Basic Study
Copyright ©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Jul 7, 2023; 29(25): 4053-4071
Published online Jul 7, 2023. doi: 10.3748/wjg.v29.i25.4053
Molecular profiling reveals potential targets in cholangiocarcinoma
Dan Liu, Yang Shi, Hongze Chen, Muhammad Azhar Nisar, Nicholas Jabara, Noah Langwinski, Sophia Mattson, Katsuya Nagaoka, Xuewei Bai, Shaolei Lu, Chiung-Kuei Huang
Dan Liu, Yang Shi, Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
Hongze Chen, Muhammad Azhar Nisar, Nicholas Jabara, Noah Langwinski, Sophia Mattson, Chiung-Kuei Huang, Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, United States
Katsuya Nagaoka, Xuewei Bai, Department of Medicine, Rhode Island Hospital and the Alpert Medical School of Brown University, Providence, RI 02903, United States
Shaolei Lu, Department of Pathology, Alpert Medical School of Brown University, Providence, RI 02903, United States
Author contributions: Huang CK contributed to the study concept and design; Liu D, Shi Y, Chen H, Nisar MA, Jabara N, Langwinski N, Mattson S, Nagaoka K, Bai X and Huang CK contributed to the acquisition of data; Liu D, Shi Y, Bai X, Huang CK and Lu S contributed to analysis and interpretation of data; Liu D, Lu S, Jabara N, Nagaoka K, Chen H and Nisar MA contributed to the technical support; Lu S contributed to the material support; Huang CK and Lu S obtained the funding; Liu D, Shi Y, Huang CK, Lu S and Nisar MA drafted the manuscript; Shi Y, Nisar MA, Huang CK, Lu S, Jabara N, Langwinski N and Mattson S revised the manuscript. Liu D and Shi Y contributed equally.
Supported by 2017 AASLD Pinnacle Research Career Development Award.
Institutional review board statement: All protocols were approved by the Institutional Animal Care and Use Committee (IACUC) at Rhode Island Hospital (CMTT # 5051-18), and all experiments were conducted in accordance with the guidelines of this IACUC.
Conflict-of-interest statement: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Data sharing statement: No additional data are available.
ARRIVE guidelines statement: The authors have read the ARRIVE Guidelines, and the manuscript was prepared and revised according to the ARRIVE Guidelines.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See:
Corresponding author: Chiung-Kuei Huang, PhD, Assistant Professor, Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, United States.
Received: January 21, 2023
Peer-review started: January 21, 2023
First decision: February 1, 2023
Revised: February 16, 2023
Accepted: May 23, 2023
Article in press: May 23, 2023
Published online: July 7, 2023

Cholangiocarcinoma (CCA) is a devastating malignancy and has a very poor prognosis if tumors spread outside the liver. Understanding the molecular mechanisms underlying the CCA progression will likely yield therapeutic approaches toward treating this deadly disease.


To determine the molecular pathogenesis in CCA progression.


In silico analysis, in vitro cell culture, CCA transgenic animals, histological, and molecular assays were adopted to determine the molecular pathogenesis.


The transcriptomic data of human CCA samples were retrieved from The Cancer Genome Atlas (TGCA, CHOL), European Bioinformatics Institute (EBI, GAD00001001076), and Gene Expression Omnibus (GEO, GSE107943) databases. Using Gene set enrichment analysis, the cell cycle and Notch related pathways were demonstrated to be significantly activated in CCA in TCGA and GEO datasets. We, through differentially expressed genes, found several cell cycle and notch associated genes were significantly up-regulated in cancer tissues when compared with the non-cancerous control samples. The associated genes, via quantitative real-time PCR and western blotting assays, were further examined in normal human cholangiocytes, CCA cell lines, mouse normal bile ducts, and mouse CCA tumors established by specifically depleting P53 and expressing KrasG12D mutation in the liver. Consistently, we validated that the cell cycle and Notch pathways are up-regulated in CCA cell lines and mouse CCA tumors. Interestingly, targeting cell cycle and notch pathways using small molecules also exhibited significant beneficial effects in controlling tumor malignancy. More importantly, we demonstrated that several cell cycle and Notch associated genes are significantly associated with poor overall survival and disease-free survival using the Log-Rank test.


In summary, our study comprehensively analyzed the gene expression pattern of CCA samples using publicly available datasets and identified the cell cycle and Notch pathways are potential therapeutic targets in this deadly disease.

Keywords: Bile duct cancer, Notch, Cell cycle, Liver cancer, Therapeutic target

Core Tip: Molecular profiling of cholangiocarcinoma (CCA) has been conducted using various cohorts. However, the identified targets vary among different cohorts. In the current study, we combined different cohorts of CCA RNA sequencing datasets and refined the potential therapeutic targets in human CCA malignancy. We validated the findings using human CCA cell lines, the KrasG12D and P53 mutation transgenic mouse model, and human CCA clinical data, thus supporting the potential of targeting the identified pathways in clinical trials.