A potential three-gene-based diagnostic signature for idiopathic pulmonary fibrosis

Frontiers in Genetics

Genetics

Lin Zhong¹  Li Qiu¹  Lina Chen¹  Yi Wu¹  Liqun Dong¹  Lin Yang¹ 

[1] Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China;Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China;NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China;

关键词: idiopathic pulmonary fibrosis;    diagnostic biomarkers;    WGCNA;    bioinformatics analysis;    differentially expressed genes;   

DOI  :  10.3389/fgene.2022.985217

 received in 2022-07-03, accepted in 2022-11-30,  发布年份 2023

来源: Frontiers

【 摘 要 】

Background: Idiopathic pulmonary fibrosis (IPF) is a life-threatening disease whose etiology remains unknown. This study aims to explore diagnostic biomarkers and pathways involved in IPF using bioinformatics analysis.Methods: IPF-related gene expression datasets were retrieved and downloaded from the NCBI Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened, and weighted correlation network analysis (WGCNA) was performed to identify key module and genes. Functional enrichment analysis was performed on genes in the clinically significant module. Then least absolute shrinkage and selection operator (LASSO) logistic regression and support vector machine-recursive feature elimination (SVM-RFE) algorithms were run to screen candidate biomarkers. The expression and diagnostic value of the biomarkers in IPF were further validated in external test datasets (GSE110147).Results: 292 samples and 1,163 DEGs were screened to construct WGCNA. In WGCNA, the blue module was identified as the key module, and 59 genes in this module correlated highly with IPF. Functional enrichment analysis of blue module genes revealed the importance of extracellular matrix-associated pathways in IPF. IL13RA2, CDH3, and COMP were identified as diagnostic markers of IPF via LASSO and SVM-RFE. These genes showed good diagnostic value for IPF and were significantly upregulated in IPF.Conclusion: This study indicates that IL13RA2, CDH3, and COMP could serve as diagnostic signature for IPF and might offer new insights in the underlying diagnosis of IPF.

【 授权许可】

Unknown   
Copyright © 2023 Wu, Zhong, Qiu, Dong, Yang and Chen.