Bioinformatics analysis of gene expression profile of peripheral blood mononuclear cells in female patients with osteoarthritis
- VernacularTitle:女性骨关节炎患者外周血单个核细胞基因表达谱的生物信息学分析
- Author:
Wei YANG
1
;
Puwei YUAN
2
;
Longlong DU
2
;
Qingmin HAN
3
Author Information
- Publication Type:Journal Article
- Keywords: osteoarthritis; peripheral blood mononuclear cells （PBMCs）; gene set enrichment analysis （GSEA）; apoptosis; inflammation
- From: Journal of Xi'an Jiaotong University(Medical Sciences) 2022;43(3):373-382
- CountryChina
- Language:Chinese
- Abstract: 【Objective】 Through bioinformatics methods to analyze the differences in the gene expression profiles of peripheral blood mononuclear cells （PBMCs） between middle-aged and elderly women and normal people， so as to explore the diagnosis and treatment targets of OA. 【Methods】 We downloaded the GSE48556 data set from GEO databases. We utilized the R language to screen out the differentially expressed genes （DEGs） between OA and NC. By gene set enrichment analysis （GSEA）， we obtained the target gene subset. The GO and KEGG pathways of the target gene subset were analyzed by DAVID. We applied STRING and Cytoscape software to construct PPI network. The module analysis was performed by the Mcode and centiscape plug-in， and the key genes were screened out by Cytohubba. 【Results】 By GSEA analysis and P.adjust <0.05 & |log2FC| >0.2， a total of 292 target genes were screened， consisting of 81 upregulated genes and 211 downregulated genes. The GO enrichment analysis of all target genes mainly focused on the biological functions， such as “regulation of NIK/NF-κB”， “monocytes”， “proliferation”， “regulation of apoptosis signaling pathway”， “TNF-mediated signaling pathway”， “regulation of Wnt signaling pathway”， “regulation of MAP kinase activity”， and “regulation of autophagy”. KEGG was mainly enriched in four pathways： cytotoxicity of natural killer cell mediation， TNF signaling pathway， MAPK signaling pathway， and apoptosis. We employed PPI network and related plug-ins to screen out eight core genes highly related to OA inflammation and apoptosis， namely， MAPK1， IL10， PTGS2， IL18， GSK3B， NFKBIA， TNFRSF1A， and EGR1. 【Conclusion】 Bioinformatics analysis revealed that the differences in PBMCs gene expressions between OA and NC were concentrated in the biological events of apoptosis and inflammation， making blood expression profile an effective breakthrough for monitoring OA target markers.
