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| Status |
Public on Aug 17, 2011 |
| Title |
Whole genome expression array profiling highlights differences in mucosal defense genes in Barrett's esophagus and esophageal adenocarcinoma. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Esophageal adenocarcinoma (EAC) has become a major concern in Western countries due to rapid rises in incidence coupled with very poor survival rates. One of the key risk factors for the development of this cancer is the presence of Barrett’s esophagus (BE), which is believed to form in response to repeated gastro-esophageal reflux. In this study we performed comparative, genome-wide expression profiling (using Illumina whole-genome Beadarray) on total RNA extracted from esophageal biopsy tissues from individuals with EAC, BE (in the absence of EAC) and those with normal squamous epithelium. We combined these data with publically accessible raw data from three similar studies to investigate key gene and ontology differences between these three tissue states. The results support the deduction that BE is a tissue with enhanced glycoprotein synthesis machinery (DPP4, ATP2A3, AGR2) designed to provide strong mucosal defenses aimed at resisting gastro-esophageal reflux. EAC exhibits the enhanced extracellular matrix remodeling (collagens, IGFBP7, PLAU) effects expected in an aggressive form of cancer, as well as evidence of reduced expression of genes associated with mucosal (MUC6, CA2, TFF1) and xenobiotic (AKR1C2, AKR1B10) defenses. When our results are compared to previous whole-genome expression profiling studies keratin, mucin, annexin and trefoil factor gene families are the most frequently represented gene families. Eleven genes identified here are also represented in at least 3 other profiling studies. We used these genes to discriminate squamous, BE and EAC within the two largest cohorts using a support vector machine leave one out cross validation analysis. While this method was satisfactory for discriminating squamous and BE, it demonstrates the need for more detailed investigations into profiling changes within BE leading to the progression towards EAC.
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| Overall design |
A comparison of three esophageal biopsy groups from separate individuals: normal squamous (n=9), Barrett's esophagus without dysplasia (n=22) & adenocarcinoma (n=23). Adenocarcinoma samples overlap with members of DNA copy number analysis GEO series GSE10506 such that, in each case genomic DNA and total RNA were extracted from the same biopsy. The matching copy number data GEO samples IDs are noted in characteristics: Matching CN Sample ID
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| Contributor(s) |
Nancarrow DJ, Clouston AD, Smithers BM, Gotley DC, Drew PA, Watson DI, Tyagi S, Hayward NK, Whiteman DC |
| Citation(s) |
21829465 |
| Submission date |
Mar 31, 2011 |
| Last update date |
Mar 23, 2012 |
| Contact name |
Derek John Nancarrow |
| E-mail(s) |
derek.nancarrow@qimr.edu.au
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| Phone |
61 7 3362 0323
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| Fax |
61 7 3845 3508
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| Organization name |
Queensland Institute of Medical Research
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| Department |
Genetics & Population Health
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| Lab |
Oncogenomics
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| Street address |
300 Herston Road
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| City |
Herston |
| State/province |
Queensland |
| ZIP/Postal code |
4006 |
| Country |
Australia |
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| Platforms (1) |
| GPL2507 |
Sentrix Human-6 Expression BeadChip |
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| Samples (54)
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| Relations |
| BioProject |
PRJNA139491 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE28302_RAW.tar |
3.7 Mb |
(http)(custom) |
TAR |
| GSE28302_non-normalized.txt.gz |
31.3 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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