Yang YC, Ma X, Zhou C, Xu N, Ding D, Ma ZZ, Zhou L, Cui PY. Functional investigation and two-sample Mendelian randomization study of primary biliary cholangitis hub genes. World J Clin Cases 2024; 12(30): 6391-6406 [DOI: 10.12998/wjcc.v12.i30.6391]
Corresponding Author of This Article
Pei-Yuan Cui, MD, Chief Doctor, Department of General Surgery, The First Affiliated Hospital of Bengbu Medical College, No. 287 Changhuai Road, Longzihu District, Bengbu 233000, Anhui Province, China. cpy666@126.com
Research Domain of This Article
Medicine, Research & Experimental
Article-Type of This Article
Clinical and Translational Research
Open-Access Policy of This Article
This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (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: http://creativecommons.org/licenses/by-nc/4.0/
World J Clin Cases. Oct 26, 2024; 12(30): 6391-6406 Published online Oct 26, 2024. doi: 10.12998/wjcc.v12.i30.6391
Functional investigation and two-sample Mendelian randomization study of primary biliary cholangitis hub genes
Yun-Chuan Yang, Xiang Ma, Chi Zhou, Nan Xu, Ding Ding, Zhong-Zheng Ma, Lei Zhou, Pei-Yuan Cui
Yun-Chuan Yang, Xiang Ma, Chi Zhou, Nan Xu, Ding Ding, Zhong-Zheng Ma, Lei Zhou, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical University, Bengbu 233000, Anhui Province, China
Yun-Chuan Yang, Xiang Ma, Medical College, Jinan University, Guangzhou 510000, Guangdong Province, China
Pei-Yuan Cui, Department of General Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China
Author contributions: Yang YC, Ma X, and Zhou C substantially contributed to the study conception and design and made revisions to the manuscript; Xu N, Ma ZZ, and Ding D were responsible for data collection, analysis, and manuscript writing; Zhou L and Cui PY made critical revisions; All authors assume full responsibility for the integrity and accuracy of the work, and any relevant queries were addressed and resolved appropriately, reviewed and approved the final manuscript.
Supported bySchool-Level Key Projects at Bengbu Medical College, No. 2021byzd109.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Open-Access: This is an open-access article that was selected by an in-house editor and comprehensively peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non-Commercial (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: https://creativecommons.org/licenses/by-nc/4.0/
Corresponding author: Pei-Yuan Cui, MD, Chief Doctor, Department of General Surgery, The First Affiliated Hospital of Bengbu Medical College, No. 287 Changhuai Road, Longzihu District, Bengbu 233000, Anhui Province, China. cpy666@126.com
Received: May 7, 2024 Revised: July 3, 2024 Accepted: August 22, 2024 Published online: October 26, 2024 Processing time: 119 Days and 13 Hours
Abstract
BACKGROUND
The identification of specific gene expression patterns is crucial for understanding the mechanisms underlying primary biliary cholangitis (PBC) and finding relevant biomarkers for diagnosis and therapeutic evaluation.
AIM
To determine PBC-associated hub genes and assess their clinical utility for disease prediction.
METHODS
PBC expression data were obtained from the Gene Expression Omnibus database. Overlapping genes from differential expression analysis and weighted gene co-expression network analysis (WGCNA) were identified as key genes for PBC. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses were performed to explore the potential roles of key genes. Hub genes were identified in protein-protein interaction (PPI) networks using the Degree algorithm in Cytoscape software. The relationship between hub genes and immune cells was investigated. Finally, a Mendelian randomization study was conducted to determine the causal effects of hub genes on PBC.
RESULTS
We identified 71 overlapping key genes using differential expression analysis and WGCNA. These genes were primarily enriched in pathways related to cytokine-cytokine receptor interaction, and Th1, Th2, and Th17 cell differentiation. We utilized Cytoscape software and identified five hub genes (CD247, IL10, CCL5, CCL3, and STAT3) in PPI networks. These hub genes showed a strong correlation with immune cell infiltration in PBC. However, inverse variance weighting analysis did not indicate the causal effects of hub genes on PBC risk.
CONCLUSION
Hub genes can potentially serve as valuable biomarkers for PBC prediction and treatment, thereby offering significant clinical utility.
Core Tip: This study identified five hub genes (CD247, IL10, CCL5, CCL3, and STAT3) associated with primary biliary cholangitis (PBC) through comprehensive bioinformatics analysis. These hub genes were enriched in immune-related pathways and strongly correlated with immune cell infiltration in PBC. Although hub genes did not have a causal effect on PBC risk, they provided valuable insights into the molecular mechanisms of PBC and showed potential as biomarkers for PBC prediction and treatment.
