Effect of vitamin D supplementation on rats' liver
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA994448 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25257502.fastq.gz | Fastqsanger.gz | |||
| SRR25257503.fastq.gz | Fastqsanger.gz | |||
| SRR25257504.fastq.gz | Fastqsanger.gz | |||
| SRR25257505.fastq.gz | Fastqsanger.gz | |||
| SRR25257506.fastq.gz | Fastqsanger.gz |
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Project description:In order to understand the molecular mechanism responsible for the therapeutic potential of vitamin D, we conducted an analysis of the liver transcriptome – a central place of metabolic changes. The experiment was carried out on adult female rats (about one year old), n=18, divided into three experimental subjects, receiving different doses of vitamin D for three months: group I - 0, group II - 1000 U/Kg, group III - 5000 U/Kg. After the experiment, the biochemical and haematological parameters of the blood were evaluated. RNA-seq was used to analyze the changes in the liver transcriptome, and Gene Set Enrichment Analysis (GSEA) was used to identify enrichments in gene expression profiles of experimental groups. qPCR was employed to evaluate the expression of several genes connected to cholesterol biosynthesis, metallothioneins, vitamin D metabolism and others. At the end of the experiment, 25(OH) vitamin D concentrations were as follows: group I: 29 ng/ml, group II 43: ng/ml, group III: 70 ng/mL. Considering blood parameters, we observed a lower platelet count (p<0,008) and significantly higher (p<0.02) number of WBC in rats supplemented with 1000 U/Kg than in rats from group III (5000 U/Kg), but no difference between rats from group I and III were detected in these parameters. Moreover, we noted a trend (p<0.06 ) in total cholesterol concentration, suggesting a linear decrease with increasing doses of vitamin D. RNA-seq analysis did not identify any differentially expressed genes with FDR<0.05 in any of the three comparisons. However, GSEA revealed significant activation of the number of processes and pathways. In the I vs III comparison, the most enriched were the genes from the “metallothionein, and TspO/MBR family” (Enrichment Score=8,170, FDR= 0.00006), the genes associated with “glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity” (Enrichment Score=5.13, FDR<00049) and the genes associated with “Negative regulation of tumour necrosis factor production” (Enrichment score=1.26, FDR0.0064. qPCR analysis identified significant upregulation of Mt1, Mt2 and Orm1 genes in animals receiving high doses of vitamin D (p<0.025, p<0.025, p<0009, respectively). Moreover, significant downregulation of Srebp2 and Insig2 was observed in both experimental groups when compared to the control group (p<0.003, p<0.036, respectively). Our results support the potential of vitamin D supplementation in ameliorating oxidative stress, inflammation and high blood cholesterol and underlie the need for further studies aimed at identifying optimal vitamin D doses with therapeutic effects.
2023-07-24 | GSE237234 | GEO
Project description:In this study, we investigated the effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model as vitamin D is known to have a spectrum of anticancer activities. Using PET, we found that tumor formation and progression were suppressed in rats fed a diet supplemented with 6 IU/g vitamin D3(+6D) as compared to the group fed a 2 IU/g vitamin D3 diet (+2D) or controls. Microarray analysis of the tumors that arose revealed that vitamin D supplementation caused significant up- and down regulation in 21 and 16 genes, respectively. There are 9 tissue samples (3 rats in each group labeled as (+6), (+2) and control). Duplicate analysis were used for each sample.
2015-08-01 | E-GEOD-48961 | biostudies-arrayexpress
Project description:In this study, we investigated the effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model as vitamin D is known to have a spectrum of anticancer activities. Using PET, we found that tumor formation and progression were suppressed in rats fed a diet supplemented with 6 IU/g vitamin D3(+6D) as compared to the group fed a 2 IU/g vitamin D3 diet (+2D) or controls. Microarray analysis of the tumors that arose revealed that vitamin D supplementation caused significant up- and down regulation in 21 and 16 genes, respectively.
2015-08-01 | GSE48961 | GEO
Project description:This SuperSeries is composed of the following subset Series:; GSE8146: Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse heart; GSE8150: Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse brain Experiment Overall Design: Refer to individual Series
2008-06-16 | E-GEOD-8162 | biostudies-arrayexpress
Project description:We report the anaysis of the effect of the supplementation of pigs feed with high doses of vitamin D on the muscle transcriptome. We observed significant changes in the expression of only one gene - IFNGR2.
2023-11-01 | GSE243386 | GEO
Project description:Background: In addition to its canonical functions, vitamin D has been proposed to be an important mediator of the immune system. Despite ample sunshine, vitamin D deficiency is prevalent (> 80%) in the Middle East, resulting in a high rate of supplementation. However, the underlying molecular mechanisms of the specific regimen and potential factors affecting an individual’s response to vitamin D are not well characterized. Objective: To characterize changes in blood transcriptomic and the potential mechanisms associated with vitamin D3 supplementation and response. Design: In this intervention study, one hundred vitamin D-deficient women were given a weekly oral dose (50,000 IU) of vitamin D3 for three months. A high-throughput targeted PCR, composed of 264 genes representing important blood transcriptomic fingerprints in health and disease states, was performed on pre- and post-supplementation blood samples to profile the molecular response to vitamin D3. Multivariate, network, gene ontology, and literature mining analyses were used for the interpretation of the transcriptomic profiling results. Results: We identified 54 differentially expressed genes that were strongly modulated by vitamin D3 supplementation. Network analyses showed significant changes in the immune-related pathways such as TLR4/CD14 and IFN receptors, and catabolic processes related to NFkB, which were subsequently confirmed by gene ontology enrichment analyses. We proposed a model for vitamin D3 response, using the reduced expression of the molecules involved and the receptor-mediated intra-cellular signaling leading to reduce cytokine production. Conclusions: Blood-transcriptomic profiles of vitamin D3 response were generated using a targeted blood gene panel. Vitamin D has a strong effect on the immune system, G-coupled protein receptor signaling, and the ubiquitin system. We highlighted the major molecular changes and biological processes induced by vitamin D3, which will help to further investigate the effectiveness of vitamin D supplementation among individuals in the Middle East.
2021-05-19 | GSE157939 | GEO
Project description:Vitamin D deficiency is common among older adults and has been linked to muscle weakness. Vitamin D supplementation has been proposed as a strategy to improve muscle function in older adults. The aim of this study was to investigate the effect of calcifediol (25-hydroxycholecalciferol) on whole genome gene expression in skeletal muscle of vitamin D deficient frail older adults. A double-blind placebo controlled trial was conducted in vitamin D deficient frail older adults (aged above 65), characterized by blood 25-hydroxycholecalciferol concentrations between 20 and 50 nmol/L. Subjects were randomized across the placebo group (n=12) and the calcifediol group (n=10, 10 µg per day). Muscle biopsies were obtained before and after six months of calcifediol or placebo supplementation and subjected to whole genome gene expression profiling using Affymetrix HuGene 2.1ST arrays. Expression of the vitamin D receptor gene was virtually undetectable in human skeletal muscle biopsies. Calcifediol supplementation led to a significant increase in blood 25-hydroxycholecalciferol levels compared to the placebo group. No difference between treatment groups was observed on strength outcomes. The whole transcriptome effects of calcifediol and placebo were very weak. Correcting for multiple testing using false discovery rate did not yield any differentially expressed genes using any sensible cut-offs. P-values were uniformly distributed across all genes, suggesting that low p-values are likely to be false positives. Partial least squares-discriminant analysis and principle component analysis was unable to separate treatment groups. Calcifediol supplementation did not affect the skeletal muscle transcriptome in frail older adults. Our findings indicate that vitamin D supplementation has no effects on skeletal muscle gene expression, suggesting that skeletal muscle may not be a direct target of vitamin D in older adults.
2019-06-10 | GSE123993 | GEO
Project description:The objective of the overall study was to determine the effects of oral vitamin D supplementation on alveolar macrophages from human subjects. In this substudy, subjects treated with vitamin D (intervention group) in paired analysis had small, but significant effects on immune-related differential gene expression pre versus post supplementation. In this study, we obtained alveolar macrophages by bronchoalveolar lavage of subjects before and after a 3 month vitamin D trial. RNA for the array was obtained shortly after bronchoscopy. Randomized Controlled Trial: This is a substudy of paired samples of subjects treated with vitamin D. Each sample was studied once. 22 individuals were studied.
2014-04-08 | E-GEOD-56583 | biostudies-arrayexpress
Project description:DNA methylation data were assayed using the Illumina MethylationEPIC microarray platform in blood samples from 48 individuals taking part in a vitamin K supplementation trial.
2020-01-09 | GSE143307 | GEO
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