Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis
Chengzhuo Yang,1,* Xinhua Chen,1,* Jin Liu,1 Wenhao Wang,1 Lihua Sun,2 Youhong Xie,1 Qing Chang1,* 1Department of The Affiliated Rehabilitation Hospital of Chongqing Medical University, Chongqing, People’s Republic of China; 2Department of Rehabilitation Medicine, The First A...
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Dove Medical Press
2025-01-01
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| Series: | Journal of Inflammation Research |
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| Online Access: | https://www.dovepress.com/identification-and-validation-of-pivotal-genes-in-osteoarthritis-combi-peer-reviewed-fulltext-article-JIR |
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| author | Yang C Chen X Liu J Wang W Sun L Xie Y Chang Q |
| author_facet | Yang C Chen X Liu J Wang W Sun L Xie Y Chang Q |
| author_sort | Yang C |
| collection | DOAJ |
| description | Chengzhuo Yang,1,* Xinhua Chen,1,* Jin Liu,1 Wenhao Wang,1 Lihua Sun,2 Youhong Xie,1 Qing Chang1,* 1Department of The Affiliated Rehabilitation Hospital of Chongqing Medical University, Chongqing, People’s Republic of China; 2Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Youhong Xie; Qing Chang, Email 172763320@qq.com; 651733149@qq.comIntroduction: The prevalence of osteoarthritis (OA), the most common chronic joint condition, is increasing due to the aging population and escalating obesity rates, leading to a significant impact on human health and well-being. Thus, analyzing the key targets of OA through bioinformatics can help discover new biomarkers to improve its diagnosis.Methods: The microarray and RNA-seq results were screened from the Gene Expression Omnibus (GEO) database. Functional enrichment analyses, protein-protein interaction (PPI) analysis, and weighted gene co-expression network analysis (WGCNA) of the DEGs were performed. RT-qPCR and WB were further performed to verify the hub gene expression in OA rat.Results: In this study, 35 key genes were identified through differential expression analysis and weighted gene co-expression network analysis (WGCNA) using the GSE169077 and GSE114007 datasets. Enrichment analysis revealed that these key genes were predominantly enriched in the HIF-1 signaling pathway, ECM-receptor interaction, and FoxO signaling pathway. Through the integration of protein-protein interaction (PPI) analysis, validation in animal models and ROC curve analysis, four pivotal genes (GADD45B, CLDN5, HILPDA and CDKN1B) were finally identified.Conclusion: In conclusion, these identified key genes could serve as novel targets for predicting and treating OA, offering fresh insights into its etiology and pathogenesis.Keywords: osteoarthritis, bioinformatics analysis, WGCNA, GSE data |
| format | Article |
| id | doaj-art-059495aa112d4da984886c7b2a1646e7 |
| institution | Kabale University |
| issn | 1178-7031 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | Journal of Inflammation Research |
| spelling | doaj-art-059495aa112d4da984886c7b2a1646e72025-02-02T15:59:40ZengDove Medical PressJournal of Inflammation Research1178-70312025-01-01Volume 181459147099774Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA AnalysisYang CChen XLiu JWang WSun LXie YChang QChengzhuo Yang,1,* Xinhua Chen,1,* Jin Liu,1 Wenhao Wang,1 Lihua Sun,2 Youhong Xie,1 Qing Chang1,* 1Department of The Affiliated Rehabilitation Hospital of Chongqing Medical University, Chongqing, People’s Republic of China; 2Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Youhong Xie; Qing Chang, Email 172763320@qq.com; 651733149@qq.comIntroduction: The prevalence of osteoarthritis (OA), the most common chronic joint condition, is increasing due to the aging population and escalating obesity rates, leading to a significant impact on human health and well-being. Thus, analyzing the key targets of OA through bioinformatics can help discover new biomarkers to improve its diagnosis.Methods: The microarray and RNA-seq results were screened from the Gene Expression Omnibus (GEO) database. Functional enrichment analyses, protein-protein interaction (PPI) analysis, and weighted gene co-expression network analysis (WGCNA) of the DEGs were performed. RT-qPCR and WB were further performed to verify the hub gene expression in OA rat.Results: In this study, 35 key genes were identified through differential expression analysis and weighted gene co-expression network analysis (WGCNA) using the GSE169077 and GSE114007 datasets. Enrichment analysis revealed that these key genes were predominantly enriched in the HIF-1 signaling pathway, ECM-receptor interaction, and FoxO signaling pathway. Through the integration of protein-protein interaction (PPI) analysis, validation in animal models and ROC curve analysis, four pivotal genes (GADD45B, CLDN5, HILPDA and CDKN1B) were finally identified.Conclusion: In conclusion, these identified key genes could serve as novel targets for predicting and treating OA, offering fresh insights into its etiology and pathogenesis.Keywords: osteoarthritis, bioinformatics analysis, WGCNA, GSE datahttps://www.dovepress.com/identification-and-validation-of-pivotal-genes-in-osteoarthritis-combi-peer-reviewed-fulltext-article-JIRosteoarthritisbioinformatics analysiswgcnagse data |
| spellingShingle | Yang C Chen X Liu J Wang W Sun L Xie Y Chang Q Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis Journal of Inflammation Research osteoarthritis bioinformatics analysis wgcna gse data |
| title | Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis |
| title_full | Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis |
| title_fullStr | Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis |
| title_full_unstemmed | Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis |
| title_short | Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis |
| title_sort | identification and validation of pivotal genes in osteoarthritis combined with wgcna analysis |
| topic | osteoarthritis bioinformatics analysis wgcna gse data |
| url | https://www.dovepress.com/identification-and-validation-of-pivotal-genes-in-osteoarthritis-combi-peer-reviewed-fulltext-article-JIR |
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