Session Title: Vasculitis
Session Type: Abstract Submissions (ACR)
Background/Purpose: Behcet’s disease (BD) is a systemic vasculitis of poorly understood etiology. Herein, we study the DNA methylome in BD for the first time and identify significant DNA methylation changes in this disease.
Methods: We studied six untreated newly diagnosed male patients with BD and six age-, sex-, and race-matched controls. Monocytes and CD4+ T cells were purified using magnetic bead separation from PBMCs. DNA was extracted from each cell subset and treated with sodium bisulfite. Genome-wide DNA methylation changes were assessed using the Illumina Infinium HumanMethylation450 BeadChip arrays. This platform allows for the interrogation of over 485,000 CpG sites within the entire genome. Percent methylation of each CpG site and differential methylation between patients and controls were determined using GenomeStudio. False discovery rate of ≤5% was applied to correct for multiple testing. Further, only CpG sites with a differential methylation score between patients and controls ≥75 (P ≤ 5X10-8), and a methylation difference of at least 1.2-fold were included in the analysis. Pathway and gene ontology analysis was performed using Ingenuity.
Results: A total of 343 hypomethylated and 337 hypermethylated CpG sites, and 232 hypomethylated and 254 hypermethylated CpG sites, were identified in BD monocytes and CD4+ T cells, respectively. The most significant DNA methylation change detected was hypomethylation in multiple CpG sites located within the HLA-C gene in both monocytes (7.9-fold) and CD4+ T cells (8.2-fold) in patients compared to controls. Differential DNA methylation between patients and controls, consistent in the two cell subsets, was also observed in HLA-DPB1, HLA-DPB2, HLA-DQA1, HLA-DQA2, HLA-DRB1, HLA-DRB6, and HLA-G. Other hypomethyled loci in BD include NOP10 (monocytes, 3.2-fold; CD4+ T cells, 4.2-fold), and SPDEF (monocytes, 2.3-fold; CD4+ T cells, 2.2-fold). Hypermethylated loci include IL17RA (monocytes, 4.0-fold; CD4+ T cells, 2.2-fold), MMP27 (monocytes, 3.8-fold; CD4+ T cells, 2.0-fold), MRPL1 (monocytes, 2.1-fold; CD4+ T cells, 5.7 fold), and SLC37A1 (monocytes, 2.0-fold; CD4+ T cells, 1.9-fold). Canonical pathway analysis of differentially methylated genes highlights the antigen-presentation pathway (monocytes, P=1.1X10-6; CD4+ T cells, P= 4.02X10-11). Indeed, transcription factor binding site analysis demonstrates enrichment of CIITA binding sites in differentially methylated genes (monocytes, P= 1.22X10-3; CD4+ T cells, P= 4.52X10-4). Cytotoxic T cell-mediated apoptosis, allograft rejection signaling, graft-versus-host disease signaling, and OX40 signaling, are also enriched pathways. Network analysis also highlights type-I interferon and NFkB signaling.
Conclusion: We performed a genome-wide DNA methylaltion study in BD using two distinct cell populations. Our data demonstrate significant genome-wide epigenetic differences between BD patients and healthy age-, sex-, and race-matched controls. We identified differential DNA methylation in the HLA locus in BD, and hypothesize that BD-associated risk alleles in the HLA might induce disease susceptibility, at least in part, by tagging a DNA methylation change.
P. S. Coit,
M. A. Jeffries,
A. H. Sawalha,
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ACR Meeting Abstracts - https://acrabstracts.org/abstract/a-genome-wide-dna-methylation-study-identifies-significant-epigenetic-changes-across-the-genome-and-in-multiple-hla-loci-in-behcets-disease/