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| Status |
Public on Jan 04, 2011 |
| Title |
Robust prognostic biomarkers for EAC identified by systems-level characterization of tumor transcriptome |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Despite continual efforts to rationalize a prognostic stratification of patients with esophageal adenocarcinoma (EAC) before treatment, current staging system only shows limited success owing to the lack of molecular and genetic markers that reflect prognostic features of the tumor. To develop molecular predictors of prognosis, we used systems-level characterization of tumor transcriptome. Using DNA microarray, genome-wide gene expression profiling was performed on 75 biopsy samples from patients with untreated EAC. Various statistical and informatical methods were applied to gene expression data to identify potential biomarkers associated with prognosis. Potential marker genes were validated in an independent cohort using quantitiative RT-PCR to measure gene expression. Distinct subgroups of EAC were uncovered by systems-level characterization of tumor transcriptome. We also identified a six-gene expression signature that could be used to predict overall survival (OS) of EAC patients. In particular, expression of SPARC and SPP1 was a strong independent predictor of OS, and a combined gene expression signature with these two genes was associated with prognosis (P < 0.024), even when all relevant pathological variables were considered together in multivariate Cox hazard regression analysis. Our findings suggest that molecular features reflected in gene expression signatures may dictate the prognosis of EAC patients, and these gene expression signatures can be used to predict the likelihood of prognosis at the time of diagnosis and before treatment.
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| Overall design |
64 primary esophageal adenocarcinoma, 15 Barrett's esophagus and 28 surrounding normal fresh frozen tissues were used for microarray. All the tissues were obtained after curative resection after pathologic confirm at UT M.D. Anderson Cancer Center (MDACC). Microarray experiment and data analysis were done in the Dept. of systems biology at MDACC
DNA microarray (Illumina human V2)
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| |
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| Contributor(s) |
Kim S, Ajani J, Lee J |
| Citation(s) |
21152079 |
| |
| Submission date |
Dec 10, 2008 |
| Last update date |
Feb 15, 2013 |
| Contact name |
Sangbae Kim |
| E-mail(s) |
sangbkim22@gmail.com
|
| Organization name |
Baylor Colleage of Medicine
|
| Department |
HGSC
|
| Street address |
1 Baylor plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL6102 |
Illumina human-6 v2.0 expression beadchip |
|
| Samples (118)
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| Relations |
| BioProject |
PRJNA110305 |
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