Background/Purpose:   Epigenetics influences pathogenic mechanisms in autoimmunity. Recently, a stable RA DNA methylation signature in fibroblast-like synoviocytes (FLS) was defined in 2375 genes. The present study compared the DML patterns of early RA (ERA) and other inflammatory arthritides to the patterns in longstanding RA (LRA) and OA.

Methods:   Genomic DNA from FLS was isolated from arthroscopic biopsies in ERA (1-13 months of symptoms; n=4), undifferentiated arthritis that progressed to RA (UA; n=2) and ACPA+ arthralgia that did not develop arthritis (Arthralg; n=2). FLS lines were obtained from juvenile idiopathic arthritis (JIA; n=3) and spondyloarthritis (SpA; n=2) at arthroplasty. Methylation was measured using the Illumina HumanMethylation450 chip. Hierarchical clustering using Pearson correlation as the metric was performed on the methylomes of 11 LRA and 11 OA FLS lines. Principle component analysis (PCA) assessed the relationships between the different FLS types. Feature selection was determined by random forest to define ERA and LRA differences. Pathway enrichment analysis was evaluated using Kyoto Encyclopedia of Genes and Genomes (KEGG).

Results: Differentially methylated loci (DMLs) for LRA and OA segregated from each other based on the methylation pattern of 15,220 DMLs. Other non-inflammatory arthritis FLS lines clustered with LRA rather than OA. Within the non-OA cluster, LRA were highly similar to each other. DML patterns for ERA FLS were closely related to each other, but differed from the LRA. FLS from other diseases, including UA, SpA and JIA had an intermediate pattern. They were more closely related to LRA but formed subgroups within the non-OA hierarchical clustering. PCA confirmed distinct methylation patterns for LRA and OA. ERA and LRA patterns partially overlapped, which could be consistent with a transition of ERA to LRA methylation. UA was in the center of the LRA region while SpA and JIA primarily localized at the edges of LRA. The 2 Arthalg FLS lines did not conform to either OA or LRA patterns. Feature selection was performed and showed that the difference between LRA and ERA was due to 317 CpG loci. Pathway analysis suggested that DML genes in ERA involving focal adhesion, chemokine signaling, complement and coagulation are differentially methylated compared with LRA, indicating that cell recruitment in synovium evolves during the transition from early to late disease.

Conclusion: These data show a methylation signature in longstanding RA, with patterns that could be differentiated from SpA and JIA. UA patients who ultimately develop RA have a longstanding RA pattern. Most interesting, early RA had a distinct but overlapping DML pattern compared with longstanding RA with changes in cell recruitment pathways that might indicate a change in how cells enter the joint as disease progresses. Therefore, differential methylation of RA FLS occurs early and evolves over time. Understanding the transition from early and established disease provides clues identifying targets causing disease progression.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/distinctive-dna-methylome-signatures-in-early-rheumatoid-arthritis-ra-synoviocytes-compared-with-longstanding-ra-and-other-inflammatory-arthritides/