Genomic DNA methylation is a modifiable epigenetic mechanism that exhibits wide-spread variation among blood cell types. Methylation can influence disease phenotypes via modulating the effects of genetic and environmental factors on gene expression. Changes in methylation at the human leukocyte antigen gene (HLA-DRB1) have been previously associated with multiple sclerosis (MS) in both T lymphocytes and monocytes. This association is influenced by the well-established MS haplotype at this locus.
To further characterise the cell-specific methylation profiles of MS by performing an epigenome-wide association study (EWAS) incorporating a statistical deconvolution of whole blood data
This was a case-control design involving subjects from the AusImmune Study. Specifically included were, 221 MS patients at first demyelination diagnosis and 468 population-based controls matched for age, sex and residential location. DNA methylation derived from whole blood was measured using Illumina EPIC arrays. EWAS analysis was performed using the ChAMP program. Cell deconvolution analysis was performed using the CellDMC function of the EpiDISH program . This method adjusts methylation levels by variation in blood cell proportions among subjects and can effectively estimate cell-specific methylation profiles without the need to do cell sorting. Gene set enrichment analysis (GSEA) was performed using the ToppGene program. All tests were assessed for statistical significance using a false discovery rate (FDR) of 0.05.
The top differentially methylated region (DMR) was HLA-DRB1, which included both hypo and hyper methylation loci (PFDR<0.05). The underlying HLA-DRB1 haplotype was strongly associated with these DMRs. Deconvolution analyses showed that the HLA-DRB1 signal specifically originated from T cells and monocytes, which is consistent with previous findings. Interestingly, cell-specific GSEA revealed associations with pathways related to axonal guidance signalling, specifically in T cells, natural killer (NK) cells, and B cells. In particular, epigenetic variation in the Netrin-1 signalling pathway in both NK and B cells was associated with MS in this cohort (PFDR<0.05). Netrin‐1, is an axon guidance protein that reduces serum levels of pro-inflammatory mediators and stabilizes the blood-brain barrier limiting the entrance of immune cells into the central nervous system. These pathways were not detected in whole blood methylation analyses, highlighting the importance of the cellular deconvolution approach.
These results provide provisional evidence that epigenetic variation in axonal signalling pathways is associated with early-stage MS in a cell-dependent manner. If validated, these findings might help guide future efforts in epigenetic medicine for MS.