Swine inflammation and necrosis syndrome is associated with plasma metabolites and liver transcriptome in affected piglets
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PROVIDER: PRJNA704808 | ENA |
REPOSITORIES: ENA
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Project description:Swine Inflammation and Necrosis Syndrome (SINS) can lead to severe clinical signs, especially in tails, ears, teats and claws in pigs. Clinical and histopathological findings in newborn piglets with in-tact epidermis indicate a primarily endogenous etiology, and microbial-associated molecular pat-terns (MAMPs), such as lipopolysaccharide (LPS) are assumed to play a central role in the devel-opment of the syndrome. We hypothesized that swine inflammation and necrosis syndrome (SINS) is indirectly triggered by gut-derived MAMPs entering the circulatory system via the liver and thereby causing derangements on liver metabolism. To test this hypothesis, metabolomes, candidate genes of the liver and liver transcriptomes of 6 piglets with high-grade clinical signs of SINS (SINS high) were examined and compared with 6 piglets without significant signs of SINS (SINS low). Several hepatic pro-inflammatory genes and genes involved in stress response were induced in piglets of the SINS high group. The most striking finding from hepatic transcript pro-filing and bioinformatic enrichment was that the most enriched biological processes associated with the approximately 220 genes induced in the liver of the SINS high group were exclusively related to metabolic pathways, such as fatty acid metabolic process. Within the genes (≈ 390) re-pressed in the liver of the SINS high group, enriched pathways were ribosome biogenesis, RNA processing, RNA splicing, spliceosome and RNA transport. The transcriptomic findings were supported by the results of the metabolome analyses. These results provide the first evidence for the induction of an inflammatory process in the liver of piglets suffering from SINS, accompanied by lipid metabolic derangement.
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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.
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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.
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Project description:MicroRNAs (miRNAs) in serum are very stable and specific. Moreover, serum miRNAs are non-destructive and convenient. Studies have shown that the changes of serum miRNAs are closely relative to the pathological stresses and diseases. Our previous studies suggested that weaning stress induced the abnormal miRNA transcriptome in the intestine of piglets. In this project, we will further screen serum miRNA expression in piglets induced by weaning stress using miRNA microarray. Microarrays containing 422 porcine unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between weaning piglets at 4 d after weaning and suckling piglets at the same days old. A total of 115 differentally expressed miRNAs were found,therein 63 miRNAs upregulated and 52 miRNA downregulated; 64 miRNAs are statistically significant but have low signals (signal < 500);122 miRNAs are not statistically significant (p > 0.01); the remaining 132 miRNAs have not detected signals.
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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.
2014-05-01 | GSE48050 | GEO
Project description:Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. Here we conducted DNA methylation (DNAm) immunoprecipitation binding high throughput sequencing (MeDIP-seq) and RNA sequencing (RNA-seq) of muscle tissues of cloned piglets to investigate the relationship of abnormal DNAm with gene dysregulation and the unusual phenotypes in cloned piglets. Results:Analysis of the methylomes revealed that abnormal cloned piglets suffered more hypomethylated differentially methylated regions (DMRs) than hypermethylated DMRs compared to the normal cloned piglets. The DNAm level in the CpG Island was higher in the abnormal cloned piglets. Some repetitive elements, such as SINE/tRNA-Glu Satellite/centr also showed significant differences. Besides we detected 1,711 differentially expressed genes (DEGs) between the two groups, of which 243 genes also changed methylation level in the abnormal cloned piglets. The altered DNA methylation mainly affected the low and silent expression genes. We also found some interesting pathways and genes, such as MAPK signalling pathway, hypertrophic cardiomyopathy pathway, TPM3 gene and the imprinted gene PLAGL1, which may played important roles in the abnormal phenotype development. Conclusions;The abnormal cloned piglets showed substantial change both in the DNAm and the gene expression levels. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals. We dissected the biceps femoris muscle from the abnormal cloned piglets and the normal cloned piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups. This represents the RNA-Seq study only
2014-09-03 | E-GEOD-51282 | biostudies-arrayexpress
Project description:Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. Here we conducted DNA methylation (DNAm) immunoprecipitation binding high throughput sequencing (MeDIP-seq) and RNA sequencing (RNA-seq) of muscle tissues of cloned piglets to investigate the relationship of abnormal DNAm with gene dysregulation and the unusual phenotypes in cloned piglets. Results:Analysis of the methylomes revealed that abnormal cloned piglets suffered more hypomethylated differentially methylated regions (DMRs) than hypermethylated DMRs compared to the normal cloned piglets. The DNAm level in the CpG Island was higher in the abnormal cloned piglets. Some repetitive elements, such as SINE/tRNA-Glu Satellite/centr also showed significant differences. Besides we detected 1,711 differentially expressed genes (DEGs) between the two groups, of which 243 genes also changed methylation level in the abnormal cloned piglets. The altered DNA methylation mainly affected the low and silent expression genes. We also found some interesting pathways and genes, such as MAPK signalling pathway, hypertrophic cardiomyopathy pathway, TPM3 gene and the imprinted gene PLAGL1, which may played important roles in the abnormal phenotype development. Conclusions;The abnormal cloned piglets showed substantial change both in the DNAm and the gene expression levels. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals. We dissected the biceps femoris muscle from the abnormal cloned piglets and the normal cloned piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups.
2014-09-03 | E-GEOD-51476 | biostudies-arrayexpress