title: An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype.
abstract: BACKGROUND
  A DNA methylation signature has been characterized that distinguishes rheumatoid arthritis (RA) fibroblast like synoviocytes (FLS) from osteoarthritis (OA) FLS. The presence of epigenetic changes in long-term cultured cells suggest that rheumatoid FLS imprinting might contribute to pathogenic behavior. To understand how differentially methylated genes (DMGs) might participate in the pathogenesis of RA, we evaluated the stability of the RA signature and whether DMGs are enriched in specific pathways and ontology categories.
  
  
  METHODS
  To assess the RA methylation signatures the Illumina HumanMethylation450 chip was used to compare methylation levels in RA, OA, and normal (NL) FLS at passage 3, 5, and 7. Then methylation frequencies at CpGs within the signature were compared between passages. To assess the enrichment of DMGs in specific pathways, DMGs were identified as genes that possess significantly differential methylated loci within their promoter regions. These sets of DMGs were then compared to pathway and ontology databases to establish enrichment in specific categories.
  
  
  RESULTS
  Initial studies compared passage 3, 5, and 7 FLS from RA, OA, and NL. The patterns of differential methylation of each individual FLS line were very similar regardless of passage number. Using the most robust analysis, 20 out of 272 KEGG pathways and 43 out of 34,400 GO pathways were significantly altered for RA compared with OA and NL FLS. Most interestingly, we found that the KEGG 'Rheumatoid Arthritis' pathway was consistently the most significantly enriched with differentially methylated loci. Additional pathways involved with innate immunity (Complement and Coagulation, Toll-like Receptors, NOD-like Receptors, and Cytosolic DNA-sensing), cell adhesion (Focal Adhesion, Cell Adhesion Molecule), and cytokines (Cytokine-cytokine Receptor). Taken together, KEGG and GO pathway analysis demonstrates non-random epigenetic imprinting of RA FLS.
  
  
  CONCLUSIONS
  The DNA methylation patterns include anomalies in key genes implicated in the pathogenesis of RA and are stable for multiple cell passages. Persistent epigenetic alterations could contribute to the aggressive phenotype of RA synoviocytes and identify potential therapeutic targets that could modulate the pathogenic behavior.
authors: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
authors: John W
authors: JW
authors: Whitaker
authors: Ignyta, Inc., San Diego, CA, USA.
authors: Robert
authors: R
authors: Shoemaker
authors: Division of Rheumatology, Allergy and Immunology, UCSD School of Medicine, La Jolla, CA, USA.
authors: David L
authors: DL
authors: Boyle
authors: Division of Rheumatology, Allergy and Immunology, UCSD School of Medicine, La Jolla, CA, USA.
authors: Josh
authors: J
authors: Hillman
authors: Ignyta, Inc., San Diego, CA, USA.
authors: David
authors: D
authors: Anderson
authors: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
authors: Wei
authors: W
authors: Wang
authors: Division of Rheumatology, Allergy and Immunology, UCSD School of Medicine, La Jolla, CA, USA.
authors: Gary S
authors: GS
authors: Firestein
references: Immunol Rev. 2010 Jan;233(1):233-55
references: 20193003
references: Arthritis Rheum. 1996 Nov;39(11):1781-90
references: 8912499
references: Arthritis Res. 2002;4(2):117-25
references: 11879547
references: Mol Immunol. 2009 Nov;47(1):12-8
references: 19232437
references: Science. 2007 Feb 16;315(5814):1006-10
references: 17255475
references: Curr Opin Rheumatol. 2003 May;15(3):274-9
references: 12707581
references: J Clin Invest. 1989 Apr;83(4):1267-76
references: 2784799
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
references: 22080510
references: Nat Genet. 2012 Nov;44(11):1207-14
references: 23064413
references: Arthritis Rheum. 1991 Sep;34(9):1094-105
references: 1657009
references: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references: 12883005
references: Nat Med. 2009 Dec;15(12):1414-20
references: 19898488
references: Clin Diagn Lab Immunol. 2003 Nov;10(6):1002-10
references: 14607859
references: BioDrugs. 2012 Jun 1;26(3):131-41
references: 22494429
references: Ann Rheum Dis. 2013 Jan;72(1):110-7
references: 22736089
references: Genome Res. 2010 Mar;20(3):320-31
references: 20133333
references: Nature. 2003 May 15;423(6937):356-61
references: 12748655
references: Nat Rev Rheumatol. 2013 Jan;9(1):24-33
references: 23147896
references: Am J Pathol. 1996 Nov;149(5):1607-15
references: 8909250
references: Arthritis Rheum. 2009 Feb;60(2):355-63
references: 19180502
references: Nature. 2009 Nov 19;462(7271):315-22
references: 19829295
references: J Immunol. 2013 Feb 1;190(3):1297-303
references: 23277489
references: Springer Semin Immunopathol. 2003 Aug;25(1):79-90
references: 12904893
references: Cell Immunol. 2005 Feb;233(2):90-6
references: 15963480
references: Arthritis Rheum. 1988 Mar;31(3):315-24
references: 3358796
references: Arthritis Rheum. 2011 Jun;63(6):1626-36
references: 21337319