O51. DNA Methylation Profiling of Synovial Fluid-Derived Fibroblast-Like Synoviocytes from Patients with Rheumatoid Arthritis Reveals Common and Distinct Changes Relative to their Tissue-Derived Counterparts

Glossop, John R.; Haworth, Kim E.; Emes, Richard D.; Nixon, Nicola B.; Packham, Jon C.; Dawes, Peter T.; Fryer, Anthony A.; Mattey, Derek L.; Farrell, William E.

Abstract

Background: Fibroblast-like synoviocytes (FLS) from patients with RA display an aggressive, invasive phenotype and play a key role in joint destruction. Increasing evidence indicates that alterations to the epigenome, including DNA methylation, contribute to the FLS phenotype in RA. Herein, we performed the first genome-wide profiling of DNA methylation in FLS derived from SF, as a more readily accessible source of disease-associated cells, in patients with RA.

Methods: Synovial fluid samples were collected during routine arthrocentesis from 12 Caucasian patients with RA and OA. FLS were isolated and expanded in vitro using standard adherent cell culture methods. Genomic DNA was extracted, bisulfite-converted and subsequently hybridized to HumanMethylation450 BeadChips for quantitative assessment of genome-wide DNA methylation at over 480 000 CpG dinucleotides. Data were analyzed using NIMBL software. A CpG was considered to be differentially methylated in RA FLS relative to OA FLS if the mean difference in methylation β-value was at least 0.1 and was statistically significant following adjustment for multiple testing. Candidate genes were validated by bisulfite pyrosequencing.

Results: Genome-wide profiling identified 328 CpGs (representing 195 genes) that were differentially methylated between RA and OA fluid-derived FLS. The majority (∼80%) of these sites/genes were hypomethylated in RA FLS. Comparison of these 195 genes with those identified in two studies of tissue-derived FLS revealed 73 genes (∼40%) that were common with at least one of these studies, and where 22 genes shared identity with both studies. Pyrosequencing analysis confirmed altered methylation of these genes and identified additional sites in some of the genes which also showed methylation changes similar to those determined at the array-identified site. We also identified 122 differentially methylated genes that were unique to fluid-derived FLS, and which perfectly segregated RA from OA-derived FLS.

Conclusion: SF-derived RA FLS show altered DNA methylation across multiple genes and a significant proportion of these are common with those identified in tissue-derived FLS. These data identify a number of potential candidate genes and support the use of fluid-derived FLS for future investigations of epigenetic dysregulation in RA synovial fibroblasts.

Citation

Glossop, J. R., Haworth, K. E., Emes, R. D., Nixon, N. B., Packham, J. C., Dawes, P. T., …Farrell, W. E. (2015). O51. DNA Methylation Profiling of Synovial Fluid-Derived Fibroblast-Like Synoviocytes from Patients with Rheumatoid Arthritis Reveals Common and Distinct Changes Relative to their Tissue-Derived Counterparts. Rheumatology, 54(S1), i48. https://doi.org/10.1093/rheumatology/kev087.003

• Journal Article Type: Conference Paper
• Online Publication Date: Apr 20, 2015
• Publication Date: 2015-04
• Deposit Date: Oct 5, 2023
• Journal: Rheumatology
• Print ISSN: 1462-0324
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 54
• Issue: S1
• Pages: i48
• DOI: https://doi.org/10.1093/rheumatology/kev087.003
• Publisher URL: https://academic.oup.com/rheumatology/article/54/suppl_1/i48/1829681