New evidence for an association between immune cells, vitamin D and MS risk SNPs

2019 , 'New evidence for an association between immune cells, vitamin D and MS risk SNPs', PhD thesis, University of Tasmania.

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Abstract

Multiple sclerosis (MS) is a chronic and inflammatory autoimmune disease that causes progressive demyelination and neuronal degeneration in the central nervous system (CNS).
Multiple factors can increase the risk to develop MS, including environmental factors such as Vitamin D level and infection with Epstein Barr virus. Furthermore, genetic factors such as MS risk single nucleotide polymorphisms (SNP), and immune dysregulation such as a break in self-tolerance causing a misguided immune response to yet undefined CNS antigens or an increased presence of inflammatory immune cells in the CNS can support the development of this autoimmune disorder.
In this study it has been my aim to integrate the roles of Vitamin D, MS risk SNPs and immune cells with the aetiology of MS by investigating Vitamin D metabolism-associated MS risk SNPs in peripheral T cell activation and studying the Vitamin D receptor super-enhancers in THP-1 monocytes.
On one hand, I collected peripheral blood mononuclear cells (PBMCs) from people with MS and from healthy controls, and genotyped these samples for the presence of the Vitamin D-associated MS risk SNPs (i.e., rs12368653, rs703842, rs2248359). These SNPs are located in the vicinity of genes encoding Vitamin D metabolism associated genes (i.e., CYP27B1 and CYP24A1). In connection with the identified genotypes, I investigated the phenotypes of peripheral immune cells and in particular T helper cell subtypes and their cytokine profile in vitro after 96 hours culture.
Firstly, I found some peripheral immune cell abnormalities ex vivo (i.e., classic monocytes and the ratio of Th17.1/Th1) that are associated with MS. Secondly, I found some MS group-specific abnormalities of inflammatory profiles in vitro after 96 hours culture (i.e., TNF, IL-6, Th17, Th1, and Th17/Th1). Interestingly, Th2 proportion is correlated with EDSS both ex vivo and in vitro in MS patients.
Furthermore, I found there is a consistent trend of effect of the risk allele rs2248359-C on the proportions of T cell subsets (i.e., Th1 and Th17.1) both ex vivo and in vitro. In addition, the double risk allele rs703842-AA reduces the IL-2 production.
On the other hand, I identified the 1,25(OH)2D3-induced super-enhancer (SE) regions bound by Vitamin D receptors (VDR) in THP-1 monocytes. I discussed the difference between VDR super-enhancer, PU.1 super-enhancer and FAIRE-seq identified super-enhancer regions. An analysis of VDR binding regions allowed me to divide all VDR SE (VSE) regions into three types (VSE1, VSE2, VSE3) according to their combination of persistent VDR binding and secondary VDR binding after 1,25(OH)$$_2$$D$$_3$$ stimulation.
Furthermore, I indicated the genes that have VSE regions and are also associated with MS.
1) The genes with VSE regions that are near (± 500 kb) MS risk SNPs in 1,25(OH)$$_2$$D$$_3$$-stimulated THP-1 monocytes.
2) The genes with MS risk SNPs overlapping with VDR SE regions in 1,25(OH)$$_2$$D$$_3$$-stimulated THP-1 monocytes, e.g., IRF8, UBASH3B and PLEC. I found that MS risk SNPs are enriched in VSE regions compared to their genomic background.
3) A cluster of ZMIZ1-positively associated genes that both have VSE2 regions and are highly regulated by 1,25(OH)$$_2$$D$$_3$$, and a cluster of ZMIZ1-positively associated genes that both have VSE3 regions and are highly expressed in THP-1 monocytes.
In conclusion, I connected MS risk and Vitamin D in two dimensions:
1) Vitamin D-associated MS risk SNPs are associated with some immune cell phenotypes (mainly to T helper cells).
2) Key Vitamin D receptor binding regions (i.e., VSE) are associated with MS risk SNPs and genes in THP-1 monocytes.
I provided new evidence for the association between MS risk SNPs, immune cells and Vitamin D, and identified MS risk genes that are under the regulation of Vitamin D via VDR super-enhancer regions.

Item Type: Thesis - PhD Lu, M Immune cell; Vitamin D; Multiple Sclerosis; risk-SNP; super-enhancer Copyright 2018 the author Chapter 1 appears to be the equivalent of a pre-print version of an article published as: Lu, M., Taylor, B. V., Körner, H., 2018. Genomic effects of the vitamin D receptor: potentially the link between vitamin D, immune cells, and multiple sclerosis. Frontiers in immunology, 9:477. Copyright © 2018 Lu, Taylor and Körner. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). https://creativecommons.org/licenses/by/4.0/ The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Chapters 5 and 6 appear to be, in part, the equivalent of a pre-print version of an article published as: Lu, M., McComish, B. J., Burdon, K. P., Taylor, B. V., Körner, H., 2019. The association between vitamin D and multiple sclerosis risk: 1,25(OH)$$_2$$D$$_3$$ induces VDR superenhancers bound by VDR, Frontiers in immunology, 10:488. Copyright © 2019 Lu, McComish, Burdon, Taylor and Körner. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). https://creativecommons.org/licenses/by/4.0/ The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. View statistics for this item