Spatial and Single-Cell Transcriptomics Decipher the Crosstalk Environment of DEFB1 ⁺ Cancer Cells and IFI30 ⁺ Macrophages in Intrahepatic Cholangiocarcinoma

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 appears to be mediated by the TGFB1 – TGFBR1 signaling pathway, contributing 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.