Abstract LT09: Integrative Multi-Omics Enhancer Activity Profiling Identifies Therapeutic Vulnerabilities in Cholangiocarcinoma of Different Etiologies
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 , Ng Sheng Rong , Yao Xiaosai , Wang Peili , Xiao Rong , Zeng Xian , Sun Yichen , Liu Wei , Koh Joanna , Wee Felicia Yu Ting , Lim Jeffrey Chun Tatt , Ng Cedric Chuan Young , Kwek Xiu Yi , 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 
Published: April 2024

Objectives: Cholangiocarcinoma (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.

Design: Integrative multi-omics enhancer activity profiling of diverse CCA was performed. A panel of diverse CCA cell lines, and 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 immunogenicity of diverse CCA.

Results: We identified 3 distinct groups, associated with different etiologies and unique pathways. Drug inhibitors of identified pathways reduced tumor growth in in-vitro and in-vivo models. The first group (ESTRO), with mostly fluke-associated CCAs, displayed activation in estrogen signaling and were sensitive to MTOR inhibitors. Another group (OXPHO), with mostly BAP1 and IDH-mutant CCAs, displayed activated oxidative phosphorylation pathways, and were sensitive 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. Intra-tumor differences in AA mutation load were correlated to intra-tumor variation of different immune cell populations.

Conclusion: Our study elucidates the mechanisms underlying enhancer dysregulation and deepens understanding of different tumorigenesis processes in distinct CCA subtypes, with potential significant therapeutics and clinical benefits.

Citation Format: Jing Han Hong, Chern Han Yong, Hong Lee Heng, Jason Yongsheng Chan, Mai Chan Lau, Jianfeng Chen, Jing Yi Lee, Abner Herbert Lim, Zhimei Li, Peiyong Guan, Pek Lim Chu, Sheng Rong Ng, Xiaosai Yao, Peili Wang, Rong Xiao, Xian Zeng, Yichen Sun, Wei Liu, Joanna Koh, Felicia Yu Ting Wee, Jeffrey Chun Tatt Lim, Cedric Chuan Young Ng, Xiu Yi Kwek, Poramate Klanrit, Yaojun Zhang, Jiaming Lai, David Wai Meng Tai, Chawalit Pairojkul, Simona Dima, Irinel Popescu, Sen-Yung Hsieh, Ming-Chin Yu, Joe Yeong, Sarinya Kongpetch, Apinya Jusakul, Watcharin Loilome, Patrick Tan, Jing Tan, Bin Tean Teh. Integrative Multi-Omics Enhancer Activity Profiling Identifies Therapeutic Vulnerabilities in Cholangiocarcinoma of Different Etiologies [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr LT09.