Ontology highlight
ABSTRACT:
PROVIDER: PRJNA764003 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15927670_1.fastq.gz | Fastqsanger.gz | |||
| SRR15927670_2.fastq.gz | Fastqsanger.gz | |||
| SRR15927671_1.fastq.gz | Fastqsanger.gz | |||
| SRR15927671_2.fastq.gz | Fastqsanger.gz | |||
| SRR15927672_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids, and to characterize the biological mechanisms related to PUFA metabolism. Polish Landrace pigs (n =12) were fed diet enriched with linoleic acid (LA, omega-6) and alpha-linolenic acid (ALA, omega-3 family) or standard diet as a control. The fatty acids profiling was assayed in order to verify how feeding influenced the fatty acids content in liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified by analysis in DAVID and Cytoscape tools. Fatty acids profile analysis indicated a higher contribution of PUFAs in liver for LA and ALA-enriched diet group, particularly for the omega-3 fatty acids family, but not omega-6. Next-generation sequencing identified 3,565 DEG, 1,484 of which were induced and 2,081 were suppressed by PUFA supplemenation. Low ratio of omega-6/-3 fatty acids resulted in modulation of fatty acids metabolism pathways and over-representation of genes involved in membrane composition, signal transduction and immune response pathways. In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and affected a set of genes involved in metabolic pathways important to animal health status. Hepatic mRNA profiles of Polish Landrace pig breed fed two different diets, were generated by deep sequencing, using Illumina MiSeq. Experimental diet was enriched with polyunsaturated fatty acids (omega-6 and omega-3), while standard diet remain as a cotrol. 2 pooled samples each containing RNA extracts from 6 individuals livers were analyzed.
2016-03-15 | E-GEOD-72123 | biostudies-arrayexpress
Project description:Background: While the mechanisms underlying the lactation-induced adaptations of intermediary metabolism and immune response have been extensively studied in rodents and dairy cows, little is known in this regard in sows. Therefore, the present study aimed to explore the lactation-induced changes in hepatic gene expression in sows during lactation. Results: Using a porcine whole-genome microarray a total of 632 differentially expressed genes in the liver of lactating compared to non-lactating sows (each n = 10) could be identified. Enrichment analysis revealed that the differentially expressed genes were mainly involved in fatty acid metabolism, pyruvate metabolism, glutathione metabolism, glycine, serine and threonine metabolism, citrate cycle, glycerophospholipid metabolism, PPAR signaling, nitrogen metabolism, and focal adhesion. The most striking observation with respect to intermediary metabolism was that genes involved in fatty acid catabolism, the catabolism of gluconeogenic amino acids, the citrate cycle and the respiratory chain were up-regulated in the liver of sows during lactation. With respect to immune response, it could be demonstrated that genes encoding acute phase proteins and genes involved in tissue repair were up-regulated and genes encoding focal adhesion molecules were down-regulated in the liver of sows during lactation. Conclusion: The results from this study indicate that energy-generating pathways and pathways involved in the delivery of gluconeogenic substrates are induced in the liver of sows during lactation. The alterations of expression of genes encoding proteins involved in immune response suggest that lactation in sows may cause an adaptive immune response which possibly counteracts hepatic inflammation. For microarray analyses, four RNA pools each, for the non-lactating group (n = 4) and the lactating group (n = 4), were prepared from eight individual sows per group. To each RNA pool, RNA from two different sows per group contributed identical amounts of RNA.
2012-05-30 | E-GEOD-38357 | biostudies-arrayexpress
Project description:The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids, and to characterize the biological mechanisms related to PUFA metabolism. Polish Landrace pigs (n =12) were fed diet enriched with linoleic acid (LA, omega-6) and alpha-linolenic acid (ALA, omega-3 family) or standard diet as a control. The fatty acids profiling was assayed in order to verify how feeding influenced the fatty acids content in liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified by analysis in DAVID and Cytoscape tools. Fatty acids profile analysis indicated a higher contribution of PUFAs in liver for LA and ALA-enriched diet group, particularly for the omega-3 fatty acids family, but not omega-6. Next-generation sequencing identified 3,565 DEG, 1,484 of which were induced and 2,081 were suppressed by PUFA supplemenation. Low ratio of omega-6/-3 fatty acids resulted in modulation of fatty acids metabolism pathways and over-representation of genes involved in membrane composition, signal transduction and immune response pathways. In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and affected a set of genes involved in metabolic pathways important to animal health status.
2016-03-15 | GSE72123 | GEO
Project description:Background: While the mechanisms underlying the lactation-induced adaptations of intermediary metabolism and immune response have been extensively studied in rodents and dairy cows, little is known in this regard in sows. Therefore, the present study aimed to explore the lactation-induced changes in hepatic gene expression in sows during lactation. Results: Using a porcine whole-genome microarray a total of 632 differentially expressed genes in the liver of lactating compared to non-lactating sows (each n = 10) could be identified. Enrichment analysis revealed that the differentially expressed genes were mainly involved in fatty acid metabolism, pyruvate metabolism, glutathione metabolism, glycine, serine and threonine metabolism, citrate cycle, glycerophospholipid metabolism, PPAR signaling, nitrogen metabolism, and focal adhesion. The most striking observation with respect to intermediary metabolism was that genes involved in fatty acid catabolism, the catabolism of gluconeogenic amino acids, the citrate cycle and the respiratory chain were up-regulated in the liver of sows during lactation. With respect to immune response, it could be demonstrated that genes encoding acute phase proteins and genes involved in tissue repair were up-regulated and genes encoding focal adhesion molecules were down-regulated in the liver of sows during lactation. Conclusion: The results from this study indicate that energy-generating pathways and pathways involved in the delivery of gluconeogenic substrates are induced in the liver of sows during lactation. The alterations of expression of genes encoding proteins involved in immune response suggest that lactation in sows may cause an adaptive immune response which possibly counteracts hepatic inflammation.
2012-05-31 | GSE38357 | GEO
Project description:In the present study, we investigated the consequences of n-3 polyunsaturated fatty acids (PUFA) depletion on hepatic lipid metabolism in mice fed during three months with a diet presenting a high n-6/n-3 PUFA ratio to induce n-3 PUFA depletion. Microarray analyses were performed to identify the molecular targets involved in the development of hepatic steatosis associated with n-3 PUFA depletion.
2011-08-26 | GSE26986 | GEO
Project description:The impact of sesamin, episesamin and sesamolin (sesame lignans) on hepatic gene expression profiles was compared with a DNA microarray. Male Sprague-Dawley rats were fed experimental diets containing 0.2% sesamin, episesamin or sesamolin, and a control diet free of lignans for 15 d. Compared to a lignan-free diet, a diet containing sesamin, episesamin and sesamolin caused 1.5- and 2-fold changes in the expression of 128 and 40, 526 and 152, and 516 and 140 genes, respectively. The lignans modified not only the mRNA levels of many enzymes involved in hepatic fatty acid oxidation, but also those of proteins involved in the transportation of fatty acids into hepatocytes and their organelles, and regulate hepatic concentrations of carnitine, CoA and malonyl-CoA. It is apparent that sesame lignans stimulate hepatic fatty acid oxidation by affecting the gene expression of various proteins regulating hepatic fatty acid metabolism. We also observed that lignans modified the gene expression of various proteins involved in hepatic lipogenesis, cholesterogenesis and glucose metabolism. The changes were generally greater with episesamin and sesamolin than with sesamin. In terms of the amounts accumulated in serum and the liver, the lignans ranked in the order sesamolin, episesamin and sesamin. The differences in bio-availability among these lignans appear to be important to their divergent physiological activities. Male Sprague-Dawley rats were divided into 4 groups with equal mean body weights consisting of 7 animals each and fed either a diet free of lignan or diets containing 0.2% lignan (sesamin, episesamin or sesamolin) for 15 d. RNA extracted from the livers of 5 rats from each group was subjected to microarray analyses. Rats with the highest and lowest body weights in each group at the time of killing were eliminated from microarray analyses.
2012-12-04 | E-GEOD-42693 | biostudies-arrayexpress
Project description:Hepatic lipid metabolism is highly dynamic, and disruption of several circadian transcriptional regulators results in hepatic steatosis. This includes genetic disruption of the glucocorticoid receptor (GR) as the liver develops. To address the functional role of GR in the adult liver, we used an acute hepatocyte-specific GR knockout model (hepGRKO) to study temporal hepatic lipid metabolism governed by GR at several pre- and postprandial timepoints. Lipidomics analysis revealed significant temporal lipid metabolism, with GR disruption resulting in impaired regulation of specific triglycerides, non-esterified fatty acids, and sphingolipids. This correlated with increased number and size of lipid droplets and mildly reduced mitochondrial respiration, most noticeably in the postprandial phase. Proteomics and transcriptomics analyses suggest that dysregulated lipid metabolism originates from pronounced induced expression of enzymes involved in fatty acid synthesis, -oxidation, and sphingolipid metabolism. Integration of GR cistromic data suggests that induced genes are a result of regulatory actions secondary to direct GR effects on transcription.
2023-09-07 | PXD041168 | Pride
Project description:The impact of sesamin, episesamin and sesamolin (sesame lignans) on hepatic gene expression profiles was compared with a DNA microarray. Male Sprague-Dawley rats were fed experimental diets containing 0.2% sesamin, episesamin or sesamolin, and a control diet free of lignans for 15 d. Compared to a lignan-free diet, a diet containing sesamin, episesamin and sesamolin caused 1.5- and 2-fold changes in the expression of 128 and 40, 526 and 152, and 516 and 140 genes, respectively. The lignans modified not only the mRNA levels of many enzymes involved in hepatic fatty acid oxidation, but also those of proteins involved in the transportation of fatty acids into hepatocytes and their organelles, and regulate hepatic concentrations of carnitine, CoA and malonyl-CoA. It is apparent that sesame lignans stimulate hepatic fatty acid oxidation by affecting the gene expression of various proteins regulating hepatic fatty acid metabolism. We also observed that lignans modified the gene expression of various proteins involved in hepatic lipogenesis, cholesterogenesis and glucose metabolism. The changes were generally greater with episesamin and sesamolin than with sesamin. In terms of the amounts accumulated in serum and the liver, the lignans ranked in the order sesamolin, episesamin and sesamin. The differences in bio-availability among these lignans appear to be important to their divergent physiological activities.
2012-12-04 | GSE42693 | GEO
Project description:The beneficial effects of dietary long-chain (LC) n-3 polyunsaturated fatty acids (PUFA) in the prevention and/or treatment of some metabolic disorders result largely from their capacity to regulate the transcription level of many genes involved in metabolic and physiological homeostasis, especially in the liver. In this respect, they are known to bind and activate the Peroxisome Proliferator-Activated Receptor alpha (PPARalpha). The precursor of LC-PUFA, a-linoleic acid (ALA, C18:3 n-3) share some beneficial metabolic effects with its LC derivatives, however its role in gene regulation is poorly documented. Here, we analysed the hepatic transcriptome of mice fed for 5 weeks diets rich in either saturated FA from palm oil (PALM group) or ALA from linseed oil (LIN group). This modification of dietary fatty acid composition in a context of a high fat diet had a subtle but significant effect on the hepatic transcriptome. We identified mainly a group of genes that were upregulated in the LIN vs the PALM group and that include several well-known PPARalpha target genes involved in lipid and xenobiotic metabolism. Liver gene expression was measured in male C57BL/6J mice fed during 5 weeks a high fat diet (51% energy from fat) containing palm oil, rich in saturated fatty acids (n=10) or linseed oil, rich in 18:3 n-3 (n=8)
2016-05-18 | E-GEOD-73290 | biostudies-arrayexpress
Project description:Cancer is a systemic disease that includes several noted features, such as pre-metastatic niche formation, cachexia, and immune dysregulation. However, the mechanisms underlying multi-organ failure remain to be further investigated. Here, we show that inflammation, fatty liver, and dysregulated metabolism are hallmarks of systemically affected livers in various animal tumor models and cancer patients in the absence of hepatic metastasis. We identify that tumor-derived extracellular vesicles and particles (EVPs) are crucial mediators of cancer-induced hepatic functional reprogramming. Tumor EVPs package multiple fatty acids, such as palmitic acid, and target Kupffer cells upregulating TNFα via Toll-like receptor 4, which in turn promotes a pro-inflammatory microenvironment leading to fatty liver disease and downregulates metabolic pathways, such as fatty acid metabolism and oxidative phosphorylation. Strikingly, ablation of Kupffer cells or TNFα blockade markedly abrogates the tumor-induced excess hepatic lipid droplet accumulation. We show that tumor implantation or pre-treatment with tumor EVPs decreases the expression of Cytochrome P450 genes and attenuates drug metabolism in mice. Notably, increased fatty livers and decreased Cytochrome P450 genes are observed in tumor-free livers in cancer patients. Thus, tumor-derived EVP uptake in the liver may lead to reduced tolerance of drug toxicity in cancer patients. Our results highlight the role of tumor EVPs in dysregulating hepatic functions and its potential to serve as therapeutic targets along with Kupffer cell-induced TNFα inhibition to prevent fatty liver disease and enhance anti-cancer chemotherapy.
2023-03-09 | GSE220446 | GEO