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ABSTRACT: Genomic analysis of methionine-induced changes in porcine intestinal epithelial cells

PROVIDER: PRJNA1149994 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30332141_1.fastq.gz	Fastqsanger.gz
	SRR30332141_2.fastq.gz	Fastqsanger.gz
	SRR30332142_1.fastq.gz	Fastqsanger.gz
	SRR30332142_2.fastq.gz	Fastqsanger.gz
	SRR30332143_1.fastq.gz	Fastqsanger.gz

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Project description:RNAseq analysis of methionine-induced changes in porcine intestinal epithelial cells

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Effect of antimicrobial peptide PR-39 on the gene expression of porcine intestinal epithelial cell line (IPEC-J2)

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Effects of busulfan, fludarabine and clofarabine treatment on human small intestinal organoids generated from healthy donors

Project description:The intestine is vulnerable to chemotherapy-induced toxicity due to its high epithelial proliferative rate, making gut toxicity an off-target effect in several cancer treatments, including conditioning regimens for allogeneic hematopoietic cell transplantation (HSCT). In HSCT, intestinal damage is an important factor in the development of Graft-versus-Host Disease (GVHD), an immune complication in which donor immune cells attack the recipient's tissues. Here, we developed a novel human intestinal organoid-based 3D model system to study the effects of chemotherapy-induced intestinal epithelial damage at the RNA level. We show that chemotherapy conditioning specifically reprograms the intestinal epithelial transcriptome after treatment with either busulfan (3.5ÃŽÂ¼M), fludarabine (15ÃŽÂ¼M) or clofarabine (0.5ÃŽÂ¼M) for 24h. This knowledge can potentially enable us to understand which changes undergo in healthy tissues upon conditioning and how those are related with immune activation typical in GVHD.

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Deciphering the porcine intestinal microRNA transcriptome

Project description:Background While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy. Results Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks. Conclusions In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.

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