CR1(+) Tumor-Associated Macrophages Orchestrate an Immunosuppressive Niche in Hepatocellular Carcinoma: A Genetic and Multi-omics Dissection

Background Hepatocellular carcinoma (HCC) is characterized by a profoundly immunosuppressive tumor microenvironment (TME), which severely limits therapeutic efficacy. By integrating a multi-omics strategy, we identified complement receptor 1 (CR1) as a central regulator of this immunosuppressive milieu. Methods We performed Mendelian randomization (MR) analyses to infer the causal relationship between genetically predicted circulating CR1 levels and HCC risk, followed by metabolite mediation analyses. Bulk, single-cell, and spatial transcriptomic datasets from public cohorts and clinical samples were systematically analyzed to characterize CR1 expression patterns and cellular localization. Tumor microbiome profiling was conducted to explore potential microbe–immune interactions. Functional validation was performed using THP-1–derived macrophages, including gain- and loss-of-function experiments, phagocytosis assays, and macrophage–CD8⁺ T-cell co-culture systems. Results MR analysis identified a causal link between genetically predicted circulating CR1 levels and increased HCC risk (IVW OR = 0.907, P  = 0.02), with specific blood metabolites potentially mediating this effect. Multi-omics profiling revealed that CR1 was overexpressed specifically in tumor tissues and predominantly enriched in tumor-associated macrophages (TAMs), where its expression strongly correlated with M2 polarization signatures. Elevated CR1 expression correlated with reduced CD8⁺ T cell infiltration, increased T cell exhaustion, and poorer patient survival. Spatial transcriptomics further confirmed significant co-localization of CR1 with the M2 marker CD206. Functionally, CR1 overexpression reprogrammed macrophages into an M2-like immunosuppressive phenotype, characterized by upregulation of CD206 and IL-10 and enhanced phagocytic activity, while CR1 knockdown promoted an M1-like state. Crucially, in co-culture systems, CR1-high macrophages markedly inhibited CD8⁺ T cell proliferation and effector functions—including IFN-γ production and granzyme B expression—concomitant with increased PD-L1 expression. Tumor microbiome analysis extended our findings, suggesting potential crosstalk between intratumoral bacteria and the CR1-driven immunosuppressive axis. Conclusions Our study identifies CR1 as an environmentally responsive master regulator that reshapes the immunological landscape of HCC by reprogramming TAMs, thereby positioning CR1 as a highly promising therapeutic target for restoring antitumor immunity.