The role of epigenetics in multiple sclerosis development, progression and treatment

The overall aim of this thesis was to determine epigenetic changes in peripheral immune cells from Multiple Sclerosis (MS) patients. MS is a chronic inflammatory neurodegenerative disease, which initially presents itself during young adulthood. Big consortia have identified over 230 different polymorphisms contributing to the risk of developing disease, with many of these polymorphisms located in immune genes. However, the odds ratios of these polymorphisms are small and many known environmental risk factors are contributing to the disease. This indicates that the risk may partially be conferred through epigenetic changes such as DNA methylation.

In this thesis, we investigate the role of DNA methylation in different peripheral immune cells using genome-wide DNA methylation arrays. We first characterized DNA methylation patterns in four different immune cell types form relapsing-remitting (RRMS), secondary-progressive (SPMS) patients and healthy controls (HC) and compared them with each other. Here we found a shared signature between all cells types, and in SPMS we found a specific neurodegenerative signal, while in MS patients, we saw lymphocyte signaling and T cell activation being affected. The top changes in CD4+ T cells indicate a change in the VMP1/MIR21 locus. We functionally investigated this and found lower miR-21 expression and an increase of miR-21 target genes. Because the most numerous methylation changes were found in CD19+ B cells, we further investigated CD19+ cells in a second larger cohort. After meta-analysis, the changes in B cells indicate differences in metabolism and activation between RRMS and HC. To analyze the shared pathway data, we developed a method to cluster pathways, which we further developed into an R package called GeneSetCluster.

We investigated the effects of dimethyl fumarate (DMF) and rituximab treatment on DNA methylation in CD4+ and CD14+ cells. The different treatments had a different cell type specific signature as well as different kinetics. After DMF treatment, we found changes in reactive oxygen species (ROS) signaling and T cell subtype associated genes. Furthermore, we identified a polymorphism associated with treatment outcome and ROS production that does not associate with disease susceptibility. After rituximab treatment, we found differences in activation, metabolism and motility associated genes.

Our findings collectively underline the importance of investigating epigenetic changes in multiple cell types to identify novel, potentially modifiable, mechanisms involved in the etiology and pathogenesis of complex diseases like MS.

List of scientific papers

I. Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression. Ewing E, Kular L, Fernandes SJ, Karathanasis N, Lagani V, Ruhrmann S, Tsamardinos I, Tegner J, Piehl F, Gomez-Cabrero D, Jagodic M. EBioMedicine. 2019 May;43:411-423.
https://doi.org/10.1016/j.ebiom.2019.04.042

II. Hypermethylation of MIR21 in CD4+ T cells from patients with relapsing-remitting multiple sclerosis associates with lower miRNA-21 levels and concomitant up-regulation of its target genes. Ruhrmann S, Ewing E, Piket E, Kular L, Cetrulo Lorenzi JC, Fernandes SJ, Morikawa H, Aeinehband S, Sayols-Baixeras S, Aslibekyan S, Absher DM, Arnett DK, Tegner J, Gomez-Cabrero D, Piehl F, Jagodic M. Mult Scler. 2018 Sep;24(10):1288-1300.
https://doi.org/10.1177/1352458517721356

III. GeneSetCluster: a tool for summarizing and integrating gene-set analysis results. Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D. [Manuscript]

IV. Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis associates with ROS pathway in monocytes. Carlström KE, Ewing E, Granqvist M, Gyllenberg A, Aeinehband S, Enoksson SL, Checa A, Badam TVS, Huang J, Gomez-Cabrero D, Gustafsson M, Al Nimer F, Wheelock CE, Kockum I, Olsson T, Jagodic M, Piehl F. Nat Commun. 2019 Jul 12;10(1):3081.
https://doi.org/10.1038/s41467-019-11139-3

V. Investigating a role of B cells and their depletion in relapsing-remitting Multiple Sclerosis using DNA methylation patterns. Ewing E, Al Nimer F, Kular L, Stridh P, Olsson T, Khademi M, Gomez-Cabrero D, Piehl F, Jagodic M. [Manuscript]