Revealing the Molecular Mechanisms of Erwei Shensu Yin in Treating Atherosclerosis: A 4D Proteomics Analysis
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ABSTRACT:
ORGANISM(S): Rattus
SUBMITTER: 
Jianfei Yang
PROVIDER: PXD055415 | iProX | Thu Aug 29 00:00:00 BST 2024
REPOSITORIES: iProX
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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: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:We isolated CD4+ T cells from draining lymph nodes 7 days post EAE from DA rats treated with vitamin D supplemented, vitamin D deprived or regular diet
2017-02-01 | GSE92680 | GEO
Project description:The aim of the study was to investigate the role of vitamin D on adipocyte development. To this end, rat dams (Sprague-Dawley rats ) were fed diets with 0 or 1,000 IU vitamin D3 per kg diet 5 weeks prior to conception until the end of lactation. By using high-density DNA microarrays, we analyzed the gene-expression profile of mesenterial adipose tissue of both groups of newborn rats.
2016-12-31 | GSE82215 | GEO
Project description:Vitamin D is an important calcium-regulating hormone with diverse functions in numerous tissues including the brain. Increasing evidence suggests that vitamin D may play a role in maintaining cognitive function and that vitamin D deficiency may accelerate age-related cognitive decline. Using aging rodents, we attempted to model the range of human serum vitamin D levels, from deficient to sufficient, to test whether vitamin D could preserve or improve cognitive function with aging. For 5-6 months, middle-aged F344 rats were fed diets containing low, medium (typical amount) or high vitamin D3 (100, 1000 or 10,000 IU/kg diet, respectively) and then hippocampal-dependent learning and memory were tested in the Morris water maze. Rats on high vitamin D achieved the highest blood levels (in the sufficient range) and significantly outperformed low and medium groups on maze reversal, a particularly challenging task that detects more subtle changes in memory. In addition to calcium-related processes, hippocampal gene expression microarrays identified pathways pertaining to synaptic transmission, cell communication and G-protein function as being up-regulated with high vitamin D. Basal synaptic transmission also was enhanced corroborating observed effects on gene expression and learning and memory. Our studies demonstrate a causal relationship between vitamin D status and cognitive function and suggest that vitamin D-mediated changes in hippocampal gene expression may improve the likelihood of successful brain aging. Sixty, middle-aged male F344 rats were divided into three groups, each receiving for 5-6 months a different dietary amount of cholecalciferol (vitamin D3; VitD3). Purified AIN-93G (Harlan-Teklad) diet was modified to contain low, medium or high VitD3 (IU/kg diet): High = 10,000, Standard (Control) = 1000; Low = 100. Animal weight and amount of food consumed was recorded 2-3 times/week. Serum levels of 25-hydroxy vitamin D were determined using liquid chromatography/tandem mass spectrometry (ZRT Laboratory). Hippocampal RNA was isolated, quantified and checked for RNA integrity. One low VitD3 sample failed RNA quality control. Remaining RNA samples were applied to Affymetrix Rat Gene 1.0 ST arrays (one array/subject). Pre-statistical filtering removed poorly annotated probe sets, low intensity signals, and outlier values (>2SD of the group mean). Filtered data were analyzed by 1-way ANOVA to identify significant differences and the False Discovery Rate (FDR) procedure was used to estimate the error of multiple testing. FDR was compared at 0.31 and 0.17. Significant genes were assigned to one of four idealized expression patterns using Pearson’s test and separated by the sign of their correlation; relative gene expression values are provided on the log-2 scale. Functional categorization for significant genes was determined using DAVID bioinformatic tools. Please note that 'Marked' and 'Unmarked' (in the sample titles) refers to whether the rat had a mark on its tail. The rats were pair-housed and this is how two rats in one cage were distinguished.
2014-09-23 | E-GEOD-61326 | biostudies-arrayexpress
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
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-D3 (VitD3) exhibits pleiotropic effects in host’s physiology by acting on several organs. To mechanistically understand how VitD3 influences the colon physiology we interrogated the gene expression profile of mouse colon in response to high or low VitD3 bioavailability. VitD3 tissue bioavailability was modulated in mice with the use of diets supplemented with different concentrations of VitD3 (0, 2 or 10 IU/g) and the use of Gc knockout mouse strain in where VitD3 bioavailability is enhanced. Vitamin-D3 (VitD3) exhibits pleiotropic effects in host’s physiology by acting on several organs. To mechanistically understand how VitD3 influences the colon physiology we interrogated the gene expression profile of mouse colon in response to high or low VitD3 bioavailability. VitD3 tissue bioavailability was modulated in mice with the use of diets supplemented with different concentrations of VitD3 (0, 2 or 10 IU/g) and the use of Gc knockout mouse strain in where VitD3 bioavailability is enhanced.
2024-11-29 | GSE219214 | GEO
Project description:<p>A rat model of slow transit constipation (STC) was induced by loperamide hydro-chloride to explore the therapeutic mechanism of Zingiber mioga (Thunb.) Rosc. (RH) using integrated metabolomic and metagenomic approaches. Thirty-six Sprague–Dawley (SD) rats were randomly assigned to 6 groups (n = 6): the con-trol group, model group, mosapride-positive control group (2 mg kg−1), and RH low- (1,350 mg kg−1), medium- (2,700 mg kg−1), and high-dose (3,400 mg kg−1) groups. The STC model was established by intragastric administration of lop-eramide hydrochloride (5 mg/kg) for 35 consecutive days, with simultaneous drug intervention. Serum levels of substance P (SP), motilin (MTL), and gastrin (GAS) were quantified; colonic pathological sections were prepared; and serum untargeted metabolomics and fecal metagenomics analyses were conducted. Key findings demonstrated that RH significantly decreased serum SP levels while elevating MTL and GAS levels in STC rats, attenuated colonic pathological lesions, and increased intestinal propulsion rate. Serum metabolomics analysis identified 15 differential metabolites, which were primarily involved in nitrogen metabolism, neuroactive ligand-receptor interaction, and amino acid metabo-lism. Fecal metagenomics analysis revealed that RH restored the Eubacteriales/ Lachnospirales ratio and increased the relative abundance of probiotic genera (e.g., Ruminococcus sp., Eubacterium sp.). In conclusion, RH exerts laxative effects in STC rats by regulating gastrointestinal hormones, mitigating colonic injury, and accelerating intestinal peristalsis. These effects may be mediated by ameliorating amino acid and nitrogen metabolic disorders and modulating gut microbiota composition. </p>
2026-02-11 | MTBLS13888 | MetaboLights
Project description:Vitamin D is an important calcium-regulating hormone with diverse functions in numerous tissues including the brain. Increasing evidence suggests that vitamin D may play a role in maintaining cognitive function and that vitamin D deficiency may accelerate age-related cognitive decline. Using aging rodents, we attempted to model the range of human serum vitamin D levels, from deficient to sufficient, to test whether vitamin D could preserve or improve cognitive function with aging. For 5-6 months, middle-aged F344 rats were fed diets containing low, medium (typical amount) or high vitamin D3 (100, 1000 or 10,000 IU/kg diet, respectively) and then hippocampal-dependent learning and memory were tested in the Morris water maze. Rats on high vitamin D achieved the highest blood levels (in the sufficient range) and significantly outperformed low and medium groups on maze reversal, a particularly challenging task that detects more subtle changes in memory. In addition to calcium-related processes, hippocampal gene expression microarrays identified pathways pertaining to synaptic transmission, cell communication and G-protein function as being up-regulated with high vitamin D. Basal synaptic transmission also was enhanced corroborating observed effects on gene expression and learning and memory. Our studies demonstrate a causal relationship between vitamin D status and cognitive function and suggest that vitamin D-mediated changes in hippocampal gene expression may improve the likelihood of successful brain aging.
2014-09-23 | GSE61326 | GEO