Divergent malignant evolution converges on shared immunosuppressive ecosystems through tumor-intrinsic TMED2-ADAR1-dependent complement signalling in multifocal hepatocellular carcinoma

Background Multifocal hepatocellular carcinoma (HCC) comprises spatially separated tumor foci with distinct evolutionary trajectories, posing a major therapeutic challenge. Whether divergent lesions retain shared immune-evasion mechanisms beyond lesion-specific heterogeneity and offer cross-focal therapeutic opportunities remains unknown. Objective To resolve malignant and microenvironmental heterogeneity across tumor foci and identify conserved immunosuppressive programs underlying multifocal HCC progression. Design Matched tumour foci and peritumoural tissues from patients with multifocal HCC underwent integrated single-cell and spatial multi-omics profiling, including scFAST-seq (n=15), scATAC-seq (n=12), and Stereo-seq (n=14). In-house RNA-seq (n=13), public scRNA-seq (HRA001748) and RNA-seq datasets (TCGA-LIHC, OEP000321) were used for validation. Multiplex immunohistochemistry (n=96) and functional assays validated key findings. Results Multifocal HCC exhibited extensive inter-focal heterogeneity in malignant genomic, transcriptional, epigenetic, and evolutionary states, accompanied by diverse immune and stromal landscapes. Despite this divergence, spatially separated tumor foci converged on shared malignant states marked by elevated TMED2 expression and conserved immunosuppressive ecosystems characterized by regulatory T-cell (Treg) and SPP1+/SPRED1+ macrophage enrichment, impaired cytotoxic CD8+ T-cell immunity, and recurrent stromal-vascular remodeling. Mechanistically, malignant hepatocytes engaged SPP1+/SPRED1+ macrophages through C3/C5 complement signaling across divergent tumor foci, while macrophages and Tregs contributed to CD8+ T-cell dysfunction through CD274-PDCD1, CD80/CD86-CTLA4/CD28, and MHC-I-CD8 interactions. A tumor-intrinsic TMED2-ADAR1-dependent A-to-I RNA editing program promoted C3/C5 complement expression and secretion, linking malignant heterogeneity to conserved tumor-immune signaling. Conclusions Despite divergent malignant evolution, multifocal HCC converges on shared immunosuppressive ecosystems. The TMED2-ADAR1-C3/C5 complement axis represents a conserved tumor-immune vulnerability that may enable therapeutic strategies targeting common immune-evasion mechanisms across heterogeneous tumor foci.