Abstract

Epigenome in Multiple Sclerosis
P. Casaccia^1,2; K. Castro¹; A. Ntranos³; S. Moyon¹; B. Inbar¹D.; Marechal¹; I. Katz Sand^3
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.

Abstract

Epigenome in Multiple Sclerosis
P. Casaccia^1,2; K. Castro¹; A. Ntranos³; S. Moyon¹; B. Inbar¹D.; Marechal¹; I. Katz Sand^3
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.

Abstract

Epigenome in Multiple Sclerosis
P. Casaccia^1,2; K. Castro¹; A. Ntranos³; S. Moyon¹; B. Inbar¹D.; Marechal¹; I. Katz Sand^3
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.

Background

Multiple Sclerosis is characterized by autoimmune destruction of myelin and neurons in the CNS leading to a variety of neurological symptoms. Primary progressive multiple sclerosis (PPMS) is characterized by accumulation of clinical disability from the onset, without relapses or remissions. The mechanisms underpinning MS progression are still largely unknown and specific clinical translations are lacking.

Objectives

To identify DNA methylation and gene expression changes that associate with progressive MS states using genetic, epigenetic and network analysis approaches.

Methods

Our methylome analysis in blood showed a striking increase in methylation at the NBPF locus specifically in PPMS (n=279, p=5x10^-6), which was validated in independent samples. We then discovered that genetic variants determine methylation levels at this locus (p-val. range 10^-21-10^-13) and that the strongest variant potentially associates with the risk of developing PPMS (n_PPMS=482, n_controls=11718, p<0.03, OR=1.2). The same variant associated with reduced expression of FMO5, PRKAB2 and CHD1L in blood (n=156, p-val. range 10^-7-10^-2).

Results

Notably, a large body of evidence strongly implicate the identified locus in nervous processes involved in brain size and neuropsychiatric disorders. Thus, we hypothesize that it harbors the gene(s) that predispose for progressive disability in PPMS. To functionally confirm the identified differentially methylated region (DMR) can potentially regulate gene expression in a DNA methylation-dependent manner, we have used an in-vitro epigenetic reporter system and our data showed that the DMR region has properties of a gene-regulatory region. Moreover, we investigated the putative relevance of the genes included in the NBPF locus in PPMS brain pathology by constructing an unbiased correlation network analysis using RNA-sequencing data from brain tissue samples of MS patients (n_PPMS=5 and n_SPMS=7) and controls (n=10). Strikingly, identified gene modules were found centered on genes from the NBPF locus in PPMS. Indeed, exploration of the biggest module, revealed CHD1L as a major central node within this network. Gene ontology analysis of each module underscored implication in nervous processes. Thus, this unbiased in-silico approach further supports the potential implication of genes of NBPF locus in nervous processes in PPMS patients.

Conclusions

Our DNA methylation studies along with the unbiased network analysis approach using the transcriptome data independently suggest that the locus on chromosome 1 predisposes for PPMS.

Background

The gut microbiota is emerging as a critical regulator of immune responses and appears to play an important role in MS. The International Multiple Sclerosis Microbiome study (iMSMS) is a global collaboration aimed at elucidating the role of commensal gut bacteria in MS by acquiring and analyzing samples from 2000 patients and 2000 household healthy controls.

Objectives

The iMSMS focuses on identifying the microbes, genes and pathways that are involved in MS pathogenesis and on investigating how the microbiome changes response to treatment.

Methods

A total of 576 case and household healthy control pairs were recruited from 7 centers located in the US (West and East coasts), Europe and South America. Stool samples were collected and evaluated by both 16S and shallow whole metagenome shotgun sequencing. Univariate and multivariate linear regression analyses were conducted to understand patterns of variation on gut microbiome.

Results

This is the largest MS microbiome study reported to date. Our results showed a statistically significant difference of beta diversity between MS and healthy controls for the first time in MS. Intriguingly, multiple species of Akkermansia, including the known mucin-degrading bacterium Akkermansia muciniphila, were significantly enriched in untreated MS patients after adjusting for confounding factors, but the difference was not detected in treated MS group versus control. Ruminococcus torques and Eisenbergiella tayi were also among the top significantly enriched bacteria in MS. Inversely, a main butyrate producer, Faecalibacterium prausnitzii, was significantly decreased in the untreated MS group. Functional pathways of L-tryptophan biosynthesis and L-threonine biosynthesis were slightly increased in untreated MS patients, while 5-aminoimidazole ribonucleotide biosynthesis I was increased in the treated group.

Conclusions

Our large household-controlled study allowed us to identify modest but statistically robust MS-associated changes in bacterial composition and functions. It provides the foundation for all future studies of the gut microbiota in MS. The strain-level genomic variation and microbiome-derived molecules need to be further explored for understanding microbial adaptation and pathogenicity.