Epigenetics can contribute to pathogenic mechanisms in autoimmunity, and we recently identified an imprinted DNA methylation pattern in rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS), involving multiple genes in pathways that have been implicated in cell migration, matrix regulation, and immune responses (1, 2). To understand when alterations in DNA methylation occur in RA and the specificity of the methylation changes in this disease, we compared differentially methylated loci in patients with early RA, juvenile idiopathic arthritis (JIA), longstanding RA, and osteoarthritis (OA).

Genomic DNA was isolated, as previously described (1–3), from FLS of 4 patients with early RA (symptom duration 1–13 months) fulfilling the American College of Rheumatology/European League Against Rheumatism 2010 criteria for the disease (4, 5). All 4 patients were female, and the mean age was 52 years. All were positive for anti–citrullinated peptide antibody. Two of the patients were being treated with methotrexate alone, 1 was being treated with methotrexate and abatacept, and 1 was not receiving antirheumatic drugs. Samples were obtained at the time of arthroscopic biopsy. FLS from 3 patients with JIA (2 female, 1 male; mean age 31 years) was isolated from synovium obtained at the time of arthroplasty. Twenty-two previously described patients (2)(11 with longstanding RA and 11 with OA) were used as controls. DNA methylation levels across 485,512 loci were measured using an Illumina Infinium HumanMethylation450 chip, and the methylation level at individual loci was reported as beta values (see Supplementary Methods, on the Arthritis & Rheumatology web site at http://onlinelibrary. wiley. com/doi/10.1002/art. 39123/abstract).