Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Altered mucosal expression of microRNAs in pediatric patients with inflammatory bowel disease

ABSTRACT: The aim of the present study was to identify a pediatric inflamatory bowel disease (pIBD) characteristic microRNA profile serving as potential Crohns disease and ulcerative colitis specific diagnostic pattern and to further analyze the related target genes. Illumina small RNA sequencing was performed on inflamed and intact colonic biopsies of Crohn's disease and control patients. Selected miRs were further investigated by real-time reverse transcription (RT)-PCR. To analyze network connection of differentially expressed miRs and their target genes the MiRTarBase database and previous transcriptome sequencing data were used. We demonstrated a characteristic colonic miR pattern in pIBD that could facilitate deeper understanding of the pathomechanism of IBD and may serve as a diagnostic tool in the future.

INSTRUMENT(S): Illumina HiScanSQ

ORGANISM(S): Homo sapiens

SUBMITTER: Apor Veres-Szkely

PROVIDER: E-MTAB-5010 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The aim of this study was to investigate whether long term intake of pea fiber would improve colonic barrier, bacterial profile and alter colonic gene expression using DNA microarray. Fifty weaned pigs were randomly allocated into 2 groups receiving control and fibrous diet with inclusion of pea fiber from weaning age until d 160. The two diets had similar nutrient levels. Pigs fed pea fiber diet (PF diet) had markedly decreased overall average daily feed intake (ADFI) and Feed:Gain in growing and finishing period (P<0.05). In addition, long term intake of PF diet induced deeper crypt (+50 %, P<0.05), increased protein expression of colonic mucin and sIgA (+13～16 %, P<0.05). Resulting from the increased lactobacillus content (P<0.05), moreover, pigs fed PF diet had significantly higher concentration of colonic total short chain fatty acid (SCFA) and acetic acid. DNA microarray results indicated that feeding PF diet induced alterations in the expression of colonic cancer, immune response and lipid metabolism-related genes, as well as genes involved in signal pathway such as intestinal immune network for IgA production, PPAR signaling pathway and nutrient metabolism-related pathways. Collectively, our results suggested that long term intake of PF diet would improve colonic health via altering colonic bacteria profile, colonic barriers, immune and metabolism related protein or gene expressions. A total of 50 weaned pigs (Duroc×Landrace×Yorkshire, initial body weight: 7.2±0.5 kg) were randomly allocated to 2 groups with 5 pens each group and 5 pig each pen. Pigs were fed control (Control) and fibrous diets (10～20 % inclusion of pea fiber, PF) from weaning at 28 day to 160 day-old-age, which is subjected to phase feeding by weaning diet (weaning to d 30 post-weaning), growing diet (d 30～90 postweaning) and finishing diet (d 90～160 postweaning) according to their physiological stage. At d 160 postweaning, four pigs each group were selected to be slaughtered for collection of colonic tissues and DNA microarray was applied to the colonic tissues for analysis of gene expression.

Project description:The Interleukin-22 (IL22) pathway plays a key role in maintaining homeostasis at the mucosal surfaces and is frequently dysregulated during infectious and inflammatory diseases. Human genome-wide association studies performed at the WTSI have identified SNPs in and around the human IL-22 gene that are associated with IBD susceptibility. The IL-22 cytokine is produced by cells of the innate and adaptive immune systems within the intestinal mucosa and acts on the IL-22 receptor (IL-22RA1) that is present specifically on intestinal epithelial cells. Studies to date have shown the that IL-22 pathway is linked to proliferative and anti-apoptotic pathways, as well as anti-microbial molecule production that help control bacterial invasion and prevent tissue damage. We are characterizing a novel IL-22RA1 KO mouse and have shown that these mice are highly susceptible to enteric bacterial pathogens, such as Citrobacter rodentium and Clostridium difficile. However, the mechanism of this protective immunity is poorly understood. The aim of this project is to identify novel molecules or pathways downstream of IL-22 signaling that provide the mechanistic link between IL-22RA1 and innate immunity. To maintain mouse colonic epithelial cells in vitro, we used an organoid culture system that faithfully recapitulates the crypt architecture of the gastrointestinal epithelium. Primary colonic epithelial crypts were isolated from age-matched wildtype and IL-22ra1 knock-out mice (n = 4 per genotype), and subsequently cultured in the presence of defined growth factors and Matrigel for 5 days. The resulting mature organoids were then either treated with Control medium (Advanced DMEM/F12) or mouse recombinant IL-22 (50ng/ml) for 16 hours. Total RNA were extracted using the QIAgen RNeasy Micro Kit, including an on-column DNAse digestion step, according to manufacturer's protocol. We are submit total RNA samples of good quality (RIN > 7) and quantity.The culture and stimulation conditions have been optimised to achieve significant and specific induction of known target genes such as the antimicrobial peptides RegIIIb, RegIIIg, S100a8 and S100a9. Two technical replicates will be available for each genotype x condition. We aim to sequence 5GBp per replicate, and 5 replicates per lane on an Illumina platform. Through this dataset, we hope to discover epithelial cell-specific pathways downstream of IL-22 signaling that are ablated in the absence of its receptor.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

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Altered mucosal expression of microRNAs in pediatric patients with inflammatory bowel disease

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