GNPS - Osteoarthritis diet study
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Pieter C. Dorrestein
PROVIDER: MSV000094097 | GNPS | Thu Feb 15 23:11:00 GMT 2024
REPOSITORIES: GNPS
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Project description:Gluten-free diet intervention: 11 individuals, 3 time points (T1: 1 week before intervention, T2: at the intervention; T3: 5 weeks after intervention. Fecal samples taken at each time point were sujbject of VLP enrichment and routine metagenomics sequencing
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Project description:Diet can regulate gene and microRNA (miRNA) expression and various biological processes in the gut. Dietary interventions have been proposed as therapeutic approaches for several diseases, including cancer. In a pilot study, we showed that a low-inflammatory Mediterranean diet reduced markers of local and systemic inflammation in patients with Familial Adenomatous Polyposis (FAP). We evaluated the changes induced by a low-inflammatory Mediterranean dietary intervention on fecal miRNome and intestinal tissue transcriptome in FAP subjects and assessed whether these changes could be associated with the beneficial effects observed in the pilot study. The diet modulated 41 fecal miRNAs, and this modulation remained for three months after the intervention. miR-5092-5p, miR-4527, and miR-3612-3p were positively correlated with adherence to the Mediterranean diet, while miR-6867-5p and miR-760-5p were negatively correlated with serum calprotectin levels. The altered miRNAs target genes mainly related to inflammatory pathways, DNA repair, metabolism, and cytoskeleton organization. Seventy genes were differentially expressed between adenoma and normal tissue. Most were different before the dietary intervention, but reached similar levels after the diet. Functional enrichment analysis identified the proinflammatory ERK1/2, cell cycle regulation and nutrient response pathways as commonly regulated by differentially expressed miRNAs and genes. These findings suggest that fecal miRNAs modulated by the diet reflect an epigenetic regulation occurring in tissues that seems to influence inflammatory pathways. miRNAs and genes with oncogenic and tumor suppressor functions are also regulated, highlighting the potential cancer-preventive effect of the low-inflammatory Mediterranean diet.
2024-01-12 | GSE222298 | GEO
Project description:Diet can regulate gene and microRNA (miRNA) expression and various biological processes in the gut. Dietary interventions have been proposed as therapeutic approaches for several diseases, including cancer. In a pilot study, we showed that a low-inflammatory Mediterranean diet reduced markers of local and systemic inflammation in 27 patients with Familial Adenomatous Polyposis (FAP). We evaluated the changes induced by a low-inflammatory Mediterranean dietary intervention on fecal miRNome and intestinal tissue transcriptome in FAP subjects and assessed whether these changes could be associated with the beneficial effects observed in the pilot study. The diet modulated 41 fecal miRNAs, and this modulation remained for three months after the intervention. miR-5092-5p, miR-4527, and miR-3612-3p were positively correlated with adherence to the Mediterranean diet, while miR-6867-5p and miR-760-5p were negatively correlated with serum calprotectin levels. The altered miRNAs target genes mainly related to inflammatory pathways, DNA repair, metabolism, and cytoskeleton organization. Seventy genes were differentially expressed between adenoma and normal tissue. Most were different before the dietary intervention, but reached similar levels after the diet. Functional enrichment analysis identified the proinflammatory ERK1/2, cell cycle regulation and nutrient response pathways as commonly regulated by differentially expressed miRNAs and genes. These findings suggest that fecal miRNAs modulated by the diet reflect an epigenetic regulation occurring in tissues that seems to influence inflammatory pathways. miRNAs and genes with oncogenic and tumor suppressor functions are also regulated, highlighting the potential cancer-preventive effect of the low-inflammatory Mediterranean diet.
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Project description:Compositional changes in the microbiota (dysbiosis) may be a basis for Irritable Bowel Syndrome (IBS) but biomarkers are currently unavailable to direct microbiota-directed therapy. We therefore examined whether changes in fecal β-defensin could be a marker of dysbiosis in a murine model. Experimental dysbiosis was induced using four interventions relevant to IBS: a mix of antimicrobials, westernized diets (high-fat/high-sugar and, high salt diets), or mild restraint stress. Fecal mouse β-defensin-3 and 16S rRNA-based microbiome profiles were assessed at baseline, during and following these interventions. Each intervention, except for mild restraint stress, altered compositional and diversity profiles of the microbiota. Exposure to antimicrobials or a high-fat/high-sugar diet, but not mild restraint stress, resulted in decreased fecal β-defensin-3 compared to baseline. In contrast, exposure to the high salt diet increased β-defensin-3 compared to baseline but this was not accompanied by discernible inflammatory changes in the host.
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Project description:This study aimed to identify the effects of replacement of saturated fat (SFA) by monunsaturated fat (MUFA) in a western-type diet and the effects of a full Mediterranean (MED) diet on whole genome PBMC gene expression and plasma protein profiles. Abdominally overweight subjects were randomized to a 8 wk completely controlled SFA-rich diet, a SFA-by-MUFA-replaced diet (MUFA diet) or a MED diet. Concentrations of 124 plasma proteins and PBMCs whole genome transcriptional profiles were assessed. Consumption of the MUFA and MED diet, compared with the SFA diet, decreased expression of oxidative phosphorylation (OXPHOS) genes, serum lipids and plasma Connective Tissue Growth Factor, myoglobin and Apo B concentrations. The MED diet additional lowered plasma α-2-macroglobulin concentration compared with the SFA diet. Within the MED diet group concentrations of several pro-inflammatory proteins were lowered. We conclude that MUFA as replacement of SFA in a western-type diet or in a MED diet had similar effects on lowering expression of OXPHOS genes. We hypothesize that replacement of SFA by MUFA increased metabolic health as reflected by lowered serum lipids and certain plasma proteins, thereby reducing metabolic stress and OXPHOS activity in PBMCs. The MED diet may have additional anti-atherogenic effects by lowering concentrations of pro-inflammatory plasma proteins. Expression profiling by array
2012-08-02 | E-GEOD-30509 | biostudies-arrayexpress
Project description:This study aimed to identify the effects of replacement of saturated fat (SFA) by monunsaturated fat (MUFA) in a western-type diet and the effects of a full Mediterranean (MED) diet on whole genome PBMC gene expression and plasma protein profiles. Abdominally overweight subjects were randomized to a 8 wk completely controlled SFA-rich diet, a SFA-by-MUFA-replaced diet (MUFA diet) or a MED diet. Concentrations of 124 plasma proteins and PBMCs whole genome transcriptional profiles were assessed. Consumption of the MUFA and MED diet, compared with the SFA diet, decreased expression of oxidative phosphorylation (OXPHOS) genes, serum lipids and plasma Connective Tissue Growth Factor, myoglobin and Apo B concentrations. The MED diet additional lowered plasma α-2-macroglobulin concentration compared with the SFA diet. Within the MED diet group concentrations of several pro-inflammatory proteins were lowered. We conclude that MUFA as replacement of SFA in a western-type diet or in a MED diet had similar effects on lowering expression of OXPHOS genes. We hypothesize that replacement of SFA by MUFA increased metabolic health as reflected by lowered serum lipids and certain plasma proteins, thereby reducing metabolic stress and OXPHOS activity in PBMCs. The MED diet may have additional anti-atherogenic effects by lowering concentrations of pro-inflammatory plasma proteins.
2012-08-03 | GSE30509 | GEO
Project description:Peripheral blood mononuclear cell (PBMC) gene expression profiling is a low-invasive tool used in human diet intervention studies. In dogs this technique has been used to investigate disease states but not to examine the effect of diet. We tested the hypothesis that diet alters dog systemic immune cell gene expression profiles by comparing PBMC gene expression in dogs fed either a premium kibbled diet or a raw red meat diet for 9 weeks. Our results showed that diet shifted the dogs’ PBMC gene expression profile and these alterations corresponded with changes in plasma IgA levels. This illustrates that PBMC microarrays are a useful tool that may be applied to study the long-term effects of diet on health outcomes for the dog.
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Project description:In a randomized controlled dietary intervention study we compared an isocaloric Healthy Nordic diet with the average Nordic diet for influence on peripheral blood mononuclear cells (PBMC) gene expression. We studied obese adults with features of the metabolic syndrom, n=66. There was no significant difference in age, BMI, or gene expression between the groups before the intervention. The intervention lasted for 18-24 weeks.
2015-05-13 | GSE68759 | GEO
Project description:In a randomized controlled dietary intervention study we compared an isocaloric Healthy Nordic diet with the average Nordic diet for influence on peripheral blood mononuclear cells (PBMC) gene expression. We studied obese adults with features of the metabolic syndrom, n=66. There was no significant difference in age, BMI, or gene expression between the groups before the intervention. The intervention lasted for 18-24 weeks. Blood samples were obtained before (W0), during (W12) and after completion (W18-24) of the dietary intervention. From the samples we extracted RNA. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix Inc.).
2015-05-13 | E-GEOD-68759 | biostudies-arrayexpress
Project description:OBJECTIVE Diet intervention in obese adults is the first strategy to induce weight loss and to improve insulin sensitivity. We hypothesized that improvements in insulin sensitivity after weight loss from a short-term dietary intervention tracks with alterations in expression of metabolic genes and abundance of specific lipid species. RESEARCH DESIGN AND METHODS Eight obese, insulin resistant, non-diabetic adults were recruited to participate in a three-week low calorie diet intervention study (1000 kcal/day). Fasting blood samples and vastus lateralis skeletal muscle biopsies were obtained before and after the dietary intervention. Clinical chemistry and measures of insulin sensitivity were determined. Unbiased microarray gene expression and targeted lipidomic analysis of skeletal muscle was performed. RESULTS Body weight was reduced, insulin sensitivity (HOMA-IR) was enhanced, and serum insulin concentration and blood lipid (triglyceride, cholesterol, LDL and HDL) levels were improved after dietary intervention. Gene set enrichment analysis of skeletal muscle revealed that oxidative phosphorylation and inflammatory processes were among the most enriched KEGG-pathways identified after dietary intervention. mRNA expression of PDK4 and MLYCD increased, while SCD decreased in skeletal muscle after dietary intervention. Dietary intervention altered the intramuscular lipid profile of skeletal muscle, with changes in content of phosphatidylcholine and triglyceride species among the pronounced. CONCLUSIONS Short-term diet intervention and weight loss in obese adults alters metabolic gene expression and reduces specific phosphatidylcholine and triglyceride species in skeletal muscle, concomitant with improvements in clinical outcomes and enhanced insulin sensitivity.
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