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Regulation of the methylome in differentiation from adult stem cells may underpin vitamin D risk in MS

Abstract

Multiple lines of evidence indicate Multiple Sclerosis (MS) is affected by vitamin D. This effect may be mediated by methylation in immune cell progenitors. We aimed to determine (1) if haematopoietic stem cell methylation constrains methylation in daughter cells and is variable between individuals, and (2) the interaction of methylation with the vitamin D receptor binding sites. We interrogated genomic methylation levels from matching purified CD34+ haematopoietic stem cells and progeny CD14+ monocytes and CD56+ NK cells from 11 individuals using modified reduced representation bisulfite sequencing. Differential methylation of Vitamin D Receptor binding sites and MS risk genes was assessed from this and using pyrosequencing for the vitamin D regulated MS risk gene ZMIZ1. Although DNA methylation states at CpG islands and other sites are almost entirely recapitulated between progenitor and progeny immune cells, significant variation was detected at some regions between cell subsets and individuals; including around the MS risk genes HLA DRB1 and the vitamin D repressor NCOR2. Methylation of the vitamin D responsive MS risk gene ZMIZ1 was associated with risk SNP and disease. We conclude that DNA methylation settings in adult haematopoietic stem cells may contribute to individual variation in vitamin D responses in immune cells.

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Fig. 1: The hypothesis underpinning this study.
Fig. 2: Specific and relative DNA methylation across cell subsets.
Fig. 3: Clustering of cell subsets based on differentially methylated CGI.
Fig. 4: Differentially methylated CGI and their overlaps with regulatory regions and MS risk genes.
Fig. 5: Individual differences in DNA methylation by subset.
Fig. 6: ZMIZ1 methylation and expression in MS and controls.

Data availability

The datasets supporting the conclusions of this article are available in the GEO database under the accession number GSE114254.

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Acknowledgements

The authors would like to thank Ellis Patrick for invaluable biostatistical advice, Nicole Fewings and Stephen Schibeci for assistance with practical aspects of this study and volunteers from the Westmead Institute for Medical Research who kindly donated samples for this project. Flow cytometry was performed at the Flow Cytometry Core Facility that is supported by Westmead Research Hub, Cancer Institute NSW and NHMRC. Bioinformatic analysis was supported by Sydney Informatics Hub, funded by the University of Sydney.

Funding

LO was supported by a National Health and Medical Research Council (NHMRC), Trish MS Foundation and MS Research Australia co-funded postgraduate scholarship. GP was supported by a MS Research Australia Postdoctoral Fellowship and a MS Research Australia/ JDRF Australia/ Macquarie Group Foundation Postdoctoral Fellowship. DB was supported by a NHMRC Senior Research Fellowship and MSRA Project Grant.

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LO, GP and DB planned the experiment, analysed the data and prepared the paper. LO conducted all genomic methylation experiments. KV analysed the ZMIZ1 pyrosequencing data. GS and CL assisted in preparation of the paper. All authors read and approved the final paper.

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Correspondence to Lawrence T. C. Ong.

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This study received ethics approval from the Western Sydney Local Health District Human Research Ethics Committee (HREC2002/9/3.6(1425)).

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Informed, written consent was obtained from subjects prior to involvement in this study.

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Ong, L.T.C., Parnell, G.P., Veale, K. et al. Regulation of the methylome in differentiation from adult stem cells may underpin vitamin D risk in MS. Genes Immun 21, 335–347 (2020). https://doi.org/10.1038/s41435-020-00114-4

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