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Identification and functional analysis of differentially expressed genes associated with cerebral ischemia/reperfusion injury through bioinformatics methods.

ABSTRACT: Cerebral ischemia/reperfusion (I/R) injury results in detrimental complications. However, little is known about the underlying molecular mechanisms involved in the reperfusion stage. The aim of the present study was to identify a gene expression profile associated with cerebral ischemia/reperfusion injury. The GSE23160 dataset, which comprised data from sham control samples and post?I/R injury brain tissues that were obtained using a middle cerebral artery occlusion (MCAO) model at 2, 8 and 24 h post?reperfusion, was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in the MCAO samples compared with controls were screened using the GEO2R web tool. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for DEGs was performed using the online tool DAVID. Furthermore, a protein?protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. In total, 32 DEGs at 2 h post?reperfusion, 39 DEGs at 8 h post?reperfusion and 91 DEGs at 24 h post?reperfusion were identified, while 15 DEGs were common among all three groups. GO analysis revealed that the DEGs at all three time?points were enriched in 'chemotaxis' and 'inflammatory response' terms, while KEGG pathway analysis demonstrated that DEGs were significantly enriched in the 'chemokine signaling pathway'. Furthermore, following PPI network construction, Cxcl1 was identified as the only hub gene that was common among all three time?points. In conclusion, the present study has demonstrated a global view of the potential molecular differences following cerebral I/R injury and may contribute to an improved understanding of the reperfusion stage, which may ultimately aid in the development of future clinical strategies.

SUBMITTER: Shao X

PROVIDER: S-EPMC6072188 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Identification and functional analysis of differentially expressed genes associated with cerebral ischemia/reperfusion injury through bioinformatics methods.

Shao Xiaoli X Bao Wangxiao W Hong Xiaoqin X Jiang Huihua H Yu Zhi Z

Molecular medicine reports 20180606 2

Cerebral ischemia/reperfusion (I/R) injury results in detrimental complications. However, little is known about the underlying molecular mechanisms involved in the reperfusion stage. The aim of the present study was to identify a gene expression profile associated with cerebral ischemia/reperfusion injury. The GSE23160 dataset, which comprised data from sham control samples and post‑I/R injury brain tissues that were obtained using a middle cerebral artery occlusion (MCAO) model at 2, 8 and 24 h ...[more]

PMID: 29901134

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Project description:BackgroundMyocardial ischemia is a prevalent cardiovascular disorder associated with significant morbidity and mortality. While prompt restoration of blood flow is essential for improving patient outcomes, the subsequent reperfusion process can result in myocardial ischemia-reperfusion injury (MIRI). Mitophagy, a specialized autophagic mechanism, has consistently been implicated in various cardiovascular disorders. However, the specific connection between ischemia-reperfusion and mitophagy remains elusive. This study aims to elucidate and validate central mitophagy-related genes associated with MIRI through comprehensive bioinformatics analysis.MethodsWe acquired the microarray expression profile dataset (GSE108940) from the Gene Expression Omnibus (GEO) and identified differentially expressed genes (DEGs) using GEO2R. Subsequently, these DEGs were cross-referenced with the mitophagy database, and differential nucleotide sequence analysis was performed through enrichment analysis. Protein-protein interaction (PPI) network analysis was employed to identify hub genes, followed by clustering of these hub genes using cytoHubba and MCODE within Cytoscape software. Gene set enrichment analysis (GSEA) was conducted on central genes. Additionally, Western blotting, immunofluorescence, and quantitative polymerase chain reaction (qPCR) analyses were conducted to validate the expression patterns of pivotal genes in MIRI rat model and H9C2 cardiomyocytes.ResultsA total of 2719 DEGs and 61 mitophagy-DEGs were identified, followed by enrichment analyses and the construction of a PPI network. HSP90AA1, RPS27A, EEF2, EIF4A1, EIF2S1, HIF-1α, and BNIP3 emerged as the seven hub genes identified by cytoHubba and MCODE of Cytoscape software. Functional clustering analysis of HIF-1α and BNIP3 yielded a score of 9.647, as determined by Cytoscape (MCODE). In our MIRI rat model, Western blot and immunofluorescence analyses confirmed a significant elevation in the expression of HIF-1α and BNIP3, accompanied by a notable increase in the ratio of LC3II to LC3I. Subsequently, qPCR confirmed a significant upregulation of HIF-1α, BNIP3, and LC3 mRNA in the MIRI group. Activation of the HIF-1α/BNIP3 pathway mediates the regulation of the degree of Mitophagy, thereby effectively reducing apoptosis in rat H9C2 cardiomyocytes.ConclusionsThis study has identified seven central genes among mitophagy-related DEGs that may play a pivotal role in MIRI, suggesting a correlation between the HIF-1α/BNIP3 pathway of mitophagy and the pathogenesis of MIRI. The findings highlight the potential importance of mitophagy in MIRI and provide valuable insights into underlying mechanisms and potential therapeutic targets for further exploration in future studies.

Dataset Information

Identification and functional analysis of differentially expressed genes associated with cerebral ischemia/reperfusion injury through bioinformatics methods.

Publications

Identification and functional analysis of differentially expressed genes associated with cerebral ischemia/reperfusion injury through bioinformatics methods.

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