Comment[ArrayExpressAccession]	E-GEOD-42781						
MAGE-TAB Version	1.1						
Public Release Date	2013-10-22						
Investigation Title	A Splice Variant of HER2 Activates Key Signaling Cascades and Evokes Mammary Tumors and Metastases						
Comment[Submitted Name]	A Splice Variant of HER2 Activates Key Signaling Cascades and Evokes Mammary Tumors and Metastases						
Experiment Description	The Epidermal Growth Factor Receptor 2 (ERBB2 or HER2) is amplified and overexpressed in approximately 20% of invasive breast cancers and is associated with metastasis and poor prognosis. Here we describe the role of a constitutively active splice variant of HER2 (Delta-HER2) in human mammary epithelial cells. Overexpression of Delta-HER2 in human mammary cells decreased apoptosis and increased proliferation and expression of epithelial-to-mesenchymal markers. It also induced invasion in three-dimensional cultures and promoted tumorigenicity and metastasis in vivo. In contrast, similar overexpression of wild-type HER2 failed to evoke the same effects. Unbiased protein-tyrosine phosphorylation profiling revealed a significant increase in phosphorylation of several key signaling proteins upon Delta-HER2 expression, some of which not previously shown to belong to the HER2 pathway. In addition, microarray analysis revealed the expression of a set of genes specifically associated with Delta-HER2 expression. We found those genes to be highly expressed in ER-negative, high grade and metastatic primary breast tumors. Altogether, these results provide new insights into the function of a tumorigenic splice variant of HER2 and the signaling cascade deriving from its activity RNA was extracted from MCF10A expressing empty vector, WT-HER2 or Delta-HER2 (n=3).						
Term Source Name	ArrayExpress	EFO					
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Roloff	Alajati	Bentires-Alj	Duss	Thiry	Roloff	
Person First Name	Tim	Abdullah	Mohamed	Stephan	Stephane	Tim	
Person Mid Initials						C	
Person Email	tim.roloff@fmi.ch						
Person Affiliation	FMI						
Person Address	Functional Genomics, FMI, Maulbeerstrasse 66, Basel, Switzerland						
Person Roles	submitter						
Protocol Name	P-GSE42781-1	P-GSE42781-5	P-GSE42781-6	P-GSE42781-2	P-GSE42781-3	P-GSE42781-4	P-GSE42781-7
Protocol Description	Expression values were normalized and probeset-level values calculated with robust multi-array average (RMA) as implemented in the R/Bioconductor package affy (R version 2.14) ID_REF =  VALUE = RMA normalized log2 expression values	GeneChip WT cDNA Synthesis Kit and a GeneChip WT Terminal Labeling Kit (Affymetrix)	Hybridized for 16 h to GeneChip Human Gene 1.0 ST arrays (Affymetrix)	Prior anaylysis the cells were grown for 16 hours in DMEM/F12 medium supplemented with 100 IU/ml penicillin, and 100 µg/ml streptomycin	MCF10A cells were cultured in DMEM/F12 medium (Invitrogen) supplemented with 5% horse serum (Hyclone), 20 ng/ml epidermal growth factor (EGF) (Peprotech), 0.5 µg/ml hydrocortisone (Sigma), 100 ng/ml cholera toxin (Sigma), 10 µg/ml insulin (Sigma), 100 IU/ml penicillin, and 100 µg/ml streptomycin. For 3D cultures, DMEM/F12 medium was supplemented with 2% horse serum, 5 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 µg/ml insulin, 100 IU/ml penicillin, and 100 µg/ml streptomycin	RNA was extracted with TRIzol reagent (Sigma)	GeneChip Scanner 3000 with an autoloader according to the manufacturer’s instructions
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	phenotype						
Experimental Factor Type	phenotype						
Publication Title	Mammary tumor formation and metastasis evoked by a HER2 splice variant.						
Publication Author List	Alajati A, Sausgruber N, Aceto N, Duss S, Sarret S, Voshol H, Bonenfant D, Bentires-Alj M						
PubMed ID	23867476						
Publication DOI	10.1158/0008-5472.CAN-12-3186						
Comment[SecondaryAccession]	GSE42781						
Comment[GEOReleaseDate]	2013-10-22						
Comment[ArrayExpressSubmissionDate]	2012-12-06						
Comment[GEOLastUpdateDate]	2013-10-22						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-42781.sdrf.txt