Spatial Transcriptomics and snRNA-seq Expose CAF Niches Orchestrating Dual Stromal-Immune Barriers in Hepatocellular...

Area of Science:

• Oncology
• Immunology
• Genomics

Background:

• Hepatocellular carcinoma (HCC) displays spatial heterogeneity, contributing to treatment resistance.
• The function of cancer-associated fibroblasts (CAFs) in creating an immunosuppressive tumor microenvironment is not fully understood.

Purpose of the Study:

• To investigate the role of CAFs in the HCC tumor microenvironment using integrated single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptomics (stRNA-seq).
• To identify specific CAF subtypes and their mechanisms of immune suppression in HCC.

Main Methods:

• snRNA-seq and stRNA-seq were employed to map cellular and molecular features of HCC.
• The Robust Cell Type Decomposition (RCTD) algorithm was used for spatial gene expression analysis.
• Immunofluorescence validated protein localization and spatial patterns.

Main Results:

• Hypoxic metabolic myofibroblasts (hmmyCAFs) were identified as key regulators, enriched at the invasive front.
• hmmyCAFs form collagen barriers excluding CD8+ T cells and secrete POSTN, inhibiting immune checkpoints.
• hmmyCAFs drive hypoxia-mediated metabolic reprogramming in T cells, correlating with reduced survival and immunotherapy resistance.

Conclusions:

• hmmyCAFs act as triple architects of physical, molecular, and metabolic immunosuppression in HCC.
• hmmyCAFs and POSTN are potential biomarkers for predicting immunotherapy efficacy in HCC.
• Targeting hmmyCAFs may enhance immunotherapy outcomes in liver cancer.