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Series GSE17958 Query DataSets for GSE17958
Status Public on Oct 04, 2009
Title Affymetrix SNP array data for 47 lung squamous cell carcinoma and 40 esophageal squamous cell carcinoma samples.
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Lineage-survival oncogenes are targeted by gene amplification in cancers arising from the tissues where these genes play a role in normal development. Here we show that the transcription factor SOX2—previously known to be mutated in hereditary human esophageal malformations, to be necessary for normal esophageal squamous development, to promote proliferation of basal tracheal cells and to co-operate in induction of pluripotent stem cells -- acts as an amplified oncogene in squamous cell carcinomas (SCC) of the lung and esophagus. We identified SOX2 at a peak of genomic amplification on chromosome 3q26.33 in SCCs of both the lung and esophagus but did not find it to be significantly amplified in adenocarcinomas from these tissues. Tumors with SOX2 amplification showed higher SOX2 mRNA expression, and suppression of SOX2 by RNAi in lung and esophageal SCC cell lines revealed that SOX2 expression is required for proliferation and anchorage-independent growth. Furthermore, ectopic expression of SOX2 cooperated with FOXE1 or FGFR2 to transform immortalized tracheobronchial epithelial cells. SOX2-driven tumors showed expression of markers of both squamous differentiation and pluripotency. These observations identify SOX2 as a novel lineage survival oncogene in lung and esophageal SCC and suggest novel connections between development, pluripotency and carcinogenesis.
Overall design SNP array experiments were performed on 87 tumor samples and cell lines. Tumor Samples were normalized against a reference panel of 1140 normal samples using tangent normalization.
Contributor(s) Bass A, Ramos A
Citation(s) 19801978
Submission date Sep 03, 2009
Last update date Aug 21, 2013
Contact name Adam Joel Bass
Organization name Dana-Farber Cancer Institute
Street address 44 Binney Street
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (87)
GSM449583 Lung squamous cell carcinoma sample 12T
GSM449584 Lung squamous cell carcinoma sample 13T
GSM449585 Lung squamous cell carcinoma sample 15T
BioProject PRJNA119921

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
GSE17958_RAW.tar 2.3 Gb (http)(custom) TAR (of CEL)
GSE17958_abass_tangent_files.tar.gz 426.2 Mb (ftp)(http) TAR
Raw data provided as supplementary file
Processed data included within Sample table

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