Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA sequencing of purified intestinal epithelial cells from paediatric biopsies including Inflammatory Bowel Disease and healthy controls

ABSTRACT: This study investigated alterations in the transcriptomic profiles of intestinal epithelial cells in Inflammatory Bowel Diseases (IBD), i.e. Crohn's Disease and Ulcerative Colitis. Biopsies were taken from treatment-naive paediatric patients at diagnostic endoscopy from terminal ileum (TI), ascending colon (AC) and sigmoid colon (SC). Intestinal epithelial cells were purified using enzyme digestion and magnetic bead separation. RNA extraction was performed on EpCAM-positive cells, using AllPrep DNA/RNA mini kit. An Agilent Bioanalyzer was used to check RNA integrity following the manufacturer’s guidelines. mRNA was sequenced at the University of Kiel, Germany.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Judith Kraiczy

PROVIDER: E-MTAB-5464 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

Howell Kate Joanne KJ Kraiczy Judith J Nayak Komal M KM Gasparetto Marco M Ross Alexander A Lee Claire C Mak Tim N TN Koo Bon-Kyoung BK Kumar Nitin N Lawley Trevor T Sinha Anupam A Rosenstiel Philip P Heuschkel Robert R Stegle Oliver O Zilbauer Matthias M

Gastroenterology 20171012 3

<h4>Background & aims</h4>We analyzed DNA methylation patterns and transcriptomes of primary intestinal epithelial cells (IEC) of children newly diagnosed with inflammatory bowel diseases (IBD) to learn more about pathogenesis.<h4>Methods</h4>We obtained mucosal biopsies (N = 236) collected from terminal ileum and ascending and sigmoid colons of children (median age 13 years) newly diagnosed with IBD (43 with Crohn's disease [CD], 23 with ulcerative colitis [UC]), and 30 children without IBD (co ...[more]

PMID: 29031501

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Project description:Goal: Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the longitudinal axis, contributes to a differential response to chemoprotective agents. Method: We assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. Crypts were isolated from the proximal and distal colonic regions from rats maintained on a semi-purified diet, and mRNA gene expression profiles were generated using RNA-Seq. The remaining isolated crypts were paraformaldehyde-crosslinked and chromatin immunoprecipitated using antibodies against H3K4me3, H3K9me3, and RNA Polymerase II. Results/Conclusion: Globally, RNA-Seq results indicated that 9,866 genes were actively expressed, of which 540 genes were differentially expressed between the proximal and distal colon. With regard to differentially expressed genes, a high correlation was observed between H3K4me3-Seq and RNA-Seq data, with 96% of the canonical pathways being similarly affected in the H3K4me3-Seq and RNA-Seq data sets. Gene ontology analysis indicated that colonic crypt location significantly impacted both chromatin and transcriptional regulation of genes involved in cell transformation, lipid metabolism, lymphatic development and immune cell trafficking. Gene function analysis indicated that the PI3-Kinase signaling pathway was regulated in a site-specific manner, e.g., pathway proto-oncogenes, c-Jun, c-Fos and ATF, were up-regulated in the distal colon. Middle and long non-coding RNAs (lncRNAs) were also detected in the colon, including select lncRNAs formerly only detected in the rat nervous system. In summary, distinct combinatorial patterns of histone modifications exist in the proximal versus distal colon. These site-specific differences may explain the differential effects of chemoprotective agents on cell transformation in the ascending (proximal) and descending (distal) colon. Examination of mRNA profiles and 2 different histone modifications (H3K4me3 and H3K9me3) in 2 tissue types (proximal and distal colon).

Dataset Information

RNA sequencing of purified intestinal epithelial cells from paediatric biopsies including Inflammatory Bowel Disease and healthy controls

Publications

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

Similar Datasets

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