PS08.01 - The Epigenome and Multiple Sclerosis
Epigenome in Multiple Sclerosis
P. Casaccia1,2; K. Castro1; A. Ntranos3; S. Moyon1; B. Inbar1D.; Marechal1; I. Katz Sand3
1Neuroscience Initiative, CUNY Advanced Science Research Center at The Graduate Center, New York, NY; 2Neuroscience, 3Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
Background: Multiple Sclerosis results from the interaction of genetic predisposition and environmental exposure. Epigenetics refers to the molecular mechanisms by which cells “interpret” external signals, and modulate gene expression. These mechanisms are unique for each cell type and age-dependent. This presentation is focused on DNA methylation.
Objectives: We previously reported differences in the genome-wide distribution of DNA methylation in the normal appearing white matter in post-mortem brains from Multiple Sclerosis patients compared to healthy controls. We generated a mouse model to test the functional relevance of those genes initially identified as hypermethylated in MS brains. In addition, I will review our epigenomic studies conducted in peripheral cells isolated from peripheral blood of RRMS patients.
Methods: DNA methylation was conducted using Illumina bead chip on monocytes from 54 relapsing-remitting therapy-naïve female patients with low or high body mass and in CD4+ lymphocytes, from 47 therapy naive patients, 35 on dimethylfumarate (DMF) and 16 glatiramer acetate (GA) . Functional characterization of novel mouse models generated to test the functional relevance of genes hypermethylated in MS brains will be presented.
Results: DNA methylation in monocytes from RRMS patients differed between high and low BMI groups. Functionally, high BMI correlated with high ceramide levels which induced DNA hypermethylation, affected gene expression and increased the number of circulating monocytes. In patients at the 2 year follow up, the high BMI group showed worsening disability, an effect that could be reproduced in animal models. The study in CD4+ lymphocytes, highlighted the effect of DMF on hypermethylation on the microRNA MIR- 21, which is critical for the differentiation of T helper-17 cells.
Conclusions: External factors, such as disease state, BMI or therapy, affect the behavior of distinct cell types by creating cell-specific DNA methylation patterns in the CNS and in the periphery. These epigenomic changes impact T cell differentiation, modulate the number of circulating monocytes and also affect the ability of oligodendrocyte progenitors to form new myelin after demyelination. Together with additional ongoing studies in mouse models, our results underscore the importance of the epigenome as mediator of the effect of external variables and life style factors on distinct cell types, eventually modulating MS disease course.
PS08.02 - Mendelian Randomization in MS
Traditional epidemiological observational studies in multiple sclerosis (MS) can be biased by confounding, which occurs when there is a common cause of the exposure and the outcome. Further, given the insidious onset of the disease, measuring the exposure prior to the date of diagnosis, does not guarantee against reverse causation, where the outcome directly influences the exposure. An established method to overcome these issues is Mendelian randomization (MR).
In this invited talk, I will discuss recent advances in MR and how they can improve causal inference in the field of MS. Specifically, I will draw upon studies from our group and others that have used MR to shed light on factors that likely influence predisposion to MS. I will discuss new and emerging methods in the field of MR and focus upon proper reporting of MS studies to ensure that they can be interpreted and applied by clinicians.
I will review recent studies in the field of MS, which use GWAS and emerging sequencing studies to better understand the causal pathways that influence this disease.
In this invited talk, I will discuss results from recent MR studies and provide practical tips on the implementation of such studies in the field of MS.
MR studies can make important contributions to our understanding of the causes of MS and in some cases can help to prioritize randomized controlled trials, as well as provide causal inference information when such trials are not impossible of unethical. Taken together, the findings from recent MR studies in MS have helped to disentangle multiple controversies in the field and help to provide orthogonal lines of evidence to test long-standing hypothesis in the field.
PS08.03 - Deconvolution of epigenetic profiles reveals blood cell-specific pathways associated with early stage Multiple Sclerosis in the AusImmune Study
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.
PS08.04 - Polygenic Risk Score Analysis in Multiple Sclerosis
The International Multiple Sclerosis Genetics Consortium (IMSGC) uncovered the contribution of inherited variants to multiple sclerosis (MS) in 115,801 individuals. Polygenic risk profiling intends to summarize and represent the genetic architecture of complex disorders and identify groups of individuals who can benefit from the knowledge of their increased susceptibility. In this context, it is important to explore the relationships between polygenic risk scores (PRS) in MS with disease status and severity in population-level and familial cohorts, in order to leverage potential clinical utilities.
To develop and assess quantifiable measures of MS susceptibility and examine their association with phenotypic variability.
We employed both the Bayesian LDPred algorithm and Pruning and Thresholding to develop multiple MS-PRS from a multi-cohort GWAS comprising 41,505 participants. Models were validated in the UK Biobank phase 1 dataset and tested in both the UK Biobank phase 2 and the Kaiser Permanente Northern California (KPNC) MS datasets. PRS of families was tested in a cohort of 34 families with one affected parent and at least one affected child. Clinical phenotype data was used in the UCSF EPIC cohort including 742 MS patients. Standard quality control of the base (IMSGC) and target datasets was performed prior to final analyses.
We observed a statistically significant difference between PRS distributions of cases and controls in both the UK Biobank and KPNC cohorts (P < 1e-70), and identified individuals at greater risk versus the rest of the population (OR > 3). We confirmed that an increased PRS in siblings of disease discordant parents is associated with a higher risk of MS and showed an enhanced power for disease prediction among siblings in a small cohort of 152 individuals. These results suggest that PRS metric shows promise for prediction of MS within sibships, but needs to be further tested in larger familial cohorts. The predictive prognostic value of PRS for selected MRI metrics and disability scores suggests that PRS modestly explain phenotypic variations.
Polygenic risk scores are currently the best estimate of the complex genetic architecture of MS and, when clinically implemented, could facilitate recognition and management of MS in early stages of the disease. These results provide a direction for translation of MS-GWAS studies into relevant biology and clinically meaningful outcomes.
PS08.05 - Functional changes associated to the Multiple Sclerosis risk polymorphism in the HHEX gene
Genome-wide association studies (GWAS) identified 233 SNPs (Single Nucleotide Polymorphisms) increasing multiple sclerosis (MS) susceptibility, with a main involvement of immune peripheral cells and microglia. One of these variants, rs7923837, described as eQTL in healthy individuals, is located near the HHEX (Hematopoietically Expressed Homeobox) gene, which encodes a key transcription factor in lymphopoiesis and contributes to metabolism-related traits and diseases.
We aimed at understanding the impact of rs7923837 polymorphism located in the 3'UTR (Untranslated Region) of the HHEX gene on MS risk
The study included 154 MS patients and 117 healthy controls. The SNP rs7923837 was genotyped by TaqMan technology. Levels of expression of the HHEX gene were ascertained by real time PCR and normalized to the GUS housekeeping gene. HHEX nuclear translocation was analyzed by confocal microscopy. Extracellular acidification (ECAR) and oxygen consumption rate (OCR) were measured in peripheral blood mononuclear cells (PBMCs) with and without phytohemagglutinin (PHA) stimulation, in a Seahorse XFp Extracellular Flux Analyzer (Agilent). Mitochondrial mass was measured by FACS in PBMCs with mitotracker florescence probe.
Lower levels of expression of the HHEX gene were detected in MS patients compared to controls (p=0.037). As previously described in whole blood of healthy controls, the risk polymorphism acts as eQTL in PBMCs of MS patients. The AA genotype not only showed reduced levels of mRNA expression in MS patients, but also an increased nuclear localization, in contrast to the lower nuclear localization found in controls with this genotype. In addition, PHA stimulation in PBMCs of AA-homozygotes significantly increased mitochondrial mass in controls compared with MS patients (p=0.009). The influence of genotypes in rs7923837 on the values of ECAR and OCR, indicative of glycolysis and oxidative phosphorylation respectively, were analyzed. Significant differences in ECAR were evidenced by comparison of either homozygous genotype between MS patients and controls. In basal conditions, a consistent trend to higher OCR was observed for MS patients compared with healthy controls. After PHA stimulation, AA-homozygous individuals presented increased mitochondrial maximal respiration and spare respiratory capacity, and AA-homozygous patients showed higher no mitochondrial oxygen consumption.
In MS patients, the homozygous AA genotype of rs7923837 in HHEX determines low levels of mRNA expression and increased nuclear location, presumably altering its function as a transcription factor. Moreover, MS patients display higher values than healthy controls in some parameters of mitochondrial respiration. Those differences are increased in minor allele homozygotes for rs7923837, and reflect a differential coupling between minor and major homozygous genotypes in MS patients.