Comment[ArrayExpressAccession]	E-GEOD-51549
MAGE-TAB Version	1.1						
Public Release Date	2013-12-13
Investigation Title	All trans-retinoic acid (ATRA) re-differentiate early transformed breast epithelial cells to normal.						
Comment[Submitted Name]	All trans-retinoic acid (ATRA) re-differentiate early transformed breast epithelial cells to normal.
Experiment Description	Retinoids have been used as potential chemotherapeutic or chemo-preventive agents because of their differentiation, anti-proliferative, pro-apoptotic, and anti-oxidant effects. We investigated the effect of all trans- retinoic acid (ATRA) at different stages of the neoplastic transformation using an in vitro model of breast cancer progression. This model was previously developed by treating the human normal-like breast epithelial MCF-10F cells with high dose of estradiol and consist of five cell lines which shown a progressive neoplastic transformation: MCF-10F (normal stage), trMCF (premalignant stage), bsMCF (invasive stage) and caMCF (tumorigenic stage).  In 3D-cultures, MCF-10F cells form tubules resembling the normal mammary gland although after treatment with high doses of estradiol, trMCF cells, formed tubules and, spherical masses which are an indication of cell transformation. By ring cloning, trMCF clone 11 which only formed spherical masses in collagen was isolated. Our results showed that the early transformed trMCF clone 11 cells shown a reduction of spherical masses and increased of tubules in collagen after being treated with 10-5M (10M-BM-5M) and 10-6M (1M-BM-5M) ATRA; the number of tubules was higher in cells treated with 10-6M ATRA  (43%  vs. 10% tubules). The invasive bsMCF and tumorigenic caMCF cells did not shown any changes in morphology after ATRA treatment. Analysis of expression studies in early transformed cells treated with 10-6M ATRA showed that 271 probes upregulated in trMCF clone 11 cells were downregulated after ATRA treatment and, 316 probes that were downregulated were upregulated after ATRA treatment in these cells to similar levels than the normal breast epithelial cells MCF-10F.  These genes were involved in the aryl hydrocarbon receptor signaling, RAR Activation, xenobiotic metabolisms signaling, molecular mechanisms of cancer and cell morphology. Our results shown that ATRA was able to re-differentiate transformed cells at early stages of the neoplastic process suggesting that ATRA could potentially be used to inhibit the progression of premalignant lesions of the breast such as ductal carcinoma in situ (DCIS). We investigated the effect of all trans- retinoic acid (ATRA) at different stages of the neoplastic transformation using an in vitro model of breast cancer progression. This model was previously developed by treating the human normal-like breast epithelial MCF-10F cells with high dose of estradiol and consist of five cell lines which shown a progressive neoplastic transformation: MCF-10F (normal stage), trMCF (premalignant stage), bsMCF (invasive stage) and caMCF (tumorigenic stage).						
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	Fernandez	Arisi	Staker	Addya	Huang	Fernandez	
Person First Name	Sandra	Maria	Rebecca	Sankar	Yong	Sandra	
Person Mid Initials	Viviana	F	A			V	
Person Email	Sandra.Fernandez@jefferson.edu						
Person Affiliation	Thomas Jefferson University						
Person Phone	(215) 503-7783						
Person Address	Medical Oncology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA, USA						
Person Roles	submitter						
Protocol Name	P-GSE51549-1	P-GSE51549-5	P-GSE51549-6	P-GSE51549-2	P-GSE51549-3	P-GSE51549-4	P-GSE51549-7
Protocol Description	Background correction and normalization were done using Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 2-fold (p-value<0.05) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses. ID_REF =  VALUE = Iterative Plier 16 normalized data	5 ug cDNAs were fragmented and chemically labeled with biotin to generate biotinylated cDNA using FL-Ovation biotin module (NuGen Technologies, Inc.).	Affymetrix U133 Plus 2.0 human oligonucleotide microarrays (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (5 ug) in 220 ul of hybridization cocktail. Target denaturation was performed at 99M-0C for 2 min. and then 45M-0C for 5 min, followed by hybridization for 18 h.	To study the effect of ATRA, trMCF clone 11 cells were treated continuously for 26 days with 10-5M to 10-8M ATRA and the media was replaced daily. As control, the cells were treated with 0.1% DMSO (vehicle).	The human breast epithelial cells were grown in vitro as described elsewhere (Fernandez et al, 2010, Mutat Res 688:28-35)	RNA was isolated from the breast epithelial cells using RNAeasy Mini Kit (Qiagen) manufacturerM-bM-^@M-^Ys protocol.	Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
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	TREATMENT	DISEASE STATE					
Experimental Factor Type	treatment	disease state					
Comment[SecondaryAccession]	GSE51549						
Comment[GEOReleaseDate]	2013-12-13						
Comment[ArrayExpressSubmissionDate]	2013-10-22						
Comment[GEOLastUpdateDate]	2014-01-09						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-51549.sdrf.txt