Multi-region spatial transcriptome analysis reveals cellular networks and pathways associated with hepatocellular carcinoma recurrence after surgical resection
Hepatocellular carcinoma (HCC) exhibits diverse aetiologies and molecular heterogeneities, with a median 5-year overall survival (OS) of less than 70% due to late diagnosis and high recurrence rates post-curative ablation or surgery. This study investigated the complex tumor microenvironment (TME) in HCC, emphasizing the interactions between various cell types and their role in disease recurrence. Using samples from the PLANet 1.0 cohort (NCT03267641), spatial transcriptomics were performed on 17 tissue samples from 4 patients, and bulk RNA-seq on multi-region tumour sectors from 91 patients. Analysis revealed extensive intra- and inter-tumour  gene expression heterogeneity, identifying a specific subset of endothelial cells (ECs), INTS6+ ECs, enriched and spatially co-localized with tumour cells in primary tumours of recurrent cases. A significant ANGPTL4-SDC1 ligand-receptor interaction was found between INTS6+ ECs and tumour cells. Interestingly, INTS6+ ECs were enriched in histologically annotated microvascular invasion (MVI). These findings suggest novel therapeutic targets focusing on endothelial cell interactions within TME. Overall design: we conducted a spatial transcriptomic analysis using visium technology from 10x genomics, on multiple sectors per primary tumour from patients with HCC treated with curative intent surgical resection who were without recurrence at 60 months after surgery (A009) and who had early tumour recurrences between 3.6 to 14.0 months (C008, B013, C004) .These patients were part of the PLANet 1.0 longitudinal cohort study and included both chronic viral hepatitis B-positive and-negative individuals. Where possible, as reference, we profiled adjacent non-tumour tissue ('normal').  Each Primary tumour was sampled from 2-5 distinct regions, and at least one section per region was obtained for spatial transcriptomic analysis. In patient C004, we examined both primary and recurrent tumour sectors.