Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes

Abstract

BackgroundThe nuclear hormone receptor superfamily acts as a genomic sensor of diverse signals. Their actions are often intertwined with other transcription factors. Nuclear hormone receptors are targets for many therapeutic drugs, and include the vitamin D receptor (VDR). VDR signaling is pleotropic, being implicated in calcaemic function, antibacterial actions, growth control, immunomodulation and anti-cancer actions. Specifically, we hypothesized that the biologically significant relationships between the VDR transcriptome and phenotype-associated biology could be discovered by integrating the known VDR transcription factor binding sites and all published trait- and disease-associated SNPs. By integrating VDR genome-wide binding data (ChIP-seq) with the National Human Genome Research Institute (NHGRI) GWAS catalog of SNPs we would see where and which target gene interactions and pathways are impacted by inherited genetic variation in VDR binding sites, indicating which of VDR’s multiple functions are most biologically significant.ResultsTo examine how genetic variation impacts VDR function we overlapped 23,409 VDR genomic binding peaks from six VDR ChIP-seq datasets with 191,482 SNPs, derived from GWAS-significant SNPs (Lead SNPs) and their correlated variants (r 2 > 0.8) from HapMap3 and the 1000 genomes project. In total, 574 SNPs (71 Lead and 503 SNPs in linkage disequilibrium with Lead SNPs) were present at VDR binding loci and associated with 211 phenotypes. For each phenotype a hypergeometric test was used to determine if SNPs were enriched at VDR binding sites. Bonferroni correction for multiple testing across the 211 phenotypes yielded 42 SNPs that were either disease- or phenotype-associated with seven predominately immune related including self-reported allergy; esophageal cancer was the only cancer phenotype. Motif analyses revealed that only two of these 42 SNPs reside within a canonical VDR binding site (DR3 motif), and that 1/3 of the 42 SNPs significantly impacted binding and gene regulation by other transcription factors, including NF-κB. This suggests a plausible link for the potential cross-talk between VDR and NF-κB.ConclusionsThese analyses showed that VDR peaks are enriched for SNPs associated with immune phenotypes suggesting that VDR immunomodulatory functions are amongst its most important actions. The enrichment of genetic variation in non-DR3 motifs suggests a significant role for the VDR to bind in multimeric complexes containing other transcription factors that are the primary DNA binding component. Our work provides a framework for the combination of ChIP-seq and GWAS findings to provide insight into the underlying phenotype-associated biology of a given transcription factor.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3481-4) contains supplementary material, which is available to authorized users.

Ancient Nuclear Receptor VDR With New Functions: Microbiome and Inflammation

“…Singh et al 53 has broadened our understanding of the interaction of VDR and NF-κB and further supports a critical role of VDR in regulating inflammatory disease. By integrating disease-associated SNPs identified by GWAS with VDR genomic binding sites identified by Chip-Seq, the authors identified 42 SNPs associated with immune phenotypes and VDR binding.…”

BsmI (rs1544410) and FokI (rs2228570) vitamin D receptor polymorphisms, smoking, and body mass index as risk factors of cutaneous malignant melanoma in northeast Italy

“…VDR can bind to thousands of VDREs on human genome and up- or down-regulate hundreds of genes. Of interest, recent evidence showed a crosstalk between VDR and immune factors 57 . VDR cistrome analyses suggested that altered expression of VDR in colon cancer changes actions of VDR, thus affecting patient outcome 58 .…”

Vitamin D Receptor Signaling and Cancer

“…In this manner, we identified genetic variation that was significant at the genome-wide level enriched in VDR binding sites that were shared with nuclear factor-κB binding regions related to immune phenotypes, including self-reported allergy. 310 However, none of the GWAS SNPs identified in VDR binding sites were neither in a DR3 type motif, again underscoring the diversity of VDR binding sites, nor related to cancer phenotypes.…”