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Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets.

ABSTRACT: BACKGROUND:Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and immune surveillance. To study the early postnatal development of the jejunum, a meta-analysis was performed on different transcriptomic datasets. These datasets were acquired from different experimental in-house studies or from experiments described in literature of porcine jejunum mucosa. Gene expression was measured under different experimental interventions, such as nutritional intervention, at various time-points (age). RESULTS:The studies included in the meta-analysis provided gene expression data for various time-points (piglet ages) for piglets that had received a treatment versus control piglets. In separate studies, treatments were administered to the sow (i.e. amoxicillin), or nutritional supplementation directly to the piglets with medium chain fatty acids (MCFAs), and oral administration of fructooligosaccharides (FOS) or a high dose of zinc-oxide, respectively. In the meta-analysis, genes were grouped into 16 clusters according to their temporal gene expression profiles for control piglets, i.e. the changes of gene expression level over time. Functional analysis showed that these temporal profile clusters had different dominant processes, such as immune related processes or barrier function. Transcriptomics data of treatment piglets was subsequently superimposed over the control temporal profiles. In this way we could investigate which temporal profile clusters (and which biological processes) were modulated by the treatments. Interestingly, not all 16 temporal profiles were modulated. CONCLUSIONS:We showed that it is possible to re-use (publicly available) transcriptomics data and produce temporal gene expression profiles for control piglets with overexpression of genes representing specific biological processes. Subsequently, by superimposing gene expression data from (nutritional) intervention studies we observed deviations from some of these reference profile(s) and thus the plasticity of the system. By employing this meta-analysis approach we highlighted the importance of birth and weaning and the underlying biological processes.

SUBMITTER: Schokker D

PROVIDER: S-EPMC6533718 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets.

Schokker Dirkjan D Hulsegge Ina I Woelders Henri H Rebel Johanna M J JMJ

BMC genomics 20190523 1

<h4>Background</h4>Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and immune surveillance. To study the early postnatal development of the jejunum, a meta-analysis was performed on different transcriptomic datasets. These datasets were acquired from different experimental in-house studies or from experiments described in literature of porc ...[more]

PMID: 31122193

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Project description:BackgroundDengue is a major arthropod-borne viral disease spreading rapidly across the globe. The absence of vaccines and inadequate vector control measures leads to further expansion of dengue in many regions globally. Hence, the identification of genes involved in the pathogenesis of dengue will help to understand the molecular basis of the disease and the genes responsible for the disease progression.MethodsIn the present study, a meta-analysis was carried out using dengue gene expression data obtained from Gene Expression Omnibus repository. The differentially expressed genes such as CCNB1 and CCNB2 (G2/mitotic-specific cyclin-B2 and B1) were upregulated in dengue fever to control (DF-CO) and severe dengue (dengue hemorrhagic fever [DHF]) to control (DHF-CO) were identified as key genes for controlling the major pathways (cell cycle, oocyte meiosis, p53 signaling pathway, cellular senescence and progesterone-mediated oocyte maturation). Similarly, interferon alpha-inducible (IFI27) genes, type-I and type-III interferon (IFN) signaling genes (STAT1 and STAT2), B cell activation and survival genes (TNFSF13B, TNFRSF17) and toll like receptor (TLR7) genes were differentially up activated during DF-CO and DHF-CO. Followed by, Cytoscape was used to identify the immune system process and topological analysis.ResultsThe results showed that the top differentially expressed genes under the statistical significance p <0.001, which is majorly involved in Kyoto Encyclopedia of Genes and Genomes orthology K05868 and K21770 with gene names CCNB1 and CCNB2. In addition to this, the immune system profile showed up-regulation of IL12A, CXCR3, TNFSF13B, IFI27, TNFRSF17, STAT, STAT2, and TLR7 genes in DF-CO and DHF-CO act as immunological signatures for inducing the immune response towards dengue infection.ConclusionsThe current study could aid in understanding of molecular pathogenesis, genes and corresponding pathway upon dengue infection, and could facilitate for identification of novel drug targets and prognostic markers.

Project description:BackgroundSexual-size dimorphism (SSD) is replete among animals, but while the selective pressures that drive the evolution of SSD have been well studied, the developmental mechanisms upon which these pressures act are poorly understood. Ours and others' research has shown that SSD in D. melanogaster reflects elevated levels of nutritional plasticity in females versus males, such that SSD increases with dietary intake and body size, a phenomenon called sex-specific plasticity (SSP). Additional data indicate that while body size in both sexes responds to variation in protein level, only female body size is sensitive to variation in carbohydrate level. Here, we explore whether these difference in sensitivity at the morphological level are reflected by differences in how the insulin/IGF-signaling (IIS) and TOR-signaling pathways respond to changes in carbohydrates and proteins in females versus males, using a nutritional geometry approach.ResultsThe IIS-regulated transcripts of 4E-BP and InR most strongly correlated with body size in females and males, respectively, but neither responded to carbohydrate level and so could not explain the sex-specific response to body size to dietary carbohydrate. Transcripts regulated by TOR-signaling did, however, respond to dietary carbohydrate in a sex-specific manner. In females, expression of dILP5 positively correlated with body size, while expression of dILP2,3 and 8, was elevated on diets with a low concentration of both carbohydrate and protein. In contrast, we detected lower levels of dILP2 and 5 protein in the brains of females fed on low concentration diets. We could not detect any effect of diet on dILP expression in males.ConclusionAlthough females and males show sex-specific transcriptional responses to changes in protein and carbohydrate, the patterns of expression do not support a simple model of the regulation of body-size SSP by either insulin- or TOR-signaling. The data also indicate a complex relationship between carbohydrate and protein level, dILP expression and dILP peptide levels in the brain. In general, diet quality and sex both affect the transcriptional response to changes in diet quantity, and so should be considered in future studies that explore the effect of nutrition on body size.

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Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets.

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Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets.

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