Single-Cell Transcriptomic Analysis Reveals Two Molecularly and Clinically Distinct Subtypes of Intrahepatic Cholangiocarcinoma

Abstract Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous cancer with limited understanding of its classification and tumor microenvironment. Here, we performed single-cell RNA sequencing on 144,878 cells from 14 pairs of iCCA tumors and non-tumor liver tissues. We found that S100P and SPP1 are two reliable markers for iCCA perihilar large duct type (iCCA phl ) and peripheral small duct type (iCCA pps ). S100P + SPP1- iCCA phl has significantly reduced levels of infiltrating CD3 + T cells, CD56 + NK cells, and increased CCL18 + macrophages compared to S100P-SPP1 + iCCA pps . The transcriptor CREB3L1 is identified to regulate the S100P expression and promote tumor cell invasion. S100P-SPP1 + iCCA pps has significantly more SPP1 + macrophage infiltration, less aggressiveness and better survival than S100P + SPP1- iCCA phl . Moreover, S100P-SPP1 + iCCA pps harbors tumor cells at different status of differentiation, such as ALB + hepatocyte differentiation and ID3 + stemness. Our study extends our understanding of the diversity of tumor cells in iCCA and provides clearer understanding of iCCA classification.