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E-GEOD-15308

Title: Expression profiling of the cell line SSC9 (human squamous carcinoma of the tongue) treated with the NSAID nimesulide and/or cisplatin. [original title: Genomics of oral cancer cells]
Organism(s): Homo sapiens
Description: Dynamic changes in RNA and protein levels after exposure to 100 umol/L nimesulide and low-dose 0.5umol/L cisplatin in oral cancer cells were screened to gain insights into the molecular mechanisms of cell death. After 48 hours of treatment, SCC9 and SCC25 cells were analyzed for apoptosis and necrosis by FACS, immunohistochemistry and analysis of nucleotides by HPLC. Microarray GeneChips and the iTRAQ system were used to measure changes in the whole genome and proteome. FACS and immunohistochemical analyses showed an increased number of apoptotic and necrotic SCC9 and SCC25 cells after nimesulide and cisplatin exposure. Simultaneously, ATP and the energy charge of the SCC9 cells were significantly decreased. In SCC25 cells, ATP only significantly decreased after combined nimesulide/cisplatin exposure. In the SCC9 cell line, gene and proteome analysis detected and quantified one gene, keratin 6a and 540 proteins, respectively. After combined treatment, significant upregulation of histone H2A, H2B and H4 could be found with a local discovery false rate of 0.003 and 0.0027 for histone H2A and histone H2B, respectively. Using gene and proteome mapping, we could show that combined treatment of oral cancer cells with nimesulide and low-dose cisplatin induce necrosis and early apoptosis by the intrinsic and extrinsic pathways. Our results suggest potential clinical benefits of a nimesulide/cisplatin combination rather than single cisplatin treatment for oral cancer patients. Cell culture: A squamous carcinoma cell line of the tongue, SCC9, was obtained from the American Type Culture Collection (ATCC, Rockville, Maryland, USA). The cell line was cultured in RPMI 1640 medium containing 10% fetal bovine serum and 100U/mL penicillin and 100 ug/mL streptomycin (all reagents from Life Technologies Ltd, Paisley, Scotland) and incubated at 37¬ĚC in a humidified atmosphere of 5% CO2. SCC9 cells were maintained in RPMI 1640 medium and seeded at equal densities of 5x10^5 cells in 10cm tissue culture dishes. 24 hours later, cells were harvested using Trypsin/EDTA (Life Technologies Ltd, Paisley Scotland) and treated with 100 umol/L nimesulide, 0.5 umol/L cisplatin or a combination of nimesulide/cisplatin. Control dishes were treated in exactly the same way without the addition of the respective compound. The concentration of 100 umol/L for nimesulide was chosen as this concentration is in a pharmacologically relevant range for humans. cDNA microarray, hybridization and image analysis: RNA isolation and preparation of cRNA, hybridization, and scanning of the arrays were performed according to protocols of the manufacturer. Hybridization was done using three sets of human U133A GeneChips (Affymetrix, Ca, USA); only two nimesulide/cisplatin Samples are included in this submission. The arrays were scanned using the GeneArray scanner (Affymetrix). Data normalization was performed using RMA. The supplementary file 'GSE15308_sample_protocols.txt' contains detailed Sample protocols.
Design(s): transcription profiling by array
Experimental factor(s):
other drug
2 recorded
none cisplatin
NSAID
2 recorded
nimesulide none
treatment
4 recorded
nimesulide cisplatin cisplatin + nimesulide none
Publication(s):
Sample attribute(s):
Material Type
1 recorded
total RNA
treatment
4 recorded
nimesulide cisplatin cisplatin + nimesulide none
cell line
1 recorded
SSC9
Label
1 recorded
biotin
Organism
1 recorded
Homo sapiens
BioSourceProvider
1 recorded
American Type Culture Collection (ATCC, Rockville, Maryland, USA).
cell type
1 recorded
oral tongue squamous cell carcinoma cell line
Contact(s): Boban Erovic
Release Date: 10/4/2011
Submission Date:
Metadata Downloads Download Study Metadata as ISAtabDownload Study Metadata as ISAtab
Assay Downloads
transcription profiling using DNA microarray
11 assays