Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney Injury
Introduction: The morbidity and mortality of acute kidney injury (AKI) are increasing. Epigenetic regulation and immune cell infiltration are thought to be involved in AKI. However, the relationship between epigenetic regulation and immune cell infiltration in AKI has not been elucidated....
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Karger Publishers
2025-01-01
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| Series: | Kidney & Blood Pressure Research |
| Online Access: | https://karger.com/article/doi/10.1159/000542787 |
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| author | Wei-Hua Liu Fang Cao Miao Lin Fu-Yuan Hong |
| author_facet | Wei-Hua Liu Fang Cao Miao Lin Fu-Yuan Hong |
| author_sort | Wei-Hua Liu |
| collection | DOAJ |
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Introduction: The morbidity and mortality of acute kidney injury (AKI) are increasing. Epigenetic regulation and immune cell infiltration are thought to be involved in AKI. However, the relationship between epigenetic regulation and immune cell infiltration in AKI has not been elucidated. This study was conducted to identify the differentially expressed genes (DEGs), differentially expressed RNA methylation genes (DEMGs), and infiltrated immune cells in the kidneys of ischemia-reperfusion induced-acute kidney injury (IRI-AKI) models and further explore their relationships in IRI-AKI. Methods: This is a bioinformatic analysis using R programming language in 3 selected IRI-AKI datasets from the Gene Expression Omnibus (GEO) database, including 16 IRI-AKI kidney tissues and 10 normal kidney tissues. The DEGs were screened, and enrichment pathways were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The DEMGs and core DEMGs were identified using the R package. The ROC curve was plotted to predict disease occurrence of 7 core DEMGs. The correlation of 7 core DEMGs and other genes was analyzed using Pearson’s correlation test. The gene set enrichment analysis (GSEA) of each DEMG was conducted using the R package. The upstream miRNAs and transcript factors of 7 core DEMGs were predicted based on the RegNetwork database and Cytoscape software. The STITCH database was used to predict the possible binding compounds of the 7 core DEMGs. Immune cell infiltration in kidney tissues between the IRI-AKI group and control group was evaluated using the R package. Results: A total of 2,367 DEGs were obtained, including 1,180 upregulated and 1,187 downregulated genes in IRI-AKI kidney associated with the cell structure, proliferation, molecule binding/interaction, and signaling pathways such as the leukocyte migration and chemokine signaling pathways. Ten DEMGs were identified, with Ythdf1, Rbm15, Trmt6, Hnrnpc, and Dnmt1 being significantly upregulated, while Lrpprc, Cyfip2, Mettl3, Ncbp2, and Nudt7 were significantly downregulated in IRI-AKI tissues. The molecules interacting with 7 core DEMGs were identified. Significant changes in the infiltration of 8 types of immune cells were observed in IRI-AKI kidneys compared to normal controls. The significant correlation between 6 core DEMGs and the infiltration of immune cells was observed. Conclusion: IRI may induce AKI through RNA methylation to regulate the expression of genes involved in immune cell infiltration. |
| format | Article |
| id | doaj-art-67c5b37c8e5f43309fa0705f23b186ab |
| institution | DOAJ |
| issn | 1423-0143 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Karger Publishers |
| record_format | Article |
| series | Kidney & Blood Pressure Research |
| spelling | doaj-art-67c5b37c8e5f43309fa0705f23b186ab2025-08-20T03:09:47ZengKarger PublishersKidney & Blood Pressure Research1423-01432025-01-01501143210.1159/000542787Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney InjuryWei-Hua LiuFang CaoMiao LinFu-Yuan Hong Introduction: The morbidity and mortality of acute kidney injury (AKI) are increasing. Epigenetic regulation and immune cell infiltration are thought to be involved in AKI. However, the relationship between epigenetic regulation and immune cell infiltration in AKI has not been elucidated. This study was conducted to identify the differentially expressed genes (DEGs), differentially expressed RNA methylation genes (DEMGs), and infiltrated immune cells in the kidneys of ischemia-reperfusion induced-acute kidney injury (IRI-AKI) models and further explore their relationships in IRI-AKI. Methods: This is a bioinformatic analysis using R programming language in 3 selected IRI-AKI datasets from the Gene Expression Omnibus (GEO) database, including 16 IRI-AKI kidney tissues and 10 normal kidney tissues. The DEGs were screened, and enrichment pathways were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The DEMGs and core DEMGs were identified using the R package. The ROC curve was plotted to predict disease occurrence of 7 core DEMGs. The correlation of 7 core DEMGs and other genes was analyzed using Pearson’s correlation test. The gene set enrichment analysis (GSEA) of each DEMG was conducted using the R package. The upstream miRNAs and transcript factors of 7 core DEMGs were predicted based on the RegNetwork database and Cytoscape software. The STITCH database was used to predict the possible binding compounds of the 7 core DEMGs. Immune cell infiltration in kidney tissues between the IRI-AKI group and control group was evaluated using the R package. Results: A total of 2,367 DEGs were obtained, including 1,180 upregulated and 1,187 downregulated genes in IRI-AKI kidney associated with the cell structure, proliferation, molecule binding/interaction, and signaling pathways such as the leukocyte migration and chemokine signaling pathways. Ten DEMGs were identified, with Ythdf1, Rbm15, Trmt6, Hnrnpc, and Dnmt1 being significantly upregulated, while Lrpprc, Cyfip2, Mettl3, Ncbp2, and Nudt7 were significantly downregulated in IRI-AKI tissues. The molecules interacting with 7 core DEMGs were identified. Significant changes in the infiltration of 8 types of immune cells were observed in IRI-AKI kidneys compared to normal controls. The significant correlation between 6 core DEMGs and the infiltration of immune cells was observed. Conclusion: IRI may induce AKI through RNA methylation to regulate the expression of genes involved in immune cell infiltration. https://karger.com/article/doi/10.1159/000542787 |
| spellingShingle | Wei-Hua Liu Fang Cao Miao Lin Fu-Yuan Hong Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney Injury Kidney & Blood Pressure Research |
| title | Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney Injury |
| title_full | Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney Injury |
| title_fullStr | Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney Injury |
| title_full_unstemmed | Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney Injury |
| title_short | Comprehensive Analysis of RNA Methylation-Regulated Gene Signature and Immune Infiltration in Ischemia/Reperfusion-Induced Acute Kidney Injury |
| title_sort | comprehensive analysis of rna methylation regulated gene signature and immune infiltration in ischemia reperfusion induced acute kidney injury |
| url | https://karger.com/article/doi/10.1159/000542787 |
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