ArticleClinical rheumatology2021
Identification of abnormally methylated-differentially expressed genes and pathways in osteoarthritis: a comprehensive bioinformatic study.
Article in Clinical rheumatology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 15 citations in OpenAlex.
- Identification of potential biomarkers related to the Bitong mixture in osteoarthritis based on bioinformatics and network pharmacology, and exploration of the mechanism involved.Frontiers in immunology · 2026Article
- Disease-Associated Signatures Persist in Extracellular Vesicles from Reprogrammed Cells of Osteoarthritis Patients.International journal of molecular sciences · 2025Article
- Integrative analyses of mendelian randomization and bioinformatics reveal casual relationship and genetic links between COVID-19 and knee osteoarthritis.BMC medical genomics · 2025Article
- Article
- Single-cell profiling uncovers synovial fibroblast subpopulations associated with chondrocyte injury in osteoarthritis.Frontiers in endocrinology · 2024Article
- ITGB1 alleviates osteoarthritis by inhibiting cartilage inflammation and apoptosis via activating cAMP pathway.Journal of orthopaedic surgery and research · 2023Article
- Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis.BMC genomics · 2023Article
- Bioinformatics and system biology approach to identify potential common pathogenesis for COVID-19 infection and osteoarthritis.Scientific reports · 2023Article
- A comprehensive analysis of biomarkers associated with synovitis and chondrocyte apoptosis in osteoarthritis.Frontiers in immunology · 2023Article
- Males and Females Have Distinct Molecular Events in the Articular Cartilage during Knee Osteoarthritis.International journal of molecular sciences · 2021Article
- Proteomic Analysis of Synovial Fibroblasts and Articular Chondrocytes Co-Cultures Reveals Valuable VIP-Modulated Inflammatory and Degradative Proteins in Osteoarthritis.International journal of molecular sciences · 2021Article
- Genetic biomarkers in osteoarthritis: a quick overview.Faculty reviews · 2021Review
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivesTo investigate abnormally methylated-differentially expressed genes (DEGs) and their related pathways in osteoarthritis (OA) by comprehensive bioinformatic analysis.
methodsGene expression profiles of GSE51588 and GSE114007, and a gene methylation microarray data GSE63695 were downloaded from the Gene Expression Omnibus (GEO) repository. Abnormally methylated DEGs were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of these genes were subsequently performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction (PPI) network was built from STRING. Module analysis and hub gene identification were performed by using Cytoscape. Co-expression analysis was also constructed using the CEMiTool package.
resultsIn total, 133 abnormally methylated DEGs were identified, including 85 hypomethylation high-expression genes and 48 hypermethylation low-expression genes. Among biological processes and KEGG pathways of abnormally methylated DEGs, collagen fibril organization was enriched most frequently, and pathways of oxidative stress and aging were enriched, including HIF-1 signaling pathway, AMPK signaling pathway, and FoxO signaling pathway. In PPI networks, the hub genes of hypomethylation high-expression genes were COL1A1, COL3A1, COL1A2, COL5A2, LUM, MMP2, SPARC, COL2A1, COL6A2, and COL7A1, and the hub genes of hypermethylation low-expression genes were VEGFA, SLC2A1, LDHA, PDK1, and BNIP3. Combined with co-expression analysis, COL3A1, LUM, and MMP2 were the critical hypomethylation high-expression hub genes in medial tibia subchondral bone.
conclusionsOur study implied abnormally methylated DEGs and dysregulated pathways in OA. Common methylation biomarkers included COL3A1, LUM, and MMP2, and we also found that THBS2 may serve as a novel biomarker in end-stage OA. Key Points • Abnormally methylated differentially expressed genes regulate osteoarthritis. • Hypomethylation high-expression genes were related to the extracellular matrix. • Hypermethylation low-expression genes were related to oxidative stress and aging. • COL3A1, LUM, and MMP2 were potential methylation biomarkers for osteoarthritis.
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