Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin Accessibility Dynamics Suggest Immune-Modulatory Effects of Vitamin D3 In Vivo

ABSTRACT: Vitamin D₃ is a key micronutrient known to support innate immunity and modulate adaptive responses, with in vitro studies suggesting the involvement of epigenetic mechanisms. However, in vivo evidence remains limited. In this study, we investigated genome-wide epigenomic responses to vitamin D₃ supplementation in a cohort of 38 individuals from a Polish population. Peripheral blood mononuclear cells (PBMCs) were collected at baseline (day 0) and 24 hours after supplementation (day 1). ATAC-seq analyses revealed widespread vitamin D₃-induced changes in chromatin accessibility.

ORGANISM(S): Homo sapiens

PROVIDER: GSE303320 | GEO | 2025/12/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Chromatin Accessibility and Gene Expression Dynamics Suggest Immune-Modulatory Effects of Vitamin D3 In Vivo [ATAC-seq]

Project description:Vitamin D3 is a key micronutrient known to support innate immunity and modulate adaptive responses, with in vitro studies suggesting involvement of epigenetic mechanisms. However, in vivo evidence for such regulation remains limited. In this proof-of-principle study, we investigated genome-wide epigenomic and transcriptomic responses to vitamin D₃ in a high responder (n=1) from the VitDHiD intervention trial. The participant received monthly oral boluses of 80,000 IU vitamin D3 over three months. Peripheral blood mononuclear cells were collected at baseline (day 0) and at 24 and 48 hours post-supplementation (days 1 and 2) for ATAC-seq and RNA-seq profiling. ATAC-seq revealed over 3,500 regions with increased chromatin accessibility, mainly at gene promoters, indicating a strong epigenomic response. Motif enrichment analysis identified immune-regulatory transcription factors, but not VDR (vitamin D receptor) motifs, suggesting indirect or cooperative regulation. RNA-seq identified 380 vitamin D target genes with time-dependent expression changes, including DUSP6 and FOS. Functional enrichment highlighted pathways related to innate immunity and interferon signaling. Integrative analysis linked 306 differentially expressed genes to nearby vitamin D-sensitive chromatin regions, including both promoters and enhancers. Many of these overlapped with VDR binding sites and promoters of neighboring non-target genes, indicating potential long-range regulatory interactions. Redundancies in regulatory elements were observed among closely located genes sharing enhancers and promoters. These findings provide in vivo evidence that vitamin D3 modulates chromatin accessibility and gene expression, supporting its role as an epigenetic regulator of immune function and highlighting its potential in personalized nutrition and immune health.

2025-11-28 | GSE295550 | GEO

Chromatin Accessibility and Gene Expression Dynamics Reveal Immune-Modulatory Effects of Vitamin D3 In Vivo [RNA-Seq]

Project description:Vitamin D₃ is a key micronutrient known to support innate immunity and modulate adaptive responses, with in vitro studies suggesting involvement of epigenetic mechanisms. However, in vivo evidence for such regulation remains limited. In this proof-of-principle study, we investigated genome-wide epigenomic and transcriptomic responses to vitamin D₃ in a high responder (n=1) from the VitDHiD intervention trial. The participant received monthly oral boluses of 80,000 IU vitamin D₃ over three months. Peripheral blood mononuclear cells were collected at baseline (day 0) and at 24 and 48 hours post-supplementation (days 1 and 2) for ATAC-seq and RNA-seq profiling. ATAC-seq revealed over 3,500 regions with increased chromatin accessibility, mainly at gene promoters, indicating a strong epigenomic response. Motif enrichment analysis identified immune-regulatory transcription factors, but not VDR (vitamin D receptor) motifs, suggesting indirect or cooperative regulation. RNA-seq identified 380 vitamin D target genes with time-dependent expression changes, including DUSP6 and FOS. Functional enrichment highlighted pathways related to innate immunity and interferon signaling. Integrative analysis linked 306 differentially expressed genes to nearby vitamin D-sensitive chromatin regions, including both promoters and enhancers. Many of these overlapped with VDR binding sites and promoters of neighboring non-target genes, indicating potential long-range regulatory interactions. Redundancies in regulatory elements were observed among closely located genes sharing enhancers and promoters. These findings provide in vivo evidence that vitamin D₃ modulates chromatin accessibility and gene expression, supporting its role as an epigenetic regulator of immune function and highlighting its potential in personalized nutrition and immune health.

2025-11-28 | GSE295549 | GEO

Chromatin Accessibility Dynamics Suggest Immune-Modulatory Effects of Vitamin D3 In Vivo

Project description:Chromatin Accessibility Dynamics Suggest Immune-Modulatory Effects of Vitamin D3 In Vivo

| PRJNA1294843 | ENA

RNA sequencing of unmanipulated and saline-injected skin in healthy old adults before and after oral vitamin D3 supplementation

Project description:Vitamin D insufficiency may exacerbate non-specific inflammation observed in older adults. Here, we tested the hypothesis that an inflammatory gene signature present in old skin following saline injection (as model for non-specific needle injury) normalizes after oral vitamin D3 supplementation. To define the saline-induced signature, we compared gene expression in skin biopsies taken six hours after saline injection in old adults (≥65 years) to biopsies from unmanipulated skin. We then assessed signature expression in saline-injected skin of old and young adults (<40 years), and in paired samples of old adults before and after oral vitamin D3 supplementation (6400 IU/day for 14 weeks), where median serum 25-hydroxyvitamin D increased from 43 nmol/L (interquartile range 36-53 nmol/L) to 131 nmol/L (interquartile range 115-147 nmol/L). This submission comprises 112 samples from 57 individuals.

2021-01-02 | E-MTAB-9789 | biostudies-arrayexpress

Modulation of the peripheral blood immune cell transcriptome by vitamin D3 supplementation in people with a first demyelinating event: a randomized placebo-controlled trial

Project description:Vitamin D deficiency is a risk factor for developing multiple sclerosis (MS). Both in vitro and animal studies suggest an immunomodulatory effect of vitamin D. The PrevANZ trial, a phase IIb randomized placebo-controlled trial of oral vitamin D3 supplementation in people with a first demyelinating event (FDE), was conducted to determine if supplementation can prevent recurrent disease activity in this cohort at high risk of developing definite MS. As a sub-study of this trial, we used whole blood transcriptomic analyses to investigate the effect of vitamin D3 supplementation on peripheral immune cells in people with an FDE, and to gain insight into potential mechanisms by which vitamin D3 may regulate MS risk and disease activity. The PrevANZ trial randomized participants to 1000 IU, 5000 IU or 10,000 IU daily of oral vitamin D3 or placebo. Peripheral blood was collected at baseline and 12 weeks in PAXgene Blood RNA tubes. Transcriptomic datasets were generated by RNA sequencing.

| EGAS00001007346 | EGA

Alzheimer's model and vitamin D

Project description:Little is known about the global molecular changes leading to neurodegeneration and brain dysfunction in Alzheimer's disease (AD). To study the molecular cascades involved, we chose to study the transcriptomic profile of an early-onset AD model, the 5xFAD mice, at different time points (1 month, 4 months, 6 months and 9 months) of the disease. We are also interested in the effects of vitamin D supplementation in AD. Vitamin D receptor belongs to the family of nuclear receptors and vitamin D can act as a neurosteroid by regulating the expression of over a 1000 genes. We therefore decided to evaluate the effect of vitamin D supplementation in this AD mouse model at the transcriptomic level, after 5 months of supplementation (i.e. from 1 month to 6 months and from 4 months to 9 months).

2014-04-30 | E-MTAB-1937 | biostudies-arrayexpress

Regulatory role of vitamin D3 on myogenesis and fibrogenesis under Vdr gene silencing and TGF-β1 stimulation in skeletal muscle cells

Project description:Vitamin D deficiency is associated with a decline in muscle function and an increasing risk of muscle injury in athletes and the elderly. Nevertheless, how vitamin D3 and vitamin D receptor (VDR) regulate skeletal muscle cells under pro-fibrotic factor stimulation that could be pronounced during repetitive muscle damage have not been elucidated. Therefore, this study aimed to investigate the regulatory role of cholecalciferol (D3), calcidiol (25D3), calcitriol (1,25D3), and the effect of Vdr gene suppression under TGF-β1 stimulation in C2C12 mouse skeletal muscle cells. All forms of vitamin D3 exerted anti-fibrotic effects under TGF-β1 stimulation by suppression of COL1A1; however, D3 preserves this effect without a negative impact on myogenesis. Moreover, LC-MS/MS-based proteomics analysis revealed that myoblast fusion protein and mitochondrial regulation were altered following Vdr knockdown. These changes were associated with exacerbation of α-SMA expression in TGF-β1-treated cells and suggested VDR modulates fibrogenesis in skeletal muscle cells regardless of ligand binding. Under TGF-β1 stimulation, anti-fibrotic effects of 1,25D3 but not D3 were diminished after Vdr knockdown, supporting D3 action is not dependent on VDR activation. Collectively, understanding anti-fibrotic effects of vitamin D3 is beneficial for providing a strategy of vitamin D supplementation to counteract fibrosis development after muscle injury.

2025-12-01 | PXD062669 | Pride

Vitamin C boosts DNA demethylation in TET2 germline mutation carriers

Project description:We recently identified a family with lymphoma predisposition where a heterozygous truncating germline mutation in TET2 segregated with nodular lymphocyte predominant Hodgkin lymphoma. In a clinical trial of one year, we investigated the effects of oral 1 g/day vitamin C supplementation on DNA methylation by analyzing genome-wide DNA methylation and gene expression patterns from the family members.

| EGAS00001006916 | EGA

Transcriptome profiling of gingival fibroblasts treated by vitamin D3

Project description:In humans, vitamin D3 is a secosteroid, a prohormonal precursor of biologically active hydroxyforms. Vitamin D3 is related to periodontitis. The third American Health and Nutrition Survey found that plasma 25(OH)D3 levels are negatively correlated with attachment loss in people aged >50 years. The relationship between vitamin D3 and periodontitis remains to be investigated. We sent human gingival fibroblasts treated by vitamin D3 for transcriptome sequencing.

2022-09-09 | GSE212728 | GEO

Scottish Colorectal Cancer Vitamin D Intervention Study (SCoViDS) [RNA-seq]

Project description:Controversy surrounds whether vitamin D reduces colorectal cancer (CRC) risk, and/or beneficially impacts on CRC survival. We sought to delineate the transcriptomic in vivo response of human colorectal epithelium to vitamin D supplementation, define inter-subject variability and develop a predictive biomarker of response consistent with anti-tumour effects. Methodology Blood and rectal normal mucosa (NM) were sampled (176 subjects) and correlation sought between circulating vitamin D (25-OHD) level and NM gene expression (HT12 microarray) in the observational study. Oral vitamin D (3200IU/day) supplements were administered to 50 participants in an intervention study. Blood and NM (sigmoidoscopic biopsy) were sampled after 12 weeks. Transcriptomic analysis (HT12 and RNAseq) of post-treatment biopsies assessed enrichment for candidate genes and GO processes prioritised in the observational study. We identified transcriptomic changes in rectum that are consistent with anti-tumour responses. We then sought blood biomarkers predicting this response using receiver-operator curves and calculation of C-statistic. An independent expression dataset (BEST-D trial) was then used to validate candidate blood biomarkers of vitamin D response.

2021-06-22 | GSE157982 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data