DNA methylation changes in brains from multiple sclerosis patients

Introduction: The mechanisms underlying brain pathology in Multiple Sclerosis (MS) are still poorly understood. The study of stable epigenetic modifications, such as DNA methylation (5mC), that orchestrates genome activity in response to environmental cues could unravel both the causes and driving mechanisms underlying neurodegeneration in MS. DNA methylation, which often associates with gene repression, can be reliably measured in postmortem brain samples. Recently, another epigenetic mark, DNA hydroxymethylation (5hmC), has gained particular attention due to high abundance in brain tissue and its specific genomic distribution and regulatory properties.
Objectives: We aim to gain more insight into MS brain pathology by profiling DNA methylation changes in affected and control brains.
Methods: Genomic DNA was extracted from snap frozen brain tissue blocks collected within 24h post-mortem (Multiple Sclerosis and Parkinson's Tissue Bank, Imperial College London). Samples were treated in parallel with oxidative bisulfite (oxBS) and BS for detection of 5mC and cumulative 5mC+5hmC levels, respectively, using the Infinium HumanMethylation450 BeadChip array, which covers 99% of RefSeq genes. We set up a bioinformatics analysis pipeline to quantify levels of both 5mC and 5hmC genome-wide. We functionally investigated DNA methylation changes using published RNAseq data and immunohistofluorescence from brain tissue of MS patients and controls.
Results: Multidimensional scaling, principal component analysis and cluster analysis revealed a significant impact of tissue composition, which is necessary to be taken into account prior to further examining differences between MS patients and controls. In total, we identified 2811 and 1534 significant (genome-wide adjusted P-Value < 0.05) 5mC and 5hmC positions differing between MS patients and controls. We found striking hypo-5mC and hyper-5hmC changes, which correlated with transcriptional differences in MS patients compared to controls.

DNA methylation Multiple sclerosis