Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Common inflammatory pathways between NEC and Crohn's disease

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE64801 | GEO | 2016/01/25

SECONDARY ACCESSION(S): PRJNA271895

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Amniotic fluid and necrotizing enterocolitis in preterm pigs

2010-03-01 | GSE13515 | GEO

Amniotic fluid and necrotizing enterocolitis in preterm pigs

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

Microbiota-associated intestinal methylation changes confer immune-metabolic gene network of NEC in preterm pig model

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

Temporal development of necrotizing enterocolitis in the preterm pig

2010-03-01 | GSE13516 | GEO

Intestinal necrotizing enterocolitis triggers hippocampal gene expression and neuronal differentiation in preterm neonates

Project description:Necrotizing enterocolitis (NEC) is an acute gut inflammatory disorder that mainly affects preterm neonates. A large proportion of NEC survivors develop neuronal deficits later in life, however the effect of early stages of NEC on the developing brain is unknown. Using preterm pigs as a NEC-sensitive animal model, we profiled the hippocampal gene expression in response to severe NEC lesions. The NEC-induced differentially expressed genes (DEGs) in the hippocampus segregated the piglets suffering from small intestinal NEC (Si-NEC) from those showing NEC lesions only in the colon (Co-NEC). Only when NEC lesions were observed in the small intestine, did piglets show reduced physical activity together with up-regulation of hippocampal genes related to inflammation and hypoxia, which was further verified by qPCR. Cluster analyses revealed key hippocampal NEC–related DEGs for Si-NEC (23 genes, including S100A8, PDK4, EDN1, IER3, Opalin, TXNIP) and Co-NEC (3 genes: GSTM3, TF, and S100A1). Both NEC phenotypes showed only two down-regulated DEGs (TMEM 167, HBB) and were devoid of any histological signs of microglia activation. Cerebrospinal fluid (CSF) from NEC-positive pigs contained elevated levels of several inflammatory proteins and in vitro exposure of immature hippocampal neurons to NEC-related CSF promoted neuritogenesis. Further in vitro experiments with neurite outgrowth indicated that VEGF, CINC-3, S100A9 and S100A8/S100A9 may play a role in NEC effects on hippocampal development. In conclusion, NEC lesions, especially when involving the small intestine, alter hippocampal gene expression with potential neuroinflammation and effects on neural circuit formation. Our results demonstrated that gut lesions affect the immature brain at early stages of disease progression. Thus, supportive care is important for preterm infants experienced with NEC to lessen possible later neurological dysfunctions.

2018-05-22 | GSE114705 | GEO

Data in support of Circulating neutrophil extracellular trap components including cell-free DNA are associated with neonatal sepsis and necrotizing enterocolitis in newborn, immature infants, pigs and mice

Project description:Preterm infants are highly susceptible to late-onset sepsis (LOS) and necrotizing enterocolitis (NEC) but specific biomarkers for diagnosis and effective treatment are lacking. Neutrophil extracellular traps (NETs) are related to sepsis in adults but not investigated in infant conditions. This is the first proteome study to document that circulating NETs are involved in neonatal LOS and NEC. cfDNA and NET proteins may provide new potential diagnostic markers for these diseases.

2018-03-05 | PXD004082 | Pride

Selective hypermethylation is evident in small intestine samples from infants with necrotizing enterocolitis [targeted_ileum]

Project description:Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal disease affecting preterm infants. NEC develops suddenly and is characterized by gut barrier destruction, an inflammatory response, intestinal necrosis and multi-system organ failure. There is currently no method for early NEC detection, and the pathogenesis of NEC remains unclear.

2022-09-13 | GSE212913 | GEO

Temporal development of necrotizing enterocolitis in the preterm pig

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, NÃ¦rum, 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

Very preterm delivery is associated with microbial signatures in maternal feces and blood and inflammatory activation in the fetus

Project description:Preterm birth is a major cause of infant mortality and morbidity. The rate of preterm birth is 5-9% in most developed countries and 12% in the United States with approximately 15 million children born prematurely each year. Globally, prematurity is the second most common cause of death in children under the age of five years. To characterize the transcriptomic changes between preterm and full term neonates, RNA-sequencing was applied altogether to 14 cord blood samples. The analysis of the RNA-sequencing data revealed that the spontaneous preterm delivery resulted in systemic inflammatory responses at the gene and pathway level in the fetus.

2020-08-31 | GSE103192 | GEO

BCG vaccination reprograms the function of myeloid cells and aggravates necrotizing enterocolitis in neonates

Project description:Bacillus Calmette–Guérin (BCG) vaccination immediately after birth provides overall protection against immune disorders in healthy infants. However, for vulnerable infants such as preterm or low birth weights, delayed BCG vaccination is usually recommended. The mechanism underlying this clinical application remains obscure. Here we reported that BCG vaccination abrogated the transitory appearance of immunosuppressive myeloid cells in neonatal mice, that is myeloid-derived suppressor cells (MDSCs) represented as the important immunoprotection against inflammatory diseases in early life. A combination of single-cell transcriptome, metabolite profiling, and functional analysis revealed that the upregulation of mTOR/HIF1a signaling and the enhanced glycolysis explained the underlying mechanism. Consequently, BCG vaccination significantly exacerbated the severity of necrotizing enterocolitis (NEC), a common clinical emergency primarily affecting preterm or low birth weight infants. Adoptive transfer of MDSCs or pharmalogical inhibition of glycolysis or mTOR signaling efficiently relieved the severity of NEC upon BCG vaccination. These observations suggest that BCG may diminish the protective mechanism of myeloid cells and enhances the susceptibility of NEC in vulnerable neonates.

2023-06-12 | GSE234153 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data