Effects of digested onion extracts on intestinal gene expression: an interspecies comparison using different intestine models
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE83908 | GEO | 2016/09/16
SECONDARY ACCESSION(S): PRJNA327381
REPOSITORIES: GEO
Similar Datasets
Project description:Rat small intestine precision cut slices were exposed for 6 hours to in vitro digested yellow (YOd) and white onion extracts (WOd) that was followed by transcriptomics analysis. The digestion was performed to mimic the digestion that in vivo takes place in the stomach and small intestine. The transcriptomics response of the rat small intestine precision cut slices was compared to that of human Caco-2 cells and the pig in-situ small intestinal segment perfusion. The microarray data for the human Caco-2 cells (GSE83893) and the pig in-situ small intestinal segment perfusion (GSE83908) have been submitted separately from the current data on rat intestine. The goal was to obtain more insight into to which extent mode of actions depend on the experimental model. A main outcome was that each of the three models pointed to the same mode of action: induction of oxidative stress and particularly the Keap1-Nrf2 pathway.
2016-07-10 | GSE84179 | GEO
Project description:Rat small intestine precision cut slices were exposed for 6 hours to in vitro digested yellow (YOd) or white onion extracts (WOd) that was followed by transcriptomics analysis. The digestion was performed to mimic the digestion that in vivo takes place in the saliva, stomach and small intestine. A main question was to which extent the outcome of the biological interpretation of the transcription analysis (pathway analysis) depend on the model used. One outcome was that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions in all three models.
2016-09-29 | E-MTAB-5120 | biostudies-arrayexpress
Project description:Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of food compounds on (intestinal) health. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were incubated with in vitro digested onion extracts for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify onion-induced gene expression profiles in Caco-2 cells, digested yellow onion and white onion samples were compared to a digest control samples. Results: We found that yellow onion (n=5586, p<0.05) had a more pronounced effect on gene expression than white onion (n=3688, p<0.05). However, a substantial number of genes (n=3281, p<0.05) were affected by both onion variants in the same direction. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Conclusion: our data indicate that the in vitro Caco-2 intestinal model can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.
2016-09-16 | GSE83893 | GEO
Project description:Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of food compounds on (intestinal) health. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were incubated with in vitro digested onion extracts for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify onion-induced gene expression profiles in Caco-2 cells, digested yellow onion and white onion samples were compared to a digest control samples. Results: We found that yellow onion (n=5586, p<0.05) had a more pronounced effect on gene expression than white onion (n=3688, p<0.05). However, a substantial number of genes (n=3281, p<0.05) were affected by both onion variants in the same direction. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Conclusion: our data indicate that the in vitro Caco-2 intestinal model can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.
2021-04-30 | GSE100541 | GEO
Project description:Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, we explored the applicability of in vitro (human Caco-2 cells) and ex vivo intestine models (rat precision cut intestine slices and the pig in-situ small intestinal segment perfusion (SISP) technique) to study the effect of food compounds. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into which extent mode of actions depend on the model. The three intestine models shared 9,140 genes which were used to compare the responses to digested onions between the models. Unsupervised clustering analysis showed that genes up- or down-regulated by WOd in human Caco-2 cells and rat intestine slices were similarly regulated by YOd, indicating comparable modes of action for the two onion species. Highly variable responses to onion were found in the pig SISP model. By focussing only on genes with significant differential expression, in combination with a fold change > 1.5, 15 genes showed similar onion-induced expression in human Caco-2 cells and rat intestine slices and 2 overlapping genes were found between the human Caco-2 and pig SISP model. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions in all three models. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Taken together, our data indicate that each of the in vitro and ex vivo intestine models used in this study, taking into account their limitations, can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.
| S-EPMC5025074 | biostudies-literature
Project description:Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses.
2012-01-15 | GSE28159 | GEO
Project description:Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses. Samples of RNA were prepared from onions of two cultivars, ‘Wellington’ (brown, long-storing) and ‘Sherpa’ (brown, average-storing), grown according to normal commercial practice at various physiological ages, viz, freshly harvested, cured, pre-sprouting and sprouting. Three biological replicates for each time (harvest, cured, before sprouting, sprouting), curing temperature (20, 28°C) and cultivar (Wellington, Sherpa) combination (n = 42).
2012-01-15 | E-GEOD-28159 | biostudies-arrayexpress
Project description:Onion is regarded as non-climacteric. In onion, ethylene can suppress sprouting however, the ethylene binding inhibitor, 1-MCP can also suppress sprout growth although it is unknown how ethylene and 1-MCP elicit the same response. In this study, onion bulbs were treated with 10 μL L-1 ethylene or 1 μL L-1 1-MCP individually or in combination for 24 h at 20°C before or after curing (six weeks) at 20 or 28°C then stored at 1°C. Following curing, a subset of these same onion bulbs was stored separately under continuous air or ethylene (10 μL L-1) at 1°C
2011-06-29 | GSE27132 | GEO
Project description:Phylloplane microbiome of the outer leaves of onion bulb
| PRJEB70900 | ENA
Project description:Onion is regarded as non-climacteric. In onion, ethylene can suppress sprouting however, the ethylene binding inhibitor, 1-MCP can also suppress sprout growth although it is unknown how ethylene and 1-MCP elicit the same response. In this study, onion bulbs were treated with 10 μL L-1 ethylene or 1 μL L-1 1-MCP individually or in combination for 24 h at 20°C before or after curing (six weeks) at 20 or 28°C then stored at 1°C. Following curing, a subset of these same onion bulbs was stored separately under continuous air or ethylene (10 μL L-1) at 1°C Six treatments were chosen for microarray analysis; four samples were taken before curing immediately after treatment with ethylene or 1-MCP or ethylene and 1-MCP in combination for 24 h at 20°C. The other two samples and two were taken at the end of storage following 6 weeks curing at 28°C andafter 29 weeks cold storage (1°C) in continuous air or continuous ethylene totalling 35 weeks storage. The four pre-curing samples used were untreated (control) or treated with EB, MB or EMB and the two samples after storage were control bulbs stored in continuous ethylene or air at 1°C. There were three biological replicates of each of the six treatments making 18 samples in total.
2011-06-29 | E-GEOD-27132 | biostudies-arrayexpress