Study of SPEN knockdown in MCF-7 cells. (2)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: StM-iphanie LM-igarM-i
PROVIDER: E-MTAB-2183 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We investigated the functions/pathways affected by SPEN in breast cancer by global expression profiling in a cell model, where the human breast cancer cell line, T47D, were transfected with an expression vector coding for SPEN.
2015-10-21 | E-MTAB-2182 | biostudies-arrayexpress
Project description:Split Ends (SPEN) is a transcriptional coregulator that have formerly identified as a tumour suppressor gene in ER-positive breast cancers. However, ER-positive breast cancers are diagnosed at similar frequencies in pre- and post-menopausal women who show significantly different circulating hormone levels. This therefore raises the possibility that SPEN functions under hormone-depleted settings may contrast with its roles in the presence of hormones. We therefore attempted to explore the cellular functions regulated by SPEN under hormone-depleted settings using a previously established model with T47D cells stably transfected with a control vector (non-target) or SPEN-expressing vector. In particular, we attempted to investigate the hormone-independent transcriptional program regulated by SPEN in breast cancer. To achieve this, we have treated previously established T47D cells stably transfected with a control vector (non-target) or SPEN-expressing vector. These cells were allowed to grow in hormone-depleted conditions for 4 days. To minimize external biases introduced by hormone depletion or any transcriptional contribution from the estrogen receptor (ER), we also performed gene expression profiling analyses on the same cells but stimulated with an estrogen receptor (ER) agonist (Estradiol) or antagonist (Tamoxifen).
2017-08-15 | E-MTAB-4975 | biostudies-arrayexpress
Project description:Cyclic indole-3-carbinol (I3C) tetrameric derivative (CTet) is an anticancer molecule that has been shown to exert an antiproliferative activity in both MCF-7 and MDA-MB-231 breast cancer cell lines. To characterize the molecular mechanisms leading to the inhibition of the cell proliferation, gene expression analyses were conducted. MCF-7 and MDA-MB-231 breast cancer cells were plated in 6-wells culture plates at density of 150,000 cells/well and cultured overnight. Cellular treatments were conducted at 6uM and 12 uM concentration of CTet, or vehicle control, for 24 h. Cell survival was evaluated by trypan blue dye exclusion assay and, after washing in phosphate buffered saline (PBS), the cells were pelletted by centrifugation and stored at -20M-0C with 300M-5l of RNA-later solution (Sigma-aldrich). Total RNA was purified from treated and control cells using the RNeasy plus kit (Qiagen). Biotin-labeled cRNA was synthesized using the CodeLink iExpress Assay reagent kit (GE Healthcare), following the manufacturerM-^Rs protocols. Biotin-labeled cRNA obtained from each biological sample was fragmented and hybridized against three independent arrays (10 ug each) at 37M-0C for 22 h. After hybridization, the arrays were washed, stained with Cy5-streptavidin and scanned using a ScanArray GX scanner (Perkin Elmer), with a resolution of 5 um. The image files generated by the scanner were processed using the Codelink Expression Analysis software (GE Healthcare). Normalized data from the Codelink software package were analyzed with GeneSifter software (www.genesifter.net; Geospiza Inc., Seattle, WA) for statistical validation and data mining. Normalized data of the two experiments were subjected to analysis of variance (ANOVA) and 5% false discovery rate calculation (Benjamini and Hochberg). The cut-off parameters for differential gene expression were p =0.01 and fold change threshold =2.<br>
2010-12-30 | E-MEXP-2989 | biostudies-arrayexpress
Project description:In this experiment, we knocked down the expression of Split Ends (SPEN), a gene that we found was involved in the regulation of primary cilia formation, in MCF10A cells, to evaluate its effects on transcription. Split Ends (SPEN) is a transcriptional coregulator that have formerly identified as a tumour suppressor gene in ER-positive breast cancers. We expect the knockdown of SPEN in MCF10A cells to be accompanied with the down-regulation of genes involved in ciliogenesis as we observed that SPEN knockdown decreases primary cilia formation in those cells. We chose MCF10A cells because they harbour lots of primary cilia and therefore represent a good model to study the effect of SPEN on primary cilia formation.
2017-08-15 | E-MTAB-4974 | biostudies-arrayexpress
Project description:We report the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using Global Run-On and sequencing (GRO-seq). We found that estrogen signaling directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein-coding genes, estrogen regulates the distribution and activity of all three RNA polymerases, and virtually every class of non-coding RNA that has been described to date. This data submission covers >95% of mapped reads comprising nearly all transcript classes described. Reads mapping to intergenic and enhancer transcripts were removed from this data submission and will be reported separately (manuscripts in preparation). Bed files are tab-separated text files in which columns represent: chrom, chromStart (5' End of the read), chromEnd (chromStart+1), name (unused always 'n'), score (the number of mismatches), and strand. Note that because of the inclusion of reads mapping to the rRNA chromosome, bed files cannot be uploaded to the UCSC genome browser directly. Instead, use the wiggle files (coming soon!) for this purpose. Using GRO-seq over a time course (0, 10, 40, 160 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.
2011-05-05 | E-GEOD-27463 | biostudies-arrayexpress
Project description:Interactions with the extracellular matrix (ECM) through integrin adhesion receptors provide cancer cells with physical and chemical cues that act in concert with growth factors to support survival and proliferation. Preclinical studies testing beta1 integrin antagonists in (breast) cancer models have shown inhibition of tumor growth and sensitization to radio- or chemotherapy and these strategies are currently evaluated in clinical trials. Here, we show that disruption of beta1 integrin-mediated ECM adhesion attenuates breast tumor growth but dissemination to the lungs from such small tumors can be markedly enhanced. beta1 integrin downregulation induces compensatory upregulation of beta3 integrins, but increased beta3 expression does not lead to enhanced lung metastasis. Instead, beta1 integrin downregulation in human and mouse triple negative, E-cadherin positive breast cancer cells elicits a switch from collective invasion to individual cell migration in 3D ECM. This involves alterations in the TGFbeta-BMP signaling network shifting the balance between miR-200 and ZEB, which causes a block in E-cadherin transcription. The switch is fully reversible: restored beta1 expression reinstates E-cadherin expression and cell cohesion. Moreover, restoring the network at the level of TGFbetaR, ZEB/miR-200 balance, or E-cadherin, restores cohesion and prevents the induction of lung metastasis without affecting tumor growth. These findings reveal that integrin-mediated ECM-attachments regulate a signaling network in control of epithelial characteristics that suppress metastatic spread. This raises concerns with respect to the use of beta1 integrins as cancer drug targets
2014-02-11 | E-MTAB-2185 | biostudies-arrayexpress
Project description:Numerous studies have described the altered expression and the causal role of miRNAs in human cancer. However, to date efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here, we find that Nucleolin (NCL), a major nucleolar protein, post-transcriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, causally involved in breast cancer initiation, progression and drug-resistance. We also show that NCL is commonly overexpressed in human breast tumors, and its expression correlates with that of NCL-dependent miRNAs. Finally, this study indicates that NCL-binding guanosine-rich aptamers affect the levels of NCL-dependent miRNAs and their target genes, reducing breast cancer cell aggressiveness, both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer. Identification of NCL regulated miRNAs by using miRNA high-throughput sequencing of HeLa cells stably expressing double-strand (ds) interfering RNA against NCL or scrambled sequences (sh-NCL or sh-Scr).
2013-02-07 | E-GEOD-44052 | biostudies-arrayexpress
Project description:N-?-acetyltransferase 10 protein (Naa10p, also called ARD1), the catalytic subunit of N-acetyltransferase A, is a critical regulator of cell death and proliferation. Naa10p is also shown to regulate cancer metastasis by inhibiting cell motility, however its role in cancer metastasis is not fully understood. In this study, we found that high expression of Naa10p is positively correlated with the survival of patients with breast cancer, while negatively correlated with lymph node metastasisr. Naa10p inhibits breast cancer cell migration and invasion in vitro and decreases the xenograft growth and metastasis in nude mice. Microarray screening revealed that Naa10p down-regulates expression of several pro-invasive genes, which was validated by qRT-PCR analysis. To gain an insight into Naa10p’s inhibitory effect on cancer metastasis, we performed microarray analysis with RNA samples extracted from Naa10p-silenced MCF-7 (MCF-7SA) and control cells (MCF-7NC).
2014-08-01 | E-GEOD-52723 | biostudies-arrayexpress
Project description:A non-functional myosin Vb motor in duodenal enterocytes results in disruption of epithelial cell polarity characterized by complete loss of microvilli and mislocalization of apical brush border proteins in the cytoplasm which finally cause a devastating disease in neonates with severe malabsorption defects accompanied by protracted diarrhea during infancy, classified as microvillus inclusion disease (MVID). The exact mechanisms how loss-of-function of MYO5B induces polarity loss are not completely understood in MVID pathogenesis. Obtaining better insights in cell polarity defects caused by loss of MYO5B, we performed microarray- in combination with protein expression-analysis in an inducible CaCo2 MYO5B RNAi cell system. Surprisingly, in MYO5B-depleted CaCo2 cells, CDH1 coding for the cell adhesion protein E-Cadherin and important for cell adhesion and therefore maintenance of cell polarity, was significantly downregulated. Interestingly, mesenchymal cell markers, specifically Vimentin and N-Cadherin, physiologically not expressed in differentiated epithelium, were upregulated and accompanied by increased phospho-c-jun levels in the nucleus. Importantly phospho-c-jun was also found in nuclei of duodenal enterocytes in MVID patients, indicating loss of MYO5B induces epithelial cell scattering in enterocytes. 3 Myosin 5B KD versus 3 control samples
2013-03-14 | E-GEOD-45134 | biostudies-arrayexpress
Project description:Here we reveal a hierarchical mechanism in the direct conversion of fibroblasts into induced neuronal (iN) cells mediated by the transcription factors Ascl1, Brn2, and Myt1l. Examination of global transcriptional changes and mapping genome-wide transcription factors occupancy at distinct time points during the transdifferentiation process
2013-04-10 | E-GEOD-43916 | biostudies-arrayexpress