DEFB1 + Cancer Cell– IFI30 + Macrophage Crosstalk Drives Immunosuppressive Niche in Intrahepatic Cholangiocarcinoma

Abstract

Intrahepatic cholangiocarcinoma (ICC) is a rare but highly aggressive primary liver malignancy distinguished by a profoundly heterogeneous tumor microenvironment, which underlies its limited response to targeted and immune-based therapies. Deciphering the cellular composition and intercellular signaling within this complex ecosystem is critical to understanding ICC progression and to identifying actionable therapeutic targets. Here, we integrated single-cell RNA sequencing and spatial transcriptomics to construct a comprehensive cellular and transcriptional atlas of human ICC. Our analyses revealed a continuous trajectory of T-cell state transition from activation to exhaustion, with CD8  + proliferating T cells exhibiting two distinct exhaustion programs, namely terminal and progenitor-like exhaustion. Notably, DEFB1  + cholangiocytes and IFI30  + macrophages displayed a strong positive correlation across independent ICC cohorts and were found in close spatial proximity within the tumor microenvironment. Mechanistically, their interaction was predicted to involve the TGFB1–TGFBR1 signaling axis, which may contribute to tumor progression and immunotherapy resistance. Together, these findings delineate the cellular architecture and spatial organization of the ICC microenvironment, uncovering a key cholangiocyte–macrophage axis that shapes immune dysfunction and offers a potential therapeutic entry point to enhance immunotherapy efficacy in ICC.