Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis
Abstract The purpose of this study was to search for genes related to ros induced oxidative stress in osteoarthritis(OA) cartilage through bioinformatics analysis, and to verify the expression of related genes in articular cartilage of OA patients. OA expression data and ROS-related genes were downl...
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Nature Portfolio
2025-08-01
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| Online Access: | https://doi.org/10.1038/s41598-025-11667-7 |
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| author | Chengze Qiu Zhiyong Zhang Haocheng Wang Na Liu Ruixin Li Zhiheng Wei Benjie Wang Nan Zhang |
| author_facet | Chengze Qiu Zhiyong Zhang Haocheng Wang Na Liu Ruixin Li Zhiheng Wei Benjie Wang Nan Zhang |
| author_sort | Chengze Qiu |
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| description | Abstract The purpose of this study was to search for genes related to ros induced oxidative stress in osteoarthritis(OA) cartilage through bioinformatics analysis, and to verify the expression of related genes in articular cartilage of OA patients. OA expression data and ROS-related genes were downloaded from GEO (GSE51588, GSE117999) and Molecular Signatures Databases. The limma package in R language was used to screen differently expressed genes (DEGs) from the GEO databases. WGCNA analysis and Venn diagrams were employed to screen genes that were differentially expressed between OA and control samples and had strong correlations with ROS as candidate genes. DEGs were screened by GO and KEGG enrichment analysis, as well as protein-protein interaction (PPI) analysis. Besides, the software Cytoscape and database STRING were utilized to screen hub genes networks. The hub genes were confirmed by analysis of the receiver operating characteristic (ROC) curve on the GSE51588 and GSE117999 databases. An artificial neural network model was constructed for the hub genes, and immune analysis was conducted using the ssGSEA algorithm. The expression of genes in OA and normal chondrocytes was verified through HE staining, immunohistochemistry, ROS detection, qRT-PCR and Western blotting test. This study identified five genes, including ALB, CDH1, HSPA8, HIST1H2BE and XDH, as hub genes. ROC curves, gene expression analysis, and artificial neural network diagrams indicated that ALB, HIST1H2BE and XDH had good diagnostic characteristics. GSEA showed that the XDH gene was significantly enriched in ROS pathways. Meanwhile, the expression of XDH were also confirmed to be significant differences between injured cartilage and normal cartilage in OA patients in vivo. Our study may provide new hub genes related to ROS-mediated oxidative stress in OA and validate the correlation between XDH gene and its transcripts with ROS pathways in OA. This offers potential clinical applications for understanding the pathology, diagnosis, and treatment of OA. |
| format | Article |
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| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-7d3be9742ccc42749fe36bb6b214f85f2025-08-20T04:03:01ZengNature PortfolioScientific Reports2045-23222025-08-0115111410.1038/s41598-025-11667-7Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysisChengze Qiu0Zhiyong Zhang1Haocheng Wang2Na Liu3Ruixin Li4Zhiheng Wei5Benjie Wang6Nan Zhang7Department of Orthopedics, Affiliated Xinhua Hospital of Dalian UniversityDepartment of Orthopedics, Affiliated Xinhua Hospital of Dalian UniversityDepartment of Orthopedics, Affiliated Xinhua Hospital of Dalian UniversityDepartment of Hematology and Rheumatology, Affiliated Xinhua Hospital of Dalian UniversityDepartment of Orthopedics, Affiliated Xinhua Hospital of Dalian UniversityDepartment of Orthopedics, Affiliated Xinhua Hospital of Dalian UniversityDepartment of Orthopedics, Affiliated Xinhua Hospital of Dalian UniversityDepartment of Orthopedics, Affiliated Xinhua Hospital of Dalian UniversityAbstract The purpose of this study was to search for genes related to ros induced oxidative stress in osteoarthritis(OA) cartilage through bioinformatics analysis, and to verify the expression of related genes in articular cartilage of OA patients. OA expression data and ROS-related genes were downloaded from GEO (GSE51588, GSE117999) and Molecular Signatures Databases. The limma package in R language was used to screen differently expressed genes (DEGs) from the GEO databases. WGCNA analysis and Venn diagrams were employed to screen genes that were differentially expressed between OA and control samples and had strong correlations with ROS as candidate genes. DEGs were screened by GO and KEGG enrichment analysis, as well as protein-protein interaction (PPI) analysis. Besides, the software Cytoscape and database STRING were utilized to screen hub genes networks. The hub genes were confirmed by analysis of the receiver operating characteristic (ROC) curve on the GSE51588 and GSE117999 databases. An artificial neural network model was constructed for the hub genes, and immune analysis was conducted using the ssGSEA algorithm. The expression of genes in OA and normal chondrocytes was verified through HE staining, immunohistochemistry, ROS detection, qRT-PCR and Western blotting test. This study identified five genes, including ALB, CDH1, HSPA8, HIST1H2BE and XDH, as hub genes. ROC curves, gene expression analysis, and artificial neural network diagrams indicated that ALB, HIST1H2BE and XDH had good diagnostic characteristics. GSEA showed that the XDH gene was significantly enriched in ROS pathways. Meanwhile, the expression of XDH were also confirmed to be significant differences between injured cartilage and normal cartilage in OA patients in vivo. Our study may provide new hub genes related to ROS-mediated oxidative stress in OA and validate the correlation between XDH gene and its transcripts with ROS pathways in OA. This offers potential clinical applications for understanding the pathology, diagnosis, and treatment of OA.https://doi.org/10.1038/s41598-025-11667-7OsteoarthritisReactive oxygen species(ROS)Oxidative stressXanthine dehydrogenase(XDH)Bioinformatics analysis |
| spellingShingle | Chengze Qiu Zhiyong Zhang Haocheng Wang Na Liu Ruixin Li Zhiheng Wei Benjie Wang Nan Zhang Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis Scientific Reports Osteoarthritis Reactive oxygen species(ROS) Oxidative stress Xanthine dehydrogenase(XDH) Bioinformatics analysis |
| title | Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis |
| title_full | Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis |
| title_fullStr | Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis |
| title_full_unstemmed | Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis |
| title_short | Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis |
| title_sort | identification and verification of xdh genes in ros induced oxidative stress response of osteoarthritis based on bioinformatics analysis |
| topic | Osteoarthritis Reactive oxygen species(ROS) Oxidative stress Xanthine dehydrogenase(XDH) Bioinformatics analysis |
| url | https://doi.org/10.1038/s41598-025-11667-7 |
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