Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

PURPOSE: Dysregulated cholesterol metabolism has emerged as a crucial driver of hepatocellular carcinoma (HCC) progression and immunotherapy resistance. This study aimed to delineate the single-cell landscape of cholesterol metabolism in HCC and identify key molecular determinants linking metabolic reprogramming to tumor aggressiveness and immune evasion. METHODS: An integrative multi-omics approach combining bulk and single-cell RNA sequencing from multiple-center cohorts was employed. Metabolic activity scoring, high-dimensional weighted gene co-expression network analysis (hdWGCNA), and a five-model integrated machine learning strategy were applied to identify hub genes associated with cholesterol metabolism. Functional assays, including genetic silencing, metabolic profiling, and orthotopic mouse models with anti-PD-1 and FDPS inhibitor (alendronic acid), were used to validate mechanistic and therapeutic relevance. RESULTS: Cholesterol metabolic activity was markedly elevated in HCC tumors and immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations. The enzyme Farnesyl Diphosphate Synthase (FDPS) emerged as a pivotal regulator, promoting tumor cell cholesterol metabolism and proliferation. Further functional experiments demonstrated that targeting FDPS suppressed tumor growth, reduced intracellular cholesterol levels and significantly enhanced anti-PD-1 efficacy in vivo, accompanied by increased lymphoid immune infiltration. CONCLUSION: Our findings establish FDPS-driven cholesterol metabolic reprogramming as a key mechanism of HCC malignancy and immunotherapy resistance. Targeting FDPS offers a promising strategy to potentiate immune checkpoint therapy and reshape metabolic vulnerabilities in liver cancer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13402-026-01177-7.