Karolinska Institutet
Clinical Neuroscience

Author Of 3 Presentations

Biomarkers and Bioinformatics Poster Presentation

P0136 - Profiling of small non-coding RNAs across cellular and biofluid compartments in patients with Multiple Sclerosis (ID 1195)

Speakers
Presentation Number
P0136
Presentation Topic
Biomarkers and Bioinformatics

Abstract

Background

Small non-coding RNAs (sncRNAs) are important regulators of gene expression at the transcriptional and post-transcriptional levels in various biological contexts, such as regulation of immune system functions, homeostasis, and autoimmunity development. While the role of microRNAs (miRNAs) in multiple sclerosis (MS) has attained major interest, studies investigating other sncRNA classes, especially in the target central nervous system compartment, are still scarce.

Objectives

We aimed to perform a comprehensive, comparative analysis of all classes of sncRNAs in matching peripheral blood mononuclear cells (PBMCs), plasma, cerebrospinal fluid (CSF) cells, and cell-free CSF from MS patients and controls.

Methods

23 relapsing-remitting (RRMS, n=12 in relapse, n=11 in remission), 6 secondary progressive (SPMS) MS patients and 16 non-inflammatory and inflammatory neurological disease controls (NINDC, n=11; INDC, n=5) were included in the analysis. We utilized Small-seq (Faridani et al., Nat Biotechnol. 2016) to quantify sncRNA transcripts.

Results

We observed distinct and variable profiles of sncRNA classes across all analyzed cellular and biofluid compartments. While miRNAs were the most abundant class of sncRNAs in PBMCs and plasma, transfer RNAs represented the most abundant class in CSF cells and cell-free CSF. Furthermore, we observed an opposing quantitative pattern of small nuclear, nucleolar, transfer RNAs, and miRNAs changes between the blood and CNS compartments. In CSF cells, 133/133 and 115/117 differentially expressed sncRNAs were increased in RRMS relapse compared to remission and RRMS compared to NINDC, respectively. In contrast, 65/67 differentially expressed PBMC sncRNAs were decreased in RRMS compared to NINDC. These findings underscore the importance of including both the peripheral and intrathecal compartments in studies investigating the role of sncRNAs in MS.

Conclusions

Our findings demonstrate widespread alterations of several classes of sncRNAs, particularly during the relapse phase in CSF cells. Genome-wide small non-coding RNA profiling provides therefore an informative moleculer panel for addressing MS pathogenesis, where further research may lead to the identification of novel biomarkers and possible treatment targets.

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Genetics and Epigenetics Poster Presentation

P0525 - Investigating a role of B cells and their depletion in relapsing-remitting Multiple Sclerosis using DNA methylation patterns (ID 892)

Speakers
Presentation Number
P0525
Presentation Topic
Genetics and Epigenetics

Abstract

Background

Multiple Sclerosis (MS) is a chronic inflammatory disease characterized by autoimmune attack and destruction of myelin and neuroaxonal degeneration in the central nervous system (CNS). Previous reports have indicated that widespread differences in DNA methylation between MS cases and healthy controls in B cells. Importantly, B cells have come under renewed interest due to the effectiveness of treatments that deplete B cells, such as rituximab.

Objectives

To characterize epigenetic changes and their functional consequences in CD19+ B cells from MS patients, and to investigate changes in CD4+ T cells and CD14+ monocytes following B cell depletion with rituximab.

Methods

We measured DNA methylation in CD19+ B cells sorted from peripheral blood from relapsing-remitting (RRMS) (n= 26) and healthy controls (HC) (n = 15), which we compared and integrated with previously analyzed cohort (RRMS n = 12, HC n = 10). We also quantified DNA methylation in CD4+ T cells (n = 17) and CD14+ monocytes (n = 17) sorted from peripheral blood at baseline and 6 months of rituximab treatment. DNA methylation was measured using Infinium HumanMethylationEPIC arrays. Rituximab results were compared with results from a dimethyl fumarate treated cohort.

Results

Meta-analysis of the two B cell cohorts revealed 3 003 differentially methylated CpGs between RRMS and HC (with adjusted p-value < 0.05). Pathway analyses of the cohorts implicated dysregulation of genes involved in cell-to-cell communication, cell migration and activation. Rituximab treatment did not yield genome-wide significant changes in DNA methylation in CD4+ and CD14+ cells likely due to the indirect action of the drugs. Nevertheless pathway analysis of candidate differentially methylated CpGs associated with changes in activation immune activation, subset differentiation and motility being affected by B cell depletion.

Conclusions

Our data establish that B cells from MS patients acquire a distinct epigenetic profile connected to changes in pathways of importance for B cell functions. Furthermore, we demonstrate changes in other cell types following B cell depletion as a therapeutic modality.

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Pathogenesis – Immunology Poster Presentation

P0956 - DNA methylation of cerebrospinal fluid cells in Multiple Sclerosis (ID 1193)

Speakers
Presentation Number
P0956
Presentation Topic
Pathogenesis – Immunology

Abstract

Background

Multiple Sclerosis (MS) is a chronic inflammatory disease of a yet unknown cause characterized by autoimmune destruction of myelin and neurons in the central nervous system. Immune cells from the cerebrospinal fluid (CSF) can provide valuable insight into the pathogenic processes occurring in the typically inaccessible target organ; however, they have not been sufficiently utilized due to low numbers. DNA methylation is an epigenetic modification that without altering the genetic code can stably change the expression of genes and thus may play an important role in MS development. Moreover, due to stability, high specificity and the ability to be measured in limited amounts of material genome-wide, methylation changes may assist in studying MS pathogenesis.

Objectives

We aimed to establish and optimize a genome-wide methylation approach to investigate methylation changes that render immune cells pathogenic in MS with the prospect of better understanding disease pathogenesis.

Methods

Cells from the CSF of relapsing-remitting MS (RRMS n=5) and age- and sex-matched non-inflammatory controls (NINDC n=5) were extracted. Whole-genome bisulfite sequencing (WGBS) libraries were generated using the post-bisulfite adaptor tagging (PBAT) protocol, which originally was designed for single-cell and adapted to the limited cell amount as previously described (1). Results were replicated in a larger cohort (RRMS n=18 and NINDC n=7), while the reliability of the methodology was confirmed with technical replication of the original cohort.

Results

We first explored the global landscape of CpG methylation levels, as well as specific genomic features including promoters, enhancers and CTCF binding sites. We conducted statistical analysis based on three distinct methods, which identified differentially methylated CpG (DMCs). Methylation levels calculated in the sequencing data were well correlated with the independent technical replicates where the sequencing depths were comparatively lower which gave more evidence the less sequenced data can reflect the true values to some degree. Besides, in the replicate sample groups, a large proportion of DMCs changed in the same direction when applying a minimal 0.2 difference. Moreover, NFATC1, NFKBID, MAPK1, MAP2K2 and other genes participated in the regulation of the immune response were differentially modified. In addition, the differentially modified genes were significantly enriched in pathways including integrin signaling pathway which is important for cell movement and activation, CD40 signaling pathway which is related with the lymphocyte activation, as well as various cytokine signaling pathways such as IL-1, IL-6, IL-17.

Conclusions

Genome-wide methylation analysis, based on a low cell-number library preparation, will enable us to study MS pathogenesis using samples that are difficult to comprehensively study by many other methods.

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