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.
The 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.



To 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 (r2> 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.



These 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.
Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA.
Prashant K
PK
Singh
Leiden institute of Physics, Leiden University, 2300 RA, Leiden, Netherlands.
Patrick R
PR
van den Berg
Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA.
Mark D
MD
Long
Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA.
Angie
A
Vreugdenhil
Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, 14214, USA.
Laurie
L
Grieshober
Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, 14214, USA.
Heather M
HM
Ochs-Balcom
Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA.
Jianmin
J
Wang
Luxembourg Centre for Systems Biomedicine, 6 Avenue du Swing, 4367, Belvaux, Luxembourg.
Sylvie
S
Delcambre
School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, 70211, Finland.
Sami
S
Heikkinen
School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, 70211, Finland.
Carsten
C
Carlberg
Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, 536 Parks Hall, The Ohio State University, Columbus, OH, 43210, USA. Campbell.1933@osu.edu.
Moray J
MJ
Campbell
Division of Pharmacy Practice and Science, College of Pharmacy, 604 Riffe Building, The Ohio State University, Columbus, OH, 43210, USA. sucheston-campbell.1@osu.edu.|Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA. sucheston-campbell.1@osu.edu.
Lara E
LE
Sucheston-Campbell
D002460:Cell Line; D055106:Genome-Wide Association Study; D023281:Genomics; D006801:Humans; D007109:Immunity / Q000235:genetics*; D015810:Linkage Disequilibrium; D016328:NF-kappa B / Q000378:metabolism*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D018167:Receptors, Calcitriol / Q000235:genetics* / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
D016328:NF-kappa B; D018167:Receptors, Calcitriol; D014157:Transcription Factors; C579457:VDR protein, human
ChIP-seq; Cistrome; DR3 motif; GWAS; Immune function; Linkage disequilibrium; NF-κB; Nuclear receptor superfamily; SNP; VDR