Integrative multiomics enhancer activity profiling identifies therapeutic vulnerabilities in cholangiocarcinoma of different etiologies

• Published in: Gut Vol. 73; no. 6; pp. 966 - 984
• Main Authors: Hong, Jing Han, Yong, Chern Han, Heng, Hong Lee, Chan, Jason Yongsheng, Lau, Mai Chan, Chen, Jianfeng, Lee, Jing Yi, Lim, Abner Herbert, Li, Zhimei, Guan, Peiyong, Chu, Pek Lim, Boot, Arnoud, Ng, Sheng Rong, Yao, Xiaosai, Wee, Felicia Yu Ting, Lim, Jeffrey Chun Tatt, Liu, Wei, Wang, Peili, Xiao, Rong, Zeng, Xian, Sun, Yichen, Koh, Joanna, Kwek, Xiu Yi, Ng, Cedric Chuan Young, Klanrit, Poramate, Zhang, Yaojun, Lai, Jiaming, Tai, David Wai Meng, Pairojkul, Chawalit, Dima, Simona, Popescu, Irinel, Hsieh, Sen-Yung, Yu, Ming-Chin, Yeong, Joe, Kongpetch, Sarinya, Jusakul, Apinya, Loilome, Watcharin, Tan, Patrick, Tan, Jing, Teh, Bin Tean
• Format: Journal Article
• Language: English
• Published: England BMJ Publishing Group Ltd and British Society of Gastroenterology 01.06.2024; BMJ Publishing Group LTD
• Subjects: Animals; Aristolochic acid; Bile Duct Neoplasms - drug therapy; Bile Duct Neoplasms - genetics; Bile Duct Neoplasms - metabolism; Bile Duct Neoplasms - pathology; CANCER; Cancer therapies; Carcinogenesis; Cell Line, Tumor; Chemotherapy; CHOLANGIOCARCINOMA; Cholangiocarcinoma - drug therapy; Cholangiocarcinoma - genetics; Cholangiocarcinoma - metabolism; Cholangiocarcinoma - pathology; DNA methylation; Epigenetics; Estrogens; Etiology; Gene expression; Gene Expression Profiling - methods; Hepatology; Humans; Immunogenicity; Immunohistochemistry; Infections; Liver; Malignancy; Mice; MOLECULAR ONCOLOGY; Multiomics; Mutation; Oxidative phosphorylation; Phosphorylation; Population studies; Signal transduction; Therapeutic targets; TOR protein; Transcriptomics; Tumorigenesis; Tumors; CHOLANGIOCARCINOMA; CANCER; MOLECULAR ONCOLOGY
• ISSN: 0017-5749; 1468-3288; 1468-3288
• DOI: 10.1136/gutjnl-2023-330483

ObjectivesCholangiocarcinoma (CCA) is a heterogeneous malignancy with high mortality and dismal prognosis, and an urgent clinical need for new therapies. Knowledge of the CCA epigenome is largely limited to aberrant DNA methylation. Dysregulation of enhancer activities has been identified to affect carcinogenesis and leveraged for new therapies but is uninvestigated in CCA. Our aim is to identify potential therapeutic targets in different subtypes of CCA through enhancer profiling.DesignIntegrative multiomics enhancer activity profiling of diverse CCA was performed. A panel of diverse CCA cell lines, patient-derived and cell line-derived xenografts were used to study identified enriched pathways and vulnerabilities. NanoString, multiplex immunohistochemistry staining and single-cell spatial transcriptomics were used to explore the immunogenicity of diverse CCA.ResultsWe identified three distinct groups, associated with different etiologies and unique pathways. Drug inhibitors of identified pathways reduced tumour growth in in vitro and in vivo models. The first group (ESTRO), with mostly fluke-positive CCAs, displayed activation in estrogen signalling and were sensitive to MTOR inhibitors. Another group (OXPHO), with mostly BAP1 and IDH-mutant CCAs, displayed activated oxidative phosphorylation pathways, and were sensitive to oxidative phosphorylation inhibitors. Immune-related pathways were activated in the final group (IMMUN), made up of an immunogenic CCA subtype and CCA with aristolochic acid (AA) mutational signatures. Intratumour differences in AA mutation load were correlated to intratumour variation of different immune cell populations.ConclusionOur study elucidates the mechanisms underlying enhancer dysregulation and deepens understanding of different tumourigenesis processes in distinct CCA subtypes, with potential significant therapeutics and clinical benefits.