Bioinformatic Analyses of Potential Key Genes in the Pathogenesis of Idiopathic Pulmonary Fibrosis

Purpose: Idiopathic pulmonary fibrosis (IPF) is an advancing, chronic and fatal interstitial lung disease with a poor prognosis and increasing incidence. Our study aimed to learn the molecular mechanisms of IPF progression to gain a better comprehension of IPF at the biological level. Methods: In our study, we used the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE15197 and GSE48149 to identify differentially expressed genes (DEGs) between IPF patients and normal controls. Then, tissue-specific gene expression, functional enrichment, and protein-protein interaction (PPI) network analyses were performed. Results: In total, 183 DEGs were identified in the differential expression analysis, including 56 downregulated genes and 127 upregulated genes. The PPI network analysis and manual screening of tissue-specific gene expression resulted in the identification of 51 tissue-specific expressed DEGs, among which 25 were tissue-specifically expressed in the respiratory system. In addition, functional enrichment and biological process analysis identified 7 upregulated genes (SERPINB5, COL17A1, CLCA2, KRT17, KRT5, CDH3) and 6 downregulated genes (CLDN18, CRTAC1, AGER, SFTPA2, SFTPA1, ABCA3) specifically expressed in the respiratory system and indicated that the processes of extracellular matrix organization, protein digestion, and absorption signaling pathway and hemidesmosome assembly played main roles in the pathogenesis of IPF. Conclusions: This bioinformatic analysis may provide useful information for elucidating novel mechanisms underlying IPF. 13 main DEGs specifically expressed in the respiratory system, which are involved in processes of hemidesmosome assembly, cell-substrate junction assembly, and cell junction assembly, may play main roles in the pathogenesis of progression of IPF.