ONTOLOGY SOURCE REFERENCE
Term Source Name	"EFO"	"SNOMEDCT"	"NCBITaxon"	"BTO"	"CHEBI"	
Term Source File	"http://www.ebi.ac.uk/efo/efo.owl"	"http://bioportal.bioontology.org/ontologies/46896"	"http://bioportal.bioontology.org/ontologies/47845"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO"	"http://bioportal.bioontology.org/ontologies/50447"	
Term Source Version	""	"46896"	"47845"	"Jun 2010"	"50447"	
Term Source Description	""	"Systematized Nomenclature of Medicine - Clinical Terms"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"BRENDA tissue / enzyme source"	"Chemical Entities of Biological Interest Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-15308"
Study 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]"
Study 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¡C 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."
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Study Public Release Date	"2011-10-04"
Study File Name	"s_E-GEOD-15308_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
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STUDY FACTORS
Study Factor Name	"treatment"	"NSAID"	"other drug"
Study Factor Type	"treatment"	"chemical compound"	"chemical compound"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-15308_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE15308-1"	"P-GSE15308-6"	"P-GSE15308-3"	"P-GSE15308-13"	"P-GSE15308-8"	"P-GSE15308-12"	"P-GSE15308-11"	"P-GSE15308-10"	"P-GSE15308-7"	"P-GSE15308-9"	"P-GSE15308-2"	"P-GSE15308-4"	"P-GSE15308-5"
Study Protocol Type	"bioassay_data_transformation"	"hybridization"	"grow"	"feature_extraction"	"image_aquisition"	"image_aquisition"	"image_aquisition"	"image_aquisition"	"image_aquisition"	"image_aquisition"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"
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Study Protocol Description	"ID_REF = <br>VALUE = RMA-normalized signals"	"Hybridization of the arrays was performed according to the manufacturer."	"The SCC9 cell line was cultured in RPMI 1640 medium containing 10% fetal bovine serum, 100U/mL penicillin and 100 ug/mL streptomycin (all reagents from Life Technologies Ltd, Paisley, Scotland) and incubated at 37¡C in a humidified atmosphere of 5% CO2."	"The Affymetrix chips were normalized using RMA (robust multi-array analysis). For the acquisition of reliable data, we used triplicate arrays although duplicate arrays are usually recommended. In a filtering step, all probe sets with inter-quartile range <0.3 were excluded, resulting in 300 probe sets for the analysis. A linear model for the comparison of the three treatment groups versus no treatment was calculated. However, due to the left-skewed distribution of the p-values (most likely induced by correlation between the probe sets), local false discovery rates were calculated for the three comparisons which give the probability of having no effect given the observed test statistics for each probe set. All probe sets with a local false discovery <0.2 were considered as "interesting". A heatmap with a dendrogram of the arrays was plotted. All pre-processing steps and analyses were performed using R.2.6 and the Bioconductor environment (www.Bioconductor.org)."	"Wavelength: 570nm for SAPE"	"Number of scans: 2"	"6 um for 50 um Chip"	"3 um for 24 um Chip"	"Arrays were scanned using the GeneArray scanner (Affymetrix)."	"Pixel size:"	"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."	"RNA isolation was performed according to protocols of the manufacturer."	"Preparation of labeled cRNA was performed according to protocols of the manufacturer."
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STUDY CONTACTS
Study Person Last Name	"Erovic"
Study Person First Name	"Boban"
Study Person Mid Initials	"M"
Study Person Email	"boban.erovic@meduniwien.ac.at"
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Study Person Address	"MUW, Waehringer Guertel 18-20, Vienna, Austria"
Study Person Affiliation	"MUW"
Study Person Roles	"submitter"
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