Vitamin D Signaling in the Context of Innate Immunity: Focus on Human Monocytes

Abstract

The vitamin D₃ metabolite 1α,25-dihydroxyvitamin D₃ (1,25(OH)₂D₃) activates at sub-nanomolar concentrations the transcription factor vitamin D receptor (VDR). VDR is primarily involved in the control of cellular metabolism but in addition modulates processes important for immunity, such as anti-microbial defense and the induction of T cell tolerance. Monocytes and their differentiated phenotypes, macrophages and dendritic cells, are key cell types of the innate immune system, in which vitamin D signaling was most comprehensively investigated via the use of next generation sequencing technologies. These investigations provided genome-wide maps illustrating significant effects of 1,25(OH)₂D₃ on the binding of VDR, the pioneer transcription factors purine-rich box 1 (PU.1) and CCAAT/enhancer binding protein α (CEBPA) and the chromatin modifier CCCTC-binding factor (CTCF) as well as on chromatin accessibility and histone markers of promoter and enhancer regions, H3K4me3 and H3K27ac. Thus, the epigenome of human monocytes is at multiple levels sensitive to vitamin D. These data served as the basis for the chromatin model of vitamin D signaling, which mechanistically explains the activation of a few hundred primary vitamin D target genes. Comparable epigenome- and transcriptome-wide effects of vitamin D were also described in peripheral blood mononuclear cells isolated from individuals before and after supplementation with a vitamin D₃ bolus. This review will conclude with the hypothesis that vitamin D modulates the epigenome of immune cells during perturbations by antigens and other immunological challenges suggesting that an optimal vitamin D status may be essential for an effective epigenetic learning process, in particular of the innate immune system.

Keywords: PBMCs; VDR; epigenome; gene regulation; monocytes; transcriptome; vitamin D; vitamin D target genes.

Figure 1

The chromatin model of vitamin D signaling. The model was defined by epigenome- and transcriptome-wide data obtained in THP-1 cells. CTCF proteins define left and right TAD borders, in which vitamin D target genes (red arrow, measured by RNA-seq) are activated by VDR [activated by 1,25(OH)₂D₃] binding to enhancer regions. The pioneer transcription factors CEBPα and PU.1 help VDR in binding to accessible genomic DNA (measured by FAIRE-seq). This paralleled with changes in markers of active TSS regions (H3K4me3) and active chromatin (H3K27ac). The genome-wide binding of VDR, CTCF, PU.1, CEBPα, and histone markers were determined by ChIP-seq in three biological repeats. The time of 1,25(OH)₂D₃ stimulation is indicated for each dataset.

Figure 2

Memory hypothesis. VDR binding and chromatin opening of the loci of the genes ZMIZ1, (A) and MYO1G (B) in vitro (THP-1) as well as in vivo (PBMCs). THP-1 cells were stimulated for 0, 24, and 48 h with 1,25(OH)₂D₃ and VDR ChIP-seq and FAIRE-seq were performed (22). In a comparable in vivo experiment an individual was challenged with a vitamin D₃ bolus (2,000 μg) and PBMCs were isolated before (day 0) and at days 1 (24 h) and 2 (48 h) (23). The peak tracks represent merger of each three biological repeats. Gene structures are shown in blue. Different types of immune challenges program the epigenome of the pool of human monocytes, which “memorize” these encounters in form of differently programmed epigenomes leading to subtype differentiation (bottom, differently colored dots of in nuclei of monocyte subpopulations, C). The recently discovered epigenome modulating effect of vitamin D [via the VDR (24)] modulates on multiple levels this epigenetic programming process. The stabilization of the epigenomes of the subtypes of monocytes, macrophages and dendritic cells by vitamin D can prevent or delay the onset of common age-related diseases.