Sus scrofa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA348306 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4420390_1.fastq.gz | Fastqsanger.gz | |||
| SRR4420390_2.fastq.gz | Fastqsanger.gz | |||
| SRR4420391_1.fastq.gz | Fastqsanger.gz | |||
| SRR4420391_2.fastq.gz | Fastqsanger.gz | |||
| SRR4420392_1.fastq.gz | Fastqsanger.gz |
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Project description:Intestinal microbiota colonization is important for intestinal development and health of preterm infants, especially those with extremely low birth weight. Recent studies indicated for a dynamic crosstalk between that gut microbiota and DNA methylome of host intestinal cells. Thereby, we sought to determine the epigenomic and metagenomic consequences of suppression of microbiota colonization in the intestine of preterm neonates to gain insights into biological pathways that shape the interface between the gut microbiota and the preterm intestinal cells. We examined 14 preterm piglets by comparing the conventional preterm neonates with those ones treated with oral antibiotics for genome wide DNA methylation and 16S rDNA microbiome. Our results demonstrated an extensive genome-wide DNA methylation changes in response to the suppression of intestinal microbe colonization, especially genes involved in neonatal immune response signaling and glycol-metabolism pathways were identified. Our study highlights several key genes that might predispose preterm neonates to NEC risk due to their key roles involved in the immune-metabolic networks. Our study not only provided rich omic-data to interpret molecular program in relation with microbiota-associated methylome-proteome network changes, but also confer clinical usage of key gene markers for potential early diagnostics of NEC of preterm neonates.
2017-10-12 | GSE88697 | GEO
Project description:Chorioamnionitis (CA), resulting from intra-amniotic inflammation, is a frequent cause of preterm birth and exposes the immature intestine to bacterial toxins and/or inflammatory mediators before birth via fetal swallowing. This may affect intestinal immune development, interacting with the effects of enteral feeding and gut microbiota colonization just after birth. Using preterm pigs as model for preterm infants, we hypothesized that prenatal exposure to gram-negative endotoxin influences postnatal bacterial colonization and gut immune development. Pig fetuses were given intra-amniotic lipopolysaccharide (LPS) 3 d before preterm delivery by cesarean section, and were compared with litter-mate controls (CON) at birth and after 5 d of formula feeding and spontaneous bacterial colonization. Amniotic fluid was collected for analysis of leukocyte counts and cytokines, and the distal small intestine was analyzed for endotoxin level, morphology and immune cell counts. Intestinal gene expression and microbiota were analyzed by transcriptomics and metagenomics, respectively. At birth, LPS-exposed pigs showed higher intestinal endotoxin, neutrophil/macrophage density and shorter villi. About 1.0% of intestinal genes were affected at birth and DMBT1, a regulator of mucosal immune defense, was identified as the hub gene in the co-expression network. Genes related to innate immune response (TLR2, LBP, CD14, C3, SFTPD), neutrophil chemotaxis (C5AR1, CSF3R, CCL5) and antigen processing (MHC II, CD4) were also affected and expression levels correlated with intestinal neutrophil/macrophage density and amniotic fluid cytokine levels. On day 5, LPS and CON pigs showed similar necrotizing enterocolitis (NEC) lesions, endotoxin levels, morphology, immune cell counts, gene expressions and microbiota (except for difference in some low-abundant species). Our results show that CA markedly affects intestinal genes at preterm birth, including genes related to immune cell infiltration. However, a few days later, following the physiological adaptations to preterm birth, CA had limited effects on intestinal structure, function, gene expression, bacterial colonization and NEC sensitivity. We conclude that short-term, prenatal intra-amniotic inflammation is unlikely to exert marked effects on intestinal immune development in preterm neonates beyond the immediate neonatal period.
2019-10-25 | GSE139366 | GEO
Project description:We hypothesized that the immature pig intestine would be highly sensitive to gene methylation changes in the immediate prenatal and neonatal periods. We performed a Reduced Representation Bisulfite Sequencing (RRBS) to assess the DNA methylation differences occurring during the last 10 days prenatally (PN, 0d-term vs. 0d-preterm), neonatally after 4 days (NN, 4d-preterm vs. 0d-preterm) and after NEC development (4d-preterm-NEC vs. 4d-preterm) in pigs (each group n=2-3). Differentially methylated gene regions (DMRs) between the groups were identified, subjected to KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis and selected genes were chosen for further validation of gene expression levels by RT-PCR (n= 6 for each group). Consistent with the need to increase expression of many intestinal genes in the perinatal period, methylation levels of most genes decreased during the prenatal and neonatal periods. We identified four intestinal genes (CYP2W1, GPR146, TOP1MT, CEND1), related to intestinal metabolism, that were significantly hyper-methylated in their promoter CGIs, and transcriptionally down-regulated in the 4 d-old preterm pigs. This down-regulation of intestinal metabolism may predispose to intestinal dysfunction and NEC. The first enteral feeds and bacterial colonization are critical factors for NEC sensitivity and it remains to be investigated whether these factors affect intestinal gene methylation and thereby predispose to, or prevent from, disease more long term.
2014-12-31 | GSE53747 | GEO
Project description:Necrotizing enterocolitis (NEC) is the most frequent life-threatening gastrointestinal disease experienced by premature infant occuring in neonatal intensive care units. NEC is associated with severe intestinal inflammation, intestinal perforation leading to mortality. The challenge for neonatologists is to detect early clinical manifestations of NEC. Therefore, one of the strategies to prevent or treat NEC would be to develop an early diagnostic tool allowing identification of preterm infants either at risk of developing NEC or at the onset of the disease. Illumina’s deep sequencing technology (RNA-seq) was used to establish the gene expression profile between resected ileal healthy preterm (control, n=5) and NEC diagnosed preterm infant (NEC, n=9) and analyzed by IPA Core analysis system. IPA analysis indicated that the most significant functional pathways overrepresented in NEC neonates were associated with innate immune functions, such as altered T and B cell signaling, B cell development, and the role of pattern recognition receptors in recognition of bacteria and viruses. Among genes that were strongly modulated in NEC neonates, we observed a high degree of similarity with those linked to the development of IBD. By comparing gene expression patterns between NEC and Crohn’s disease, we identified several new potential protein targets for helping to predict and/or diagnose NEC in preterm infant. Gene expression profile revealed an uncontrolled innate immune response in the intestine of NEC neonates. Moreover, comparative analysis between NEC and Crohn’s disease evidenced high degree of similarity between these two inflammatory diseases and allowed us to identify several new potential NEC biomarkers.
2016-01-25 | GSE64801 | GEO
Project description:Large White and Meishan pigs were either non-treated or injected with mammalian 1-24 ACTH (Immediate Synachten, Novartis France) at the dose of 250 µg per animal. Pigs were sacrificed either immediately after capture from their home cage (non-treated animals) or 1 hour following ACTH injection. Adrenal glands were immediately collected from pigs and frozen on dry ice and then stored at -80°C until RNA isolation. Keywords: stress response, adrenal, gene expression, pig
2008-01-07 | GSE8377 | GEO
Project description:Large White and Meishan pigs were either non-treated or injected with mammalian 1-24 ACTH (Immediate Synachten, Novartis France) at the dose of 250 µg per animal. Pigs were sacrificed either immediately after capture from their home cage (non-treated animals) or 1 hour following ACTH injection. Adrenal glands were immediately collected from pigs and frozen on dry ice and then stored at -80°C until RNA isolation. Keywords: stress response, adrenal, gene expression, pig 47 samples
2010-06-29 | E-GEOD-8377 | biostudies-arrayexpress
Project description:Preterm neonates are susceptible to gastrointestinal (GI) disorders such as necrotizing enterocolitis (NEC). Maternal milk, and especially colostrum, protects against NEC via growth promoting, immunomodulatory and antimicrobial factors. The fetal enteral diet, amniotic fluid (AF), contains similar bioactive components and we hypothesized that postnatal AF administration would reduce inflammatory responses and NEC in preterm neonates. Thirty preterm pigs (92% gestation) were delivered by caesarean section and fed total parental nutrition (TPN) for 48 h followed by enteral porcine colostrum (COLOS, n=7), infant formula (FORM, n=13) or formula + porcine AF (AF, n=10). Using a previously validated model of NEC in preterm pigs, we determined the structural, functional, microbiological and immunological responses to AF when administered prior to and after introduction of a suboptimal enteral formula diet. Keywords: Healthy versus inflammed tissues in relation to necrotizing enterocolitis Pigs from each treatment group (COLOS, n=4; FORM, n=6; and AF, n=7) were randomly selected for microarray analysis of frozen distal small intestine samples. The FORM group was further divided into formula-fed healthy pigs (F-HEA, n=3) and formula-fed NEC pigs (F-NEC, n=3) in order to compare sick versus healthy formula fed pigs. Equal amounts of total distal small intestinal RNA from all pigs were pooled to make the reference sample. Samples and reference pool were labelled with Oyster 550 and 650, respectively. The in-house spotted porcine oligonucleotide microarray version 4 (POM4) is a low density microarray consisting of 384 different oligonucleotide probes representing more than 200 different immune related genes.
2010-05-06 | E-GEOD-13515 | biostudies-arrayexpress
Project description:Temporal development of necrotizing enterocolitis in the preterm pig
| PRJNA110123 | ENA
Project description:Necrotizing enterocolitis (NEC), a severe gut disorder in preterm infants, is difficult to predict due to poor specificity and sensitivity of clinical signs and biomarkers. Using preterm piglets as a model, we hypothesized that early development of NEC affects blood gene expression, potentially related to early systemic immune responses. In this animal model, variable severity of gut NEC lesions were detected in 5d-old piglets with limited clinical signs. NEC (n=20) and control piglets (CON, n=19) were analyzed for whole blood transcriptome, revealing 344 differentially expressed genes (DEGs) between NEC and CON piglets. Co-expression network analyses and qPCR suggested AOAH, FKBP5, PAK2 as three NEC-specific genes associated with severe gut lesions. These results suggest that whole blood gene expressions are affected in preterm piglets when clinical symptoms of NEC are minimal. Blood transcriptome may be a novel tool to identify early biomarkers of NEC.
2021-06-01 | GSE166152 | GEO
Project description:Necrotizing enterocolitis (NEC), a serious gastrointestinal disease that afflicts 5-10% of preterm infants, often progresses rapidly from mild food intolerance into extensive haemorrhage, inflammation and necrosis. Events leading to NEC have remained poorly defined. Similar disease characteristics are observed in preterm pigs 24-48 h after feeding formula. Using this model, we aimed to characterize the temporal development of NEC, and describe the functional and immunological response of the preterm intestine preceding NEC. Keywords: time course Pigs from treatment groups TPN (n=5), and 8 h (n=5) and 24 h (n=5-6) FORM and COLOS were randomly selected for microarray analysis. Equal amounts of total distal small intestinal RNA from all pigs was pooled to make the reference sample. Samples and reference pool were labelled with Oyster 550 and 650, respectively. The in-house spotted porcine oligonucleotide microarray version 4 (POM4) is a low density microarray consisting of 384 different oligonucleotide probes representing more than 200 different immune related genes and eight different array control oligonucleotides (ArrayControl; Ambion, Nærum, Denmark). The immunologically relevant 60-70mer oligonucleotide probes represent interferons and interleukins (and receptors), chemokines (and receptors), acute phase proteins, apoptosis-related factors and sequences with relevance to Toll-like receptors and their intracellular signalling pathways.
2010-05-07 | E-GEOD-13516 | biostudies-arrayexpress