Figure 2.

Methylation differences at the MHC class II locus are the largest between controls and pwMS. (a) Combined analysis of all three cohorts identified DMPs associated with MS. Volcano plot representing the 452,453 CpGs analyzed in the combined cohort DMP analysis. Red dots indicate DMPs that passed both the adjusted p-value (−log10(p) ≤ 7) and delta beta (±0.02) thresholds. Blue dots represent DMPs that passed the p-value threshold only and green dots indicate DMPs that passed the delta beta threshold only. The locus to which each DMP is mapped is indicated for genes that passed both the p-value and delta beta thresholds. (b) Genotype at HLA-DRB1 mediates methylation. Results of the CIT analysis measuring haplotype-related mediation of MS risk through methylation. p CIT: overall Omnibus CIT p-values. Dotted horizontal line represents significance threshold of p ≤ 0.05. The CpGs used for HLA-DRB1 are indexed CpGs for each of the 4 DMRs associated with MS. Dark gray = discovery dataset, light gray = validation dataset 1. (c) Correlation between HLA-DRB1 expression and CpG methylation. Top panel: cell types are listed in rows, CpGs are in columns, except for column 1, which represents gene-of-interest expression in each cell type. The correlation coefficient (R) is represented through circle size and color. A larger circle area indicates a high absolute R value (maximum 1). Red indicates negative values; blue indicates positive values. The black rectangle represents the hypomethylated DMR 2 at HLA-DRB1 identified in whole blood and cell-specific analysis. Bottom panel: whole blood methylation differences (Δβ) between pwMS and controls. Pink represent hypermethylation and blue represents hypomethylation.