Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes

Nat Commun. 2016 Jun 10;7:11849. doi: 10.1038/ncomms11849.


Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. Using genome-wide methods, we show differences between RA knee and hip FLS in the methylation of genes encoding biological pathways, such as IL-6 signalling via JAK-STAT pathway. Furthermore, differentially expressed genes are identified between knee and hip FLS using RNA-sequencing. Double-evidenced genes that are both differentially methylated and expressed include multiple HOX genes. Joint-specific DNA signatures suggest that RA disease mechanisms might vary from joint to joint, thus potentially explaining some of the diversity of drug responses in RA patients.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arthritis, Rheumatoid / genetics*
  • Arthritis, Rheumatoid / pathology*
  • Cluster Analysis
  • DNA Methylation / genetics*
  • Databases as Topic
  • Female
  • Fibroblasts / metabolism
  • Fibroblasts / pathology
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Hip / pathology
  • Humans
  • Interleukin-6 / metabolism
  • Joints / metabolism*
  • Joints / pathology*
  • Knee / pathology
  • Middle Aged
  • Organ Specificity / genetics
  • Osteoarthritis / genetics
  • Osteoarthritis / pathology
  • Principal Component Analysis
  • Reproducibility of Results
  • Signal Transduction / genetics
  • Synoviocytes / metabolism
  • Synoviocytes / pathology
  • Transcriptome / genetics*


  • Interleukin-6