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Abstract
Objective Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible, high-mortality lung disease, but its pathogenesis is still unclear. Our purpose was to explore potential genes and molecular mechanisms underlying IPF. Methods IPF-related data were obtained from the GSE99621 dataset. Differentially expressed genes (DEGs) were identified between IPF and controls. Their biological functions were analyzed. The relationships between DEGs and microRNAs (miRNAs) were predicted. DEGs and pathways were validated in a microarray dataset. A protein-protein interaction (PPI) network was constructed based on these common DEGs. Western blot was used to validate hub genes in IPF cell models by western blot. Results DEGs were identified for IPF than controls in the RNA-seq dataset. Functional enrichment analysis showed that these DEGs were mainly enriched in immune and inflammatory response, chemokine-mediated signaling pathway, cell adhesion, and other biological processes. In the miRNA-target network based on RNA-seq dataset, we found several miRNA targets among all DEGs, like RAB11FIP1, TGFBR3, and SPP1. We identified 304 upregulated genes and 282 downregulated genes in IPF compared to controls both in the microarray and RNA-seq datasets. These common DEGs were mainly involved in cell adhesion, extracellular matrix organization, oxidation-reduction process, and lung vasculature development. In the PPI network, 3 upregulated and 4 downregulated genes could be considered hub genes, which were confirmed in the IPF cell models. Conclusion Our study identified several IPF-related DEGs that could become potential biomarkers for IPF. Large-scale multicentric studies are eagerly needed to confirm the utility of these biomarkers.
Highlights
Idiopathic pulmonary fibrosis (IPF) is a progressive, chronic, irreversible lung disease, characterized by an irreversible decline in lung function, progressive pulmonary scarring, and common interstitial pneumonia [1,2,3]
GPX8 and VCAM1 were both downregulated in IPF cells than controls
We identified IPF-related Differentially expressed genes (DEGs) and analyzed potential pathways by comprehensively analyzing IPFrelated RNA-seq and microarray datasets
Summary
Idiopathic pulmonary fibrosis (IPF) is a progressive, chronic, irreversible lung disease, characterized by an irreversible decline in lung function, progressive pulmonary scarring, and common interstitial pneumonia [1,2,3]. It affects more than 3 million people worldwide [4,5,6,7]. The prognosis of IPF remains poor, and the median survival time of patients is only 2-4 years [8, 9]. It is still challenging to diagnose IPF in BioMed Research International
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