Gene profiling: U87 IRE1 dominant negative cells vs. U87ctrl cells in culture
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Auf G
PROVIDER: S-ECPF-GEOD-22385 | biostudies-other | 2010 Aug
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Transcriptome analysis was performed from human U87 glioblastoma cell clones: U87 IRE1.NCK DN (U87dn, IRE1 dominant negative) and U87 control (U87ctrl, empty plasmid). Cells were grown in DMEM supplemented with 10% FBS and glutamine for 16 hours in culture prior mRNA isolation and analyses
2010-08-08 | GSE22385 | GEO
Project description:Transcriptome analysis was performed from human U87 glioblastoma cell clones: U87 IRE1.NCK DN (U87dn, IRE1 dominant negative) and U87 control (U87ctrl, empty plasmid). Cells were grown in DMEM supplemented with 10% FBS and glutamine for 16 hours in culture prior mRNA isolation and analyses U87dn cells expressing a dominant negative transgene of IRE1alpha were compared to U87ctrl cells transfected with the corresponding empty plamid to identify genes associated to tumor invasion and angiogenesis.
2010-08-08 | E-GEOD-22385 | biostudies-arrayexpress
Project description:Overall study: Identification of PDGF-dependent patterns of gene expression in U87 glioblastoma cells. RNA was obtained from triplicate dishes of 5 different groups of U87 cells, each (total 15) analyzed with one U95 microarray chip.,Three different comparisons were made:,1) Clone 3.1 (34580-34582) vs. clone 3.3 (34583-34585) vs. parent U87 (34592-34594).,Purpose: demonstrate that the gene expression profiles between these 3 cell lines are not different, so they could be pooled as a single untreated group.,2) Pooled control group (34580-34585, 34592-34594) vs. clone 8.1 (34586-34588).,Purpose: identify genes specifically controlled by autocrine PDGF activity.,3) Clone 8.1 (34586-34588),vs. clone 8.1 treated with PDGF (34589-34591),Purpose: Identify genes specifically induced by exogenous PDGF.
| S-ECPF-GEOD-1923 | biostudies-other
Project description:Epidermal growth factor (EGF) receptors contribute to the development of malignant glioma. Here we considered the possible implication of the EGFR ligand epiregulin (EREG) in glioma development in relation to the activity of the unfolded protein response (UPR) sensor IRE1?. We also examined EREG status in several glioblastoma cell lines and in malignant glioma.Expression and biological properties of EREG were analyzed in human glioma cells in vitro and in human tumor xenografts with regard to the presence of ErbB proteins and to the blockade of IRE1?. Inactivation of IRE1? was achieved by using either the dominant-negative strategy or siRNA-mediated knockdown.EREG was secreted in high amounts by U87 cells, which also expressed its cognate EGF receptor (ErbB1). A stimulatory autocrine loop mediated by EREG was evidenced by the decrease in cell proliferation using specific blocking antibodies directed against either ErbB1 (cetuximab) or EREG itself. In comparison, anti-ErbB2 antibodies (trastuzumab) had no significant effect. Inhibition of IRE1? dramatically reduced EREG expression both in cell culture and in human xenograft tumor models. The high-expression rate of EREG in U87 cells was therefore linked to IRE1?, although being modestly affected by chemical inducers of the endoplasmic reticulum stress. In addition, IRE1-mediated production of EREG did not depend on IRE1 RNase domain, as neither the selective dominant-negative invalidation of the RNase activity (IRE1 kinase active) nor the siRNA-mediated knockdown of XBP1 had significant effect on EREG expression. Finally, chemical inhibition of c-Jun N-terminal kinases (JNK) using the SP600125 compound reduced the ability of cells to express EREG, demonstrating a link between the growth factor production and JNK activation under the dependence of IRE1?.EREG may contribute to glioma progression under the control of IRE1?, as exemplified here by the autocrine proliferation loop mediated in U87 cells by the growth factor through ErbB1.
| S-EPMC3878670 | biostudies-literature
Project description:Overall study: Identification of PDGF-dependent patterns of gene expression in U87 glioblastoma cells. RNA was obtained from triplicate dishes of 5 different groups of U87 cells, each (total 15) analyzed with one U95 microarray chip.,Three different comparisons were made:,1) Clone 3.1 (34580-34582) vs. clone 3.3 (34583-34585) vs. parent U87 (34592-34594).,Purpose: demonstrate that the gene expression profiles between these 3 cell lines are not different, so they could be pooled as a single untreated group.,2) Pooled control group (34580-34585, 34592-34594) vs. clone 8.1 (34586-34588).,Purpose: identify genes specifically controlled by autocrine PDGF activity.,3) Clone 8.1 (34586-34588),vs. clone 8.1 treated with PDGF (34589-34591),Purpose: Identify genes specifically induced by exogenous PDGF.
2007-12-12 | E-GEOD-1923 | biostudies-arrayexpress
Project description:A novel suicide gene therapy approach was tested in U87 MG glioblastoma multiforme cells. A 26nt G-rich double-stranded DNA aptamer (AS1411) was integrated into a vector at the 5' of a mammalian codon-optimized saporin gene, under CMV promoter. With this plasmid termed "APTSAP", the gene encoding ribosome-inactivating protein saporin is driven intracellularly by the glioma-specific aptamer that binds to cell surface-exposed nucleolin and efficiently kills target cells, more effectively as a polyethyleneimine (PEI)-polyplex. Cells that do not expose nucleolin at the cell surface such as 3T3 cells, used as a control, remain unaffected. Suicide gene-induced cell killing was not observed when the inactive saporin mutant SAPKQ DNA was used in the (PEI)-polyplex, indicating that saporin catalytic activity mediates the cytotoxic effect. Rather than apoptosis, cell death has features resembling autophagic or methuosis-like mechanisms. These main findings support the proof-of-concept of using PEI-polyplexed APTSAP for local delivery in rat glioblastoma models.
| S-EPMC8082512 | biostudies-literature
Project description:Parvin-beta is a focal adhesion protein downregulated in human breast cancer cells. Loss of Parvin-beta contributes to increased integrin-linked kinase activity, cell-matrix adhesion, and invasion through the extracellular matrix in vitro. The effect of ectopic Parvin-beta expression on the transcriptional profile of MDA-MB-231 breast cancer cells, which normally do not express Parvin-beta was evaluated. Particular emphasis was placed upon propagating MDA-MB-231 breast cancer cells in three-dimensional culture matrices. Gene expression profiles of vector control and Parvin-beta transfected MDA-MB-231 cells cultured on (A) monomeric type I collagen coated plastic, (B) embedded in a type I collagen gel, and (C) embedded in basement membrane (growth factor reduced Matrigel), were compared. Interestingly, Parvin-beta re-expression in MDA-MB-231 cells increased the mRNA expression, serine 82 phosphorylation (mediated by CDK9), and activity of the nuclear hormone receptor, peroxisome proliferator-activated receptor gamma (PPARgamma) and a concomitant increase in lipogenic gene expression as a downstream effector of PPARgamma. Importantly, Parvin-beta suppressed breast cancer growth in vivo with associated decreased proliferation. These data suggest that Parvin-beta might influence breast cancer progression.. Experiment Overall Design: The MDA-MB-0231 transfectants were cultured for 7 days in each growth condition and total RNA isolated using Trizol reagent (Invitrogen). Genes either upregulated or downregulated in Parvin-beta transfectants versus vector control cells were compared among the 3 different growth conditions. Venn diagrams were generated using GeneSpring software and used to produce gene lists that were unique to a particular growth condition, or shared between two or all three growth conditions. The focus was primarily on gene expression alterations observed in the 3D collagen type I and 3D Matrigel conditions.
| S-ECPF-GEOD-9747 | biostudies-other
Project description:Gene expression profiling of ABCB1 positive and ABCB1 negative OCM1A cells. ABCB1 is an ATP-dependent transporter efflux pump. OCM1A cell line is derived from uveal melanomas. 6 samples (3 ABCB1 positive and 3 ABCB1 negative) from 3 independent ABCB1 shift assays were analysed
| S-ECPF-GEOD-21425 | biostudies-other
Project description:An orthotopic model of lung cancer was established in Rag-2 null mice by injecting 1 x 106 GFP-A549 cells into the mouse lung via the trachea. After 6 weeks a primary tumor develops in the right lung. RNA was collected from tumors established in the orthotopic model after 6 weeks in three separate mice and from the right lung of three sham control mice that were injected with PBS by the same method. RNA was also collected from the A549 cells in culture. RNA was applied to an Affymetrix Customized Protease Microarray (HuMu ProtIn chip). This custom chip is able to distinguish human and mouse genes by using oligonucleotides specific for each species. The chip contains all known human and mouse proteases and protease inhibitors. A distribution of gene expression from a comparison of all human and mouse genes present in the tumor vs. the control lung was indentified as well as a distribution of gene expression from a comparison of all human and mouse genes present in the tumor vs. the cells in culture. Human and mouse genes differentially expressed in each group were identifed.
| S-ECPF-MEXP-489 | biostudies-other
Project description:Survivin (BIRC5, product of the BIRC5 gene) is highly expressed in many tumor types and has been widely identified as a potential target for cancer therapy. However, effective anti-survivin drugs remain to be developed. Here we report that both vector-delivered and cell-penetrating dominant-negative (dn) forms of the transcription factor ATF5 that promote selective death of cancer cells in vitro and in vivo cause survivin depletion in tumor cell lines of varying origins. dn-ATF5 decreases levels of both survivin mRNA and protein. The depletion of survivin protein appears to be driven at least in part by enhanced proteasomal turnover and depletion of the deubiquitinase USP9X. Survivin loss is rapid and precedes the onset of cell death triggered by dn-ATF5. Although survivin downregulation is sufficient to drive tumor cell death, survivin over-expression does not rescue cancer cells from dn-ATF5-promoted apoptosis. This indicates that dn-ATF5 kills malignant cells by multiple mechanisms that include, but are not limited to, survivin depletion. Cell-penetrating forms of dn-ATF5 are currently being developed for potential therapeutic use and the present findings suggest that they may pose an advantage over treatments that target only survivin.
| S-EPMC6760124 | biostudies-literature