ArticleThe Journal of pediatrics2013
A genome-wide methylation study of severe vitamin D deficiency in African American adolescents.
Article in The Journal of pediatrics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 3 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
58 citing papers in PubMed, 3 syntheses or guidelines pooled it, 103 citations in OpenAlex.
- Effect of epigenetics on vitamin D levels: a systematic review until December 2020.Archives of public health = Archives belges de sante publique · 2023Pooled it
- Vitamin D Deficiency Is Inversely Associated with Homeostatic Model Assessment of Insulin Resistance.Nutrients · 2021Pooled it
- Pooled it
- Effects of Maternal Vitamin D3 Supplementation on Offspring Epigenetic Clock of Gestational Age at Birth: A Post-hoc Analysis of a Randomized Controlled Trial.Epigenetics · 2020Trial
- Gestational Vitamin D Supplementation Leads to Reduced Perinatal RXRA DNA Methylation: Results From the MAVIDOS Trial.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2019Trial
- Effects of Vitamin D3 Supplementation on Epigenetic Aging in Overweight and Obese African Americans With Suboptimal Vitamin D Status: A Randomized Clinical Trial.The journals of gerontology. Series A, Biological sciences and medical sciences · 2019Trial
- Race/Ethnicity-Specific Association of Vitamin D and Global DNA Methylation: Cross-Sectional and Interventional Findings.PloS one · 2016Trial
- Vitamin D-Related Signaling and Epigenetic Regulation: Evidence from Experimental, Observational, and Interventional Studies.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Vitamin D deficiency in mice modulates oral microbiome stability over time and leads to changes in host inflammatory gene expression pathways.Frontiers in cellular and infection microbiology · 2026Article
- Nutri-Epigenetic Regulation of Vitamin D-Impact on Metabolism and Biological Functions: Narrative Review.Metabolites · 2025Review
- Vitamin D, B9, and B12 Deficiencies as Key Drivers of Clinical Severity and Metabolic Comorbidities in Major Psychiatric Disorders.Nutrients · 2025Article
- Gene expression profiling of vitamin D metabolism enzymes in leukemia and lymphoma patients: molecular aspect interplay of VDR, CYP2R1, and CYP24A1.Molecular biology reports · 2024Article
- Review
- Hypermethylation and down-regulation of vitamin D receptor (VDR) as contributing factors for polycystic ovary syndrome (PCOS): a case-control study from Kashmir, North India.Archives of gynecology and obstetrics · 2024Article
- Association of DNA methylation of vitamin D metabolic pathway related genes with colorectal cancer risk.Clinical epigenetics · 2023Article
- Review
- Correlation ofThe Indian journal of medical research · 2023Article
- Nutriepigenomics in Environmental-Associated Oxidative Stress.Antioxidants (Basel, Switzerland) · 2023Review
- Genomic or Non-Genomic? A Question about the Pleiotropic Roles of Vitamin D in Inflammatory-Based Diseases.Nutrients · 2023Review
- Vitamin D supplementation is associated with slower epigenetic aging.GeroScience · 2022Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
objectivesTo 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. STUDY
designWe 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.
resultsA 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).
conclusionSevere 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.