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bioRxiv · 10.1101/2025.11.22.689892

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

Wang, G.·Meng, H.·Li, M.·Fang, X.·Zou, W.·Qu, H.
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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 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.

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Wang, G., Meng, H., Li, M., Fang, X., Zou, W., Qu, H.. 2025-11-25. Spatial and Single-Cell Transcriptomics Decipher the Crosstalk Environment of DEFB1+ Cancer Cells and IFI30+ Macrophages in Intrahepatic Cholangiocarcinoma. https://doi.org/10.1101/2025.11.22.689892

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