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Liu W, Wang H, Zhao Q, Tao C, Qu W, Hou Y, Huang R, Sun Z, Zhu G, Jiang X, Fang Y, Gao J, Wu X, Yang Z, Ping R, Chen J, Yang R, Chu T, Zhou J, Fan J, Tang Z, Yang D, Shi Y. Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma. Cancer Commun (Lond) 2024; 44:226-250. [PMID: 38143235 PMCID: PMC10876206 DOI: 10.1002/cac2.12513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/23/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous and lethal hepatobiliary tumor with few therapeutic strategies. The metabolic reprogramming of tumor cells plays an essential role in the development of tumors, while the metabolic molecular classification of iCCA is largely unknown. Here, we performed an integrated multiomics analysis and metabolic classification to depict differences in metabolic characteristics of iCCA patients, hoping to provide a novel perspective to understand and treat iCCA. METHODS We performed integrated multiomics analysis in 116 iCCA samples, including whole-exome sequencing, bulk RNA-sequencing and proteome analysis. Based on the non-negative matrix factorization method and the protein abundance of metabolic genes in human genome-scale metabolic models, the metabolic subtype of iCCA was determined. Survival and prognostic gene analyses were used to compare overall survival (OS) differences between metabolic subtypes. Cell proliferation analysis, 5-ethynyl-2'-deoxyuridine (EdU) assay, colony formation assay, RNA-sequencing and Western blotting were performed to investigate the molecular mechanisms of diacylglycerol kinase α (DGKA) in iCCA cells. RESULTS Three metabolic subtypes (S1-S3) with subtype-specific biomarkers of iCCA were identified. These metabolic subtypes presented with distinct prognoses, metabolic features, immune microenvironments, and genetic alterations. The S2 subtype with the worst survival showed the activation of some special metabolic processes, immune-suppressed microenvironment and Kirsten rat sarcoma viral oncogene homolog (KRAS)/AT-rich interactive domain 1A (ARID1A) mutations. Among the S2 subtype-specific upregulated proteins, DGKA was further identified as a potential drug target for iCCA, which promoted cell proliferation by enhancing phosphatidic acid (PA) metabolism and activating mitogen-activated protein kinase (MAPK) signaling. CONCLUSION Via multiomics analyses, we identified three metabolic subtypes of iCCA, revealing that the S2 subtype exhibited the poorest survival outcomes. We further identified DGKA as a potential target for the S2 subtype.
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Affiliation(s)
- Weiren Liu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Huqiang Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Qianfu Zhao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Chenyang Tao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Weifeng Qu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Yushan Hou
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Run Huang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zimei Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Guiqi Zhu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Xifei Jiang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Yuan Fang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jun Gao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Xiaoling Wu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zhixiang Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Rongyu Ping
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Jiafeng Chen
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Rui Yang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Tianhao Chu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jian Zhou
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jia Fan
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zheng Tang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Dong Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Yinghong Shi
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
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