The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation
Background. Inflammation within areas of interstitial fibrosis and tubular atrophy (IF/TA) is associated with kidney allograft failure. The aim of this study was to reveal new diagnostic markers of IF/TA based on bioinformatics analysis. Methods. Raw data of IF/TA samples after kidney transplantatio...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2022-01-01
|
| Series: | Journal of Immunology Research |
| Online Access: | http://dx.doi.org/10.1155/2022/7212852 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832554800973086720 |
|---|---|
| author | Bin Yang Dike Shi Yahong Chen Yi Zhu |
| author_facet | Bin Yang Dike Shi Yahong Chen Yi Zhu |
| author_sort | Bin Yang |
| collection | DOAJ |
| description | Background. Inflammation within areas of interstitial fibrosis and tubular atrophy (IF/TA) is associated with kidney allograft failure. The aim of this study was to reveal new diagnostic markers of IF/TA based on bioinformatics analysis. Methods. Raw data of IF/TA samples after kidney transplantation and control samples after kidney transplantation were extracted from the Gene Expression Omnibus (GEO) database (GSE76882 and GSE120495 datasets), and genes that were differentially expressed between the two groups (DEGs) were screened. Gene Set Enrichment Analysis (GSEA), ESTIMATE and single sample GSEA (ssGSEA), least absolute shrinkage and selection operator (LASSO) regression analysis, and competing endogenous RNA (ceRNA) network were used to analyze the data. Results. The results of GSEA revealed that multiple immune-related pathways were enriched in the IF/TA group, and subsequent immune landscape analysis also showed that the IF/TA group had higher immune and stromal scores and up to 15 types of immune cells occupied them, such as B cells, cytotoxic cells, and T cells. LASSO regression analysis selected 6 (including ANGPTL3, APOH, LTF, FCGR2B, HLA-DQA2, and EGF) out of 14 DE-IRGs as diagnostic genes to construct a diagnostic model. Then, receiver operating characteristic (ROC) curve analysis showed the powerful diagnostic value of the model, and the area under the curve (AUC) of a single diagnostic gene was greater than 0.75. The results of ingenuity pathway analysis (IPA) also indicated that DEGs were involved in the immune system and kidney disease-related pathways. Finally, we found multiple miRNAs that could regulate diagnostic genes from the ceRNA network. Conclusion. This study identified 6 IF/TA-related genes, which might be used as a new diagnosis model in the clinical practice. |
| format | Article |
| id | doaj-art-e8b761302a2f4a658b9e469cddc2976d |
| institution | Kabale University |
| issn | 2314-7156 |
| language | English |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Immunology Research |
| spelling | doaj-art-e8b761302a2f4a658b9e469cddc2976d2025-02-03T05:50:30ZengWileyJournal of Immunology Research2314-71562022-01-01202210.1155/2022/7212852The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney TransplantationBin Yang0Dike Shi1Yahong Chen2Yi Zhu3Department of Hepato-Pancreato-Biliary SurgeryDepartment of Gastrointestinal SurgeryDepartment of Hepato-Pancreato-Biliary SurgeryDepartment of Hepato-Pancreato-Biliary SurgeryBackground. Inflammation within areas of interstitial fibrosis and tubular atrophy (IF/TA) is associated with kidney allograft failure. The aim of this study was to reveal new diagnostic markers of IF/TA based on bioinformatics analysis. Methods. Raw data of IF/TA samples after kidney transplantation and control samples after kidney transplantation were extracted from the Gene Expression Omnibus (GEO) database (GSE76882 and GSE120495 datasets), and genes that were differentially expressed between the two groups (DEGs) were screened. Gene Set Enrichment Analysis (GSEA), ESTIMATE and single sample GSEA (ssGSEA), least absolute shrinkage and selection operator (LASSO) regression analysis, and competing endogenous RNA (ceRNA) network were used to analyze the data. Results. The results of GSEA revealed that multiple immune-related pathways were enriched in the IF/TA group, and subsequent immune landscape analysis also showed that the IF/TA group had higher immune and stromal scores and up to 15 types of immune cells occupied them, such as B cells, cytotoxic cells, and T cells. LASSO regression analysis selected 6 (including ANGPTL3, APOH, LTF, FCGR2B, HLA-DQA2, and EGF) out of 14 DE-IRGs as diagnostic genes to construct a diagnostic model. Then, receiver operating characteristic (ROC) curve analysis showed the powerful diagnostic value of the model, and the area under the curve (AUC) of a single diagnostic gene was greater than 0.75. The results of ingenuity pathway analysis (IPA) also indicated that DEGs were involved in the immune system and kidney disease-related pathways. Finally, we found multiple miRNAs that could regulate diagnostic genes from the ceRNA network. Conclusion. This study identified 6 IF/TA-related genes, which might be used as a new diagnosis model in the clinical practice.http://dx.doi.org/10.1155/2022/7212852 |
| spellingShingle | Bin Yang Dike Shi Yahong Chen Yi Zhu The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation Journal of Immunology Research |
| title | The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation |
| title_full | The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation |
| title_fullStr | The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation |
| title_full_unstemmed | The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation |
| title_short | The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation |
| title_sort | potential diagnostic value of immune related genes in interstitial fibrosis and tubular atrophy after kidney transplantation |
| url | http://dx.doi.org/10.1155/2022/7212852 |
| work_keys_str_mv | AT binyang thepotentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation AT dikeshi thepotentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation AT yahongchen thepotentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation AT yizhu thepotentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation AT binyang potentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation AT dikeshi potentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation AT yahongchen potentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation AT yizhu potentialdiagnosticvalueofimmunerelatedgenesininterstitialfibrosisandtubularatrophyafterkidneytransplantation |