A methylome-wide study of immune cells in relapsing-remitting multiple sclerosis
Bioinformatics and Theoretical Biology
Human Genetics
Final Report Abstract
Multiple sclerosis (MS) is a CNS disease characterized by inflammation, progressive axonal injury and neurodegeneration. In the pathophysiology of the disease, overactivated B and T cells have closely related roles in an inflammatory but also in regulatory manner. A complex interaction between genetic and environmental factors through epigenetic modifications can cause MS. DNA methylation is a cell-type-specific epigenetic mechanism involved in the aetiology of autoimmune diseases like MS. We recruited 10 relapsing remitting MS patients and 10 age-, gender- and education-matched controls. Additionally, 10 secondary progressive MS patients gender-matched with the RRMS group were enrolled in the study. Fresh whole peripheral blood was collected from the MS patients and their controls (100 mL per subject), and on the same day they were subjected to a battery of neuropsychological tests. Memory B and regulatory T cells were isolated from blood using flow cytometry and cell sorting. DNA was purified from both immune cell types, sonicated, repaired, ligated and finally immunoprecipitated. DNA libraries were subjected to single-end sequencing with a 50-bp read length and 25 million reads per sample. Candidate genes were validated by gene expression arrays. We found 453,110 and 847,248 differentially methylated regions in memory B cells derived from relapsing remitting MS and secondary progressive MS, respectively. A total of 31% of the differentially methylated regions were hypermethylated while 69% were hypomethylated in relapsing remitting MS when compared to their controls. In contrast, 71% of the differentially methylated regions were hypermethylated and 29% hypomethylated in secondary progressive MS in comparison with relapsing remitting MS. In regulatory T cells, we found 406,017 and 2,291,588 differentially methylated regions derived from relapsing remitting MS and secondary progressive MS, respectively. In relapsing remitting MS, 37% of the differentially methylated regions were hypermethylated while the remaining were hypomethylated. A total of 59% of differentially methylated regions were hypermethylated and the remaining DNA regions were hypomethylated in secondary progressive MS. The candidate genes were further studied. We found the following from subjects in the relapsing remitting MS group. In memory B cells, we found a hypomethylation in the GCC1 promoter and, consequently, enhanced mRNA levels. We determined that the expression of GCC1 followed an inverse relationship with the amount of T2 lesions. We also found a hypermethylated pattern in the first intron adjacent to the IL21R promoter that was accompanied by lower mRNA expression. In regulatory T cells, we discovered a hypermethylated region within the ECEL1P2 promoter that was associated with lower mRNA expression. The expression of ECEL1P2 was inversely correlated with the IgG index. We report common widespread hypermethylated regions within HLA-DRB5 in both immune cell types. Memory B cells: GCC1 codifies a protein required in trans-Golgi membrane transport. The Golgi apparatus acts as a signalling platform towards immune response. Alterations in Golgi structure can lead to neurodegenerative diseases. Thus, we hypothesize that an increase in GCC1 mRNA content could be a compensatory mechanism for vesicular trafficking of cytokines and chemokines to the extracellular matrix. IL21R participates in the proliferation and differentiation of distinct immune cells and contributes to the humoral immune response mediated by memory B cells. Mice lacking IL21R and subjected to autoimmune encephalomyelitis displayed severe neurological deficits. A decrease in IL21R expression as a result of DNA hypermethylation could compromise the immune response in MS. Regulatory T cells: ECEL1P2 is a pseudogene expressed in almost all human tissues including the brain and blood cells. In line with our findings, a hypermethylation of ECEL1P2 has been reported in patients with Alzheimer disease indicating that the DNA methylation status of ECEL1P2 could be related to loss of the myelin sheath around axons. Memory B and regulatory T cells: Genetic variants of the HLA-DRB locus have been reported in autoimmune diseases. However, HLA-DRB5 variant has been described to confer neuroprotection whereas MS patients lacking this variant of HLA displayed more vulnerability to develop progressive forms of MS. Additionally, we found that a hypermethylation within HLA-DRB5 could impair antigen presentation to naïve CD4+ T cells. Then, we can speculate that a hypermethylation of HLA-DRB5 might compromise either antigen presentation or neuroprotection favouring the development of progressive forms of the disease. Relevance to MS: The study of DNA methylation could be used as a predictive tool to evaluate health risks and also to design personalized health plans in MS patients. We created a crowdfunding platform with FECYT (Spain) support that had a significant impact on the Spanish communications media (for further details see: https://www.precipita.es/proyectos/A-un-paso-de-conocer-lascausas-epigenticas-de-la-Esclerosis-Mltiple).
Publications
- Effects of repeated longterm psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders. CNS Neurosci Ther. 2018;24(6)
Tomas-Roig J, Piscitelli F, Gil V, Quintana E, Ramió-Torrentà LL, del Río JA, et al.
(See online at https://doi.org/10.1111/cns.12810) - Analysis of miRNA signatures in CSF identifies upregulation of miR-21 and miR-146a/b in patients with multiple sclerosis and active lesions. J Neuroinflammation. 2019
Munõz-San Martín M, Reverter G, Robles-Cedenõ R, Buxò M, Ortega FJ, Gómez I, et al.
(See online at https://doi.org/10.1186/s12974-019-1590-5) - Changes in Deoxyribonucleic Acid Methylation Contribute to the Pathophysiology of Multiple Sclerosis. Front Genet. 2019;10
Celarain N, Tomas-Roig J
(See online at https://doi.org/10.3389/fgene.2019.01138) - Gene expression signature in brain regions exposed to long-term psychosocial stress following acute challenge with cannabinoid drugs. Psychoneuroendocrinology. 2019;102
Tomas-Roig J, Havemann-Reinecke U
(See online at https://doi.org/10.1016/j.psyneuen.2018.11.023) - Long lasting behavioural effects on cuprizone fed mice after neurotoxicant withdrawal. Behav Brain Res. 2019;363
Tomas-Roig J, Torrente M, Cabré M, Vilella E, Colomina MT
(See online at https://doi.org/10.1016/j.bbr.2019.01.036) - Aberrant DNA methylation profile exacerbates inflammation and neurodegeneration in multiple sclerosis patients. Journal of Neuroinflammation. 2020
Celarain N, Tomas-Roig J
(See online at https://doi.org/10.1186/s12974-019-1667-1) - Dosedependent effect of cannabinoid WIN-55,212-2 on myelin repair following a demyelinating insult. Sci Rep. 2020
Tomas-Roig J, Agbemenyah HY, Celarain N, Quintana E, Ramió-Torrentà L, Havemann-Reinecke U
(See online at https://doi.org/10.1038/s41598-019-57290-1)
