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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transriptional profiling upon heat shock and recovery in cells deficient for FBXW7 and their wild type counterpart.

ABSTRACT: FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. Genes positively regulated by HSF1 show increeased expression during heat shock while their expression is reduced during recovery. Genes negatively regulated by HSF1 show the opposite pattern. In this study we utilized the HCT116 FBXW7 KO colon cell line and its wild type counterpart to monitor gene expression changes during heat shock (42oC, 1 hour) and recovery (37oC for 2 hours post heat shock) using RNA sequencing. These results revealed that the heat-shock response pathway is prolonged in cells deficient for FBXW7. Whole RNA was extracted from 1 million HCT116 WT or FBXW7KO cells using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed for each matched recovery versus heat-shock pairs, separately in each biological replicate and cell line (WT or KO). Two types of comparisons were tested: (a) WT recovery vs WT heat shock, (b) FBXW7 KO recovery vs heat shock.

ORGANISM(S): Homo sapiens

SUBMITTER: Nikos Kourtis

PROVIDER: E-GEOD-57397 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transriptional profiling upon heat shock and recovery in cells deficient for FBXW7 and their wild type counterpart.

Project description:FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. Genes positively regulated by HSF1 show increeased expression during heat shock while their expression is reduced during recovery. Genes negatively regulated by HSF1 show the opposite pattern. In this study we utilized the HCT116 FBXW7 KO colon cell line and its wild type counterpart to monitor gene expression changes during heat shock (42oC, 1 hour) and recovery (37oC for 2 hours post heat shock) using RNA sequencing. These results revealed that the heat-shock response pathway is prolonged in cells deficient for FBXW7.

2015-02-20 | GSE57397 | GEO

Genome-wide characterization of HSF1 binding in human WT and FBXW7 KO colon cancer cells under basal conditions and upon heat shock

Project description:FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. In this study we assayed for genome-wide localization of HSF1 enrichment in the HCT116 FBXW7 KO colon cells and their wild type counterpart in untreated cells and upon heat shock. These results revealed that accumulation of nuclear HSF1 in FBXW7 KO cells results in rewiring of the HSF1 transcriptional program.

2015-02-20 | GSE57398 | GEO

Genome-wide characterization of HSF1 binding in human WT and FBXW7 KO colon cancer cells under basal conditions and upon heat shock

Project description:FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. In this study we assayed for genome-wide localization of HSF1 enrichment in the HCT116 FBXW7 KO colon cells and their wild type counterpart in untreated cells and upon heat shock. These results revealed that accumulation of nuclear HSF1 in FBXW7 KO cells results in rewiring of the HSF1 transcriptional program. Five million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1

2015-02-20 | E-GEOD-57398 | biostudies-arrayexpress

Aggregation and disaggregation features of the human proteome

Project description:The aim of the project was to quantify protein aggregation and disaggregation in human cells after transient non-lethal heat shock and during recovery. In addition, the non-aggregating proteins were analyzed by two-dimensional proteome profiling to detect changes in thermal stability upon heat shock. For aggregation/disaggregation study, K562 cells were grown in light SILAC medium which was changed to heavy medium 90 minutes before heat treatment (10 minutes at 44C). After heat shock, cells were let to recover at 37C. Samples were collected before and after the heat shock as well as on multiple time points during recovery (one, two, three and five hours). Protein intensities from soluble fraction (extracted with mild detergent - NP40) was compared to a control samples that on parallel were treated with mock shock (10 minutes at +37C). Samples were labelled with TMT labels and pooled. The medium switch prior to heat shock also allowed to monitor changes in protein synthesis caused by the heat shock. For control, an analysis of total protein amount (extracted with strong detergent - SDS) was conducted. For two-dimensional proteome profiling, aliquots of heat shocked and mock shocked samples were exposed to a temperature gradient (from 37.0C to 66.3C). Samples from two adjacent temperatures were labelled with TMT and pooled. Proteins from soluble fractions were quantified and heat shock-induced changes in thermal stability were analyzed.

2020-09-22 | PXD017291 | Pride

SACL, a bHLH gene that restricts vascular cell proliferation in plants.

Project description:The final size and arrangement of the plant vasculature requires precise adjustment of cell proliferation. In particular, radial growth of vascular bundles is to a large extent controlled by a bHLH transcription factor heterodimer formed by TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW). Excess activity of this TMO5/LHW dimer causes excessive proliferation of vascular cell divisions and thus suggests the existence of a molecular mechanism that restricts its activity in space and time. Here we show that this overproliferation phenotype is similar to acaulis5 (acl5) mutants, suggesting a role for ACL5 in controlling TMO5/LHW activity. We further identify the clade of SAC51-LIKE (SACL) bHLH transcription factors whose translation is regulated by ACL5, as inhibitors of TMO5/LHW activity. We show that SACL proteins interact with LHW impairing activation of downstream targets and alleviating the overproliferation caused by TMO5/LHW misexpression. Given that transcription of SACL genes is induced by TMO5/LHW and its upstream trigger auxin, we propose that SACL proteins represent a feedback mechanism that limits activity of this pathway and controls periclinal cell divisions. Three biological replicates were generated per sample. The goal of this experiment is to compare different genotypes that suppress the acl5 mutant as Columbia-0, acl5 + pHS::SACL3 and acl5 ajax2-31, against the acl5 mutant. Every pair of samples that were compared in the same array, were also growth in the same plate. The acl5 + pHS::SACL3 seedlings (and the acl5 ones against they are went compared) were treated to 37C degrees heat shock and then collected at the different times (30 and 210 min) after heat shock. In each comparison 1 or 2 or the replcates were reversed-labeled.

2015-09-01 | E-GEOD-70157 | biostudies-arrayexpress

An optimized RNA amplification method for prokaryotic expression profiling analysis

Project description:Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model. To identify an optimal RNA labeling method for prokaryotic microarray analysis, experiments were performed with starting RNA obtained from E.coli growing at control (37Â°C) or heat shock (43Â°C) condition. We employed 0.5 Î¼g of total RNA for a single round of amplification using PAOD and RPA methods coupling to IVT to generate cDNA targets. In addition, an approach using DL method was also performed. Three types of cDNA mixtures containing Cy5-labeled (or Cy3-labeled) control DNA and Cy3-labeled (or Cy5-labeled) DNA targets were hybridized with E.coli microarrays in a dye-swap strategy. Replicate experiments were conducted from the same batch of total RNA to assess technique reproducibility of each approach.

2010-05-15 | E-GEOD-17074 | biostudies-arrayexpress

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock using microarrays

Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of heat shock on E. coli O157:H7, global transcript levels of strain EDL933 cells shifted from 37°C to 50°C for 15 min were compared to cells left at 37°C using microarrays. Keywords: Stress Response Twelve independent RNA samples from heat shocked cultures were paired with twelve independent RNA samples from control cultures for hybridization to twelve two-color microarrays. For six arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.

2009-04-01 | E-GEOD-11463 | biostudies-arrayexpress

Transient Genotype-by-Environment Interactions in the Yeast Genomic Expression Response to Heat Shock

Project description:Microarray time courses followed the response of 5 yeast strains to heat shock. Expression variation due to genetic, environmental, and genotype-by-environment interactions were identified. Keywords: Timecourse and single timepoint expression studies of stress response in yeast The genomic expression response to heat shock was measured in 5 different yeast strains over the course of 2 hours. Basal expression at 25C was also compared in 4 non-lab strains to the S288c refernce. All experiments were done in duplicate, for a total of 68 Samples.

2010-05-18 | E-GEOD-15147 | biostudies-arrayexpress

The Rpd3L HDAC complex is essential for the heat stress response in yeast

Project description:To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. Global gene expression analysis showed that Rpd3 partially regulated gene expression upon heat shock. The Hsf1 and Msn2/4 transcription factors are the main regulators of gene activation in response to heat stress. RPD3-deficient cells had impaired activation of Msn2/4-dependent genes, while activation of genes controlled by Hsf1 was deacetylase independent. Rpd3 bound to heat stress-dependent promoters through the Msn2/4 transcription factors, allowing entry of RNA Pol II and activation of transcription upon stress. Finally, we found that the large, but not the small Rpd3 complex regulated cell adaptation in response to heat stress. Three independent 200 ml cultures of wild-type and rpd3Δ mutant strains were grown to mid-log phase in YPD rich medium at 25ºC (control) or at 39 ºC for 20 min (heat stressed). Results were analyzed comparing thermo-responsive gene expression respect to the control in each individual strain.

2010-04-23 | E-GEOD-17514 | biostudies-arrayexpress

A census of Hsp70-mediated proteome solubility changes upon recovery from severe heat stress

Project description:Eukaryotic cells respond to heat shock through several regulatory processes including upregulation of stress responsive chaperones and reversible shutdown cellular activities through formation of protein assemblies. However, the underlying regulatory mechanisms of the recovery of these heat-induced protein assemblies remain largely elusive. Here, we measured the proteome abundance and solubility changes during recovery from severe heat shock in the mouse Neuro2a cell line. We found that prefoldins and translation machinery are rapidly down-regulated as the first step in the heat shock response. Analysis of proteome solubility reveals a rapid mobilization of protein quality control machineries, changes in cellular energy metabolism, changes in translational activity and nucleocytoplasmic transport are fundamental to the early stress responses, while the longer term adaptation to stress involves renewal of core cellular components. Hsp70 inhibition negatively affects the ribosomal machinery and delays the solubility recovery of many nuclear proteins.

2022-03-08 | PXD030069 | Pride

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