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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of esophagus samples from eight human patients with Barretts associated adenocarcinomas

ABSTRACT: Samples were obtained from 8 patients with Barrett's associated adenocarcinomas after transhiatal esophagectomy. Samples representative of the normal esophageal epithelium (N), BarrettÃ¢ÂÂs esophagus (B) and esophageal adenocarcinomas (ADC) were obtained from every patient by experienced GI pathologists. RNA were extracted and samples were profiled for detection of genes differentially expressed in B and ADC relative to N and in ADC relative to B.

ORGANISM(S): Homo sapiens

SUBMITTER: Nikolai Khodarev

PROVIDER: E-GEOD-1420 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Progression of Barrett's metaplasia to adenocarcinoma is associated with the suppression of the transcriptional programs of epidermal differentiation.

Kimchi Erik T ET Posner Mitchell C MC Park James O JO Darga Thomas E TE Kocherginsky Masha M Karrison Theodore T Hart John J Smith Kerrington D KD Mezhir James J JJ Weichselbaum Ralph R RR Khodarev Nikolai N NN

Cancer research 20050401 8

We did expressional profiling on 24 paired samples of normal esophageal epithelium, Barrett's metaplasia, and esophageal adenocarcinomas. Matching tissue samples representing the three different histologic types were obtained from each patient undergoing esophagectomy for adenocarcinoma. Our analysis compared the molecular changes accompanying the transformation of normal squamous epithelium with Barrett's esophagus and adenocarcinoma in individual patients rather than in a random cohort. We tes ...[more]

PMID: 15833844

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Barrett's esophagus, Barrett's-associated adenocarcinomas and normal esophageal epithelium

Project description:Samples were obtained from 8 patients with Barrett's associated adenocarcinomas after transhiatal esophagectomy. Samples representative of the normal esophageal epithelium (N), Barrett’s esophagus (B) and esophageal adenocarcinomas (ADC) were obtained from every patient by experienced GI pathologists. RNA were extracted and samples were profiled for detection of genes differentially expressed in B and ADC relative to N and in ADC relative to B. Keywords: other

2004-11-18 | GSE1420 | GEO

Barrett's esophagus

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Project description:SAGE libraries made of squamous esophagus tissue, primary cell culture or esophageal squamous cell carcinoma Keywords: SAGE analysis of different tissues squamous esophagus biopsy was taken from 1 male metaplastic Barrett's esophagus patient. primary cell culture was from 1 male Barrett's esophagus patient. Esophageal squamous cell carcinoma was from a patient known to have ESCC

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microRNA expression in Barrett's esophagus and esophageal adenocarcinoma

Project description:Barrett's esophagus is a metaplastic condition of the distal esophagus, characterized by the replacement of normal squamous epithelium by columnar epithelium. Patients with BE have an increased risk of developing esophageal adenocarcinoma. MicroRNAs have been implicated to be disease and tissue specific, however limited data of microRNA expression in the esophagus is available. Therefore we evaluated microRNA expression profiles of esophageal adenocarcinoma and compared these with Barrett's esophagus and normal squamous esophagus.

2012-03-15 | GSE29965 | GEO

A Qualitative Transcriptional Signature for the Histological Classification of Non-Small Cell Lung Cancer

Project description:Histological classification by routine pathology assessment with hematoxylin-eosin staining and immunostaining for poorly differentiated tumors, particularly those from small biopsies, is still challenging. In this study, using gene expression profiles of pathologically-determined lung squamous cell carcinomas and adenocarcinomas, denoted as pSCC and pADC respectively, we developed a qualitative transcriptional signature, based on the within-sample relative gene expression orderings (REOs) of gene pairs, to individually distinguish ADC from SCC. The signature was validated in the frozen tissues, FFPE materials, mixed tumors, small biopsy specimens and poorly differentiated samples.In summary, the qualitative signature, independent of the subjective diagnosis of pathologists, would be an effective auxiliary tool in distinguishing ADC from SCC.

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Gene expression profiling reveals stromal genes expressed in common between Barrett's esophagus and adenocarcinoma.

Project description:samples contain normal, Barrett and duodenum and adenocarcinoma BACKGROUND & AIMS: Barrett's esophagus is a precursor of esophageal adenocarcinoma. DNA microarrays that enable a genome-wide assessment of gene expression enhance the identification of specific genes as well as gene expression patterns that are expressed by Barrett's esophagus and adenocarcinoma compared with normal tissues. Barrett's esophagus length has also been identified as a risk factor for progression to adenocarcinoma, but whether there are intrinsic biological differences between short-segment and long-segment Barrett's esophagus can be explored with microarrays. METHODS: Gene expression profiles for endoscopically obtained biopsy specimens of Barrett's esophagus or esophageal adenocarcinoma and associated normal esophagus and duodenum were identified for 17 patients using DNA microarrays. Unsupervised and supervised approaches for data analysis defined similarities and differences between the tissues as well as correlations with clinical phenotypes. RESULTS: Each tissue displays a unique expression profile that distinguishes it from others. Barrett's esophagus and esophageal adenocarcinoma express a unique set of stromal genes that is distinct from normal tissues but similar to other cancers. Adenocarcinoma also showed lower and higher expression for many genes compared with Barrett's esophagus. No difference in gene expression was found between short-segment and long-segment Barrett's esophagus. CONCLUSIONS: The genome-wide assessment provided by current DNA microarrays reveals many candidate genes and patterns not previously identified. Stromal gene expression in Barrett's esophagus and adenocarcinoma is similar, indicating that these changes precede malignant transformation. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design

2006-10-18 | GSE6059 | GEO

Homo sapiens

Project description:Barrett's esophagus, Barrett's-associated adenocarcinomas and normal esophageal epithelium

| PRJNA90021 | ENA

SOX15 governs a transcriptional program in human esophageal stratified epithelium and in a subset of esophageal adenocarcinomas

Project description:We identified spatially restricted transcription factors and found SOX15 expression confined to stratified esophageal epithelium, with attenuation in Barrett's esophagus. SOX15 binds esophagus-specific loci and its loss in human esophageal cells affected esophagus-specific transcripts

2015-11-09 | GSE62909 | GEO

Expression data from nonrandomized trial of vitamin D in Barrett's esophagus

Project description:Vitamin D deficiency has been associated with increased esophageal cancer risk. Vitamin D controls many downstream regulators of cellular processes including proliferation, apoptosis, and differentiation. We evaluated the effects of vitamin D supplementation on global gene expression in patients with Barrett's esophagus. We used microarrays to assess global gene expression in Barrett's esophagus patients who received vitamin D supplementation.

2017-07-06 | GSE100843 | GEO

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