Comprehensive tumor microenvironment analysis identifies a suppressive immune landscape in stemness-high hepatocellular carcinoma

Introduction : Hepatocellular carcinoma (HCC) remains a leading cause of cancer mortality, driven by late detection and limited therapeutic efficacy. A prior molecular classification defined five transcriptomic subtypes, among which the stemness-high (STM) subtype exhibits the poorest survival and pronounced stemness programs. Given the scarcity of effective treatments for this high-risk population, it is critical to characterize their tumor immune landscape and evaluate potential sensitivity to immune checkpoint inhibitors (ICIs). Here, we systematically profiled the immunologic features of STM tumors to assess their immunogenicity and likelihood of benefiting from ICIs. Methods : Four resectable HCC transcriptomic cohorts (Korea, Samsung, Zhongshan, and Modena) were analyzed. STM subtype assignment was performed using the Bayesian Compound Covariate Predictor (BCCP) with previously defined STM signatures. Immune deconvolution was conducted using TIMER 3.0 (CIBERSORT, MCP-counter, EPIC), and immune cell states were assessed by EcoTyper. Immune dysfunction and exclusion were quantified using TIDE. Survival outcomes were evaluated by Kaplan-Meier analysis. Results : Across all cohorts, STM tumors demonstrated significantly worse overall survival and recurrence-free survival. Clinically, STM tumors were enriched for adverse pathological features, including higher T stage, poor differentiation, and increased vascular invasion.Immune profiling revealed a profoundly suppressive tumor microenvironment, characterized by elevated M0 macrophages, regulatory T cells, myeloid-derived suppressor-like signatures, and abundant cancer-associated fibroblasts (CAFs). EcoTyper identified enrichment of pro-migratory fibroblasts, exhausted and Treg-like CD4⁺ T cell states, and tumor-associated endothelial and epithelial programs.TIDE analysis demonstrated high exclusion and dysfunction scores, along with increased CD274 (PD-L1) and Merck18 expression, collectively indicating an immune-excluded, poorly immunogenic, and ICI-resistant profile. Conclusions : The STM subtype of HCC is defined by a markedly immunosuppressive and immune-excluded tumor microenvironment with dysfunctional T cell states, CAF/MDSC infiltration, and angiogenic activity. These features are strongly associated with resistance to ICIs, suggesting that immune checkpoint blockade alone is unlikely to be effective. Alternative or combination therapeutic strategies will be required to improve outcomes in this high-risk molecular subtype.