Page 59 - GPD-3-4

Gene & Protein in Disease

ORIGINAL RESEARCH ARTICLE
Bioinformatics analysis of therapeutic targets for

idiopathic pulmonary fibrosis and exploration of
immune cell infiltration patterns

Zhendong Lu , Umair Ali Khan Saddozai 2 , Siyun Fu , Lingqin Zhu , and
1
1
3
Jinghui Wang *
1,3
1 Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute,
Beijing Chest Hospital, Capital Medical University, Beijing, China
2 Department of Clinical Medicine, Institute of Translational Medicine, Medical College, Yangzhou
University, Yangzhou, Jiangsu, China
3 Cancer Research Center, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing
Chest Hospital, Capital Medical University, Beijing, China

Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe progressive lung disease
characterized by fibrotic changes in lung tissue, with limited treatment options.
This study analyzed gene expression data from three gene expression omnibus
datasets (GSE2052, GSE53845, and GSE110147) using R and LIMMA to identify
differentially expressed genes (DEGs) in IPF samples. We identified 215 DEGs,
comprising 106 upregulated and 109 downregulated genes. Weighted gene
coexpression network analysis revealed five gene modules, with the module
*Corresponding author: eigengene yellow showing the strongest correlation with IPF. Functional
Jinghui Wang
(wangjinghui@bjxkyy.cn) enrichment analysis of 40 consensus genes in this module indicated their
significant involvement in extracellular matrix (ECM) organization. Kyoto
Citation: Lu Z, Saddozai UAK,
Fu S, Zhu L, Wang J. Encyclopedia of Genes and Genomes pathway analysis revealed pathways
Bioinformatics analysis of related to protein digestion, cell adhesion molecules, and the advanced glycation
therapeutic targets for idiopathic end product–receptor for advanced glycation end product signaling pathway.
pulmonary fibrosis and exploration
of immune cell infiltration patterns. Based on protein–protein interaction network analysis, collagen type XV alpha
Gene Protein Dis. 2024;3(4):4101. 1 chain (COL15A1) and collagen type VI alpha 3 chain (COL6A3) were identified
doi: 10.36922/gpd.4101 as upregulated hub genes in IPF, which were regulated by microRNAs and
Received: July 1, 2024 transcription factors. Immune cell infiltration analysis showed significant
Accepted: August 13, 2024 changes in immune cell populations in IPF samples, with increases in memory B
Published Online: October 10, 2024 cells, plasma cells, and M0 macrophages and decreases in CD8 T cells, and resting
Copyright: © 2024 Author(s). natural killer cells. Potential drugs targeting COL15A1 and COL6A3 were predicted
This is an Open-Access article using multiple databases, revealing compounds such as (+)-JQ1, aristolochic acid
distributed under the terms of the
Creative Commons Attribution I, and dexamethasone with promising binding potential. These findings suggest
License, permitting distribution, that COL15A1 and COL6A3 are central hub genes in IPF, are associated with ECM
and reproduction in any medium, organization and immune response, and serve as therapeutic targets for IPF.
provided the original work is
properly cited.
Publisher’s Note: AccScience Keywords: Idiopathic pulmonary fibrosis; Weighted gene coexpression network analysis;
Publishing remains neutral with Immune cell infiltration; MicroRNA-transcription factor-mRNA network; Molecular
regard to jurisdictional claims in
published maps and institutional docking
affiliations.

Volume 3 Issue 4 (2024) 1 doi: 10.36922/gpd.4101