Functional investigation and two-sample Mendelian randomization study of primary biliary cholangitis hub genes

doi:10.12998/wjcc.v12.i30.6391

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World Journal of Clinical Cases

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Clinical and Translational Research

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 by School-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.

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.

Keywords: Primary biliary cholangitis; Weighted gene co-expression network analysis; Hub genes; Mendelian randomization; Bioinformatic analysis

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.