Email updates

Keep up to date with the latest news and content from BMC Medicine and BioMed Central.

Journal App

google play app store
Open Access Research article

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease

Adam E Handel12, Geir K Sandve3, Giulio Disanto1, Antonio J Berlanga-Taylor1, Giuseppe Gallone1, Heather Hanwell1, Finn Drabløs4, Gavin Giovannoni2, George C Ebers1 and Sreeram V Ramagopalan12*

Author affiliations

1 Medical Research Council Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK

2 Blizard Institute, Queen Mary University of London, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK

3 Department of Informatics, University of Oslo, Gaustadalléen 23 B, N-0373, Oslo, Norway

4 Bioinformatics & Gene Regulation, Norwegian University of Science and Technology, Erling Skjalgsons gt. 1, N-7006, Trondheim, Norway

For all author emails, please log on.

Citation and License

BMC Medicine 2013, 11:163  doi:10.1186/1741-7015-11-163

Published: 12 July 2013

Abstract

Background

Vitamin D insufficiency has been implicated in autoimmunity. ChIP-seq experiments using immune cell lines have shown that vitamin D receptor (VDR) binding sites are enriched near regions of the genome associated with autoimmune diseases. We aimed to investigate VDR binding in primary CD4+ cells from healthy volunteers.

Methods

We extracted CD4+ cells from nine healthy volunteers. Each sample underwent VDR ChIP-seq. Our results were analyzed in relation to published ChIP-seq and RNA-seq data in the Genomic HyperBrowser. We used MEMEChIP for de novo motif discovery. 25-Hydroxyvitamin D levels were measured using liquid chromatography–tandem mass spectrometry and samples were divided into vitamin D sufficient (25(OH)D ≥75 nmol/L) and insufficient/deficient (25(OH)D <75 nmol/L) groups.

Results

We found that the amount of VDR binding is correlated with the serum level of 25-hydroxyvitamin D (r = 0.92, P= 0.0005). In vivo VDR binding sites are enriched for autoimmune disease associated loci, especially when 25-hydroxyvitamin D levels (25(OH)D) were sufficient (25(OH)D ≥75: 3.13-fold, P<0.0001; 25(OH)D <75: 2.76-fold, P<0.0001; 25(OH)D ≥75 enrichment versus 25(OH)D <75 enrichment: P= 0.0002). VDR binding was also enriched near genes associated specifically with T-regulatory and T-helper cells in the 25(OH)D ≥75 group. MEME ChIP did not identify any VDR-like motifs underlying our VDR ChIP-seq peaks.

Conclusion

Our results show a direct correlation between in vivo 25-hydroxyvitamin D levels and the number of VDR binding sites, although our sample size is relatively small. Our study further implicates VDR binding as important in gene-environment interactions underlying the development of autoimmunity and provides a biological rationale for 25-hydroxyvitamin D sufficiency being based at 75 nmol/L. Our results also suggest that VDR binding in response to physiological levels of vitamin D occurs predominantly in a VDR motif-independent manner.

Keywords:
Vitamin D; Autoimmune disease; ChIP-seq; Functional genomics