Intestinal DNA methylome of preterm pigs
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE108284 | GEO | 2018/12/18
REPOSITORIES: GEO
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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:Genome wide DNA methylation differences in umbilical cord blood (UCB) of preterm and term born neonates. The Illumina 450K Human DNA methylation Beadchip was used to obtain the DNA methylation profiles of 12 preterm and 12 term UCB samples across 450,000 CpGs. 2 samples were removed due to failed quality control, and BMIQ normalization was done with 11 preterm and 11 term samples.
2015-08-17 | GSE66459 | 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: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:Development of the gut microbiota is greatly impacted in preterm infants. Despite increasing knowledge about microbiota composition in preterm infants, knowledge about the functional signatures of the intestinal microbiota remains limited. The aim was to study transitions in microbiota activity during the first six postnatal weeks in ten preterm infants. A total of 64 stool samples were measured by LC-MS/MS.
2017-07-14 | PXD005574 | Pride
Project description:Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD haves been increased. Therapeutic options are limited for prevention and treatment. This study was designed to explore the relationship between gestational age (GA), birth weight and estímate blood cell-type composition in premature infants and to elucidate early epigenetic biomarkers associated with BPD. Cord blood DNA from preterm neonates that went on to develop BPD (n = 14) or not (nonBPD, n = 93) was applied to Illumina 450K methylation arrays. Using DNA methylation analysis of cord blood DNA, we investigated association of GA and birth weight with the estimated distribution of cord blood cell types, particularly the nucleated red blood cell (NRBC) in a pilot-size cohort of preterm infants with or without BPD. We describe changes in methylation-based estimates of blood cell-type composition in relation to GA and birth weight. After adjusting for covariates (GA, birth weight, cell type proportions, etc.) we identify differentially methylated CpGs and genes associated with BPD.
2022-05-05 | GSE188949 | GEO
Project description:Development of the gut microbiota is greatly impacted in preterm infants. Despite increasing knowledge about microbiota composition in preterm infants, knowledge about the functional signatures of the intestinal microbiota remains limited. The aim was to study transitions in microbiota activity during the first six postnatal weeks in ten preterm infants. A total of 64 stool samples were measured by LC-MS/MS.
2017-10-17 | MSV000081616 | MassIVE
Project description:Genome wide placental DNA methylation profiling of full term and preterm deliveries sampled from 5 full term deliveries and 4 preterm deliveries. The Illumina HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 485,577 CpGs in formalin fixed samples. Samples included 4 placental tissues from 4 women with preterm delivery and 5 placental tissues from 5 women with full term delivery. 9 women's placental DNA (4 women had perterm deliveries and 5 women had full term deliveries) were hybridised to the Illumina HumanMethylation450 Beadchip
2016-07-25 | E-GEOD-49504 | biostudies-arrayexpress
Project description:Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD haves been increased. Therapeutic options are limited for prevention and treatment. This study was designed to explore the relationship between gestational age (GA), birth weight and estímate blood cell-type composition in premature infants and to elucidate early epigenetic biomarkers associated with BPD. Peripheral blood DNA (at days 14 and 28) from preterm neonates that went on to develop BPD (n = 14) or not (nonBPD, n = 93) was applied to Illumina EPIC methylation arrays. Using DNA methylation analysis of cord blood DNA, we investigated association of GA and birth weight with the estimated distribution of cord blood cell types, particularly the nucleated red blood cell (NRBC) in a pilot-size cohort of preterm infants with or without BPD. We describe changes in methylation-based estimates of blood cell-type composition in relation to GA and birth weight. After adjusting for covariates (GA, birth weight, cell type proportions, etc.) we identify differentially methylated CpGs and genes associated with BPD at different time points.
2023-07-05 | GSE225313 | GEO
Project description:To characterize the molecular profile of the chorioamniotic membranes of preterm neonates with and without neurocognitive impairment at 18-24 months and (2) to determine if neonates who developed neurocognitive impairment can be identified at birth. Paired two-group design
2015-01-21 | E-GEOD-61822 | biostudies-arrayexpress