Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1086386 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31147607_1.fastq.gz | Fastqsanger.gz | |||
| SRR31147607_2.fastq.gz | Fastqsanger.gz | |||
| SRR31147608_1.fastq.gz | Fastqsanger.gz | |||
| SRR31147608_2.fastq.gz | Fastqsanger.gz | |||
| SRR31147609_1.fastq.gz | Fastqsanger.gz |
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Project description:Objective The imbalance between Th17 cells and regulatory T cells in the gut of inflammatory bowel disease (IBD) patients promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate, enforce or repress gene expression patterns and ultimately promote the induction and maintenance of dysregulated intestinal CD4 T cells. Design Here, we characterized the chromatin landscape and the heterogeneity of CD4 T cells from blood samples and biopsies of IBD patients using in house generated ATAC-Seq and single cell RNA-Seq libraries as well as publicly available datasets. Results We found that chromatin accessibility profiles specific to CD4 T cells from inflamed intestinal biopsies associate to inflammatory genes capable of promoting γδT, NK, T and B cell activation and proliferation. Our data show that the chromatin accessibility changes of CD4 T cells are associated with a higher predominance of pathogenic Th17 cells (pTh17 cells) in inflamed biopsies of IBD patients. In addition, we found that IBD risk loci in CD4 T cells are colocalized with accessible chromatin changes near pTh17-related genes. For instance, the IBD risk locus rs12942547 lies within an intronic STAT3 region enriched in areas of active intestinal inflammation from IBD patients. A similar profile was observed in a region near IL23R. Moreover, single cell RNA-Seq analysis of CD4 T cells from patient biopsies shows a population of CD4 T cells that resembles pTh17 cells with co-expression of Th1 and Th17 transcriptional programs, including a cytotoxic gene signature. Conclusion Altogether, our data suggest that cytotoxic pTh17 cells are associated with intestinal inflammation of IBD patients and specifically associate some IBD genetic variants with this CD4 T cell subset.
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Project description:We purified the intestinal epithelial cells from biopsies taken from the ileum and colon of a paediatric cohort of IBD patients and healthy controls
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Project description:We used microarrays to identify mucosal gene signatures predictive of response to infliximab (IFX) in patients with inflammatory bowel disease (IBD) and to gain more insight into the pathogenesis of IBD. Keywords: drug response and treatment effect Mucosal biopsies were obtained at endoscopy in actively inflamed mucosa from 61 IBD patients (24 ulcerative colitis (UC), 19 Crohnâs colitis (CDc) and 18 Crohnâs ileitis (CDi)), refractory to corticosteroids and/or immunosuppression, before and 4-6 weeks after (except for 1 CDc patient) their first infliximab infusion and in normal mucosa from 12 control patients (6 colon and 6 ileum). The patients were classified for response to infliximab based on endoscopic and histologic findings at 4-6 weeks after first infliximab treatment. Total RNA was isolated from intestinal mucosal biopsies, labelled and hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays.
2009-11-02 | E-GEOD-16879 | biostudies-arrayexpress
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Project description:Microarrays were used to analyze the gene expression in endoscopic-derived intestinal mucosal biopsies from patients with inflammatory bowel disease (IBD) and controls Mucosal biopsies were obtained at endoscopy from the colon of 97 ulcerative colitis (UC), 8 Crohn's disease (CD) patients and 11 controls. The biopsies were taken at the most affected sites but at a distance of ulcerations. Disease activity was endoscopically assessed. Total RNA extracted from mucosal biopsies was used to analyze mRNA expression via Affymetrix Human Gene 1.0 ST arrays
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Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
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Project description:We sought to identify proteins that enable differentiation between CD and UC in children with new onset IBD. Mucosal biopsies were obtained from children undergoing baseline diagnostic endoscopy prior to therapeutic interventions. Using a super-stable isotope labeling with amino acids in cell culture (SILAC)-based approach, the proteomes of 99 paediatric control and biopsies of patients with CD and UC were compared. Multivariate analysis of a subset of these (n=50) was applied to identify novel biomarkers, which were validated in a second subset (n=49). In the discovery cohort, a panel of five proteins was sufficient to distinguish control from IBD-affected tissue biopsies with an AUC of 1.0 (95% CI 0.99 to 1.0); a second panel of 12 proteins segregated inflamed CD from UC within an AUC of 0.95 (95% CI 0.86 to 1.0). Application of the two panels to the validation cohort resulted in accurate classification of 95.9% (IBD from control) and 80% (CD from UC) of patients. 116 proteins were identified to have correlation with the severity of disease, four of which were components of the two panels, including visfatin and metallothionein-2. This study has identified two panels of candidate biomarkers for the diagnosis of IBD and the differentiation of IBD subtypes to guide appropriate therapeutic interventions in paediatric patients.
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