Comment[ArrayExpressAccession]	E-GEOD-39297
MAGE-TAB Version	1.1						
Public Release Date	2014-04-07
Investigation Title	PEA15 regulates the DNA damage induced cell cycle checkpoint and oncogene-directed transformation						
Comment[Submitted Name]	PEA15 regulates the DNA damage induced cell cycle checkpoint and oncogene-directed transformation
Experiment Description	Regulation of the DNA damage response and cell cycle progression is critical for maintaining genome integrity. Here we report that in response to DNA damage, COPS5 deubiquitinates and stabilizes PEA15 in an ATM kinase-dependent manner. PEA15 expression oscillates throughout the cell cycle, and the loss of PEA15 accelerates cell cycle progression by activating CDK6 expression via the c-JUN transcription factor. Cells lacking PEA15 exhibit a DNA damage-induced G2/M checkpoint defect due to increased CDC25C activity and consequentially higher CDK1/Cyclin B activity and accordingly have an increased rate of spontaneous mutagenesis. We find that oncogenic RAS inhibits PEA15 expression and ectopic PEA15 expression blocks RAS-mediated transformation, which can be partially rescued by ectopic expression of CDK6. Finally, we show that PEA15 expression is down regulated in colon, breast and lung cancer samples. Collectively, our results demonstrate that tumor suppressor PEA15 is a regulator of genome integrity and is an integral component of the DNA damage response pathway that regulates cell cycle progression, the DNA-damage-induced G2/M checkpoint and cellular transformation. HCT116 cells stably expressing a non-silencing shRNA or two individual shRNAs against PEA15 were used to prepare the total RNA, which was then used to analyze for gene expression using Illumina expression array.						
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	wajapeyee	Nagarajan	Dogra	Liu	Green	Wajapeyee	
Person First Name	narendra	Arvindhan	Shaillay	Alex	Michael	Narendra	
Person Mid Initials				Y	R		
Person Email	narendra.wajapeyee@yale.edu						
Person Affiliation	Yale University						
Person Phone	203-737-5070						
Person Address	Department of Pathology, Yale University, LH-214A, 310 Cedar Street, New Havem, CT, USA						
Person Roles	submitter						
Protocol Name	P-GSE39297-1	P-GSE39297-5	P-GSE39297-6	P-GSE39297-2	P-GSE39297-3	P-GSE39297-4	P-GSE39297-7
Protocol Description	Signal intensities of probes were log2-transformed and Quantile normalized (lumi package in R/Bioconductor) ID_REF =  VALUE = Log2 transformed and Quantile-Normalized Signal Intensity  (lumi package in R/Bioconductor) Detection Pval = 	Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays	Standard Illumina hybridization protocol	HCT116 cells that either expressed Non-silencing shRNA (NS shRNA) or shRNAs targeting PEA15 (PEA15 shRNA #1 and PEA15 shRNA #2 were used for preparing the total RNA and to perfrom gene expression array.	HCT116 NS shRNA, HCT16 PEA15 shRNA#1 and HCT116 PEA15 shRNA #2 cell lines were grown in DEMEM media with 10% Fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition	Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instruction	Standard Illumina scanning protocol
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	SHRNA						
Experimental Factor Type	shRNA						
Comment[SecondaryAccession]	GSE39297						
Comment[GEOReleaseDate]	2014-04-07						
Comment[ArrayExpressSubmissionDate]	2012-07-12						
Comment[GEOLastUpdateDate]	2014-04-07						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE39297_matrix_non-normalized_data.txt						
SDRF File	E-GEOD-39297.sdrf.txt