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Series GSE135770 Query DataSets for GSE135770
Status Public on Feb 07, 2020
Title Rheumatoid arthritis patients, both newly diagnosed and methotrexate treated, show more DNA methylation differences in CD4+ memory than in CD4+ naïve T cells
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary 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. 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 harbour both the lead RA risk SNP and two DMPs in CD4+ memory T cells. 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.
Overall design Two cohorts of Rheumatoid Arthritis patiens and controls.
Contributor(s) Guderud K, Lie BA
Citation(s) 32117312
Submission date Aug 13, 2019
Last update date Mar 09, 2020
Contact name Kari Guderud
Organization name University of Oslo
Department Medical Genetics
Street address Kirkeveien 166
City Oslo
ZIP/Postal code 0450
Country Norway
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (94)
GSM4029508 IRC5101A-4m: Control CD4mem 1
GSM4029509 IRC5102A-4m: Control CD4mem 2
GSM4029510 IRC5103A-4m: Control CD4mem 3
BioProject PRJNA560040
SRA SRP218228

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Supplementary file Size Download File type/resource
GSE135770_RAW.tar 2.7 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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