A Genome-Wide Methylation Study of Severe Vitamin D Deficiency in African American Adolescents

• Published in: The Journal of pediatrics Vol. 162; no. 5; pp. 1004 - 1009.e1
• Main Authors: Zhu, Haidong, Wang, Xiaoling, Shi, Huidong, Su, Shaoyong, Harshfield, Gregory A., Gutin, Bernard, Snieder, Harold, Dong, Yanbin
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2013; Mosby, Inc
• Subjects: Adolescent; adolescents; African Americans; analogs & derivatives; Black or African American; blood; blood serum; body mass index; DNA; DNA Methylation; genes; genetics; Genome-Wide Association Study; Humans; Leukocytes; Male; males; metabolism; Pediatrics; vitamin D; Vitamin D - analogs & derivatives; Vitamin D - blood; vitamin D deficiency; Vitamin D Deficiency - genetics; Young Adult; LC-MS/MS; GWAS; IL; FDR; 25(OH)D; GO; NHANES; Interleukin; Gene ontology; False discovery rate; National Health and Nutrition Examination Survey; Liquid chromatography tandem mass spectroscopy; 25-Hydroxyvitamin D; Genome-Wide Association Studies
• ISSN: 0022-3476; 1097-6833; 1097-6833
• DOI: 10.1016/j.jpeds.2012.10.059

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. 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. 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). 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.