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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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P53 amplifies Toll-like receptor 5 response in MCF-7 cells

ABSTRACT: Using gene expression profiling we characterize the global effect of p53 on the TLR5-mediated transcription in MCF7 cells. We found that combined activation of p53 and TLR5 pathways synergistically increases expression of over 200 genes, mostly associated with immunity and inflammation. The synergy was observed in several human cancer cells and primary lymphocytes. Oncotarget. 2015 Jul 10;6(19):16963-80, PMID 26220208 10 experimental conditions, each in triplicate, several samples were hybridized twice at two separate ocasions as indicated in 'description' field. 29 samples total and 35 arrays total.

ORGANISM(S): Homo sapiens

SUBMITTER: NIEHS Microarray Core

PROVIDER: E-GEOD-72359 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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p53 amplifies Toll-like receptor 5 response in human primary and cancer cells through interaction with multiple signal transduction pathways.

Shatz Maria M Shats Igor I Menendez Daniel D Resnick Michael A MA

Oncotarget 20150701 19

The p53 tumor suppressor regulates transcription of genes associated with diverse cellular functions including apoptosis, growth arrest, DNA repair and differentiation. Recently, we established that p53 can modulate expression of Toll-like receptor (TLR) innate immunity genes but the degree of cross-talk between p53 and TLR pathways remained unclear. Here, using gene expression profiling we characterize the global effect of p53 on the TLR5-mediated transcription in MCF7 cells. We found that comb ...[more]

PMID: 26220208

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p53 amplifies Toll-like receptor 5 response in MCF-7 cells

Project description:Using gene expression profiling we characterize the global effect of p53 on the TLR5-mediated transcription in MCF7 cells. We found that combined activation of p53 and TLR5 pathways synergistically increases expression of over 200 genes, mostly associated with immunity and inflammation. The synergy was observed in several human cancer cells and primary lymphocytes. Oncotarget. 2015 Jul 10;6(19):16963-80, PMID 26220208

2015-08-26 | GSE72359 | GEO

Transcriptome and translatome profiling of MCF7 vector cells after p53 activation

Project description:Several genome-wide transcriptome analyses that focused on p53-induced cellular responses in many cellular contexts have continued to expand the already vast p53-regulated transcriptional networks. To investigate post-transcriptional controls as an additional dimension of p53-directed gene expression responses we performed translatome analysis by polysomal profiling on MCF7 cells treated with Doxorubicin and Nutlin-3a. A comparison between the transcriptome and the translatome revealed a large number of uncoupled genes, whose transcription changes did not correlate with translation changes. Overall, we establish p53 as a master regulator of translational control and identify many p53 target genes affecting translation that can contribute to p53-dependent cellular responses. Keywords: p53, transcriptome, translatome, polysomal RNA, subpolysomal RNA, uncoupling, Doxorubicin, Nutlin-3a Total RNA (tot) was extracted from MCF7 vector cells after 16h of treatment with Doxorubicin (1.5uM) and Nutlin-3a (10uM) or DMSO (solvent, as control treatment). Polysomal profiling was performed after the same conditions. We collected all subpolysomal mRNA fractions (sub) and the polysomal ones (pol) after sucrose gradient fractionation of cytoplasmic lysates to analyze separately mRNAs that are not actively translated from those that are considered in active translation, respectively. Experiments were performed in three biological replicates.

2014-04-17 | E-GEOD-50650 | biostudies-arrayexpress

Human BJ fibroblasts containing control vs. BRD7 shRNA

Project description:Transcriptional profiling of human BJ fibroblasts comparing control FF shRNA expressing cells vs. BRD7 shRNA expressing cells under two conditions, either untreated or treated with 8uM nutln-3a for 8 hours. This experiment was done using two independent shRNAs targeting BRD7. Nutlin-3a was used to stabilize p53 and induce its transcriptional activity. Two-condition experiment, FF shRNA cells vs. BRD7 shRNAs cells in two experimental conditions, either untreated or treated with nutlin-3a.

2010-07-01 | E-GEOD-22607 | biostudies-arrayexpress

Mouse-specific skin and blood transcriptional responses after intradermal administration of flagellin

Project description:The study aimed at defining the local and systemic innate responses after intradermal injection of flagellin. For this purpose, mice were immunized by intradermal route with flagellin. Skin and blood were then sampled at selected times for microarray analyses. Mice were then immunized with the TLR5 agonist flagellin by intradermal route. Blood samples and punch biopsies of skin were sampled post-immunization and on mock animals. Total RNA was extracted and microarray experiments were performed as single-color hybridizations on Agilent 4x44K mouse whole genome catalog arrays (Agilent-014868) according supplier's recommendations.

2016-07-03 | E-GEOD-72016 | biostudies-arrayexpress

Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells (Affymetrix)

Project description:The effects of diverse stresses on promoter selectivity and transcription regulation by the tumor suppressor p53 are poorly understood. We have taken a comprehensive approach to characterizing the human p53 network that includes p53 levels, binding, expression and chromatin changes under diverse stresses. Human osteosarcoma U2OS cells treated with anti-cancer drugs Doxorubicin or Nutlin-3 led to strikingly different p53 gene binding patterns based on ChIP-seq experiments. While two contiguous RRRCWWGYYY decamers is the consensus binding motif, p53 can bind a single decamer and function in vivo. Although the number of sites bound by p53 was 6-times greater for Nutlin-3 than Doxorubicin, expression changes induced by Nutlin-3 were much less dramatic compared to Doxorubicin. Unexpectedly, the solvent DMSO alone induced p53 binding to many sites common to Doxorubicin; however, this binding had no effect on target gene expression. Together, these data imply a two-stage mechanism for p53 transactivation where p53 binding only constitutes the first stage. Furthermore, both p53 binding and transactivation were associated with increased active histone modification H3K4me3. We discovered 149 putative new p53 target genes including several that are relevant to tumor suppression, revealing potential new targets for cancer therapy and expanding our understanding of the p53 regulatory network. Gene expression analysis (using Affymetrix Human Genome U133 Plus 2.0 GeneChipÂ® arrays) of the p53 response in U2OS cells treated with either Doxorubicin or Nutlin-3, relative to their controls No Treatment and DMSO, respectively.

2013-07-01 | E-GEOD-46493 | biostudies-arrayexpress

Gene Expression Profiling on Stably Expressing ICD JM-a CYT-1 or CYT-2 ERBB4 isoforms in MCF10A cells

Project description:Convergent and divergent effects of two ICD ERBB4 isoforms on gene expression in normal-like MCF10A mammary epithelial cells lacking endogeneous ERBB4 expression. Control vector (VEC) and ERBB4 expression MCF10A cells (ICD CYT1 or CYT2) maintained in regular medium containing 10% serum, were collected and RNA samples were collected and analyzed.

2014-05-07 | E-GEOD-57339 | biostudies-arrayexpress

Global gene expression analysis in macrophages treated with Nutlin-3

Project description:The goal of the study is to identify p53 target genes specific to macrophages using the p53 stabilizer, Nutlin-3. Macrophages were differentiated x-vivo from monocytes obtained from healthy volunteers either left untreated or treated for 2 hours with 100 ng/mL of lipopolysaccharide (LPS), 0.1%v/v of DMSO (vehicle control for Nutlin-3) or 10 micromolar Nutlin-3. Three replicates were included for each treatment group.

2014-05-21 | E-GEOD-43596 | biostudies-arrayexpress

MicroRNA profiling by array of human multiple myloma p53 wild type cells treated with nutlin 3A

Project description:The miRNA profiles were analyzed for nutlin 3A treated and untreated multiple myloma p53 wild type cells

2010-07-22 | E-TABM-1038 | biostudies-arrayexpress

Expression data from H226 squamous cell carcinoma cells

Project description:To define the contribution of p53 versus DNp63a to gene expression control, we performed a series of microarray assays for cells where p53 was activated using Nutlin-3 or DNp63a was knocked down using a stably transduced tetracycline inducible shRNA. We determined that p53 transcriptionally activates and DNp63a transcriptionally represses a non-overlapping subset of genes. Total RNA from H226 cells harvested using Tri reagent (Sigma-Aldrich) was used for gene expression analysis on Affymetrix HuGene 1.0 ST arrays following the manufacturer’s instructions. Differential gene expression was determined with Partek software using one-way ANOVA.

2012-11-06 | E-GEOD-40462 | biostudies-arrayexpress

p53-dependent transcription program in HepG2 cells

Project description:In order to obtain a global picture regarding regulation of p53 in liver cells we used HepG2 hepatoma cells.We created two isogenic sub-cultures of HepG2 cells with altered expression of p53. HepG2 cells were infected with a retroviral vector harboring either small-hairpin RNA targeting p53 (termed HepG2sh-p53) or a non relevant small-hairpin RNA (termed HepG2sh-con). Cells were treated with two different p53 stimulators - Nutlin and AICAR

2012-03-30 | E-GEOD-30137 | biostudies-arrayexpress

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