Inhibition of ACLY enhances tumor immunogenicity and resolves MASH-driven HCC [scRNA-seq]

Immunosuppressive tumor microenvironments are common in cancers such as metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma (HCC). While immune cell metabolism influences effector function, the impact of tumor metabolism on immunogenicity is less understood. ATP citrate lyase (ACLY), a key enzyme linking catabolic and anabolic processes, supports lipid metabolism and gene regulation. Although ACLY inhibition shows anti-proliferative effects in various tumors, clinical translation has been limited by challenges in inhibitor development and compensatory metabolic pathways. Using a mouse model of MASH-driven HCC that mirrors human disease, genetic inhibition of ACLY in hepatocytes and tumors reduced neoplastic lesions by over 70%. To evaluate the therapeutic potential of this pathway, a novel small-molecule ACLY inhibitor, EVT0185 (6-[4-(5-carboxy-5-methyl-hexyl)-phenyl]-2,2-dimethylhexanoic acid), was identified via phenotypic screening. EVT0185 is converted to a CoA thioester in the liver by SLC27A2 with cryo-EM structural analysis revealing EVT0185-CoA directly interacts with ACLY's CoA binding site. Oral delivery of EVT0185 in four mouse models of MASH-HCC dramatically reduces tumor burden as monotherapy and enhances efficacy of current standards of care including tyrosine kinase inhibitors and immunotherapies. Transcriptomic and spatial profiling in mice and humans linked reduced tumor ACLY with increases in CXCL13, tumor infiltrating B-cells and tertiary lymphoid structures. Remarkably, the depletion of B cells blocked the anti-tumor effects of ACLY depletion. Together, these findings illustrate how targeting tumor metabolism can rewire immune function and suppress cancer progression in MASH-HCC. Overall design: To investigate the transcriptional effects of EVT0185, single-cell RNA sequencing was performed on snap-frozen livers from two mouse models of MASH-HCC: the WD-CCl4 and WD-DEN models. Each of the four experimental conditions (WD-CCl4 + vehicle, WD-CCl4 + EVT0185, WD-DEN + vehicle, WD-DEN + EVT0185) included 3 biological replicates, for a total of 12 samples. To enable high-throughput processing, these 12 samples were multiplexed across four pooled libraries, with each pool comprising cells from multiple samples. While 16 samples were processed and sequenced in total, only 12 are relevant to the present study; the remaining 4 were part of the same sequencing run but are not analyzed or discussed here. Sample-specific count matrices are provided for the 12 relevant samples.