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

Abstract

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.