E-GEOD-3167 - Transcription profiling of human urinary superficial transitional cell carcinoma with surrounding carcinoma in situ (CIS) lesions, without surrounding CIS lesions, and muscle invasive carcinoma

Status
Submitted on 19 August 2005, released on 28 November 2007, last updated on 27 March 2012
Organism
Homo sapiens
Samples (60)
Array (1)
Protocols (2)
Description
The presence of carcinoma in situ (CIS) lesions in the urinary bladder is associated with a high risk of disease progression to a muscle invasive stage. In this study, we used microarray expression profiling to examine the gene expression patterns in superficial transitional cell carcinoma (sTCC) with surrounding CIS (13 patients), without surrounding CIS lesions (15 patients), and in muscle invasive carcinomas (mTCC; 13 patients). Hierarchical cluster analysis separated the sTCC samples according to the presence or absence of CIS in the surrounding urothelium. We identified a few gene clusters that contained genes with similar expression levels in transitional cell carcinoma (TCC) with surrounding CIS and invasive TCC. However, no close relationship between TCC with adjacent CIS and invasive TCC was observed using hierarchical cluster analysis. Expression profiling of a series of biopsies from normal urothelium and urothelium with CIS lesions from the same urinary bladder revealed that the gene expression found in sTCC with surrounding CIS is found also in CIS biopsies as well as in histologically normal samples adjacent to the CIS lesions. Furthermore, we also identified similar gene expression changes in mTCC samples. We used a supervised learning approach to build a 16-gene molecular CIS classifier. The classifier was able to classify sTCC samples according to the presence or absence of surrounding CIS with a high accuracy. This study demonstrates that a CIS gene expression signature is present not only in CIS biopsies but also in sTCC, mTCC, and, remarkably, in histologically normal urothelium from bladders with CIS. Identification of this expression signature could provide guidance for the selection of therapy and follow-up regimen in patients with early stage bladder cancer. Experiment Overall Design: See publication
Experiment types
transcription profiling by array, individual comparison
Contact
Citation
Gene expression in the urinary bladder: a common carcinoma in situ gene expression signature exists disregarding histopathological classification. Lars Dyrskjøt, Mogens Kruhøffer, Thomas Thykjaer, Niels Marcussen, Jens L Jensen, Klaus Møller, Torben F Ørntoft. Cancer Res 64(11):4040-8 (2004)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-3167.idf.txt
Sample and data relationshipE-GEOD-3167.sdrf.txt
Raw data (2)E-GEOD-3167.raw.1.zip, E-GEOD-3167.raw.2.zip
Processed data (1)E-GEOD-3167.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-3167.eSet.r
Links