Key result
In a rat model of renal ischemia-reperfusion injury, expression of 9 out of 10 identified hub genes (including STAT3) was significantly increased compared to controls.
Why the study?
This study aimed to identify hub genes and pathways in a rat model of renal ischemia-reperfusion injury using bioinformatics analysis of GEO datasets.
Bioinformatics analysis and in vivo validation identified the HIF-1alpha signaling pathway and STAT3 as key components in renal ischemia-reperfusion injury.
Answers are grounded in this paper and cite their sources.
Rat IRI hub gene findings require human validation; leaves open whether STAT3 or HIF-1α signaling informs clinical renal protection.
BACKGROUND This study aimed to identify hub genes and pathways in a rat model of renal ischemia-reperfusion injury (IRI) using bioinformatics analysis of the Gene Expression Omnibus (GEO) microarray dataset and integration of gene expression profiles. MATERIAL AND METHODS GEO software and the GEO2R calculation method were used to analyze two mRNA profiles, including GSE 39548 and GSE 108195. The co-expression of differentially expressed genes (DEGs) were identified and searched in the DAVID and STRING databases for pathway and protein-protein interaction (PPI) analysis. Cytoscape was used to draw the PPI network. DEGs were also analyzed using the Molecular Complex Detection (MCODE) algorithm. Cytoscape and cytoHubba were used to analyze the hub genes and visualize the molecular interaction networks. Rats (n=20) included the IRI model group (n=10) and a control group (n=10). Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to measure and compare the expression of the identified genes in rat renal tissue in the IRI model and the control group. RESULTS Ten hub genes were identified, STAT3, CD44, ITGAM, CCL2, TIMP1, MYC, THBS1, IGF1, SOCS3, and CD14. Apart from IGF1, qRT-PCR showed that expression of these genes was significantly increased in renal tissue in the rat model of IRI. The HIF-1alpha signaling pathway was involved in IRI in the rat model, which was supported by MCODE analysis. CONCLUSIONS In a rat model of renal IRI, bioinformatics analysis of the GEO dataset and integration of gene expression profiles identified involvement of HIF-1alpha signaling and the STAT3 hub gene.
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Guo et al. (2019) studied Renal ischemia-reperfusion injury (n=20). Renal ischemia-reperfusion injury (IRI) model vs. Control group was evaluated on Expression of identified hub genes in renal tissue. In a rat model of renal ischemia-reperfusion injury, expression of 9 out of 10 identified hub genes (including STAT3) was significantly increased compared to controls.
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