Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease
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.
We extracted CD4+ cells from nine healthy volunteers. Each sample underwent VDR ChIP-seq.
Our results were analysed 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 (VD>75 nmol/L) and insufficient (VD<75 nmol/L).
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 vitamin D levels (VD) were sufficient (VD>75: 3.13-fold, p<0.0001; VD<75: 2.76-fold, p<0.0001; VD>75 enrichment vs.
VD<75 enrichment: p=0.0002). VDR binding was also enriched near genes associated specifically with T-regulatory and T-helper cells in the VD>75 group.
MEME ChIP did not identify any VDR-like motifs underlying our VDR ChIP-seq peaks.
Our results show a direct correlation between in vivo 25-hydroxyvitamin D levels and the number of VDR binding sites. Our study further implicates VDR binding as important in gene-environment interactions underlying the development of autoimmunity and provides a biological rationale for vitamin D sufficiency being based at 75nmol/L.
Our results also suggest that VDR binding in response to physiological levels of vitamin D occurs predominantly in a VDR motif-independent manner.