Comment[ArrayExpressAccession]	E-GEOD-51798
MAGE-TAB Version	1.1				
Public Release Date	2014-04-22
Investigation Title	Transcriptional dissection of pancreatic tumors engrafted in mice				
Comment[Submitted Name]	Transcriptional dissection of pancreatic tumors engrafted in mice
Experiment Description	Engraftment of primary pancreas ductal adenocarcinomas (PDAC) in mice to generate patient derived xenograft (PDX) models is a promising platform to for biological and therapeutic studies in this disease. However, these models are still incompletely characterized. Here, we measured the impact of the murine environment on the gene expression of the engrafted human tumoral cells. We have analyzed gene expression profiles from 35 new PDX models and compared them with previously published microarray data from PDAC and hepatocellular carcinoma (HCC). Our results showed that PDX models derived from PDAC, or HCC, were clearly different to the cell lines derived from the same cancer tissues. Indeed, PDAC- and HCC-derived cell lines are indistinguishable one from the other based in their gene expression profiles. In contrast, the transcriptomes of PDAC and HCC PDX models are clearly different and more similar to their original tumor than to PDX models from the other tumor type. Interestingly, the main differences between pancreatic PDX models and human PDAC is the expression of genes involved in pathways related with extracellular matrix interactions and cell cycle regulation likely reflecting the adaptations of the tumors to the new environment. Furthermore, most of these differences are detected in the first passages after the tumor engraftment, indicating early phases of the adaptation process. In conclusion, different from conventional cancer cell lines, PDX models of PDAC retain similar gene expression profiles of PDAC. Expression changes are mainly related to genes involved in stromal pathways likely reflecting the adaptation to new environments. We also provide evidence of the stability of gene expression patterns over subsequent passages. We have analyzed gene expression profiles from 35 new PDX models and compared them with previously published in GEO microarray data. We used PDX models, primary tumors and cell lines from PDAC and hepatocellular carcinoma. All these public data were re-process in order to compare with our 35 samples				
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	Hidalgo	Martínez-García	Valencia	Hidalgo	
Person First Name	Manuel	Raquel	Alfonso	Manuel	
Person Email	mhidalgo@cnio.es				
Person Affiliation	CNIO				
Person Phone	+34917328000				
Person Address	Clinical Research Programme, CNIO, C/Melchor Fernandez Almagro 3, Madrid, Madrid, Spain				
Person Roles	submitter				
Protocol Name	P-GSE51798-1	P-GSE51798-3	P-GSE51798-4	P-GSE51798-2	P-GSE51798-5
Protocol Description	The data were analyzed with frozenRMA (fRMA) using rma and quantile as background correction and normalization methods. ID_REF =  VALUE = fRMA signal intensity	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix).	Following fragmentation, cRNA was hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array.	Extraction of total RNA was performed by using Qiagen mini- RNA kit according to the manufacturer's instructions.	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	ORGANISM PART				
Experimental Factor Type	organism part				
Publication Title	Transcriptional dissection of pancreatic tumors engrafted in mice.				
Publication Author List	Martinez-Garcia R, Juan D, Rausell A, Mu�oz M, Ba�os N, Men�ndez C, Lopez-Casas PP, Rico D, Valencia A, Hidalgo M				
PubMed ID	24739241				
Publication DOI	10.1186/gm544				
Comment[SecondaryAccession]	GSE51798				
Comment[GEOReleaseDate]	2014-04-22				
Comment[ArrayExpressSubmissionDate]	2013-10-28				
Comment[GEOLastUpdateDate]	2014-04-23				
Comment[AEExperimentType]	transcription profiling by array				
Comment[AEExperimentType]	unknown experiment type				
Comment[AdditionalFile:Data1]	GSE51798_PDX_and_PT_data_plus_reprocessed_data.txt				
SDRF File	E-GEOD-51798.sdrf.txt