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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human CEACAM1-S wild-type or double-A mutant MCF7 cells to identify genes inoved in lumen formation

ABSTRACT: Identification of genes involved in lumen formation: gene chip analysis was performed on mRNA isolated from both wild type and T457A,S459A mutated CEACAM1-4S transfected MCF7 cells grown in Matrigel Experiment Overall Design: Microarray analysis of RNA isolated from MCF7 cells transfected with CEACAM1-S wild-type (SW) or CEACAM1-S double-A mutant T457A,S459A (DA) grown in Matrigel for 4 days

ORGANISM(S): Homo sapiens

SUBMITTER: Xiwei Wu

PROVIDER: E-GEOD-17540 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Invasion-mediating genes in breast cancer

Project description:From the parental breast cancer cell line MCF7 (weakly invasive), we progressively selected hyperinvasive subclones. We compared the gene expression between the parental MCF7-I0 and the hyper-invasive cells MCF7-I6. We used Affymetrix U133 Plus 2 microarrays to detail the global programme of gene expression underlying weakly and highly invasive breast cancer cells derived from the human breast cancer cell line MCF7. The hyper-invasive subclones were selected using Matrigel invasion chambers as a model for the invasion process in vivo. The cells that invaded through the membrane were cultured and re-introduced into an additional invasion assay. This methodology was repeated to give rise to a subclone of MCF7 cells that had invaded six times; these were termed MCF7-I6 cells. The invasive capacity of MCF7-I6 cells was shown to be more than 11 times greater than the parental cells, which we denote as MCF7-I0. Thus, these hyper-invasive cells were present within the heterogeneous population, and we speculated that differences in gene expression between the MCF7-I6 cells and the parental cells MCF7-I0 may be involved in the invasion process.

2011-12-10 | E-GEOD-17889 | biostudies-arrayexpress

Gene expression analysis of MCF7 breast cancer cells cultured as xenografts, in two dimensional cultures, in polyHEMA anchorage independent three dimansional cell culture models and in Matrigel three dimensional cultures.

Project description:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures. Gene expression analysis of MCF7 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.

2013-10-30 | E-GEOD-47583 | biostudies-arrayexpress

Identification of genes involved in CEACAM1-4S mediated lumen formation in a 3D model of mammary morphogenesis

Project description:Identification of genes involved in lumen formation: gene chip analysis was performed on mRNA isolated from both wild type and T457A,S459A mutated CEACAM1-4S transfected MCF7 cells grown in Matrigel

2009-10-01 | GSE17540 | GEO

Effect of knock down of LASP-1 on luminal breast cancer cells (MCF7)

Project description:Nuclear LASP-1 has a direct correlation with the overall survival of breast cancer patients. Gene expression analysis of MCF7 human breast cancer cells cultured in 3D-Matrigel was performed. Up regulation of cell junction proteins, extracellular matrix proteins and down regulation of MMP 9 and 2 were observed. This corroborates well with the involvement of LASP-1 in cell migration and chemotaxis. Non-silencing (control) and LASP-1 knock down MCF7 cells were cultured on 3D-Matrigel, total RNA was extracted and anlyzed - 4 biological replicates each. The first biological replicate was done as a pilot. Biological replicates 2-4 were run as a second set after pilot.

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Cyclin D1 determines estrogen dependent signaling in human breast cancer cell line MCF7

Project description:The CCND1 gene, which is frequently overexpressed in cancers, encodes the regulatory subunit of a holoenzyme that phosphorylates the retinoblastoma protein (pRb). It is known that cyclin D1 regulates ERM-NM-1 transactivation using heterologous reporter systems, the significance of this observation to E2 dependent gene activation is unknow. E2 stimulated MCF7 cells treated with cyclin D1 siRNA in order to analyze the genes regulated by estradiol in a cyclin D1 dependent manner. Hormone deprived MCF7 cells were treated with cyclin D1 siRNA or control siRNA and stimulated with E2 or vehicle Four separate 10cm plates of MCF7 cells treated with control siRNA were compared to four 10cm plates of MCF7 cells treated with cyclin D1 siRNA. 2 plates in each group treated with vehicle and two plates treated with E2.

2013-07-18 | E-GEOD-48989 | biostudies-arrayexpress

Timecourse total transcriptome sequencing of MCF10A cells undergoing acinus formation.

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Enzymatic Methyl-seq (EM-seq) of doxycycline induced tumor and residual mouse primary mammary epithelial cells grown in 3D cell cultures against non-induced controls

Project description:This experiment investigates the genome wide DNA methylation landscape of residual breast cancer cells. Primary mammary epithelial cells taken from female mice with doxycycline-inducible hMyc- and Neu/Her2-oncogenes were grown in 3D organoid cultures. Upon the addition of doxycycline (200ng/mL) to the medium the expression of the oncogenes gets activated and the cells start uncontrolled proliferation resembling tumor growth. Tumor samples were taken after 5 days of oncogene induction. Subsequently, doxycycline was removed from the medium, which silences oncogene expression and results in rapid tumor regression. Residual samples reminiscent to the non-induced (normal) structures were taken after 7 days of de-induction (12 days overall). Non-induced structures were grown and sampled in parallel to the residual structures.

2021-10-03 | E-MTAB-10979 | biostudies-arrayexpress

H3K27me3 ChIP-seq profiling in MCF7 cell lines under hypoxia

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2014-09-26 | E-GEOD-61740 | biostudies-arrayexpress

Transcription profiling of human mammary epithelial cells with MycER activation using 4-hydroxytamoxifen following growth in 2D monoloyers with or without EGF and insulin or in 3D Matrigel culture

Project description:MCF10A MycER cells were grown either on 2D monolayer culture in the presence of complete growth medium, in the absence of EGF and insulin or in 3D Matrigel culture for 20 days to form acinar structures. MycER was activated with 4-hydroxytamoxifen (4-OHT) in all samples for 2 or 48 h. Control cells were treated with ethanol. The aim of the study was to explore the effect of different growth conditions on gene expression changes in response to c-Myc activation.

2006-12-31 | E-MEXP-765 | biostudies-arrayexpress

Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with Eralpha

Project description:Background: The ZNF217 gene, encoding a C2H2 zinc finger protein, is located at 20q13 and found amplified and overexpressed in greater than 20% of breast tumors. Current studies indicate ZNF217 drives tumorigenesis, yet the regulatory mechanisms of ZNF217 are largely unknown. Because ZNF217 associates with chromatin modifying enzymes, we postulate that ZNF217 functions to regulate specific gene signaling networks. Here, we present a large-scale functional genomic analysis of ZNF217, which provides insights into the regulatory role of ZNF217 in MCF7 breast cancer cells. Results: ChIP-seq analysis reveals that the majority of ZNF217 binding sites are located at distal regulatory regions associated with the chromatin marks H3K27ac and H3K4me1. Analysis of ChIPseq transcription factor binding sites shows clustering of ZNF217 with FOXA1, GATA3 and ERalpha binding sites, supported by the enrichment of corresponding motifs for the ERalpha-associated cisregulatory sequences. ERalpha expression highly correlates with ZNF217 in lysates from breast tumors (n=15), and ERalpha co-precipitates ZNF217 and its binding partner CtBP2 from nuclear extracts. Transcriptome profiling following ZNF217 depletion identifies differentially expressed genes co-bound by ZNF217 and ERalpha; gene ontology suggests a role for ZNF217-ERalpha in expression programs associated with ER+ breast cancer studies found in the Molecular Signature Database. Data-mining of expression data from breast cancer patients correlates ZNF217 with reduced overall survival in multiple subtypes. Conclusions: Our genome-wide ZNF217 data suggests a functional role for ZNF217 at ERalpha target genes. Future studies will investigate whether ZNF217 expression contributes to aberrant ERalpha regulatory events in ER+ breast cancer and hormone resistance Differential RNA-seq profiling from triplicate biological replicates of MCF7 cells treated with scrambled siRNA or siZNF217.

2014-06-15 | E-GEOD-58326 | biostudies-arrayexpress

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