Ann Rheum Dis doi:10.1136/annrheumdis-2012-201526
  • Basic and translational research
  • Extended report

DNA methylome signature in rheumatoid arthritis

  1. Gary S Firestein1
  1. 1Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
  2. 2Department of Chemistry and Biochemistry, University of California San Diego School of Medicine, La Jolla, California, USA
  1. Correspondence to Dr Gary S Firestein, Division of Rheumatology, Allergy and Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive, Mail code 0656, La Jolla, CA 92093-0656, USA; gfirestein{at}
  1. Contributors KN, DB and GF designed methods and experiments, analysed the data, and interpreted the results. KN also carried out the laboratory experiments, JW and WW developed the bioinformatic algorithms and analysed array data. KN, WW, JW and GF wrote the paper. All authors have contributed to, seen and approved the manuscript.

  • Received 14 February 2012
  • Accepted 31 May 2012
  • Published Online First 26 June 2012


Objectives Epigenetics can influence disease susceptibility and severity. While DNA methylation of individual genes has been explored in autoimmunity, no unbiased systematic analyses have been reported. Therefore, a genome-wide evaluation of DNA methylation loci in fibroblast-like synoviocytes (FLS) isolated from the site of disease in rheumatoid arthritis (RA) was performed.

Methods Genomic DNA was isolated from six RA and five osteoarthritis (OA) FLS lines and evaluated using the Illumina HumanMethylation450 chip. Cluster analysis of data was performed and corrected using Benjamini–Hochberg adjustment for multiple comparisons. Methylation was confirmed by pyrosequencing and gene expression was determined by qPCR. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes.

Results RA and control FLS segregated based on DNA methylation, with 1859 differentially methylated loci. Hypomethylated loci were identified in key genes relevant to RA, such as CHI3L1, CASP1, STAT3, MAP3K5, MEFV and WISP3. Hypermethylation was also observed, including TGFBR2 and FOXO1. Hypomethylation of individual genes was associated with increased gene expression. Grouped analysis identified 207 hypermethylated or hypomethylated genes with multiple differentially methylated loci, including COL1A1, MEFV and TNF. Hypomethylation was increased in multiple pathways related to cell migration, including focal adhesion, cell adhesion, transendothelial migration and extracellular matrix interactions. Confirmatory studies with OA and normal FLS also demonstrated segregation of RA from control FLS based on methylation pattern.

Conclusions Differentially methylated genes could alter FLS gene expression and contribute to the pathogenesis of RA. DNA methylation of critical genes suggests that RA FLS are imprinted and implicate epigenetic contributions to inflammatory arthritis.


  • ▸ Additional data are published online only. To view these files please visit the journal online (

  • Funding This project was supported by grant number UL1RR031980 from the NIH National Center for Advancing Translational Science.

  • Competing interests GSF and WW are on the Scientific Advisory Board of NexDx, Inc.

  • Patient consent Written, informed consent was obtained from participants at the time of sample collection.

  • Ethics approval All study protocols related to human studies were approved by the Institutional Review Board of the University of California San Diego.

  • Provenance and peer review Not commissioned; externally peer reviewed.