Background Pulmonary fibroblast to myofibroblast trans-differentiation is a critical symbol of silicosis progression from inflammation to fibrosis, among which transforming growth factorbeta 1 (TGF-β1) is the most important cytokine. In recent years, with the development of highthroughput sequencing and microarray, more and more TGF-β1-induced fibroblast trans-differentiation data have been concerned.
Objective The current study is designed to explore and screen differentially expressed genes (DEGs) and hub transcription factors (TFs) in trans-differentiation of pulmonary fibroblasts induced by TGF-β1 through bioinformatics strategies.
Methods GSE17518, GSE97829, and GSE119007 datasets linking TGF-β1 and pulmonary fibroblasts were downloaded from Gene Expression Omnibus (GEO) database to screen upregulated and downregulated DEGs. Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to the selected DEGs. All obtained DEGs sequences were blast with the TFs sequences downloaded from HumanTFDB database. The selected genes of TFs were validated in TGF-β1 stimulated MRC-5 cells.
Results Altogether 145 upregulated DEGs and 88 downregulated DEGs were gained based on the three datasets. The results of GO functional enrichment analysis were mostly enriched in extracellular matrix organization, actin cytoskeleton, endoplasmic reticulum cavity, and other components; they were related to biological processes such as actin binding, growth factor activity, extracellular matrix structural components, collagen binding, and TGF-β1 receptor binding; in addition, they were also related to extracellular matrix tissue, cell migration and apoptosis, mitogen-activated protein kinase (MAPK) pathway activation, MAPK activation, and positive regulation of peptide tyrosine phosphorylation. The results of KEGG pathway enrichment analysis were significantly enriched in TGF-β1 signaling pathway, extracellular matrix-receptor interaction, focal adhesion, and phosphoinositide 3-kinase-protein kinase B (PI3K-Akt) signaling pathway, etc. After comparing with the sequences downloaded from HumanTFDB, 7 upregulated TFs and 11 downregulated TFs were obtained. Early growth response 2 (EGR2), SNAIL family transcriptional repressor 1 (SNAIL1), thymocyte selection-associated high mobility group box protein (TOX), and peroxisome proliferators-activated receptor gamma (PPARG) were validated by qRT-PCR in TGF-β1 stimulated MRC-5 cells, and the results showed that EGR2 and SNAIL1 were upregulated, and TOX and PPARG were downregulated.
Conclusion Among the 18 screened genes of TFs related to pulmonary fibrosis trans-differentiation, EGR2 and SNAIL1 are upregulated, and TOX and PPARG are downregulated in TGF-β1 stimulated MRC-5 cells.
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