Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithm
AbstractObjective The aim of our study was to identify key biomarkers of glomeruli in focal glomerulosclerosis (FSGS) and analyze their relationship with the infiltration of immune cells.Methods The expression profiles (GSE108109 and GSE200828) were obtained from the GEO database. The differentially...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2023-12-01
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| Series: | Renal Failure |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/0886022X.2023.2202264 |
| _version_ | 1797658495828361216 |
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| author | Yun Xia Zhang Juan Lv Jun Yuan Bai XiaoWei Pu En Lai Dai |
| author_facet | Yun Xia Zhang Juan Lv Jun Yuan Bai XiaoWei Pu En Lai Dai |
| author_sort | Yun Xia Zhang |
| collection | DOAJ |
| description | AbstractObjective The aim of our study was to identify key biomarkers of glomeruli in focal glomerulosclerosis (FSGS) and analyze their relationship with the infiltration of immune cells.Methods The expression profiles (GSE108109 and GSE200828) were obtained from the GEO database. The differentially expressed genes (DEGs) were filtered and analyzed by gene set enrichment analysis (GSEA). MCODE module was constructed. Weighted gene coexpression network analysis (WGCNA) was performed to obtain the core gene modules. Least absolute shrinkage and selection operator (LASSO) regression was applied to identify key genes. ROC curves were employed to explore their diagnostic accuracy. Transcription factor prediction of the key biomarkers was performed using the Cytoscape plugin IRegulon. The analysis of the infiltration of 28 immune cells and their correlation with the key biomarkers were performed.Results A total of 1474 DEGs were identified. Their functions were mostly related to immune-related diseases and signaling pathways. MCODE identified five modules. The turquoise module of WGCNA had significant relevance to the glomerulus in FSGS. TGFB1 and NOTCH1 were identified as potential key glomerular biomarkers in FSGS. Eighteen transcription factors were obtained from the two hub genes. Immune infiltration showed significant correlations with T cells. The results of immune cell infiltration and their relationship with key biomarkers implied that NOTCH1 and TGFB1 were enhanced in immune-related pathways.Conclusion TGFB1 and NOTCH1 may be strongly correlated with the pathogenesis of the glomerulus in FSGS and are new candidate key biomarkers. T-cell infiltration plays an essential role in the FSGS lesion process. |
| first_indexed | 2024-03-11T17:59:46Z |
| format | Article |
| id | doaj.art-38ba99ee81004b10b28300f8bfa7677f |
| institution | Directory Open Access Journal |
| issn | 0886-022X 1525-6049 |
| language | English |
| last_indexed | 2024-03-11T17:59:46Z |
| publishDate | 2023-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Renal Failure |
| spelling | doaj.art-38ba99ee81004b10b28300f8bfa7677f2023-10-17T09:23:24ZengTaylor & Francis GroupRenal Failure0886-022X1525-60492023-12-0145110.1080/0886022X.2023.2202264Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithmYun Xia Zhang0Juan Lv1Jun Yuan Bai2XiaoWei Pu3En Lai Dai4College of Integrated Traditional and Western Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, ChinaCollege of Integrated Traditional and Western Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, ChinaCollege of Integrated Traditional and Western Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, ChinaCollege of Integrated Traditional and Western Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, ChinaCollege of Integrated Traditional and Western Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, ChinaAbstractObjective The aim of our study was to identify key biomarkers of glomeruli in focal glomerulosclerosis (FSGS) and analyze their relationship with the infiltration of immune cells.Methods The expression profiles (GSE108109 and GSE200828) were obtained from the GEO database. The differentially expressed genes (DEGs) were filtered and analyzed by gene set enrichment analysis (GSEA). MCODE module was constructed. Weighted gene coexpression network analysis (WGCNA) was performed to obtain the core gene modules. Least absolute shrinkage and selection operator (LASSO) regression was applied to identify key genes. ROC curves were employed to explore their diagnostic accuracy. Transcription factor prediction of the key biomarkers was performed using the Cytoscape plugin IRegulon. The analysis of the infiltration of 28 immune cells and their correlation with the key biomarkers were performed.Results A total of 1474 DEGs were identified. Their functions were mostly related to immune-related diseases and signaling pathways. MCODE identified five modules. The turquoise module of WGCNA had significant relevance to the glomerulus in FSGS. TGFB1 and NOTCH1 were identified as potential key glomerular biomarkers in FSGS. Eighteen transcription factors were obtained from the two hub genes. Immune infiltration showed significant correlations with T cells. The results of immune cell infiltration and their relationship with key biomarkers implied that NOTCH1 and TGFB1 were enhanced in immune-related pathways.Conclusion TGFB1 and NOTCH1 may be strongly correlated with the pathogenesis of the glomerulus in FSGS and are new candidate key biomarkers. T-cell infiltration plays an essential role in the FSGS lesion process.https://www.tandfonline.com/doi/10.1080/0886022X.2023.2202264Focal segmental glomerulosclerosisweighted gene coexpression network analysisleast absolute shrinkage and selection operatorimmune cell infiltrationTGFB1NOTCH1 |
| spellingShingle | Yun Xia Zhang Juan Lv Jun Yuan Bai XiaoWei Pu En Lai Dai Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithm Renal Failure Focal segmental glomerulosclerosis weighted gene coexpression network analysis least absolute shrinkage and selection operator immune cell infiltration TGFB1 NOTCH1 |
| title | Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithm |
| title_full | Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithm |
| title_fullStr | Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithm |
| title_full_unstemmed | Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithm |
| title_short | Identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on WGCNA and the LASSO algorithm |
| title_sort | identification of key biomarkers of the glomerulus in focal segmental glomerulosclerosis and their relationship with immune cell infiltration based on wgcna and the lasso algorithm |
| topic | Focal segmental glomerulosclerosis weighted gene coexpression network analysis least absolute shrinkage and selection operator immune cell infiltration TGFB1 NOTCH1 |
| url | https://www.tandfonline.com/doi/10.1080/0886022X.2023.2202264 |
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