Analysis of co-expressed genes in myocardial ischemia-reperfusion injury and necrotic apoptosis utilizing bioinformatics
10.12007/j.issn.0258-4646.2024.01.011
- VernacularTitle:基于生物信息学的心肌缺血/再灌注损伤与坏死性凋亡共表达基因分析
- Author:
Yaowei ZHAO
1
;
Hongyu LI
;
Xiyuan MA
;
Xianghong MENG
;
Qiang TANG
Author Information
1. 黑龙江中医药大学 研究生院,哈尔滨 150006
- Keywords:
myocardial ischemia/reperfusion injury;
necrotic apoptosis;
co-expressed gene;
bioinformatics
- From:
Journal of China Medical University
2024;53(1):67-74
- CountryChina
- Language:Chinese
-
Abstract:
Objective To identify and validate co-expressed genes associated with myocardial ischemia/reperfusion injury(MI/RI)and necrotic apoptosis by bioinformatics analysis.Methods Gene expression profile data for MI/RI were obtained by GSE67308 and GSE19875 datasets from the Gene Expression Omnibus(GEO)database.Differential expression analysis was conducted on the GSE67308 dataset to identify differentially expressed genes(DEGs),followed by gene set enrichment analysis and biological pathway analysis.More-over,immune cell infiltration analysis was performed on the GSE67308 dataset.Necrotic apoptosis-related genes were retrieved from the Molecular Signatures Database and the Kyoto Encyclopedia of Genes and Genomes(KEGG).A protein-protein interaction(PPI)network was constructed by overlapping DEGs with these necrotic apoptosis-related genes to identify key genes.Furthermore,the expression pat-terns of these key genes across various cardiac cell types were analyzed using a single-cell sequencing analysis platform,and validation of key gene expression was performed using the GSE19875 dataset.Results A total of 1054 DEGs were identified,comprising 363 upregu-lated and 691 downregulated genes.Gene enrichment analysis revealed that DEGs were primarily associated with processes related to apoptosis,immune responses,and intracellular signaling regulation.Moreover,biological pathway analysis demonstrated that DEGs were predominantly involved in the regulation of signaling pathways such as tumor necrosis factor(TNF)and NF-κB.Immune infiltration anal-ysis indicated a high degree of immune infiltration,particularly with natural killer cells and monocytes,in MI/RI myocardial tissue.PPI network analysis identified Il1b,TNF,Birc3,and Ripk1as crucial genes in the context of necrotic apoptosis.Single-cell sequencing anal-ysis showed the elevated expression of key genes within white blood cells.In comparison to the control group,the MI/RI model group in the GSE19875 dataset exhibited significantly increased expression of Il1b,TNF,Birc3,and Ripk1(P<0.01).Conclusion MI/RI is strongly correlated with the TNF signaling pathway and the NF-κB signaling pathway,both of which play pivotal roles in regulating necrotic apop-tosis.Il1b,TNF,Birc3,and Ripk1emerge as key genes that concurrently regulate both MI/RI and necrotic apoptosis.It is plausible that IL-1b,TNF,Birc3,and Ripk1 may serve as critical regulatory factors in the context of necrotic apoptosis during MI/RI.
