MRC1⁺ macrophages and endothelial PTPRM signalling characterize a microvascular invasion–associated tumor ecosystem in hepatocellular carcinoma

The intercellular interactions and molecular features underlying microvascular invasion (MVI) in hepatocellular carcinoma (HCC) remain incompletely understood. We aimed to characterize the MVI-associated multicellular ecosystem at single-cell resolution and to derive prognostic and therapeutic hypotheses from the identified interaction axes. Single-cell RNA sequencing was performed on tumour samples from 4 MVI-positive and 4 MVI-negative HCC patients. Macrophage, endothelial and tumour compartments were compared between groups, and cell–cell communication was inferred with CellChat and NicheNet. Findings were examined in an independent HCC single-cell cohort and in public Visium spatial transcriptomics sections. Candidate genes from the MRC1⁺ macrophage, endothelial and tumour compartments were used for Connectivity Map (CMap) analysis and to construct a direction-weighted compartment programme score, which was evaluated in TCGA-LIHC, GSE14520 and ICGC LIRI-JP. MVI-positive tumours exhibited altered macrophage composition and endothelial capillarization, accompanied by strengthened PTPRM–PTPRM homophilic signalling between MRC1⁺ macrophages, endothelial cells and tumour cells. Both features were reproduced in the external cohort, and spatial transcriptomics localized PTPRM expression to endothelial-enriched regions adjacent to macrophage-rich areas in MVI-positive tumours. CMap analysis nominated compounds predicted to reverse the MVI-associated expression pattern, with geldanamycin ranking first. The compartment programme score was associated with overall survival across the three cohorts (log-rank p = 1.44 × 10⁻⁶, 1.82 × 10⁻⁴ and 8.57 × 10⁻⁵) and remained an independent prognostic factor in TCGA-LIHC and ICGC LIRI-JP after adjustment for available clinicopathological variables. Our study characterizes an MVI-associated tumour ecosystem in HCC, in which endothelial PTPRM signalling is strengthened in association with MRC1⁺ macrophage enrichment and endothelial capillarization. These findings provide a cellular and molecular framework for MVI stratification and hypothesis-generating therapeutic exploration.