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Transcriptomic heterogeneity of Coeliac Disease biopsies from the duodenum

ABSTRACT: Transcriptomic heterogeneity of Coeliac Disease biopsies from the duodenum

PROVIDER: PRJNA692367 | ENA |

REPOSITORIES: ENA

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Transcriptomic heterogeneity of Coeliac Disease biopsies from the duodenum

Project description:Here, we present a high-resolution analysis of the transcriptomes extracted from duodenal probes of 25 children and adolescents with active CD and 21 children without CD but with diverse intestinal afflictions as controls. We found that the transcriptomes of CD patients divide into three subgroups, a mixed group resembling part of control cases and a CD-low and CD-high groups referring to lower and higher levels of CD severity Despite generally increased inflammation, considerable variation in inflammation-level between subgroups was observed, which was further de-chiffred into immune cell types using immune cell de-convolution

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Analysis of expression of genes involved in celiac disease

Project description:Celiac disease (CD) is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of candidate genes in biopsies from duodenum.

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human duodenum biopsy data

Project description:Using a systems biology approach, we discovered and dissected a three-way interaction between the immune system, the intestinal epithelium, and the microbiota. We found that mice lacking B lymphocytes, or lacking IgA, have low intestinal expression of lipid metabolism genes regulated by the transcription factor GATA4, and a consequent decrease in fat absorption in the intestine. The defect disappeared in germ free mice, suggesting that it is dependent on the microbiota; and sequencing analysis of the bacteria showed subtle differences between normal and B-cell deficient mice. Analysis of gene expression of gut biopsies from patients with common variable immunodeficiency and intestinal dysfunction revealed a high similarity to mouse B-cell knockout profiles. These data provide an explanation for a longstanding enigmatic association between immunodeficiency and defective lipid absorption in humans. this series represents the subsection of the study where we analize gene epxression in duodenum biopsies from CVID patients and contols with unrelated pathologies Reference sample is from normal duodenum (Clontech). Log2 ratio Cy5/Cy3 was used.

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Transcription profiling of biopsies from human squamous cell carcinomas to quantify intra-tumoral heterogeneity

Project description:Heterogeneity of gene expression profiles in head and neck cancer Background: Results of gene expression profiling studies from different institutes often lack consistency. This could be due to the use of different microarray platforms and protocols, or to intra-tumoral heterogeneity in mRNA expression. The aim of our study was to quantify intra-tumoral heterogeneity in head and cancer. Methods: Forty-four fresh frozen biopsies were taken from 22 patients, two per tumor. RNA was extracted, tested for quality, amplified, labeled and hybridized to a 35k oligoarray. Results: Unsupervised clustering analyses using all genes, the most variable genes, or random gene sets showed that 80-90% of biopsy pairs clustered together. A within-pair-between-pair scatter ratio analysis showed that the similarity between matching pairs was significantly greater than that between random pairs (p < 0.00001). Conclusions: Two biopsies from the same tumor show far greater similarity in gene expression than biopsies from different tumors, supporting the use of one biopsy for expression profiling.

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insulin resistant duodenum vs. non-insulin resistant duodenum

Project description:Transcriptional profiling of duodenum from non-obese patients and patients with morbid obesity comparing non-insulin resistance vs. insulin resistande. Goal was to determine the involvement of the duodenum in the development of insulin resistance and the possible influence of obesity.

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Expression of candidate genes in Celiac Disease - Associated genes and regulatory elements (part 1)

Project description:Celiac disease is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of candidate genes and regulatory elements in biopsies from duodenum.

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insulin resistant duodenum vs. non-insulin resistant duodenum

Project description:insulin resistant duodenum vs. non-insulin resistant duodenum

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Project description:As duodenum is an important Vitamin D target organ, transcriptomic analyses were performed in this tissue. We analysed RNA extracted from duodenum of three 10 week-old wild-type and VDR-null mice using the Affymetrix Mouse Gene 2.0 ST.

2015-04-16 | E-GEOD-67904 | biostudies-arrayexpress

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Project description:Celiac disease is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of regulatory elements (4) and some of their targets in biopsies from duodenum.

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