Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis
Kuihan Tang,1 Li Sun,2 Long Chen,2 Xiaobo Feng,1 Jiarui Wu,2 Hao Guo,2 Yong Zheng1 1Department of Orthopedics, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang, 550014, People’s Republic of China; 2Department of Orthopedics, Guizhou Provincial People’s Hospital, Guiyang, 550000, People’s Republi...
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| Format: | Article |
| Language: | English |
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Dove Medical Press
2024-02-01
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| Series: | International Journal of General Medicine |
| Subjects: | |
| Online Access: | https://www.dovepress.com/bioinformatics-analysis-and-experimental-validation-of-mitochondrial-a-peer-reviewed-fulltext-article-IJGM |
| _version_ | 1797295345761255424 |
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| author | Tang K Sun L Chen L Feng X Wu J Guo H Zheng Y |
| author_facet | Tang K Sun L Chen L Feng X Wu J Guo H Zheng Y |
| author_sort | Tang K |
| collection | DOAJ |
| description | Kuihan Tang,1 Li Sun,2 Long Chen,2 Xiaobo Feng,1 Jiarui Wu,2 Hao Guo,2 Yong Zheng1 1Department of Orthopedics, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang, 550014, People’s Republic of China; 2Department of Orthopedics, Guizhou Provincial People’s Hospital, Guiyang, 550000, People’s Republic of ChinaCorrespondence: Yong Zheng, Email 1210244258@qq.comBackground: Mitochondrial autophagy is closely related to the pathogenesis of osteoarthritis, In order to explore the role of mitochondrial autophagy related genes in knee osteoarthritis (KOA) and its molecular mechanism.Methods: KOA-related transcriptome data were extracted from the Gene Expression Omnibus (GEO) database. Differentially expressed mitochondrial autophagy gene (DEMGs) were screened in patients with KOA by differential expression analysis. The STRING website was used to construct a protein-protein interaction (PPI) network among DEMGs. Molecular complex detection (MCODE) method in Cytoscape software was performed to identify hub DEMGs. Support vector machine recursive feature elimination (SVM-RFE) method was used to construct the hub DEMG diagnosis model. Genes with diagnostic value were identified as biomarkers by plotting receiver operating characteristic (ROC) curves and Expression validation. CIBERSORT algorithm was used to calculate the proportion of 22 immune cells in each sample in the GSE114007 dataset. Finally, biomarker expression was verified by qPCR.Results: A total of 15 DEMGs were obtained and enrichment analyses showed that these DEMG strains were mainly enriched in the mitophagy-animal, shigellosis, autophagy-animal and FoxO signal pathways. The PPI network unveiled 13 DEMGs with interactions. In addition, 8 hub DEMGs (ULK1, CALCOCO2, MAP1LC3B, BNIP3L, GABARAPL1, BNIP3, FKBP8 and FOXO3) were obtained for KOA. And 5 model DEMGs (BNIP3L, BNIP3, MAP1LC3B, ULK1 and FOXO3) were screened. The ROC curves revealed that BNIP3 and FOXO3 has strong diagnostic value in these models of DEMG. Immune-infiltration and correlation analysis showed that BNIP3 and FOXO3 were significantly correlated with three different immune cells, including primary B cells, M0 macrophage and M2 macrophage. The cartilage tissue samples qPCR verification results show that FOXO3 and BNIP3 were all down-regulated in KOA (p < 0.01), and the validation results are consistent with the above analysis.Conclusion: BNIP3 and FOXO3 have been identified as biomarkers for the diagnosis of KOA, which might supply a new insight for the pathogenesis and treatment of KOA.Keywords: Gene Expression Omnibus, diagnostic, bioinformatics analysis, immune infiltration, biomarkers |
| first_indexed | 2024-03-07T21:45:25Z |
| format | Article |
| id | doaj.art-6818bb9bf9eb4752a61703881329f347 |
| institution | Directory Open Access Journal |
| issn | 1178-7074 |
| language | English |
| last_indexed | 2024-03-07T21:45:25Z |
| publishDate | 2024-02-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | International Journal of General Medicine |
| spelling | doaj.art-6818bb9bf9eb4752a61703881329f3472024-02-25T18:46:48ZengDove Medical PressInternational Journal of General Medicine1178-70742024-02-01Volume 1763965090677Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee OsteoarthritisTang KSun LChen LFeng XWu JGuo HZheng YKuihan Tang,1 Li Sun,2 Long Chen,2 Xiaobo Feng,1 Jiarui Wu,2 Hao Guo,2 Yong Zheng1 1Department of Orthopedics, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang, 550014, People’s Republic of China; 2Department of Orthopedics, Guizhou Provincial People’s Hospital, Guiyang, 550000, People’s Republic of ChinaCorrespondence: Yong Zheng, Email 1210244258@qq.comBackground: Mitochondrial autophagy is closely related to the pathogenesis of osteoarthritis, In order to explore the role of mitochondrial autophagy related genes in knee osteoarthritis (KOA) and its molecular mechanism.Methods: KOA-related transcriptome data were extracted from the Gene Expression Omnibus (GEO) database. Differentially expressed mitochondrial autophagy gene (DEMGs) were screened in patients with KOA by differential expression analysis. The STRING website was used to construct a protein-protein interaction (PPI) network among DEMGs. Molecular complex detection (MCODE) method in Cytoscape software was performed to identify hub DEMGs. Support vector machine recursive feature elimination (SVM-RFE) method was used to construct the hub DEMG diagnosis model. Genes with diagnostic value were identified as biomarkers by plotting receiver operating characteristic (ROC) curves and Expression validation. CIBERSORT algorithm was used to calculate the proportion of 22 immune cells in each sample in the GSE114007 dataset. Finally, biomarker expression was verified by qPCR.Results: A total of 15 DEMGs were obtained and enrichment analyses showed that these DEMG strains were mainly enriched in the mitophagy-animal, shigellosis, autophagy-animal and FoxO signal pathways. The PPI network unveiled 13 DEMGs with interactions. In addition, 8 hub DEMGs (ULK1, CALCOCO2, MAP1LC3B, BNIP3L, GABARAPL1, BNIP3, FKBP8 and FOXO3) were obtained for KOA. And 5 model DEMGs (BNIP3L, BNIP3, MAP1LC3B, ULK1 and FOXO3) were screened. The ROC curves revealed that BNIP3 and FOXO3 has strong diagnostic value in these models of DEMG. Immune-infiltration and correlation analysis showed that BNIP3 and FOXO3 were significantly correlated with three different immune cells, including primary B cells, M0 macrophage and M2 macrophage. The cartilage tissue samples qPCR verification results show that FOXO3 and BNIP3 were all down-regulated in KOA (p < 0.01), and the validation results are consistent with the above analysis.Conclusion: BNIP3 and FOXO3 have been identified as biomarkers for the diagnosis of KOA, which might supply a new insight for the pathogenesis and treatment of KOA.Keywords: Gene Expression Omnibus, diagnostic, bioinformatics analysis, immune infiltration, biomarkershttps://www.dovepress.com/bioinformatics-analysis-and-experimental-validation-of-mitochondrial-a-peer-reviewed-fulltext-article-IJGMgene expression omnibusdiagnosticbioinformatics analysisimmune infiltrationbiomarkers |
| spellingShingle | Tang K Sun L Chen L Feng X Wu J Guo H Zheng Y Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis International Journal of General Medicine gene expression omnibus diagnostic bioinformatics analysis immune infiltration biomarkers |
| title | Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis |
| title_full | Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis |
| title_fullStr | Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis |
| title_full_unstemmed | Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis |
| title_short | Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis |
| title_sort | bioinformatics analysis and experimental validation of mitochondrial autophagy genes in knee osteoarthritis |
| topic | gene expression omnibus diagnostic bioinformatics analysis immune infiltration biomarkers |
| url | https://www.dovepress.com/bioinformatics-analysis-and-experimental-validation-of-mitochondrial-a-peer-reviewed-fulltext-article-IJGM |
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