E-MEXP-1828
Ontology highlight
ABSTRACT:
PROVIDER: E-MEXP-1828 | ExpressionAtlas | 2025-01-22
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MEXP-1828-analysis-methods.tsv | Tabular | |||
| E-MEXP-1828-atlasExperimentSummary.Rdata | Rdata | |||
| E-MEXP-1828-configuration.xml | Xml | |||
| E-MEXP-1828-percentile-ranks.tsv | Tabular | |||
| E-MEXP-1828.condensed-sdrf.tsv | Tabular |
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Project description:Study on the effects of long term, dietary, consumption of gliadin (gluten) in patients with celiac disease. Comparison of expression profiles of biopsies from normalized patients treated with gluten-free diet >2 years (FU-follow-up samples) versus biopsies from patients with active disease (Dx-at diagnosis samples)
2009-06-01 | E-MEXP-1828 | biostudies-arrayexpress
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Project description:Differential diagnosis in inflammatory bowel disease (IBD) patients from the start of the diagnosis is challenging. In this study we tried to discriminate two subtypes of IBD such as Chron's disease(CD) and Ulcerative colitis (UC) using differential expression of genes from formalin-fixed paraffin-embedded mucosal biopsies of 33 IBD patients and 10 healthy controls.
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Project description:This dataset includes RNA-seq data from ileal and colonic biopsies at time of diagnosis for treatment-naive, uncomplicated Crohn's disease (CD) patients and matched controls. This is includes 56 CD patients each for ileal and colonic tissue and for controls, 46 colonic samples and 45 ileal samples. Clinical characteristics such as development of complications, disease remission, or progression to surgery were recorded with a mean follow-up of 6 years.
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Project description:We investigated the biological features of FL and their relationship to patients’ outcome. Gene expression analysis was carried out on diagnosis biopsies from 148 follicular lymphoma patients enrolled in the PRIMA clinical trial. We developed a gene expression-based predictor of progression-free survival (PFS) in high-tumour burden FL patients and we analysed gene-expression signatures reflecting different aspects of tumour biology for their association with outcome. proposition SH: We investigated the biological features of FL and their relationship to patients’ outcome. Gene expression analysis was carried out on diagnosis biopsies from 148 follicular lymphoma patients enrolled in the PRIMA clinical trial. We developed a gene expression-based predictor of progression-free survival (PFS) in high-tumour burden FL patients and we analysed gene-expression signatures reflecting different aspects of tumour biology for their association with outcome.
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Project description:About 5% of celiac disease (CeD) patients do not respond to a gluten-free diet and progress to refractory celiac disease (RCD), a severe progression that is characterized by infiltration of intraepithelial T-lymphocytes (IELs). RCD type II (RCDII) patients show clonal expansions of IELs that result in a poor prognosis and a high mortality rate through development of aggressive enteropathy-associated T-cell lymphoma.<br>RCDII has a poor prognosis (5-year survival rate <50%) also because of the development of enteropathy-associated T-cell lymphoma. Diagnosis of RCDII is complex and involves a combination of several techniques such as multiplex PCR analysis to determine the clonality of T-cell receptor gene rearrangements and immunohistochemistry or flow-cytometry to define the cell surface markers of IELs. Therefore studying the genetics and genomics of RCD2 susceptibility may provide novel insights into mechanistic basis for RCD2 development. The aim of this experiment was to profile the global gene expression changes in order to understand the dysregulated pathways in RCD2 biopsies and to uncover downstream pathways affected by RCD2 genetic susceptibility loci. <br>All patients were diagnosed with RCD2 and gut biopsies were collected from these patients to perform microarray based gene expression analysis. RNA from eleven RCD2 biopsy samples were analyzed using Illumina Human Ref8 v1 array.
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Project description:This study describes a comparison of global proteome expression in small intestinal tissue collected from celiac disease patients at different stages of disease. We have analyzed sections from FFPE biopsy blocks and identified more than 4500 protein without sample pre-fractionation. We have compared protein expression in two sample cohorts that were chosen retrospectively from patients participating in research protocols at our facility. First we compared biopsies from 10 patients collected at the time of diagnoses (untreated CD) with biopsies collected 1 year later following gluten free diet (treated CD). We observed overall good agreement between differential expression of proteins and histological changes that occur in the intestine. We identified biological pathways that are known to operate in the disease lesion. We also observed a strong signal for neutrophil infiltration. By use of a dedicated immunoglobulin variable gene family database we found that differential expression of IGHV5-51 distinguished our untreated from treated CD patients. We also compared protein expression in 4 treated CD patients that developed histological changes in the small intestine in response to a 3 day gluten challenge. Although these patients develop an intestinal lesion resembling the lesion observed in untreated patients, we observed differential expression of proteins involved in acute tissue remodeling that were not seen when we compared UCD to TCD samples. Our study presents a proof-of-concept to demonstrate that analysis of material from FFPE tissue block material can provide a comprehensive overview of many disease processes that occur in the celiac small intestine. Changes in protein expression will reveal information on disease state that may not be observed by histological evaluation
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Project description:Background Identification of the molecular determinants of invasion and metastatic potential may guide the development of a rational strategy for devising specific therapies that target the pathways leading to osteosarcoma. Methods In this study, we used pathway-focused GEarrays to screen for candidate genes related to tumor progression. Expression patterns of the selected genes were validated by real time PCR on 61 osteosarcoma patient tumor samples and correlated with clinical and pathological data. Results THBS3, SPARC and SPP1 were identified with pathway-focused GEarrays as genes differentially expressed in osteosarcoma. In particular, THBS3 was expressed at significantly high levels (p=0.0001) in biopsies from patients with metastasis at diagnosis, which is a predictor of worse overall survival, event-free survival and relapse free survival at diagnosis. After chemotherapy, patients with tumors over-expressing THBS3 have worse relapse free survival. High SPARC expression was found in 51 of 55 (96.3%) osteosarcoma samples and correlated with the worst event-free survival (p=0.03) and relapse free survival (p=0.07). Overexpression of SPP1 was found in 47 of 53 (89%) osteosarcomas correlating with better overall survival, event-free survival and relapse free survival at diagnosis. Conclusion With pathway-focused Gearrays, we identified three genes, which interestingly all encode for proteins involved in extracellular remodeling suggesting potential roles in osteosarcoma progression. This is the first report on the THBS3 gene working as a stimulator of tumor progression. Higher levels of THBS3 maintain the capacity of angiogenesis. High levels of SPARC are not required for tumor progression but are necessary for tumor growth and maintenance. SPP1 is not necessary for tumor progression in osteosarcoma and may be associated with inflammatory response and bone remodeling, functioning as a good biomarker. Keywords: disease state analysis using Superarray Pathway focused arrays
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