title: A genome-wide methylation study of severe vitamin D deficiency in African American adolescents.
abstract: OBJECTIVE
  To test the hypothesis that changes in DNA methylation are involved in vitamin D deficiency-related immune cell regulation using an unbiased genome-wide approach combined with a genomic and epigenomic integrative approach.
  
  
  METHODS
  We performed a genome-wide methylation scan using the Illumina HumanMethylation 27 BeadChip on leukocyte DNA of 11 cases of vitamin D deficiency (serum 25-hydroxyvitamin D [25(OH)D] ≤ 25 nmol/L) and 11 age-matched controls ([25(OH)D] > 75 nmol/L); the subjects were African American normal-weight (body mass index <85th percentile) males aged 14-19 years. The Limma package was used to analyze each CpG site for differential methylation between cases and controls. To correct for multiple testing, the set of raw P values were converted to false discovery rates (FDRs). We also compared our findings with the recent data from Genome-Wide Association Studies of circulating 25(OH)D levels and then performed a permutation test to examine whether the "double hit" genes were randomly enriched.
  
  
  RESULTS
  A total of 79 CpG sites achieved raw P < .001. Of the 79 CpG sites, 2 CpG sites survived multiple testing: cg16317961 (raw P = 3.5 × 10(-6), FDR = 0.078, in MAPRE2) and cg04623955 (raw P = 5.9 × 10(-6), FDR = 0.078, in DIO3). Furthermore, 3 out of the 4 genes previously identified in the 2 Genome-Wide Association Studies were also significant at the methylation level (DHCR7: cg07487535, P = .015 and cg10763288, P = .017; CYP2R1: cg25454890, P = .040; CYP24A1: cg18956481, P = .022), reflecting significant enrichment (P = .0098).
  
  
  CONCLUSIONS
  Severe vitamin D deficiency is associated with methylation changes in leukocyte DNA. The genomic and epigenomic approach reinforce the crucial roles played by the DHCR7, CYP2R1, and CYP24A1 genes in vitamin D metabolism.
authors.affiliation: Department of Pediatrics, Georgia Prevention Institute, Georgia Health Sciences University, Augusta, GA 30912, USA. hzhu@georgiahealth.edu
authors.forename: Haidong
authors.initials: H
authors.lastname: Zhu
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Wang
authors.forename: Huidong
authors.initials: H
authors.lastname: Shi
authors.forename: Shaoyong
authors.initials: S
authors.lastname: Su
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Harshfield
authors.forename: Bernard
authors.initials: B
authors.lastname: Gutin
authors.forename: Harold
authors.initials: H
authors.lastname: Snieder
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Dong
mesh_terms: D000293:Adolescent; D001741:Black or African American; D019175:DNA Methylation; D055106:Genome-Wide Association Study; D006801:Humans; D007962:Leukocytes; D008297:Male; D014807:Vitamin D / Q000031:analogs & derivatives* / Q000097:blood; D014808:Vitamin D Deficiency / Q000235:genetics*; D055815:Young Adult
chemical_list: D014807:Vitamin D; C104450:25-hydroxyvitamin D