Bioinformatics Analysis Identifies Potential Key Genes of Peripheral Blood Mononuclear Cell in Idiopathic Pulmonary Fibrosis

Lijun Liu,Yi Wu,Daxia Cai

doi:10.11648/j.cbb.20200802.17

Abstract

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic interstitial pneumonia with progressive worsening of dyspnea and lung function. The etiology of IPF is unknown, and the pathogenesis remains unclear. Our study aimed to investigate the key genes of the peripheral blood mononuclear cell in IPF by bioinformatics analysis. Our study used the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE28042 to identify differentially expressed genes (DEGs) between IPF patients and healthy controls. We performed the Gene Ontology (GO) and pathway enrichment analyses of genes for annotation, visualization, and integrated discovery. The STRING database constructed Protein-protein interaction (PPI) network analysis, and hub genes were identified by the CytoHubba plugin. Moreover, we used the receiver operating characteristic (ROC) curve to assess the diagnostic value of the hub genes. In total, 28 upregulated and 44 downregulated genes were identified in the differential expression analysis. The protein-protein interaction network (PPI) was established with 69 nodes and 68 edges. The top 10 hub genes were JUN, FOS, STAT3, SOCS3, JUNB, DUSP1, IL4, FCER1A, MS4A2, and CPA3. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched for the important module containing hub genes contained Fc epsilon RI signaling pathway, TNF signaling pathway, Jak-STAT signaling pathway, and MAPK signaling pathway. Additionally, the identified hub genes show high functional similarity and diagnostic value in IPF. Our study used bioinformatics analysis to provide new insight into the mechanisms underlying IPF. However, more experiments are needed to explore the relationships between the top 10 hub genes and IPF in the future.

Highlights

Idiopathic pulmonary fibrosis (IPF) is defined as a specific form of chronic, progressive fibrosing interstitial pneumonia and its cause is unknown [1]
107 upregulated and 244 downregulated genes were identified between male IPF patients and male healthy controls
54 upregulated and 212 downregulated genes were identified between female IPF patients and female healthy controls

Summary

Introduction

Idiopathic pulmonary fibrosis (IPF) is defined as a specific form of chronic, progressive fibrosing interstitial pneumonia and its cause is unknown [1]. Its clinical features are unexplained exertional dyspnea, chronic dry cough, or Velcro rale on examination [2]. The histopathology of this disease is interstitial fibrosis with spatial heterogeneity and patchy involvement of lung parenchyma, and microscopic honeycombing [3]. The incidence of IPF is high and its incidence rates increased over time in most countries. Median survival from the time of diagnosis is only 2.5 to 3.5 years [5]. The risk factors of IPF are environmental, genetic, epigenetic alterations, and aging [6].

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