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Stromal gene expression in human esophageal cancer

ABSTRACT: The incidence of esophageal and junctional adenocarcinoma has increased 6 fold in the last 30 years and 5 year survival remains less than 14%. Once considered an inert scaffold, the stromal compartment is now recognized to play a central role in invasive cancer. However, whether the stroma plays a role in the transition from pre-invasive to invasive disease is unknown. In this study we hypothesized that the altered expression of stromal genes influences the progression from pre-invasive to invasive disease. Using Barrett's esophagus as a model system, we performed an unbiased, genome-wide analysis of gene expression in micro-dissected stroma from different disease progression stages.

ORGANISM(S): Homo sapiens

PROVIDER: GSE19632 | GEO | 2010/01/22

SECONDARY ACCESSION(S): PRJNA122519

REPOSITORIES: GEO

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Stromal gene expression in human esophageal cancer

Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6 fold in the last 30 years and 5 year survival remains less than 14%. Once considered an inert scaffold, the stromal compartment is now recognized to play a central role in invasive cancer. However, whether the stroma plays a role in the transition from pre-invasive to invasive disease is unknown. In this study we hypothesized that the altered expression of stromal genes influences the progression from pre-invasive to invasive disease. Using Barrett's esophagus as a model system, we performed an unbiased, genome-wide analysis of gene expression in micro-dissected stroma from different disease progression stages. Total RNA isolated from laser-capture microdissected stromal cells from human tissue sections was used to make fluorescently labeled cRNA that was hybridized to DNA oligonucleotide microarrays. Briefly, 4 Âµg of total RNA was used to synthesize dsDNA through reverse transcription. cRNA was produced by in vitro transcription and labeled postsynthetically with Cy3 or Cy5. Two populations of labeled cRNA, a reference population and an experimental population, were compared with each other by competitive hybridization to microarrays. Two hybridizations were done with each cRNA sample pair using a fluorescent dye reversal strategy. Human microarrays contained oligonucleotide probes corresponding to approximately 21,000 genes. All oligonucleotide probes on the microarrays were synthesized in situ with inkjet technology (Agilent Technologies, Palo Alto, CA). After hybridization, arrays were scanned and fluorescence intensities for each probe were recorded. Ratios of transcript abundance (experimental to control) were obtained following normalization and correction of the array intensity data. Gene expression data analysis was done with the Rosetta Resolver gene expression analysis software (version 7.0, Rosetta Biosoftware, Seattle, WA).

2010-06-24 | E-GEOD-19632 | biostudies-arrayexpress

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

Epigenetic array data of saliva samples in individiduals with esophageal cancer with controls

Project description:We took saliva samples from 89 people with oesophageal cancer (plus 9 with high grade dysplasia, also labelled here as cancer) and 167 controls. We took replicate samples on 6 cancer samples and 4 controls to assess reproducibility. The cancer groups comprise people with invasive adenocarcinoma (61 and also 6 replicates), 28 people with intramucosal adenocarcinoma, 9 people with high-grade dysplasia arising in Barrett's esophagus, 52 patients with non-dysplastic Barrett's esophagus, 42 people with no positive diagnosis after endoscopy (ie no Barrett's, + 1 replicate), and 73 self-reported healthy volunteers (with 3 duplicates)

2024-02-07 | GSE232332 | GEO

Barrett's esophagus

Project description:Barrett's esophagus transcriptome was analysed and compared with Barrett's esophagus primary cell culture and esophageal adenocarcinoma. Keywords: SAGE analysis to compare tissues Barrett's esophagus biopsy was taken from 1 male metaplastic Barrett's esophagus patient. Barrett's esophagus primary cell culture was cultures from a biopsy taken from a Barrett's esophagus patient and cultured for about 4 to 5 weeks. Esophageal adenocarcinoma was taken from a patient known to have cancer and previously Barrett's esophagus

2006-06-28 | E-GEOD-5155 | biostudies-arrayexpress

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

gene expression profiles of Barrett's esophagus, squamous esophagus and gastric cardia

Project description:SAGE performed on biopsies of Barrett's esophagus, squamous esophagus and gastric cardia taken from a metaplastic Barrett's esophagus patient. Keywords: SAGE

2005-06-20 | GSE2769 | GEO

microRNA/UCR expression profiling of human Barrett's carcinogenesis

Project description:To test the hypothesis that there are specific miRNA/UCR expression signature which characterizes Barrett's esophagus development and progression, we performed miRNA/UCR microarray analysis comparing normal esophageal squamous epithelium with all the phenotypic lesions seen in the Barrett's carcinogenic process

2010-01-30 | GSE20099 | GEO

gene expression profiles of Barrett's esophagus, squamous esophagus and gastric cardia

Project description:SAGE performed on biopsies of Barrett's esophagus, squamous esophagus and gastric cardia taken from a metaplastic Barrett's esophagus patient. Keywords: SAGE comparative analysis of gene expression profiles of Barrett's esophagus, normal squamous esophagus and gastric cardia tissue

2005-06-20 | E-GEOD-2769 | biostudies-arrayexpress

Barrett's esophagus

2006-06-28 | GSE5155 | GEO

Stromal molecular signatures of breast and prostate cancer

Project description:Primary tumor growth induces host tissue responses that are believed to support and promote tumor progression. Identification of the molecular characteristics of the tumor microenvironment and elucidation of its crosstalk with tumor cells may therefore be crucial for improving our understanding of the processes implicated in cancer progression, identifying potential therapeutic targets, and uncovering stromal gene expression signatures that may predict clinical outcome. A key issue to resolve, therefore, is whether the stromal response to tumor growth is largely a generic phenomenon, irrespective of the tumor type, or whether the response reflects tumor-specific properties. To address similarity or distinction of stromal gene expression changes during cancer progression, oligonucleotide-based Affymetrix microarray technology was used to compare the transcriptomes of laser-microdissected stromal cells derived from invasive human breast and prostate carcinoma. Invasive breast and prostate cancer-associated stroma was observed to display distinct transcriptomes, with a limited number of shared genes. Interestingly, both breast and prostate tumor-specific dysregulated stromal genes were observed to cluster breast and prostate cancer patients, respectively, into two distinct groups with statistically different clinical outcomes. By contrast, a gene signature that was common to the reactive stroma of both tumor types did not have survival predictive value. Univariate Cox analysis identified genes whose expression level was most strongly associated with patient survival. Taken together, these observations suggest that the tumor microenvironment displays distinct features according to the tumor type that provides survival-predictive value. 6 samples of stroma surrounding invasive breast primary tumors; 6 matched samples of normal stroma. 6 samples of stroma surrounding invasive prostate primary tumors; 6 matched samples of normal stroma.

2011-03-31 | E-GEOD-26910 | biostudies-arrayexpress

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