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E-GEOD-13525 - Transcription profiling of human epithelial ovarian cancer cell lines treated with Carboplatin reveals carboplatin induced gene expression changes in vitro are prognostic of survival - time series

Status
Submitted on 7 November 2008, released on 14 January 2009, last updated on 27 March 2012
Organism
Homo sapiens
Samples (12)
Array (1)
Protocols (5)
Description
We performed a time-course microarray experiment to define the transcriptional response to carboplatin in vitro, and to correlate this with clinical outcome in epithelial ovarian cancer (EOC). RNA was isolated from carboplatin and control-treated 36M2 ovarian cancer cells at several time points, followed by oligonucleotide microarray hybridization. Carboplatin induced changes in gene expression were assessed at the single gene as well as at the pathway level. Clinical validation was performed in publicly available microarray datasets using disease free and overall survival endpoints. Time-course and pathway analyses identified 317 genes and 40 pathways (designated time-course and pathway signatures) deregulated following carboplatin exposure. Both types of signatures were validated in two separate platinum-treated ovarian and NSCLC cell lines using published microarray data. Expression of time-course and pathway signature genes distinguished between patients with unfavorable and favorable survival in two independent ovarian cancer datasets. Among the pathways most highly induced by carboplatin in vitro, the NRF2, NF-kB, and cytokine and inflammatory response pathways were also found to be upregulated prior to chemotherapy exposure in poor prognosis tumors. Experiment Overall Design: we treated the 36M2 cell line with carboplatin 100μM or vehicle-control for 24hrs and cells were harvested and processed for RNA isolation at 24, 30 and 36hrs after treatment.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer. Panagiotis A Konstantinopoulos, Elena Fountzilas, Kamana Pillay, Luiz F Zerbini, Towia A Libermann, Stephen A Cannistra, Dimitrios Spentzos.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-13525.idf.txt
Sample and data relationshipE-GEOD-13525.sdrf.txt
Raw data (1)E-GEOD-13525.raw.1.zip
Processed data (1)E-GEOD-13525.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-13525.eSet.r
Links