Identification of HLA‐DQA1 and HLA‐DRB5 as Risk Factors for Multiple Sclerosis: An Epigenome‐Wide Methylation Haplotype Association Analysis

Multiple sclerosis (MS) is a chronic central nervous system inflammatory disease of autoimmune aetiology. The disease is mostly considered due to a complex interaction between different genetic and environmental factors. DNA methylation is an epigenetic mechanism that can influence gene expression and has the potential to mediate the effects of environmental factors on MS. This study aimed to identify MS risk methylation haplotypes (meplotypes) and their associated genes by integrating epigenome-wide meplotype association analysis with gene optimisation. We conducted the first epigenome-wide meplotype association study for MS using methylation data from peripheral blood lymphocytes (PBLs) of 140 MS patients and 139 normal controls. The analytical procedure comprised the following steps: (1) conversion of DNA methylation level into menotypes; (2) identification of methylation disequilibrium (MD) block and performance of meplotype association analysis; (3) screening of risk meplotypes and their mapping to genes; (4) conducting functional analysis of the candidate genes; and (5) final identification of MS risk genes through gene optimisation. Our analysis identified 286 meplotypes across 191 MD blocks that were significantly associated with MS (p value < 0.05). Of these, 120 meplotypes were found to confer increased risk for MS susceptibility and were mapped to 134 candidate genes. Gene optimisation identified four MS risk meplotypes on three key genes: HLA-DQA1, HLA-DRB5 and HLA-DRB1. These results not only confirm the pivotal role of HLA-DRB1 in MS but also report, for the first time, an association between MS and DNA methylation patterns in HLA-DQA1 and HLA-DRB5. This study demonstrates that epigenome-wide methylation haplotype analysis offers a powerful and novel perspective for identifying MS-related genes.