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Series GSE10288 Query DataSets for GSE10288
Status Public on Jun 22, 2009
Title Gene expression profiling reveals novel molecular marker candidates of laryngeal squamous cell carcinoma
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Laryngeal squamous cell carcinoma is a very common in head and neck cancer, accounting for 25% of all cases, with high mortality rates and poor prognosis. In this study, we compared expression profiles of clinical samples from15 larynx tumors and 10 non-neoplastic larynx tissue using a custom-built cDNA microarray containing 332 probes for 285 genes previously identified as up- or down-regulated in head and neck tumors by the Head and Neck Annotation Consortium (Reis et al., Cancer Res 65:1693-99, 2005).
Thirty-five genes showed statistically significant differences (SNR ≥|1.0|,p-value ≤ 0.001) in expression between tumor and non-tumor larynx tissue samples. Functional annotation indicated that these genes are involved in cellular processes relevant to the cancer phenotype, such as apoptosis, cell cycle, DNA repair, proteolysis, protease inhibition, signal transduction, and transcription regulation. Six of the identified transcripts map to intronic regions of protein-coding genes and may comprise unannotated exons or yet uncharacterized long ncRNAs with a regulatory role in the gene expression program of larynx tissue.
Differential expression of 10 of these genes (ADCY6, AES, AL2SCR3, CRR9, CSTB, DUSP1, MAP3K5, PLAT, UBL1 and ZNF706) was independently confirmed by quantitative real-time RT-PCR. Among these, the CSTB gene product has cysteine protease inhibitor activity that has been associated to an antimetastatic function. Interestingly, CSTB showed low expression in all tumor samples analyzed (p-value < 0.0001).
The set of genes identified here contribute to a better understanding of the molecular basis of larynx cancer, and at the same time provide novel candidate markers for improving diagnosis, prognosis and treatment of this carcinoma.
Keywords: Gene expression profiling of larynx tumors and non-neoplastic adjacent tissue
 
Overall design Total RNA was isolated from snap-frozen tissue samples from 13 larynx tumors and 10 non-neoplastic larynx tissue.Labeled targets for hybridizations were generated from total mRNA in reverse transcription reactions using oligo-dT primers. The Cy5 (tumor or non-tumor sample) labeled cDNAs were hybridized separately with microarrays on an Automated Slide Processor (ASP, GE Healthcare) and incubated for 16 h at 42ºC. Processed slides were scanned with a 700 V PMT setting. Background-subtracted artifact-removed median intensities of Cy5 emissions were extracted for each spot from raw images, using the ArrayVision V.7.2 software (Imaging Research Inc., Ontario, Canada).
To make the experiments comparable, intensity data derived from Cy5-labeled test samples from different hybridizations were LOWESS normalized by, using as reference the intensity data from a sample with total energy comparable to the average intensity of all samples.
 
Contributor(s) Reis EM
Citation(s) 19212623
Submission date Jan 28, 2008
Last update date Mar 19, 2012
Contact name Eduardo Moraes Reis
E-mail(s) emreis@iq.usp.br
Phone +55-11-30912173
Organization name University of São Paulo
Department Biochemistry
Street address Av. Prof. Lineu Prestes, 748
City São Paulo
State/province SP
ZIP/Postal code 05508-900
Country Brazil
 
Platforms (1)
GPL6426 CAGE Lab - Head and Neck carcinoma cDNA microarray
Samples (46)
GSM259768 Larynx tumor_sample T3_Replicate 1
GSM259769 Larynx tumor_sample T3_Replicate 2
GSM259770 Larynx tumor_sample T7_Replicate 1
Relations
BioProject PRJNA108497

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10288_RAW.tar 380.0 Kb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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