Single-Cell Transcriptomic Analysis Reveals an Aggressive Basal-Like Tumor Cell Subpopulation Associated With Poor Prognosis in Intrahepatic Cholangiocarcinoma

Abstract

Background and Aim

Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver cancer whose incidence is increasing globally. However, the high tumor heterogeneity of ICC restricts the efficacy of available systematic therapies. We aim to dissect the tumor heterogeneity of ICC utilizing high-resolution single-cell RNA sequencing to identify novel therapeutic targets.

Methods

We performed single-cell RNA sequencing (scRNA-seq) of 26 tumor samples from 23 ICC patients and spatial transcriptomic sequencing of six tumor sections from six ICC patients. Bulk RNA-seq data from two public datasets were used for validation. Additionally, immunohistochemical staining and multiplex immunofluorescence staining were conducted to validate the infiltration and distribution of cells in the tumor microenvironment.

Results

We discovered that malignant cells in ICC samples exhibited a remarkably high degree of tumor heterogeneity. We identified a basal-like tumor cell subpopulation characterized by the expression of basal epithelial related genes including KRT5, KRT6A, and KRT17. The basal-like tumor subpopulation was characterized by activation of MET signaling and extracellular matrix organization associated with tumor invasion and correlated with poor prognosis. Cell–cell communication analysis further showed significant HGF-MET interaction between inflammatory cancer–associated fibroblasts (iCAFs) and basal-like tumor cells. We found that iCAFs were the major source of HGF in tumor environment and contributed to the basal-like phenotype formation of tumor cells by HGF-MET axis.

Conclusions

We identified an aggressive basal-like tumor cell subpopulation, which correlated with poor prognosis in ICC. The MET pathway contributes to the aggressiveness of basal-like tumor cells and serves as a novel therapeutic target for ICC.