Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4+ Memory Than in CD4+ Naïve T Cells.

Kari Guderud,Sören Franzenburg,Espen A Haavardsholm,Simon Rayner,Marthe T Mæhlen,Maria D Mjaavatten,Andre Franke,Siri Lillegraven,Ida M Evenrød,Bettina K Andreassen,Kristina Gervin,Benedicte A Lie,Siri T Flåm,Ellen S Norli,Line H Sunde,Anna-Birgitte Aga

doi:10.3389/fimmu.2020.00194

Abstract

Background: Differences in DNA methylation have been reported in B and T lymphocyte populations, including CD4+ T cells, isolated from rheumatoid arthritis (RA) patients when compared to healthy controls. CD4+ T cells are a heterogeneous cell type with subpopulations displaying distinct DNA methylation patterns. In this study, we investigated DNA methylation using reduced representation bisulfite sequencing in two CD4+ T cell populations (CD4+ memory and naïve cells) in three groups: newly diagnosed, disease modifying antirheumatic drugs (DMARD) naïve RA patients (N = 11), methotrexate (MTX) treated RA patients (N = 18), and healthy controls (N = 9) matched for age, gender and smoking status.Results: Analyses of these data revealed significantly more differentially methylated positions (DMPs) in CD4+ memory than in CD4+ naïve T cells (904 vs. 19 DMPs) in RA patients compared to controls. The majority of DMPs (72%) identified in newly diagnosed and DMARD naïve RA patients with active disease showed increased DNA methylation (39 DMPs), whereas most DMPs (80%) identified in the MTX treated RA patients in remission displayed decreased DNA methylation (694 DMPs). Interestingly, we also found that about one third of the 101 known RA risk loci overlapped (±500 kb) with the DMPs. Notably, introns of the UBASH3A gene harbor both the lead RA risk SNP and two DMPs in CD4+ memory T cells.Conclusion: Our results suggest that RA associated DNA methylation differences vary between the two T cell subsets, but are also influenced by RA characteristics such as disease activity, disease duration and/or MTX treatment.

Highlights

Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes pain and swelling of multiple joints in the body
We investigated whether any of the significant differentially methylated positions (DMPs) overlapped with RA susceptibility loci [30] (±500 kb from the lead single nucleotide polymorphisms (SNPs)) in CD4+ memory T cells (Supplementary Table 4). 32 of the 101 tested RA risk SNPs were within 500 kb of at least one DMP
We observed a higher global mean methylation in CD4+ naïve T cells than in CD4+ memory T cells, which is in accordance with observations on a whole genome-wide level, where a loss of DNA methylation occurs upon transition from naïve to memory CD4+ T cells [16]

Summary

Introduction

Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes pain and swelling of multiple joints in the body. Environmental and epigenetic factors are thought to be involved in the RA disease pathogenesis [3] of which smoking is the only established environmental risk factor [4, 5]. Differences in DNA methylation have been reported in B and T lymphocyte populations, including CD4+ T cells, isolated from rheumatoid arthritis (RA) patients when compared to healthy controls. We investigated DNA methylation using reduced representation bisulfite sequencing in two CD4+ T cell populations (CD4+ memory and naïve cells) in three groups: newly diagnosed, disease modifying antirheumatic drugs (DMARD) naïve RA patients (N = 11), methotrexate (MTX) treated RA patients (N = 18), and healthy controls (N = 9) matched for age, gender and smoking status

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