic AcCoA production from citrate. We hypothesized that ACLY converts excess citrate, generated by heightened TCA cycling, to AcCoA to promote FAS and storage in chemoresistant TNBC. We found elevated protein levels of ACLY and an activating phosphorylation mark in TNBC cells surviving treatment with conventional chemotherapies doxorubicin and carboplatin. ACLY knockdown or inhibition potently reduced chemotherapy-induced accumulation of AcCoA and LDs and elicited lipidomic rewiring largely characterized by increased PUFAs. Notably, combining ACLY inhibition or KD with conventional chemotherapy treatments provided significant improvement of tumor cell growth inhibition. These data indicate that NACT can cause accumulation of citrate, AcCoA, LDs, and overall lipidomic rewiring through ACLY. ACLY is a novel functional dependency of chemo-refractory TNBC and should be further explored as a potential therapeutic target. We posit that TNBC cells adapt to the stress of NACT by upregulating lipid synthesis and storage in conjunction with glucose catabolism, enhancing metabolic flexibility and cell survival.