THU0005 VARIABILITY OF DNA METHYLATION IS A DRIVER OF LYMPHOCYTE DYSREGULATION IN EARLY RHEUMATOID ARTHRITIS.
Authors: A. Clark, N. Naamane, N. Nair, A. Anderson, N. Thalayasingam, J. Diboll, A. Barton, S. Eyre, J. D. Isaacs, L. Reynard, A. Pratt
Journal: Annals of the Rheumatic Diseases (2020)

Background: DNA methylation patterns differ between leukocyte subsets and mediate the impact of environmental exposures on the molecular and functional phenotype of immune cells. Besides differences in mean methylation of CpG positions amongst patients with immune mediated diseases, recent evidence indicates variability of site-specific DNA methylation also contributes to pathogenesis 1,2 . Objectives: To seek evidence of altered DNA methylation patterns in RA, controlling for systemic inflammation and immunotherapy use. Methods: Patients with confirmed clinical diagnoses were enrolled from the Northeast Early Arthritis Cohort (NEAC). CD4 + and CD19 + lymphocytes were isolated from fresh blood by positive selection prior to therapeutic immune modulation. Methylation was quantified in cell subset-specific DNA (Infinium MethylationEPIC BeadChip, Illumina) 3 . Differentially methylated positions and regions (DMPs, DMRs) between RA and non-RA patients were identified (linear modelling, filtering on 5% pairwise difference in mean DNA methylation, and DMRcate package). Next, to identify instances where methylation variance differed between comparator groups, Bartlett’s test was performed using the iEVORA package, which accounts for outlier values 4 . Findings were controlled for technical confounders and subject to multiple test correction (FDR). A validated hypergeometric test was used to annotate enriched pathways. Results: After sample- and probe-level quality control, CD4+ and B lymphocyte specific data were respectively available for 45 and 49 RA patients, and 64 and 81 disease controls matched for systemic inflammation (CRP, ESR). No DMPs were identified in either cell type at FDR &lt; 0.05 and Δβ ≥0.05. Only following relaxation of multiple test correction was it possible to identify DMRs in either cell type, most notably encapsulating 10 CpGs relatively hypomethylated at the promoter of the endosome protein-encoding RUFY1 gene in CD4+ lymphocytes of RA patients (Δβ = 0.076). By contrast, striking evidence for differential variation in DNA methylation was observed at 291 and 601 CpGs of CD4+ and B lymphocytes, respectively (exemplars depicted in Figure 1). Only 15 of these differentially variable positions (DVPs) were common to both cell types. Pathway analysis highlighted potential functional consequences of DVP associations; for example, RA-specific hypervariability implicates prostaglandinsignalling in CD4+ lymphocytes. Conclusion: We highlight a role for altered variability in DNA methylation during the molecular pathogenesis of RA, and emphasise the importance of its study in relevant cell subsets. References: [1]Paul DS et al . Nature Communications 7, 13555 doi: 10.1038/ncomms13555 (2016). [2]Webster AP et al. Genome Medicine 10, 64 (2018) doi: 10.1186/s13073-018-0575-9. [3]Clark AD et al. Journal of Allergy and Clinical Immunology 2019; doi: 10.1016/j.jaci.2019.12.910 [4]Teschendorff AE et al. Nature Communications 2016; 7:12. Disclosure of Interests: Alexander Clark: None declared, Najib Naamane: None declared, Nisha Nair: None declared, Amy Anderson: None declared, Nishanthi Thalayasingam: None declared, Julie Diboll: None declared, Anne Barton Consultant of: AbbVie, Stephen Eyre: None declared, John D Isaacs Consultant of: AbbVie, Bristol-Myers Squibb, Eli Lilly, Gilead, Janssen, Merck, Pfizer, Roche, Louise Reynard: None declared, Arthur Pratt Grant/research support from: Pfizer, GlaxoSmithKlein