Genome‐Wide DNA Methylation Study Identifies Significant Epigenomic Changes in Osteoarthritic Cartilage

<jats:sec><jats:title>Objective</jats:title><jats:p>To perform a genome‐wide DNA methylation study to identify DNA methylation changes in osteoarthritic (OA) cartilage tissue.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>The contribution of differentially methylated genes to OA pathogenesis was assessed by bioinformatic analysis, gene expression analysis, and histopathologic severity correlation. Genome‐wide DNA methylation profiling of >485,000 methylation sites was performed on eroded and intact cartilage from within the same joint of 24 patients undergoing hip arthroplasty for OA. Genes with differentially methylated CpG sites were analyzed to identify overrepresented gene ontologies, pathways, and upstream regulators. The messenger RNA expression of a subset of differentially methylated genes was analyzed by reverse transcription–polymerase chain reaction. Histopathology was graded by modified Mankin score and correlated with DNA methylation.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We identified 550 differentially methylated sites in OA. Most (69%) were hypomethylated and enriched among gene enhancers. We found differential methylation in genes with prior links to OA, including <jats:italic>RUNX1</jats:italic>, <jats:italic>RUNX2</jats:italic>, <jats:italic>DLX5</jats:italic>, <jats:italic>FURIN</jats:italic>, <jats:italic>HTRA1</jats:italic>, <jats:italic>FGFR2</jats:italic>, <jats:italic>NFATC1</jats:italic>, <jats:italic>SNCAIP</jats:italic>, and <jats:italic>COL11A2</jats:italic>. Among these, <jats:italic>RUNX1</jats:italic>, <jats:italic>HTRA1</jats:italic>, <jats:italic>FGFR2</jats:italic>, and <jats:italic>COL11A2</jats:italic> were also differentially expressed. Furthermore, we found differential methylation in approximately one‐third of known OA susceptibility genes. Among differentially methylated genes, upstream regulator analysis showed enrichment of <jats:italic>TGFB1</jats:italic> (<jats:italic>P</jats:italic> = 4.40 × 10<jats:sup>−5</jats:sup>) and several microRNAs including miR‐128 (<jats:italic>P</jats:italic> = 4.48 × 10<jats:sup>−13</jats:sup>), miR‐27a (<jats:italic>P</jats:italic> = 4.15 × 10<jats:sup>−12</jats:sup>), and miR‐9 (<jats:italic>P</jats:italic> = 9.20 × 10<jats:sup>−10</jats:sup>). Finally, we identified strong correlations between 20 CpG sites and the histologic Mankin score in OA.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>Our data implicate epigenetic dysregulation of a host of genes and pathways in OA, including a number of OA susceptibility genes. Furthermore, we identified correlations between CpG methylation and histologic severity in OA.</jats:p></jats:sec>