Epigenetic differences at the HTR2A locus in progressive multiple sclerosis patients

Abstract

The pathology of progressive multiple sclerosis (MS) is poorly understood. We have previously assessed DNA methylation in the CD4⁺ T cells of relapsing-remitting (RR) MS patients compared to healthy controls and identified differentially methylated regions (DMRs) in HLA-DRB1 and RNF39. This study aimed to investigate the DNA methylation profiles of the CD4⁺ T cells of progressive MS patients. DNA methylation was measured in two separate case/control cohorts using the Illumina 450K/EPIC arrays and data was analysed with the Chip Analysis Methylation Pipeline (ChAMP). Single nucleotide polymorphisms (SNPs) were assessed using the Illumina Human OmniExpress24 arrays and analysed using PLINK. Expression was assessed using the Illumina HT12 array and analysed in R using a combination of Limma and Illuminaio. We identified three DMRs at HTR2A, SLC17A9 and HDAC4 that were consistent across both cohorts. The DMR at HTR2A is located within the bounds of a haplotype block; however, the DMR remained significant after accounting for SNPs in the region. No expression changes were detected in any DMRs. HTR2A is differentially methylated in progressive MS independent of genotype. This differential methylation is not evident in RRMS, making it a potential biomarker of progressive disease.

Figure 1

HTR2A DMR plot. The mean beta value at the eight HTR2A CpG sites for controls (solid red line) and SPMS patients (dotted blue line) located within the transcription start site. Error bars show standard error of the mean.

Figure 2

Haplotype block at HTR2A. Haploview chart showing the 7 haplotype blocks at HTR2A. Blocks are indicated by a bold black outline. SNPs contained within the block are in bold and the length of the block is indicated (in base pairs) in parentheses. This plot provides information on both the r² and D′ values for better clarification of any linkage disequilibrium. The number within each diamond represents the r² value between each diagonally corresponding SNP pairs and the colour of each diamond represents the strength/value of D′ (white to bright red/0 < 100).

Figure 3

HTR2A mQTL. Mean delta beta values at cp09798090 for SNP rs6313 in either the non-risk allele (T/T) or risk allele (C/C or T/C). Healthy controls (HC) are shown in blue, SPMS are shown in read. Error bars are standard error of the mean.