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Gene expression profiles induced by shRNA-mediated knockdown of PDEF in MCF7 mammary epithelial cell line

ABSTRACT: Microarray gene expression analysis was performed in MCF7 cells transduced with a non-specific shRNA or PDEF-targeting shRNA, and both subjected to hormone depletion for 48 hours. Analyses of differentially expressed genes combined with gene ontology revealed a downregulation of cell cycle related-genes and an upregulation of apoptosis-related genes in PDEF knockdown cells. These target genes constitute potential effectors of the pro-survival role of PDEF.

ORGANISM(S): Homo sapiens

PROVIDER: GSE40985 | GEO | 2014/03/29

SECONDARY ACCESSION(S): PRJNA175497

REPOSITORIES: GEO

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Gene expression profiles induced by shRNA-mediated knockdown of PDEF in MCF7 mammary epithelial cell line

Project description:Microarray gene expression analysis was performed in MCF7 cells transduced with a non-specific shRNA or PDEF-targeting shRNA, and both subjected to hormone depletion for 48 hours. Analyses of differentially expressed genes combined with gene ontology revealed a downregulation of cell cycle related-genes and an upregulation of apoptosis-related genes in PDEF knockdown cells. These target genes constitute potential effectors of the pro-survival role of PDEF. Four samples were harvested after lentiviral infection with either non-specific shRNA control or PDEF-targetting shRNA. All samples were subjected to hormone depletion for 48 hours. Each condition was performed in duplicate

2014-03-29 | E-GEOD-40985 | biostudies-arrayexpress

CEACAM6 is a PDEF induced gene in breast cancer

Project description:Identifying PDEF regulated genes may shed light on the mechanism by which PDEF may induce breast cancer progression. To that purpose, we have used the MCF-7 human breast tumor cell line model to identify PDEF induced genes. Briefly, PDEF expression was down regulated by shRNA in MCF-7 cells and RNA probes from PDEF-down regulated and control MCF-7 cells were used to screen the Affymetrics HG-U133A Gene Chips. This analysis found 62 genes that were induced 2-fold or higher by PDEF. Further analysis of 3 of these genes namely S100A7, CEACAM6 and B7-H4 in primary breast tumors showed CEACAM6 as a frequently elevated and co-exressed gene with PDEF in these tumors. We previously reported a role for PDEF (prostate derived Ets transcription factor) in breast tumor progression and its association with poor clinical outcome in ER+ breast cancer. To gain further insights into PDEF action in breast cancer, we down regulated PDEF expression by shRNA in MCF-7 human breast tumor cell line, and screened the HG-U133A human gene chips with probes from PDEF down-regulated and control MCF-7 cells. This analysis identified CEACAM6 as one of the genes induced by PDEF. Further analysis of CEACAM6 expression in relation to PDEF in 93 ER+ primary breast tumors showed largely concordant expression of these molecules. To our knowledge, our findings of CEACAM6 as a PDEF induced gene and their elevated co-expression in breast cancer have not been described before.

2012-05-01 | GSE37662 | GEO

CEACAM6 is a PDEF induced gene in breast cancer

2012-04-30 | E-GEOD-37662 | biostudies-arrayexpress

Expression data from MCF7 cells: control or tuberin-depleted

Project description:Analysis of the expression profiles of MCF7 cells transduced with a control shRNA and an TSC2-targeted shRNA (leading to tuberin depletion).

2015-04-28 | GSE68324 | GEO

Expression data from MCF7 cells: control or tuberin-depleted

Project description:Analysis of the expression profiles of MCF7 cells transduced with a control shRNA and an TSC2-targeted shRNA (leading to tuberin depletion). MCF7 cells were cultured in standard conditions, transduced, selected with puromycin (pLKO.1 shRNA vectors) and processed for expression profiling.

2015-04-28 | E-GEOD-68324 | biostudies-arrayexpress

Identification of a PDEF regulatory network that inhibits prostate cancer metastasis

Project description:To investigate the role of PDEF in prostate cancer metastasis, we employed microarray analysis of PC3 cells ectopically expressing a pBABE vector control (PC3-SCR) or PDEF-containing vector (PC3-PDEF).

2020-01-24 | GSE108641 | GEO

Gene expression profiles induced by overexpression of PDEF in MCF10A mammary epithelial cell line

Project description:Recent studies suggest that PDEF is required for secretory cell differentiation in several epithelial tissues. To investigate PDEF in the mammary gland, we examined the effect of this transcription factor on gene expression using microarray based profiling of MCF-10A cells. These cells are non-transformed mammary epithelial cells that express protein and gene expression programs of basal epithelial cells and undetectable levels of endogenous PDEF. Bioinformatics analysis of the genes induced or repressed by PDEF overexpression in MCF10A cells revealed a striking effect on expression of luminal and myoepithelial cell markers.

2014-03-29 | GSE40986 | GEO

Prostate cancer cell line with slienceing of PDEF or control (GFP) gene using siRNA.

Project description:PDEF(Prostate Derived Ets factor) is a member of Ets transcription factor with specific expression in Prostate. We identified target genes for PDEF in prostate cancer cell line PC-3 using Affymetrix Genechip Microarray technology. Keywords: target gene identification for transcription factor

2007-12-20 | GSE6576 | GEO

Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description:In order to investigate the role of reptin methylation on the expression of hypoxia-responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shRNA) or reptin shRNA (shreptin) in normoxic and hypoxic conditions. MCF7 cells were transiently transfected with either non-specific shRNA or reptin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 18 hours. Cells were then lysed and RNA was isolated.

2010-07-13 | E-GEOD-15530 | biostudies-arrayexpress

Gene expression profiles induced by overexpression of PDEF in MCF10A mammary epithelial cell line

2014-03-29 | E-GEOD-40986 | biostudies-arrayexpress

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