Unknown,Transcriptomics,Genomics,Proteomics

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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. 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 µg 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).

ORGANISM(S): Homo sapiens

SUBMITTER: N Clemons 

PROVIDER: E-GEOD-19632 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Stromal genes discriminate preinvasive from invasive disease, predict outcome, and highlight inflammatory pathways in digestive cancers.

Saadi Amel A   Shannon Nicholas B NB   Lao-Sirieix Pierre P   O'Donovan Maria M   Walker Elaine E   Clemons Nicholas J NJ   Hardwick James S JS   Zhang Chunsheng C   Das Madhumita M   Save Vicki V   Novelli Marco M   Balkwill Frances F   Fitzgerald Rebecca C RC  

Proceedings of the National Academy of Sciences of the United States of America 20100113 5


The stromal compartment is increasingly recognized to play a role in cancer. However, its role in the transition from preinvasive to invasive disease is unknown. Most gastrointestinal tumors have clearly defined premalignant stages, and Barrett's esophagus (BE) is an ideal research model. Supervised clustering of gene expression profiles from microdissected stroma identified a gene signature that could distinguish between BE metaplasia, dysplasia, and esophageal adenocarcinoma (EAC). EAC patient  ...[more]

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