Molecular Subgroups of Intrahepatic Cholangiocarcinoma Discovered by Single-Cell RNA Sequencing-Assisted Multiomics Analysis.

Abstract

Intrahepatic cholangiocarcinoma (ICC) is a relatively rare but highly aggressive tumor type that responds poorly to chemotherapy and immunotherapy. Comprehensive molecular characterization of ICC is essential for the development of novel therapeutics. Here, we constructed two independent cohorts from two clinic centers. A comprehensive multiomics analysis of ICC via proteomic, whole-exome sequencing (WES), and single-cell RNA sequencing (scRNA-seq) was performed. Novel ICC tumor subtypes were derived in the training cohort (n = 110) using proteomic signatures and their associated activated pathways, which were further validated in a validation cohort (n = 41). Three molecular subtypes, chromatin remodeling, metabolism, and chronic inflammation, with distinct prognoses in ICC were identified. The chronic inflammation subtype was associated with a poor prognosis. Our random forest algorithm revealed that mutation of lysine methyltransferase 2D (KMT2D) frequently occurred in the metabolism subtype and was associated with lower inflammatory activity. scRNA-seq further identified an APOE+C1QB+ macrophage subtype, which showed the capacity to reshape the chronic inflammation subtype and contribute to a poor prognosis in ICC. Altogether, with single-cell transcriptome-assisted multiomics analysis, we identified novel molecular subtypes of ICC and validated APOE+C1QB+ tumor-associated macrophages as potential immunotherapy targets against ICC.

• Authors: Xuanwen Bao, Qiong Li, Jinzhang Chen, Diyu Chen, Chanqi Ye, Xiaomeng Dai, Yanfang Wang, Xin Li, Xiaoxiang Rong, Fei Cheng, Ming Jiang, Zheng Zhu, Yongfeng Ding, Rui Sun, Chuan Liu, Lingling Huang, Yuzhi Jin, Bin Li, Juan Lu, Wei Wu, Yixuan Guo, Wenguang Fu, Sarah Raye Langley, Vincent Tano, Weijia Fang, Tiannan Guo, Jianpeng Sheng, Peng Zhao, Jian Ruan
• Journal: Cancer immunology research (Cancer Immunol Res) Vol. 10 Issue 7 Pg. 811-828 (07 01 2022) ISSN: 2326-6074 [Electronic] United States
• PMID: 35604302 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: ©2022 American Association for Cancer Research.

Chemical References

• Apolipoproteins E

Topics

• Apolipoproteins E
• Bile Duct Neoplasms (genetics, metabolism, pathology)
• Bile Ducts, Intrahepatic (metabolism, pathology)
• Cholangiocarcinoma (genetics, metabolism, pathology)
• Humans
• Inflammation (pathology)
• Prognosis
• Proteomics
• Sequence Analysis, RNA
• Exome Sequencing