Identification of RNF213 as a potential suppressor of local invasion in intrahepatic cholangiocarcinoma

Khajeelak Chiablaem; Artit Jinawath; Jiratchaya Nuanpirom; Jantarika Kumar Arora; Sirawit Nasaree; Thanastha Thanomchard; Nilubon Singhto; Pamorn Chittavanich; Bhoom Suktitipat; Varodom Charoensawan; Arthit Chairoungdua; Jim Jinn-Chyuan Sheu; Kazuma Kiyotani; Jisnuson Svasti; Yusuke Nakamura; Natini Jinawath

doi:10.1016/j.labinv.2024.102074

Identification of RNF213 as a potential suppressor of local invasion in intrahepatic cholangiocarcinoma

Lab Invest. 2024 May 7:102074. doi: 10.1016/j.labinv.2024.102074. Online ahead of print.

Authors

Khajeelak Chiablaem¹, Artit Jinawath², Jiratchaya Nuanpirom³, Jantarika Kumar Arora⁴, Sirawit Nasaree⁵, Thanastha Thanomchard⁶, Nilubon Singhto⁶, Pamorn Chittavanich⁵, Bhoom Suktitipat⁷, Varodom Charoensawan⁸, Arthit Chairoungdua⁹, Jim Jinn-Chyuan Sheu¹⁰, Kazuma Kiyotani¹¹, Jisnuson Svasti¹², Yusuke Nakamura¹³, Natini Jinawath¹⁴

Affiliations

¹ Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand.
² Molecular Histopathology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
³ Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand.
⁴ Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
⁵ Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
⁶ Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
⁷ Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand; Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
⁸ Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
⁹ Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand.
¹⁰ Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹¹ Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
¹² Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand.
¹³ Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan; National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
¹⁴ Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand; Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bang Phli, Samut Prakan, Thailand. Electronic address: jnatini@hotmail.com.

PMID: 38723854
DOI: 10.1016/j.labinv.2024.102074

Abstract

Intrahepatic cholangiocarcinoma (ICC) is a lethal cancer with poor survival especially when it spreads. The histopathology of its rare intraductal papillary neoplasm of the bile duct type (IPNB) characteristically shows cancer cells originating within the confined bile duct space. These cells eventually invade and infiltrate the nearby liver tissues, making it a good model to study the mechanism of local invasion, which is the earliest step of metastasis. To discover potential suppressor genes of local invasion in ICC, we analyzed the somatic mutation profiles and performed clonal evolution analyses of the 11 pairs of macrodissected IPNB tissues with local invasion (LI-IPNB) and IPNB tissues without local invasion from the same patients. We identified a protein-truncating variant (PTV) in an E3 ubiquitin ligase, RNF213 (c.6967C>T; p.Gln2323X; chr17: 78,319,102 [hg19], exon 29), as the most common PTV event in LI-IPNB samples (4/11 patients). Knockdown of RNF213 in HuCCT1 and YSCCC cells showed increased migration and invasion, and reduced vasculogenic mimicry, but maintained normal proliferation. Transcriptomic analysis of the RNF213-knockdown versus control cells was then performed in the HuCCT1, YSCCC, and KKU-100 cells. Gene Ontology (GO) enrichment analysis of the common differentially expressed genes revealed significantly altered cytokine and oxidoreductase-oxidizing metal ions activities, as confirmed by western blotting. Gene Set Enrichment Analysis (GSEA) identified the most enriched pathways being oxidative phosphorylation, fatty acid metabolism, reactive oxygen species, adipogenesis, and angiogenesis. In sum, loss of function of RNF213 is a common genetic alteration in LI-IPNB tissues. RNF213 knockdown leads to increased migration and invasion of ICC cells, potentially through malfunctions of the pathways related inflammation, and energy metabolisms.

Keywords: Clonal evolution; Intraductal papillary neoplasm of the bile duct; Intrahepatic cholangiocarcinoma; Local invasion; RNF213; Somatic mutation.