Combined bioinformatics analysis reveals gene expression and DNA methylation patterns in osteoarthritis

Song,Delei; Qi,Wei; Lv,Ming; Yuan,Chun; Tian,Kangsong; Zhang,Feng

doi:10.3892/mmr.2018.8874

Combined bioinformatics analysis reveals gene expression and DNA methylation patterns in osteoarthritis

Authors:
- Delei Song
- Wei Qi
- Ming Lv
- Chun Yuan
- Kangsong Tian
- Feng Zhang
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Affiliations: Trauma Department of Orthopedics, Zibo Central Hospital, Zibo, Shandong 255036, P.R. China
Published online on: April 12, 2018 https://doi.org/10.3892/mmr.2018.8874
Pages: 8069-8078
Copyright: © Song et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Osteoarthritis (OA) is a common type of arthritis, which may cause pain and disability. Alterations in gene expression and DNA methylation have been proven to be associated with the development of OA. The aim of the present study was to identify potential therapeutic targets and associated processes for OA via the combined analysis of gene expression and DNA methylation datasets. The gene expression and DNA methylation profiles were obtained from the Gene Expression Omnibus, and differentially expressed genes (DEGs) and differentially methylated sites (DMSs) were identified in the present study, using R programming software. The enriched functions of DEGs and DMSs were obtained via the Database for Annotation, Visualization and Integrated Discovery. Finally, cross analysis of DEGs and DMSs was performed to identify genes that exhibited differential expression and methylation simultaneously. The protein‑protein interaction (PPI) network of overlaps between DEGs and DMSs was obtained using the Human Protein Reference Database; the topological properties of PPI network overlaps were additionally obtained. Hub genes in the PPI network were further confirmed via reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). The results of the present study revealed that the majority of DEGs and DMSs were upregulated and hypomethylated in patients with OA, respectively. DEGs and DMSs were primarily involved in inflammatory, immune and gene expression regulation‑associated processes and pathways. Cross analysis revealed 30 genes that exhibited differential expression and methylation in OA simultaneously. Topological analysis of the PPI network revealed that numerous genes, including G protein subunit α1 (GNAI1), runt related transcription factor 2 (RUNX2) and integrin subunit β2 (ITGB2), may be involved in the development of OA. Additionally, RT‑qPCR analysis of GNAI1, RUNX2 and ITGB2 provided further confirmation. Numerous known and novel therapeutic targets were obtained via network analysis. The results of the present study may be beneficial for the diagnosis and treatment of OA.

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