Comment[ArrayExpressAccession]	E-GEOD-40058
MAGE-TAB Version	1.1						
Public Release Date	2013-06-03
Investigation Title	A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells [HuGene-1_0-st]						
Comment[Submitted Name]	A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells [HuGene-1_0-st]
Experiment Description	In this study we performed a systematic evaluation of functional miRNA-mRNA interactions associated with the aggressiveness of breast cancer cells using a combination of integrated miRNA and mRNA expression profiling, bioinformatics prediction, and functional assays. Analysis of the miRNA expression identified 11 miRNAs that were differentially expressed, including 7 down-regulated (miR-200c, miR-205, miR-203, miR-141, miR-34a, miR-183, and miR-375) and 4 up-regulated miRNAs (miR-146a, miR-138, miR-125b1 and miR-100), in aggressive cell lines when compared to normal and less aggressive cell lines. Transient overexpression of miR-200c, miR-205, and miR-375 in MDA-MB-231 cells led to the inhibition of cell migration and invasion. The integrated analysis of miRNA and mRNA expression identified 35 known and novel target genes of miR-200c, miR-205, and mir-375, including CFL2, LAMC1, TIMP2, ZEB1, CDH11, PRKCA, PTPRJ, PTPRM, LDHB, and SEC23A. Surprisingly, the majority of these genes (27 genes) were target genes of miR-200c, suggesting that it plays a more important role in regulating the aggressiveness of breast cancer cells. We characterized one of the target genes of miR-200c, CFL2, and demonstrated that CFL2 is overexpressed in aggressive breast cancer cell lines and can be significantly down-regulated by exogenous miR-200c. Tissue microarray analysis further revealed that CFL2 expression in primary breast cancer tissue correlated with tumor grade. To our knowledge, this study is the first systematic screening of functional miRNA target genes in aggressive breast cancer cells. The results obtained from this study may improve our understanding of the role of these candidate miRNAs and their target genes in relation to breast cancer aggressiveness and ultimately lead to the identification of novel biomarkers associated with prognosis. Affymetrix Gene 1.0 ST arrays were performed according to the manufacturer's directions on RNA extracted from breast cancer cell lines which are treated with miRNA mimic						
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	Shi	Shi	Luo	Harvel			
Person First Name	Huidong	Huidong	Daya	Nikki			
Person Email	hshi@georgiahealth.edu						
Person Affiliation	Georgia Health Sciences University						
Person Phone	706-721-6000						
Person Address	Cancer Center, Georgia Health Sciences University, 1120 15th Street, CN2138, Augusta, GA, USA						
Person Roles	submitter						
Protocol Name	P-GSE40058-1	P-GSE40058-5	P-GSE40058-6	P-GSE40058-2	P-GSE40058-3	P-GSE40058-4	P-GSE40058-7
Protocol Description	CEL files was uploaded into Partek Genomics Suites 6.5 and processed using the mRNA expression pipeline. The data was quantile-normalized, summarized (median polish), and log2-transformed. ID_REF =  VALUE = signal intensities	The cRNA was synthesized using Ambion WT Expression Kit and labeled using Affymetix GeneChip WT Terminal Labeling Kit.	The array hybridization followed the standard affymetrix protocols.	miRNA mimic was transfected into MDA-MB-231 cells using Lipofectamine™ 2000 reagent (Invitrogen).	Breast cancer cell line MDA-MB-231was cultured in DMEM media with 10% fetal bovine serum (FBS).	Total RNA was extracted using Trizol.	The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
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	TRANSFECTED WITH						
Experimental Factor Type	transfected with						
Publication Title	A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells.						
Publication Author List	Luo D, Wilson JM, Harvel N, Liu J, Pei L, Huang S, Hawthorn L, Shi H						
PubMed ID	23497265						
Publication DOI	10.1186/1479-5876-11-57						
Comment[SecondaryAccession]	GSE40058						
Comment[GEOReleaseDate]	2013-06-03						
Comment[ArrayExpressSubmissionDate]	2012-08-11						
Comment[GEOLastUpdateDate]	2013-06-05						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-40058.sdrf.txt