Bioinformatics analysis of the impact of immune infiltration in retinal ischemia-reperfusion injury
10.3760/cma.j.cn115989-20231026-00152
- VernacularTitle:免疫浸润在视网膜缺血再灌注损伤中作用的生物信息学分析
- Author:
Wenting WANG
1
;
Na LIANG
;
Wenjing HA
;
Shaomin PENG
Author Information
1. 安徽医科大学爱尔眼科医学中心，合肥 230022
- Keywords:
Ischemia-reperfusion injury;
Retina;
Bioinformatics;
Differentially expressed genes;
Immunoinfiltration
- From:
Chinese Journal of Experimental Ophthalmology
2024;42(11):997-1005
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To investigate the potential biomarkers associated with immune cells in retinal ischemia-reperfusion injury (RIRI).Methods:The RIRI gene expression profile dataset GSE20521 was obtained from the Gene Expression Omnibus database, and the differentially expressed genes (DEGs) were screened.The GSE20521 gene set was subjected to Gene Set Enrichment Analysis (GSEA) and Immune Cell Abundance Identifier (ImmuCellAI), yielding information pertaining to enriched pathways and immune cell infiltration.The Weighted Correlation Network Analysis (WGCNA) and Pearson correlation analysis were employed to identify the hub modules and candidate genes exhibiting the strongest correlation with immune infiltration.Subsequently, the protein-protein interaction (PPI) network of candidate genes was constructed, and key genes were screened using CytoHubba plugin.Results:The significant GSEA enrichment pathways in the RIRI group including the interferon-γ (IFN-γ), apoptosis, tumor necrosis factor-α/nuclear factor-κB, IFN-α, complement pathway, interleukin-6 (IL-6)-(signal transducer and activator of transcription 3)(STAT3) and IL2-STAT5 signaling pathways, as well as inflammatory response.Compared with the normal control group, the results of ImmuCellAI evaluation revealed significant increases in the proportions of cDC2 cells, monocyte-derived DC cells, M2 macrophages, and CD8_Tc cells and decreases in the proportions of pDC cells, CD4_T cells, CD4_Tm cells, helper T cells, regulatory T cells, follicular B cells, and eosinophils in the RIRI group (all at P<0.05).A total of 144 DEGs were obtained between the two groups of samples.Taking the intersection of DEGs and hub module genes, 140 candidate genes were obtained.GO analysis showed significant enrichment of positive regulation of cytokine production, leukocyte mediated immunity, wound healing, adaptive immune response, niacinamide adenine dinucleotide phosphate oxidase complex, and chemokine binding, etc.KEGG analysis enriched 50 pathways, including phagosome, pertussis, leishmaniasis tuberculosis, and complement and coagulation cascades.Three key genes were finally obtained, namely Cd68, Tlr2 and Hmox1, which were screened by PPI and different CytoHubba algorithms. Conclusions:The bioinformatics analysis reveals a distinct immune microenvironment in the retina of the RIRI group and normal control group, suggesting a correlation between RIRI and infiltration of multiple immune cell types.
