Genome-wide DNA methylation changes in CD19+ B cells from relapsing-remitting multiple sclerosis patients

Abstract

Multiple Sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system. The inflammatory process in MS is driven by both T and B cells and current therapies are targeted to each of these cell types. Epigenetic mechanisms may provide a valuable link between genes and environment. DNA methylation is the best studied epigenetic mechanism and is recognized as a potential contributor to MS risk. The objective of this study was to identify DNA methylation changes associated with MS in CD19⁺ B-cells. We performed an epigenome-wide association analysis of DNA methylation in the CD19⁺ B-cells from 24 patients with relapsing-remitting MS on various treatments and 24 healthy controls using Illumina 450 K arrays. A large differentially methylated region (DMR) was observed at the lymphotoxin alpha (LTA) locus. This region was hypermethylated and contains 19 differentially methylated positions (DMPs) spanning 860 bp, all of which are located within the transcriptional start site. We also observed smaller DMRs at 4 MS-associated genes: SLC44A2, LTBR, CARD11 and CXCR5. These preliminary findings suggest that B-cell specific DNA-methylation may be associated with MS risk or response to therapy, specifically at the LTA locus. Development of B-cell specific epigenetic therapies is an attractive new avenue of research in MS treatment. Further studies are now required to validate these findings and understand their functional significance.

Figure 1

A genome-wide differential methylation plot. Data points outside the circle (red) represent increased methylation (i.e. ∆_meth)_, in multiple sclerosis (MS) patients compared to controls whereas points inside the circle (blue) represent decreased methylation in MS patients compared to healthy controls.

Figure 2

Distribution of DMPs over each of the genomic regions Y-axis represents proportion of total DMPs (7618) in each category (shown as percentage).

Figure 3

Tukey box plot showing distribution of beta values for (A) a probe where the SNP is driving the methylation values and (B) the top LTA site from this study. The box plot shows the data within the interquartile range and the median is represented by a solid black line. Whiskers show maximum and minimum values. Grey bars indicate region for each genotype (homozygous allele 1 (1/1), heterozygous (1/2), and homozygous allele 2 (2/2)). Each point represents either an individual control (blue) or MS patients (red). Y axis shows β values.

Figure 4

DMPs within the LTA TSS/5′UTR region Line graph showing the methylation level (β value) of MS cases (blue) versus controls (red) for the genomic region 31539601-31540461 for (A) CD19⁺ B cells (B) CD4⁺ T cells^, and (C) CD8⁺ T cells. The region covers 19 probes contained within the LTA gene.

Figure 5

Methylation at the MHC locus in CD19⁺ B cells Manhattan plot showing methylation level (Δ_meth) for all probes that fall within the MHC locus (Chr6: 29054321-32978719). Points above 0 represent hypermethylated sites, points below 0 represent hypomethylated sites. Grey dotted line indicates 10% change in methylation.