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Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA and miRNA profiling

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana Bos taurus Mus musculus Rattus norvegicus Saccharomyces cerevisiae Homo sapiens Caenorhabditis elegans Gallus gallus Drosophila melanogaster Macaca mulatta

PROVIDER: GSE18693 | GEO | 2010/05/21

SECONDARY ACCESSION(S): PRJNA121479

REPOSITORIES: GEO

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Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA profiling

Project description:The overall study explores differential sensitivity of estrogen-receptor-positive and -negative breast carcinoma cells to retinoids via gene expression and microRNA profiling in MCF7 and MDA-MB-231 cells. This Series reports results of transcriptional profiling of breast carcinoma cell lines comparing the effects of retinoic acid treatment (6 and 48 hours) on estrogen-receptor-positive (MCF7) and estrogen-receptor-negative (MDA-MB-231) cells. mRNA profiling: Retinoic-acid-treated (1microM) vs vehicle-treated cells, two time points (6 and 48h), two cell lines (MCF7 and MDA-MB-231). Two biological replicates for each condition, balanced dye design.

| S-ECPF-GEOD-18390 | biostudies-other

Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA and miRNA profiling

Project description:This SuperSeries is composed of the following subset Series: GSE18390: Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA profiling GSE18628: MicroRNA profiling shows different response to retinoids in estrogen-receptor positive and negative cells Refer to individual Series

2010-05-21 | E-GEOD-18693 | biostudies-arrayexpress

Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA profiling

2010-05-21 | GSE18390 | GEO

Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA profiling

2010-05-21 | E-GEOD-18390 | biostudies-arrayexpress

mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.

Project description:BackgroundRecent studies have shown that the regulatory effect of microRNAs can be investigated by examining expression changes of their target genes. Given this, it is useful to define an overall metric of regulatory effect for a specific microRNA and see how this changes across different conditions.ResultsHere, we define a regulatory effect score (RE-score) to measure the inhibitory effect of a microRNA in a sample, essentially the average difference in expression of its targets versus non-targets. Then we compare the RE-scores of various microRNAs between two breast cancer subtypes: estrogen receptor positive (ER+) and negative (ER-). We applied this approach to five microarray breast cancer datasets and found that the expression of target genes of most microRNAs was more repressed in ER- than ER+; that is, microRNAs appear to have higher RE-scores in ER- breast cancer. These results are robust to the microRNA target prediction method. To interpret these findings, we analyzed the level of microRNA expression in previous studies and found that higher microRNA expression was not always accompanied by higher inhibitory effects. However, several key microRNA processing genes, especially Ago2 and Dicer, were differentially expressed between ER- and ER+ breast cancer, which may explain the different regulatory effects of microRNAs in these two breast cancer subtypes.ConclusionsThe RE-score is a promising indicator to measure microRNAs' inhibitory effects. Most microRNAs exhibit higher RE-scores in ER- than in ER+ samples, suggesting that they have stronger inhibitory effects in ER- breast cancers.

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Comparison between Estrogen receptor positive and Estrogen receptor negative breast cancer samples

Project description:Comparison between Estrogen receptor positive and Estrogen receptor negative breast cancer samples Keywords: breast cancer type comparison 152 unique breast cancer tissue sample are included in the analysis. The total mRNA has been labeled with Cy5 and then hybridized on a two color arrays against the stratagen Human common reference that was previously labelled with Cy3.

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Integrated miRNA and mRNA profiling of tumor-educated macrophages identifies prognostic subgroups in estrogen receptor-positive breast cancer.

Project description:INTRODUCTION:Various studies have identified aberrantly expressed miRNAs in breast cancer and demonstrated an association between distinct miRNAs and malignant progression as well as metastasis. Even though tumor-associated macrophages (TAM) are known mediators of these processes, little is known regarding their miRNA expression upon education by malignant cells in vivo. METHODS:We profiled miRNA and mRNA expression of in vitro tumor-educated macrophages (TEM) by indirectly co-culturing with estrogen-receptor-positive (ER+) MCF-7 breast cancer cells. The prognostic power of the resulting miRNA list was investigated in primary breast cancer datasets and compared to other signatures. Furthermore, miRNA expression levels were correlated to mRNA expression of macrophage markers and the impact on prognosis was assessed. RESULTS:Through the evaluation of the group effects between differentially-expressed miRNAs and their target mRNAs in TEM, the power of detecting regulated miRNAs was greatly increased. The resulting list of 96 miRNAs predicts disease-free survival (DFS) in external datasets of ER+ breast cancer patients and performs well in comparison with other miRNA signatures. Clustering with the predefined miRNA list revealed a significant difference in survival between the two resulting patient groups. Furthermore, an optimized miRNA list, based on correlations with macrophages markers, proved even more capable at identifying patient clusters significantly differing in DFS. CONCLUSIONS:In vitro profiling of TEM and subsequent bioinformatic verification identified miRNAs with a high prognostic power for DFS when transferred into the clinical setting of primary breast cancer. The resulting miRNAs not only verify previously established findings but also lead to new prognostic markers. Furthermore, our data suggest that TAM contribute to the total miRNA expression profile of ER + breast cancers.

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Comparison between Estrogen receptor positive and Estrogen receptor negative breast cancer samples

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MicroRNA profiling shows different response to retinoids in estrogen-receptor positive and negative cells

Project description:This Series reports results of miRNA profiling of estrogen-receptor-positive (MCF7) and estrogen-receptor-negative (MDA-MB-231) cells. Retinoic Acid (RA) induces mir-21 in MCF-7 but not in MDA-MB-231 cells. MCF-7 and MDA-MB-231 cells were treated (or not) with retinoic acid (RA) and grown for either 6 hours or 48 hours.

2010-05-21 | GSE18628 | GEO

MicroRNA profiling shows different response to retinoids in estrogen-receptor positive and negative cells

2010-05-21 | E-GEOD-18628 | biostudies-arrayexpress