Analysis of potential differently expressed genes and miRNAs for sepsis-associated mortality based on GEO database
- VernacularTitle:基于GEO数据库分析脓毒症相关性死亡的潜在差异表达基因和微小RNAs
- Author:
Zhuochen LYU
1
;
Shiyuan LUO
;
Yao TONG
;
Yao ZHOU
;
Ying WANG
Author Information
- Keywords: GEO database; Sepsis-associated mortality; Differential expression genes; MicroRNAs
- From: The Journal of Clinical Anesthesiology 2024;40(11):1184-1191
- CountryChina
- Language:Chinese
- Abstract: Objective To identify the potential differently expressed genes and microRNAs(mi-RNAs)in sepsis survivors and non-survivors through bioinformatics-based research based on gene expression omnibus(GEO).Methods Two gene expression profile microarray datasets of human blood samples(GSE48080 and GSE54514)were downloaded from the GEO database.The differential expression genes(DEGs)between sepsis survivors and non-survivors at two time points(diagnosis of sepsis,course of sep-sis)were screened with the GEO2R online tool.The gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment analysis were used to study the pathophysiological processes and potential signaling pathways involved in sepsis related death DEGs.STRING online tool was used to construct the DEGs protein-protein interaction(PPI).Cytoscape with CytoHubba was used to investigate the potential hub genes.NetworkAnalyst was used to construct targeted miRNAs of the hub genes.Real-time quantitative PCR(RT-qPCR)was established to evaluate the expression of potential hub genes in our sepsis survivors and non-survivors.Results During the course of sepsis,there was heterogeneity in gene expre-ssion between sepsis survivors and non-survivors.Fifteen DEGs were found to be remarkably differentially expressed between sepsis survivors and non-survivors during the course of sepsis.Four KEGG pathways,in-cluding staphylococcus aureus infection,NOD-like receptor signaling pathway,sulfur metabolism and col-lecting duct acid secretion,were significantly enriched.In combination with the results of the PPI network and CytoHubba,ten hub genes(SLC4A1,EPB42,LTF,LCN2,DEFA4,HBM,HBG1,GMPR,CAMP,OLFM4)were selected as potential biomarkers for sepsis-associated mortality.With NetworkAnalyst analysis,ten miRNAs were predicted as potential key miRNAs.RT-qPCR confirmed that the expressions of five of these genes(SLC4A1,EPB42,LCN2,DEFA4,OLFM4)were in accordance with the microarray results.Conclusion Bioinformatics analysis based on GEO database showed DEGs between sepsis suvivors and non-survivors in the course of sepsis,which contributed to identification of potential biomarkers and risk factors for sepsis-associated mortality.
