Multimodal sequencing identifies synergistic mechanisms driving resistance to neoadjuvant nivolumab treatment in hepatocellular carcinoma.

The tumor immune microenvironment (TIME) critically modulates therapeutic responses to immune checkpoint inhibitors (ICIs) in hepatocellular carcinoma (HCC). Relative to the other solid tumors, HCC is characterized by more pronounced intratumoral heterogeneity and has comparatively poorer responsiveness to ICI blockade treatment. Importantly, the correlation of the underlying mechanism of TIME and the molecular underpinnings of immunotherapy resistance in HCC remains elusive. Employing an integrative multi-omics approach, including spatially resolved transcriptomics, single-cell and bulk RNA sequencing, and lipidomics, we delineated the spatiotemporal dynamics and mechanistic basis of resistance to anti-PD-1 therapy in HCC. Our analyses revealed a profoundly immunosuppressive TIME in non-responsive patients, marked by sparse immune cell infiltration within the tumor niche, in contrast to the immune-inflamed TIME observed in the responders. Multidimensional profiling further uncovered dysregulated lipogenesis and aberrant lipid accumulation in tumor cells of the non-responder cases. Notably, tumor-associated macrophages (TAMs), exhausted CD8 T cells, and lipid-enriched tumor cells co-localize at the tumor-immune interface, forming a physical and functional barrier that precludes effective immune cell infiltration into the tumor niche. We also identified the pivotal TAM-tumor cell crosstalk via the ADM-RAMP1-EBP signaling axis, orchestrating lipid metabolism reprogramming and contributing to the attenuated PD-1 therapeutic efficacy. Collectively, these findings provide a comprehensive mechanistic framework for anti-PD1 resistance, unveiling actionable biomarkers and a translational vulnerability to enhance precision therapeutics in HCC.