Weighted gene co-expression network analysis to investigate the key genes implicated in global brain ischemia/reperfusion injury in rats.

Abstract

Ischemia/reperfusion (I/R) refers to situations where blood is perfused into ischemic or hypoxic tissues, potentially resulting in an inflammatory response and oxidative injury. This study was conducted to explore the pathogenesis of I/R injury. GSE82146 was extracted from the Gene Expression Omnibus, consisting of 15 complete global brain ischemia (CGBI) reperfusion hippocampus samples and 12 non-ischemic control (NIC) hippocampus samples. The differentially expressed genes (DEGs) between the CGBI and NIC samples were selected using LIMMA package, and were then analyzed with weighted gene co-expression network analysis (WGCNA). Using DAVID software, the DEGs in significant modules were run through enrichment analysis. The DEGs in significant modules were merged, and then a protein-protein interaction (PPI) network was built for them using Cytoscape software. After miRNAs and transcription factors (TFs) were predicted for the DEGs using the WebGestalt tool, a TF-miRNA-target regulatory network was built using Cytoscape software. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was conducted to detect the levels of key genes. There were 390 DEGs in the CGBI samples. Based on WGCNA, brown and turquoise modules were screened as CGBI-associated modules. In the PPI network, key nodes HSP90AA1 and HSPA5 were able to interact with each other. In the regulatory network, MYC, HSF1 and miR-22 had higher degree values. Moreover, HSPA5 was targeted by MYC in the regulatory network. In addition, upregulated HSPB1 and HMOX1, as well as downregulated NR4A2, were confirmed with qRT-PCR analysis. HSPB1, HMOX1 and NR4A2 were the key genes correlated with I/R injury. Additionally, HSP90AA1, HSPA5, MYC, HSF1, and miR-22 might be related to the pathogenesis of I/R injury.