Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Predicting response to vedolizumab therapy using mucosal transcriptomics in IBD patients

ABSTRACT: In this study we wanted to identify baseline predictors of successful vedolizumab therapy in patients with inflammatory bowel disease.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Bram Verstockt

PROVIDER: E-MTAB-7845 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Expression Levels of 4 Genes in Colon Tissue Might Be Used to Predict Which Patients Will Enter Endoscopic Remission After Vedolizumab Therapy for Inflammatory Bowel Diseases.

Verstockt Bram B Verstockt Sare S Veny Marisol M Dehairs Jonas J Arnauts Kaline K Van Assche Gert G De Hertogh Gert G Vermeire Séverine S Salas Azucena A Ferrante Marc M

Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association 20190822 5

<h4>Background & aims</h4>We aimed to identify biomarkers that might be used to predict responses of patients with inflammatory bowel diseases (IBD) to vedolizumab therapy.<h4>Methods</h4>We obtained biopsies from inflamed colon of patients with IBD who began treatment with vedolizumab (n = 31) or tumor necrosis factor (TNF) antagonists (n = 20) and performed RNA-sequencing analyses. We compared gene expression patterns between patients who did and did not enter endoscopic remission (absence of ...[more]

PMID: 31446181

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Project description:Gene expression profiling was performed on biopsies of affected and unaffected psoriatic skin and normal skin from seven Japanese patients to obtain insights into the pathways that control this disease. U95A Affymetrix DNA chips that contain oligonucleotide arrays of approximately 12,000 well-characterized human genes were used in the study. The statistical analysis of the Affymetrix data, based on the ranking of the Student-test statistic, revealed a complex regulation of molecular stress and immune gene responses. The majority of the 266 induced-genes in affected and unaffected psoriatic skin were involved with interferon mediation, immunity, cell-adhesion, cytoskeleton restructuring, protein trafficking and degradation, RNA regulation and degradation, signaling transduction, apoptosis and atypical epidermal cellular proliferation and differentiation. The disturbances in the normal protein degradation equilibrium of skin were reflected by the significant increase in the gene expression of various protease inhibitors and proteinases including the induced components of the ATP/ubiquitin-dependent non-lysosomal proteolytic pathway that is involved with peptide processing and presentation to T-cells. Some of the upregulated genes, such as TGM1, IVL, CSTA, FABP5 and SPRR, are well known psoriatic markers involved in atypical epidermal cellular organization and differentiation. In the comparison between the affected and unaffected psoriatic skin, the transcription factor JUNB was found at the top of the statistical rankings for the 51 significantly upregulated genes in affected skin, suggesting that it has an important but as yet undefined role in psoriasis. Our gene expression data and analysis suggest that psoriasis is a chronic IFN and T-cell-mediated immune disease of the skin where the imbalance in epidermal cellular structure, growth and differentiation arises from the molecular antiviral stress signals initiating inappropriate immune responses. Experiment Overall Design: Analysis of the expression profile of skin samples for each of three conditions (states) of psoriasis activity Experiment Overall Design: 3 samples were from psoriasis negative individuals (biological replicates) Experiment Overall Design: 4 samples were from psorasis free skin areas of psoriasis active individuals (biological replicates) Experiment Overall Design: 4 samples were from psorasis active skin areas of psoriasis active individuals (biological replicates)

Dataset Information

Predicting response to vedolizumab therapy using mucosal transcriptomics in IBD patients

Publications

Expression Levels of 4 Genes in Colon Tissue Might Be Used to Predict Which Patients Will Enter Endoscopic Remission After Vedolizumab Therapy for Inflammatory Bowel Diseases.

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