Gene expression profiling of MCF-7 cells treated with 6-shogaol
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Leong Chee-Onn
PROVIDER: S-ECPF-GEOD-36973 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description:A total of 18 genes were up-regulated and 11 genes were down-regulated > 2-fold following 6-shogaol treatment
2012-09-01 | GSE36973 | GEO
Project description:A total of 18 genes were up-regulated and 11 genes were down-regulated > 2-fold following 6-shogaol treatment Microarray experiments were performed in duplicate as follows: MCF-7 cells were treated with 10 uM of 6-shogaol or control vehicle (0.1% DMSO) for 48 h. Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturersM-bM-^@M-^Y protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm. The microarray hybridizations were carried out using the Affymetrix Human Gene 1.0 ST arrays.
2012-09-01 | E-GEOD-36973 | biostudies-arrayexpress
Project description:Blackcurrants (Ribes nigrum L., Grossulariaceae) have a high content of anthocyanin polyphenols and these have been shown to have beneficial effects on health, owing to their antioxidant and anti-carcinogenic properties. This study analyzed the constituents of blackcurrant extract (BCE) and investigated its potential phytoestrogenic effects using a breast cancer cell line (MCF-7) overexpressing the estrogen receptor (ER) α. Microarray and ingenuity pathway analysis showed that BCE activated upstream genes such as ERα and transforming growth factor beta 1, and upregulated the expression of many genes downstream of ERα. MCF-7 cells were seeded in culture dish and maintain to confluent. Then medium replace with phenol-red-serum-free DMEM medium with or without BCE (50μg/ml). After the cells were incubated for 24 h at 37 °C 5% CO2.
| S-ECPF-GEOD-58304 | biostudies-other
Project description:Lacciac Acid A was indentified as an inhibitor of DMNT1. MCF-7 cells were treated with Lacciac Acid A (200 uM) for 5 days. Changes in gene expression were identified by using Affymetrix Human gene ST1.0 arrays. We used microarrays to determine global changes in gene expression upon treatment with Lacciac Acid A an inhibitor of DMNT1. MCF-7 cells near mid passage were treated with Lacciac Acid A for 5 days. RNA was extracted and hybridized on Affymetrix microarrays. Treated and untreated cells were from the same cell passage. Two sample sets from the same passage and the third set from the previous passage were used.
| S-ECPF-GEOD-45804 | biostudies-other
Project description:Cadmium (Cd2+) is an environmental toxicant and a human carcinogen. Several studies show an association of Cd2+ exposure to the development of breast cancer. Previously, we have transformed the immortalized non-tumorigenic cell line MCF-10A with Cd2+ and have demonstrated that the transformed cells have anchorage independent growth. In a separate study, we showed that transformation of the immortalized urothelial cells with the environmental carcinogen arsenite (As3+) results in an increase in expression of genes associated with the basal subtype of bladder cancer. In this study, we determined if transformation of the MCF-10A cells with Cd2+ would have a similar effect on the expression of basal genes. The results of our study indicate that there is a decrease in expression of genes associated with keratinization and cornification and this gene signature includes the genes associated with the basal subtype of breast cancer. An analysis of human breast cancer databases indicates an increased expression of this gene signature is associated with a positive correlation to patient survival whereas a reduced expression/absence of this gene signature is associated with poor patient survival. Thus, our study suggests that transformation of the MCF-10A cells with Cd2+ produces a decreased basal gene expression profile that correlates to patient outcome.
| S-EPMC7533076 | biostudies-literature
Project description:The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and the archetype of a molecular therapeutic target. We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells. Combining this unique resource with gene expression data demonstrates distinct temporal mechanisms of estrogen-mediated gene regulation,particularly in the case of estrogen-suppressed genes. Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer. Experiment Overall Design: This Series currently contains the gene expression data accompaning Carroll JS et al. Nature Genetics 38,1289-1297(2006). MCF7 cells were stimulated with 100 nM estrogen for 0, 3, 6, or 12h. All experiments were performed in triplicate.
| S-ECPF-GEOD-11324 | biostudies-other
Project description:Microarray technology (Human OneArray microarray, phylanxbiotech.com) was used to compare gene expression profiles of non-invasive MCF-7 and invasive MDA-MB-231 breast cancer cells exposed to dioscin (DS), a steroidal saponin isolated from the roots of wild yam, (Dioscorea villosa). Initially the differential expression of genes (DEG) was identified which was followed by pathway enrichment analysis (PEA). Of the genes queried on OneArray, we identified 4641 DEG changed between MCF-7 and MDA-MB-231 cells (vehicle-treated) with cut-off log2 |fold change|≧1. Among these genes, 2439 genes were upregulated and 2002 were downregulated. DS exposure (2.30 μM, 72 h) to these cells identified 801 (MCF-7) and 96 (MDA-MB-231) DEG that showed significant difference when compared with the untreated cells (p<0.05). Within these gene sets, DS was able to upregulate 395 genes and downregulate 406 genes in MCF-7 and upregulate 36 and downregulate 60 genes in MDA-MB-231 cells. Further comparison of DEG between MCF-7 and MDA-MB-231 cells exposed to DS identified 3626 DEG of which 1700 were upregulated and 1926 were down-regulated. Regarding to PEA, 12 canonical pathways were significantly altered between these two cell lines. However, there was no alteration in any of these pathways in MCF-7 cells, while in MDA-MB-231 cells only MAPK pathway showed significant alteration. When PEA comparison was made on DS exposed cells, it was observed that only 2 pathways were significantly affected. Further, we identified the shared DEG, which were targeted by DS and overlapped in both MCF-7 and MDA-MB-231 cells, by intersection analysis (Venn diagram). We found that 7 DEG were overlapped of which six are reported in the database. This data highlight the diverse gene networks and pathways in MCF-7 and MDA-MB-231 human breast cancer cell lines treated with dioscin.
| S-EPMC4905937 | biostudies-literature
Project description:BACKGROUND: The goal of this study was to evaluate changes in gene expression in SW-620 cells in response to SN-38 in order to further elucidate the mechanisms by which SN-38 causes apoptosis and cell cycle arrest. METHODS: We used a quantitative gene expression microarray assay to identify the genes regulated by SN-38 treatment in colon cancer cells and confirmed our results with RT-PCR. By gene expression profiling, we first screened a proprietary list of about 22,000 genes. RESULTS: Treatment with SN-38 cells resulted in two-fold or greater alteration in the level of expression of 192 genes compared to control treatment. Most of the affected genes were not known to be responsive to SN-38 prior to this study. SN-38 treatment of these cells was found to affect the expression of various genes involved in DNA replication, transcription, signal transduction, growth factors, cell cycle regulation, and apoptosis, as well as other genes with unknown function. Changes in expression of 14 genes were confirmed by quantitative real-time polymerase chain reaction (RT-PCR). CONCLUSION: This study leads to an increased understanding of the biochemical pathways involved in SN-38-induced apoptosis and possibly to the identification of new therapeutic targets.
| S-EPMC1368997 | biostudies-literature
Project description:Traditional Chinese medicines (TCM), usually composed of a mixture of components, may simultaneously target multiple genes/pathways and thus achieve superior efficacy for complex diseases such as cancer. To identify novel mechanisms of action and potential health benefits for a TCM formula Si-Wu-Tang (SWT) widely used for women’s health, we obtained the DNA microarray expression profiles for SWT, its active component ferulic acid, and estradiol in human breast cancer cell line MCF-7 and analyzed the gene expression signatures associated with each treatment using the “Connectivity Map” (cMAP). This study indicates that DNA microarray profiling analysis and cMAP data mining provide a powerful approach to discover unknown mechanisms of actions and identify potential new health benefits for TCM. We profiled the gene expression of MCF-7 cell lines to SWT, its active component FA, as well as estradiol using Affymetrix human genome U133 plus 2.0 arrays. The data set includes profiles for 24 samples, divided into eight groups of treatment: 0.001% DMSO used as the vehicle control (C), 0.1 µM estradiol (EM), FA at three concentrations (0.1, 1, and 10 µM) (FL, FM and FH) and SWT at three concentrations (0.0256, 0.256, and 2.56 mg/ml) (SL, SM and SH). For each treatment group, 3 biological replicates were included, resulting in 24 (8 groups × 3 replicates/group) RNA samples.
| S-ECPF-GEOD-23610 | biostudies-other
Project description:Among the eight naturally occurring vitamin E analogs, ?-tocotrienol (GT3) is a particularly potent radioprophylactic agent in vivo. Moreover, GT3 protects endothelial cells from radiation injury not only by virtue of its antioxidant properties but also by inhibition of 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase and by improving the availability of the nitric oxide synthase cofactor tetrahydrobiopterin. Nevertheless, the precise mechanisms underlying the superior radioprotective properties of GT3 compared with other tocols are not known. This study, therefore, examined the differences in gene expression profiles between GT3 and its tocopherol counterpart, ?-tocopherol, as well as between GT3 and ?-tocopherol in human endothelial cells. Cells were treated with vehicle or the appropriate tocol for 24 h, after which total RNA was isolated and genome-wide gene expression profiles were obtained using the Illumina platform. GT3 was far more potent in inducing gene-expression changes than ?-tocopherol or ?-tocopherol. In particular, GT3 induced multiple changes in pathways known to be of importance in the cellular response to radiation exposure. Affected GO functional clusters included response to oxidative stress, response to DNA damage stimuli, cell cycle phase, regulation of cell death, regulation of cell proliferation, hematopoiesis, and blood vessel development. These results form the basis for further studies to determine the exact importance of differentially affected GO functional clusters in endothelial radioprotection by GT3.
| S-EPMC3250525 | biostudies-literature