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Transcriptomic profile of intestinal epithelial cells obtained from ileal endoscopic biopsies from newly-diagnosed, pediatric Crohn's disease patients and healthy controls.

ABSTRACT: Transcriptomic profile of intestinal epithelial cells obtained from ileal endoscopic biopsies from newly-diagnosed, pediatric Crohn's disease patients and healthy controls.

PROVIDER: PRJNA483489 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7624160.fastq.gz	Fastqsanger.gz
	SRR7624161.fastq.gz	Fastqsanger.gz
	SRR7624162.fastq.gz	Fastqsanger.gz
	SRR7624163.fastq.gz	Fastqsanger.gz
	SRR7624164.fastq.gz	Fastqsanger.gz

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Transcriptomic profile of intestinal epithelial cells obtained from ileal endoscopic biopsies from newly-diagnosed, pediatric Crohn's disease patients and healthy controls.

Project description:Purpose: To uncover differentially-regulated transcripts and pathways/biological processes in newly-diagnosed, pediatric Crohn's disease in comparison to healthy controls. Methods: Intestinal epithelial cells were dissociated from ileal endoscopic biopsies, and stored at -80C in RNAlater. The polyA RNA fraction was purified, and single-end, 50 bp reads were sequenced and aligned to the Hg19 genome using the TopHat2 aligner. Differential analysis was performed using Bioconductor packages including edgeR, where significance was defined as p<0.05 and fold change>2. Results: We obtained 15788 reasonably-expressed transcripts that were included in differential analyses. Conclusions: Our study characterizes the dysregulation of intestinal epithelial cells in treatment-naïve Crohn's disease using RNA sequencing for transcriptomic profile of cells obtained through ileal endoscopic biopsies.

2018-10-30 | GSE117875 | GEO

Characterization of H3K4me3 histone modifications in intestinal epithelial cells among healthy controls and newly-diagnosed pediatric Crohn's disease patients.

Project description:We report profiling of H3Kme3 histone modifications in intestinal epithelial cells from ileal endoscopic biopsies obtained from healthy controls and newly-diagnosed Crohn's disease (CD). We identified 1066 shared sites, corresponding to 1038 genes with increased H3K4me3 in CD, and 539 sites corresponding to 548 genes with reduced H3K4me3 in CD.

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Crohn's Disease patients and non-IBD controls : ileal gene expression

Project description:Comparison of gene expression from ileal biopsies of Crohn's Disease patients and non-IBD controls

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Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

Project description:Management of terminal ileal Crohn's disease (CD) is difficult due to fibrotic prognosis and failure to achieve mucosal healing. A limited number of synchronous analyses have been conducted on the transcriptome and microbiome in unpaired terminal ileum tissues. Therefore, our study focused on the transcriptome and mucosal microbiome in terminal ileal tissues of CD patients with the aim of determining the role of cross-talk between the microbiome and transcriptome in the pathogenesis of terminal ileal CD. Mucosa-attached microbial communities were significantly associated with segmental inflammation status. Interaction-related transcription factors (TFs) are the panel nodes for crosstalk between the gene patterns and microbiome for terminal ileal CD. The transcriptome and microbiome in terminal ileal CD can be different related to local inflammatory status, and specific differentially expressed genes (DEGs) may be targeted for mucosal healing. TFs connect gene patterns with the microbiome by reflecting environmental stimuli and signals from microbiota.

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Differential early pathogenic changes in human ileal gene expression in Crohn's disease and ulcerative colitis

Project description:The aim of this study is to identify early pathogenic changes in ileal gene expression that precede the development of macroscopic disease in inflammatory bowel diseases (IBDs). We focused on two IBD phenotypes that were unlikely to overlap: 1) ileal Crohn‚Äôs disease (CD) patients undergoing initial ileocolic resection of diseased ileum; and 2) ulcerative colitis (UC) patients undergoing total colectomy. The Control patients were those patients without IBD undergoing initial right hemicolectomy or total colectomy. In order to identify early pathogenic changes in the human ileum in inflammatory bowel diseases, we analyzed 99 two-color whole human genome expression profiles (Agilent 4410A) of a test human ileal cRNA probe vs. a common reference human ileal RNA from a Control patient (N17). A minimum of four biopsies were taken from the macroscopically disease-unaffected proximal ileal margin of freshly resected specimens from 47 ileal Crohn's disease patients undergoing initial ileocolic resection, 27 ulcerative colitis patients undergoing total colectomy and 25 Control patients undergoing either right hemicolectomy or total colectomy. The test and common reference probes were synthesized using the Agilent Low Input Linear Amplification Kit. Hybridization was carried out in DNA hybridization chambers, washed and scanned on an Axon GenePix 4000B scanner. The preprocessing, filtering and normalization of the array data was carried out using the R package LIMMA.

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Crohn's Disease patients and non-IBD controls : ileal gene expression

Project description:Crohn's Disease patients and non-IBD controls : ileal gene expression

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RNA sequencing for endoscopic biopsy tissue samples from controls and Crohn's disease patients, and organoids derived from these specimens.

Project description:RNA sequencing for endoscopic biopsy tissue samples from controls (jejunum [S170], n=1; ileum [SN2], n=1) and patients with Crohn's disease (jejunum [non-inflamed area, A2/L2+L4/B2, infliximab maintenance therapy, S93], n=1; ileum, [non-inflamed area, A2/L2/B2, infliximab maintenance therapy, S95], n=1). Organoid culture was performed using intestinal crypts derived from these specimens, as described previously (Sato et al. Nature 2009; 459: 262–265]. Organoids were sub-cultured at least 6 passages. RNA sequencing was conducted for organoids on day 3, day 6, and day 9 [S170 and S93], and organoids treated with TNFɑ 30 ng/ml on day 3, day 6, and day 9 [S170 and S93]. RNA sequencing was conducted for organoids on day 6 and day 9 [N2 and S95], and organoids treated with TNFɑ 30 ng/ml on day 6 and day 9.

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Ileal immune maturation in Pediatric Crohn's Disease

Project description:We report the global pattern of ileal gene expression in a cohort of 310 treatment-naïve pediatric Crohn Disease patients and controls. We focus on genes with consistent altered expression in the ileum of younger (Paris age A1a) vs older (Paris age A1b) patients.

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Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

Project description:Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

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