263. Genome-Wide DNA Methylation Profiling Identifies Distinct Changes in T- and B-Cell Populations from Patients with Rheumatoid Arthritis

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

Abstract

Background: DNA methylation is one of several epigenetic mechanisms that impacts on gene expression without underlying changes to the DNA sequence. Recent studies describe changes to the DNA methylome in RA. To date however, no systematic genome-wide analysis of DNA methylation in individual lymphocyte populations has been described in patients with RA. Following previous work in which we described intrinsic genome-wide methylation differences between matched T- and B-cells in healthy individuals, we now describe genome-wide methylation profiles in T- and B-cell populations from patients with RA.

Methods: Peripheral blood samples were collected from 12 Caucasian, seropositive female patients with established RA, and from 12 age-matched, healthy Caucasian females. CD3+ T-cells and CD19+ B-cells were isolated and genomic DNA was extracted, bisulphite-converted, and hybridized to HumanMethylation450 BeadChips for quantitative assessment of DNA methylation at over 450,000 CpG dinucleotides. Array data processing and analysis were performed using NIMBL software. CpGs differentially methylated in T- and B-cells were defined as those for which six or more RA samples showed a methylation level greater than the healthy group mean ± two-times the standard deviation.

Results: Initial analysis of global DNA methylation levels by assessment of LINE-1 methylation revealed a subtle but statistically significant increase in methylation in B-cells compared with T-cells (p ≤ 0.01). These differences were apparent in RA patients and healthy individuals alike. Comparison of genome-wide DNA methylation profiles in RA derived T- and B-cells revealed significant differences in methylation, differences that were similar to those we previously observed in healthy individuals. Moreover, in RA patients we identified methylation differences at multiple individual CpG sites that were disease-specific and distinct to either T- or B-cell populations. In these cases, 32 CpGs in T-cells and 20 CpGs in B-cells, representing 15 and 10 genes respectively, were differentially methylated in multiple RA samples compared with healthy controls. Of the CpGs identified in T-cells, approximately equal numbers were hypermethylated as were hypomethylated. Conversely, all of the CpGs identified in B-cells were hypomethylated in RA patients. Approximately 60% of sites in T-cells and 40% in B-cells were associated with a CpG island or the surrounding island shores/shelves. Hierarchical clustering of RA derived CpG candidates was suggestive for patients and healthy controls clustering separately. The lack of perfect segregation may reflect the absolute numbers in the analysis.

Conclusion: These findings, whilst preliminary, suggest disease-specific changes in DNA methylation for a restricted and distinct set of CpGs in T- and B-cells from patients with RA. Our on-going studies and those of other investigators will help to define the role of these changes in the genesis and progression of RA, and their potential utility in clinical management.

Citation

Glossop, J. R., Nixon, N. B., Emes, R. D., Haworth, K. E., Packham, J. C., Dawes, P. T., …Farrell, W. E. (2014, April). 263. Genome-Wide DNA Methylation Profiling Identifies Distinct Changes in T- and B-Cell Populations from Patients with Rheumatoid Arthritis. Paper presented at Rheumatology 2014, Liverpool, UK

• Presentation Conference Type: Conference Paper (unpublished)
• Conference Name: Rheumatology 2014
• Conference Location: Liverpool, UK
• Start Date: Apr 29, 2014
• End Date: May 1, 2014
• Deposit Date: Oct 5, 2023
• Publisher: Oxford University Press
• DOI: https://doi.org/10.1093/rheumatology/keu122.001
• Keywords: Pharmacology (medical); Rheumatology
• Publisher URL: https://academic.oup.com/rheumatology/article/53/suppl_1/i157/1796246