Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed Part I: Serum proteomes
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ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Elite
ORGANISM(S): Sus Scrofa Domesticus (domestic Pig)
TISSUE(S): Blood Serum
SUBMITTER: 
Thi Xuan Nguyen
LAB HEAD: Richard Burchmore
PROVIDER: PXD032327 | Pride | 2023-04-17
REPOSITORIES: Pride
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Project description:Transcriptional profiling of 25d old piglets comparing control untreated suckling jejunum with weaned piglets' jejunum. The goal was to gain new insight into the interaction between weaning and intestinal function.A keen interest is paid in deciphering expression changes of apoptosis or cell cycle control genes. The statistical analysis of gene ontology revealed that most of these altered genes are metabolic-related enzymes and regulators which may involved in the biological regulation, developmental process, and cellular process. Weaning also causes alterations in various immune response pathways. Results likely indicate that weaning induced cell cycle arrest, enhanced apoptosis, and inhibited cell proliferation. Two-condition experiment, suckling control piglets' jejunum vs. weaned piglets' jejunum. Biological replicates: 4 control replicates, 4 weaned replicates.
2014-05-01 | E-GEOD-48050 | biostudies-arrayexpress
Project description:Background: The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the breast epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained. Results: One third (n = 102) of all murine miRNAs analysed were present during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show significant changes, we observed inverse patterns of miRNA and target expression. The datasets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research. Conclusions: MicroRNAs were expressed in co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation and its correlation with mRNA expression provide new avenues for research into mammary gland biology and generates candidates for functional validation. This SuperSeries is composed of the following subset Series: GSE15054: Characterisation of microRNA expression in post-natal mouse mammary gland development [gene] GSE15055: Characterisation of microRNA expression in post-natal mouse mammary gland development [miRNA] Refer to individual Series
2010-06-25 | E-GEOD-15057 | biostudies-arrayexpress
Project description:Background: The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the breast epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained. Results: One third (n = 102) of all murine miRNAs analysed were present during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show significant changes, we observed inverse patterns of miRNA and target expression. The datasets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research. Conclusions: MicroRNAs were expressed in co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation and its correlation with mRNA expression provide new avenues for research into mammary gland biology and generates candidates for functional validation. Developmental time course over 17 time points with 2-3 independent biological replicates per time point and four pairs of technical replicates, 48 samples in total
2010-06-25 | E-GEOD-15054 | biostudies-arrayexpress
Project description:Background: Epidemiological studies suggest an association between maternal obesity and adverse neurodevelopmental outcomes in offspring. Objective: To compare the global proteomic portrait in the cerebral cortex between mice born to mothers on a high-fat or control diet who themselves were fed a high-fat or control diet. Methods: Male mice born to dams fed a control (C) or high fat (H) diet four weeks before conception and during gestation and lactation were assigned to either C or H diet at weaning. Mice (n=24) were sacrificed at 19-weeks and their cerebral cortices were pooled into 8 samples and analysed using an iTRAQ based 2D LC-MS methodology. Results: A total of 6,695 proteins were identified and fully quantified (q<0.01). Approximately 10% of these proteins demonstrated a minimum of one Standard Deviation of regulation across all biological replicates in at least one of the experimental groups (CH, HC, HH) relative to the control (CC). Principal component analysis and hierarchical clustering analysis showed that mice clustered based on the diet of the mother and not their current diet. In silico bioinformatics analysis revealed that maternal high-fat diet was significantly associated with response to hypoxia/oxidative stress and apoptosis in the cerebral cortex of the adult offspring. Conclusion: Maternal high-fat diet was associated with distinct endophenotypic changes of the adult mouse cerebral cortex independent of the diet of the offspring. The identified modulated proteins could represent novel therapeutic targets for the prevention of neuropathological features resulting from maternal obesity.
2018-01-29 | PXD001540 | Pride
Project description:Background: The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the breast epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained. Results: One third (n = 102) of all murine miRNAs analysed were present during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show significant changes, we observed inverse patterns of miRNA and target expression. The datasets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research. Conclusions: MicroRNAs were expressed in co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation and its correlation with mRNA expression provide new avenues for research into mammary gland biology and generates candidates for functional validation. Developmental time course over 16 time points with 1-3 independent biological replicates per time point and three pairs of technical replicates, 40 samples in total
2010-06-25 | E-GEOD-15055 | biostudies-arrayexpress
Project description:Epidemiological surveys first indicated that obesity and type II diabetes generated by lipid rich diets may be efficiently inherited, both paternally and maternally. This apparent exception to the fundamental law of non heritability of acquired characters was more recently documented in laboratory organisms but the transgenerational signal remained a matter of speculation. Here we show that experimental transfer to healthy one-cell embryos of testis RNA prepared from males raised on high-fat-diet (HFD) results in the development of obesity and diabetes in the adult. Body weight, fasting glucose levels, response to insulin, glucose tolerance, RNA levels of leptin and stearoyl-CoA desaturase were all affected in mice born after RNA microinjection to the same extent as in the progenitors and in their sexual offspring. Surprisingly, neither microarray hybridization nor deep sequencing of the inducer and control RNAs showed a differential expression of known regulators of adipogenesis, but only modest variations in a series of transcripts. Transgenerational maintenance appears as one instance of the RNA-mediated heredity of epigenetic traits previously demonstrated in experimental systems ranging from the worm to the mouse. The relationship between lipid-rich diet and changes in testicular RNAs on one side and the nature of the mark imprinted on the one-cell embryo by RNA transfer and responsible for pathological developments at later stages are questions of interest for future studies. Two experimental groups composed of four individuals. Controls = M1N,M2N,TN1,TN2 and Experimentals= M1W,M2W,M3W,M5W.
2014-01-16 | E-GEOD-43555 | biostudies-arrayexpress
Project description:The aim of this study was to investigate whether long term intake of pea fiber would improve colonic barrier, bacterial profile and alter colonic gene expression using DNA microarray. Fifty weaned pigs were randomly allocated into 2 groups receiving control and fibrous diet with inclusion of pea fiber from weaning age until d 160. The two diets had similar nutrient levels. Pigs fed pea fiber diet (PF diet) had markedly decreased overall average daily feed intake (ADFI) and Feed:Gain in growing and finishing period (P<0.05). In addition, long term intake of PF diet induced deeper crypt (+50 %, P<0.05), increased protein expression of colonic mucin and sIgA (+13～16 %, P<0.05). Resulting from the increased lactobacillus content (P<0.05), moreover, pigs fed PF diet had significantly higher concentration of colonic total short chain fatty acid (SCFA) and acetic acid. DNA microarray results indicated that feeding PF diet induced alterations in the expression of colonic cancer, immune response and lipid metabolism-related genes, as well as genes involved in signal pathway such as intestinal immune network for IgA production, PPAR signaling pathway and nutrient metabolism-related pathways. Collectively, our results suggested that long term intake of PF diet would improve colonic health via altering colonic bacteria profile, colonic barriers, immune and metabolism related protein or gene expressions. A total of 50 weaned pigs (Duroc×Landrace×Yorkshire, initial body weight: 7.2±0.5 kg) were randomly allocated to 2 groups with 5 pens each group and 5 pig each pen. Pigs were fed control (Control) and fibrous diets (10～20 % inclusion of pea fiber, PF) from weaning at 28 day to 160 day-old-age, which is subjected to phase feeding by weaning diet (weaning to d 30 post-weaning), growing diet (d 30～90 postweaning) and finishing diet (d 90～160 postweaning) according to their physiological stage. At d 160 postweaning, four pigs each group were selected to be slaughtered for collection of colonic tissues and DNA microarray was applied to the colonic tissues for analysis of gene expression.
2013-01-30 | E-GEOD-43917 | biostudies-arrayexpress
Project description:Background: Consumption of high fat diets has negative impacts on health and well-being, some of which may be epigenetically regulated. Selenium and folate are two compounds which influence epigenetic mechanisms. We investigated the hypothesis that post-weaning supplementation with adequate levels of selenium and folate in mouse offspring fed a high fat, low selenium and folate diet during gestation and lactation will lead to epigenetic changes of potential importance for long-term health. Female offspring of mothers fed the experimental diet were either maintained on this diet (HF-low-low), or weaned onto a high-fat diet with sufficient levels of selenium and folate (HF-low-suf), for 8 weeks. Gene and protein expression, DNA methylation, and histone modifications were measured in colon and liver of female offspring. Results: Adequate levels of selenium and folate post-weaning affected gene expression in colon and liver of offspring, including decreasing Slc2a4 gene expression. Protein expression was only altered in the liver. There was no effect of adequate levels of selenium and folate on global histone modifications in the liver. Global liver DNA methylation was decreased in mice switched to adequate levels of selenium and folate, but there was no effect on methylation of specific CpG sites within the Slc2a4 gene in liver. Conclusions: Post-weaning supplementation with adequate levels of selenium and folate in female offspring of mice fed high-fat diets during gestation and lactation can alter global DNA methylation in liver. This may be one mechanism by which the negative effects of a poor diet during early life can be ameliorated. Further research is required to establish what role epigenetic changes play in mediating observed changes in gene and protein expression, and the relevance of these changes to health. Female wild type C57BL/6 mice (Animal Resource Centre, Western Australia) were fed a High Fat diet containing low levels of selenium and folate (HF-Low) for 7 days prior to mating with male C57BL/6 mice (Ruakura Small Animal Facility, Hamilton, New Zealand). Mothers were maintained on the HF-Low diet throughout gestation and lactation. Offspring of these female mice were randomly assigned to one of two different dietary treatments: either the same diet as the mothers (HF-Low), or a High Fat diet containing adequate selenium and folate (HF-Suf). At 12 weeks of age, mice were euthanized and colon and liver samples taken for microarray, proteomics, and DNA methylation analyses. Genomic DNA, total RNA and protein from whole colon and liver tissue was extracted using an AllPrepM-BM-. DNA/RNA/Protein mini kit (Qiagen, Cat number 80004). Colon and liver RNA from six female offspring on the HF-Low diet was compared with colon and liver RNA from six female offspring on the HF-Suf diet. All individual RNA samples were hybridized against a common reference RNA on separate arrays. The reference RNA was prepared by pooling in equimolar proportions RNA extracted from the intestine and liver of twelve female C57BL/6 mice, these being all of the mice from which samples were derived for microarray analysis in the current study.
2013-06-01 | E-GEOD-43038 | biostudies-arrayexpress
Project description:The objectives of the study were to use RNA-Seq to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1) and 8 days after weaning (d 8). RNA-seq analysis was carried out on RNA extracted from whole blood. Gradual weaning had no effect on gene expression (P>0.05).There were 550 differentially expressed genes at a false discovery rate of 10% and with a â¥1.5-fold change, between Holstein-Friesian and Jersey calves on d -14, 490 on d 1, and 411 on d 8. GOseq/KEGG pathway analysis showed that the cytokine-cytokine receptor interaction pathway and the neuroactive ligand-receptor interaction pathway were over-represented between breeds on all days (P<0.01; Qâ¤0.1). These results demonstrate that the gradual weaning practiced here does not compromise the welfare of artificially-reared dairy calves, evidenced by the lack of expression changes in any genes in response to gradual weaning. These data also suggest differences in cell signalling and immune responses between breeds. Eight Holstein-Friesian and eight Jersey bull calves were group housed indoors and individually fed milk replacer and concentrate using an automatic feeder. Calves were gradually weaned by reducing milk-replacer from 6 litres to 0 litres over 14 days (d) (d -13 to d 0). Calves were blood sampled on d -14, 1, and 8, relative to weaning (d 0). RNA-seq analysis was carried out on RNA extracted from whole blood.
2016-08-19 | E-GEOD-76841 | biostudies-arrayexpress
Project description:Background: This study examines the impact of dietary fatty acids on regulation of gene expression in the mammary epithelial cells before and during puberty. Methods: The diets primarily consisted of n-9 monounsaturated fatty acids (olive oil), n-6 polyunsaturated fatty acids (safflower), saturated acids (butter), and the reference AIN-93G diet (soy oil). The dietary regimen mimics the repetitive nature of fatty acid exposure in Western diets. Dietary-induced changes in gene expression were examined in the LCM (Laser Capture Microdissected) captured mammary ductal epithelial cells at day of weaning (21 days) and at the end of puberty (50 days after birth). PCNA immunohistochemistry analysis was used to compare proliferation rates between diets. Results: Genes differentially expressed between each of the test diets and the reference diet in both age groups were significantly enriched by cell cycle genes. Some of these genes were involved in the activation of the cell cycle pathway or the G2/M check point pathway. Although there were some differences in the level of differential expression, all diets showed qualitatively same pattern of differential expression compared to the reference diet. Cluster analysis identified an expanded set of cell cycle as well as immunity and sterol metabolism related clusters of differentially expressed genes. Conclusion: Fatty acid-enriched diets significantly up-regulated proliferation above the normal physiological level at day 50. The higher cellular proliferation during puberty caused by enriched fatty acid diets pose a potential increase risk of mammary cancer in later life. The human homologs of 27 of 62 cell cycle cluster of rat genes are included in a human breast cancer cluster of 45 cell cycle related genes further emphasizing the importance of our findings in the rat model. Female, virgin Spraque-Dawley rats were obtained from Taconic Farms (Germantown, NY) at approximately 7 weeks of age and placed on one of 9 pelleted purified diets for one month. After one month of diet exposure, female rats were bred with male Sprague-Dawley rats of approximately 3 months of age. Litters were weighed and monitored throughout gestational period. Pups had access to dam’s milk as well as tap water and food throughout gestation. Pups were weaned at DOL 21 and individually housed with tap water and diets ad libitum. Rats were killed by CO2 asphyxiation and decapitated at the following two ages, DOW (DOL21) and DOL 50 with no other treatments.
2009-04-01 | E-GEOD-14933 | biostudies-arrayexpress