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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Christina Yau

PROVIDER: E-GEOD-73371 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index.

Yau Christina C Meyer Laurence L Benz Stephen S Vaske Charles C Scott Gary G Egan Brian B Labhart Paul P Pourmand Nader N Benz Christopher C CC

Breast cancer research and treatment 20151012 1

FOXM1 is a key transcription factor regulating cell cycle progression, DNA damage response, and a host of other hallmark cancer features, but the role of the FOXM1 cistrome in driving estrogen receptor-positive (ER+) versus estrogen receptor-negative (ER-) breast cancer clinical outcomes remains undefined. Chromatin immunoprecipitation sequencing (ChIP-Seq) coupled with RNA sequencing (RNA-Seq) analyses was used to identify FOXM1 target genes in breast cancer cells (MCF-7) where FOXM1 expression ...[more]

PMID: 26456572

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FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index [ChIP-Seq]

Project description:FOXM1 is a key transcription factor regulating cell cycle progression, DNA damage response, and a host of other hallmark cancer features, but the role of the FOXM1 cistrome in driving estrogen receptor-positive (ER+) vs. ER- breast cancer clinical outcomes remains undefined. Chromatin immunoprecipitation sequencing (ChIP-Seq) coupled with RNA sequencing (RNA-Seq) analyses was used to identify FOXM1 target genes in breast cancer cells (MCF-7) where FOXM1 expression was either induced by cell proliferation or repressed by p53 upregulation.

2015-10-26 | E-GEOD-72977 | biostudies-arrayexpress

FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index [RNA-Seq]

2015-10-26 | E-GEOD-73370 | biostudies-arrayexpress

Inhibition of PARP14 restores response to α-PD1 immune checkpoint inhibition in tumours with resistance driven by IFNγ. PARP14 study.

Project description:While immune checkpoint blockade therapy (ICBT) benefits cancer patients, many fail to maintain their response due to adaptive resistance mechanisms. IFNγ is critical for cellular immunity, but also promotes adaptive resistance to ICBT. We have established a role for PARP14 in mediating IFNγ-induced adaptive resistance. We confirm that chronic pre-treatment of tumour cells with IFNγ confers resistance to α-PD-1 antibodies in syngeneic mouse tumour models. We identified that PARP14 was consistently upregulated in cancer cells treated chronically with IFNγ as well as in IFNγ-high melanoma samples. Further, we showed that PARP14 knockdown or pharmacological inhibition restores sensitivity to α-PD-1 antibodies accompanied by increased immune cell infiltration into tumours but the decreased presence of regulatory T cells. RNA sequencing analysis of tumours and cultured cells treated with PARP14 inhibitor showed an upregulation of inflammatory-related pathways. In conclusion, PARP14 is an actionable target for reversing IFNγ-driven adaptive resistance to ICBT.

2023-08-08 | E-MTAB-12195 | biostudies-arrayexpress

Early Response Genes in Osteoblasts Exposed to Dynamic Fluid Flow

Project description:Cyclic mechanical loads applied to the skeleton increase bone formation. Dynamic fluid flow is a potent anabolic stimulus for cultured osteoblasts. In this study, gene profiles involved in mediating the anabolic response of MC3T3 osteoblasts to dynamic fluid flow are investigated. MC3T3 osteoblast RNA was harvested 30-minutes and 1-hour post-stimulation respectively as experimental samples for comparison to the control group without dynamic fluid flow.

2010-05-18 | E-GEOD-16211 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae oxidative stress response

Project description:Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress. We used microarrays to study the genome-wide temporal response of the yeast S. cerevisiae to oxidative stress induced by cumene hydroperoxide. Experiment Overall Design: The effects of oxidative stress induced by CHP on the transcriptional profile of S. cerevisiae was studied from a dynamical perspective. Yeast cultures were grown in controlled batch conditions, in 1 L fermentors. Three replicate cultures in mid-exponential phase were exposed to 0.19 mM CHP, while three non-treated cultures were used as controls. Samples were collected at t=0 (immediately before adding CHP) and at 3,6,12,20,40,70 and 120 min after adding the oxidant. Samples were processed for RNA extraction and profiled using Affymetrix Yeast Genome S98 arrays.

2008-06-15 | E-GEOD-7645 | biostudies-arrayexpress

Expression data for Saccharomyces cerevisiae oxidative stress response

Project description:Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress. We used microarrays to study the genome-wide temporal response of the yeast S. cerevisiae to oxidative stress induced by cumene hydroperoxide. Keywords: time course The effects of oxidative stress induced by CHP on the transcriptional profile of S. cerevisiae was studied from a dynamical perspective. Yeast cultures were grown in controlled batch conditions, in 1 L fermentors. Three replicate cultures in mid-exponential phase were exposed to 0.19 mM CHP, while three non-treated cultures were used as controls. Samples were collected at t=0 (immediately before adding CHP) and at 3, 6, 12 and 20 min after adding the oxidant. Samples were processed for RNA extraction and profiled using Affymetrix Yeast Genome S98 arrays.

2013-12-17 | E-GEOD-26169 | biostudies-arrayexpress

Expression data from human carcinoma (MCF7) derived cells that have been exposed to insulin analogues

Project description:Insulin analogues are designed to improve the pharmacokinetic parameters compared to regular human insulin. This provides a sustained control of blood glucose levels in diabetic patients. All novel insulin analogues are tested for their mitogenic side effects, however these assays do not take into account the molecular mode-of-action of different insulin analogues. Insulin analogues can bind the insulin receptor (INSR) and the insulin-like growth factor-1 receptor (IGF1R) with different affinities and consequently will activate different downstream signaling pathways. Here we used a panel of MCF7 human breast cancer cell lines that selectively express either one of the isoforms of the INSR (IRA or IRB) or the IGF1R. We sought to study the role of the different receptors (IRA, IRB and IGF1R) in the mitogenic signaling of insulin-like molecules (including insulin, glargine, X10 (or AspB10) and IGF1). MCF7 IRA, MCF7 IRB or MCF7 IGF1R cells (as described in Arch Toxicol. 2014 Apr;88(4):953-66. doi: 10.1007/s00204-014-1201-2. Epub 2014 Jan 25.) were cultured in RPMI supplemented with 5% (v/v) CDFBS (Hyclone) and used for experiments. Cells have been exposed for 1 or 6 hours to 10 nM of the indicated insulin-like molecule. As a control sample a vehicle stimulation was performed that contained everything except the active compound.

2015-01-29 | E-GEOD-65398 | biostudies-arrayexpress

Transcription profiling of human response to carboplatin in chemosensitive and chemoresistant ovarian cancer cells.

Project description:Use of expression arrays to identify genes from ovarian cancer cells that are associated with carboplatin sensitivity and resistance as defined by ChemoFX assay.

2007-09-01 | E-GEOD-1926 | biostudies-arrayexpress

Gene expression effects of morpholino directed spRunt-1 knockdown on hatched blastula stage embryos

Project description:Runt domain (Runx) transcription factors constitute a metazoan family of sequence specific DNA binding proteins that are essential for animal development. The sea urchin Runx gene SpRunt-1, which is expressed globally during early embryogenesis, is required for blastula stage cell proliferation and subsequently for cell survival. To obtain a comprehensive list of SpRunt-1 regulatory targets we screened a custom microarray representing the blastula stage transcriptome of Strongylocentrotus purpuratus, comparing relative hybridization signals generated by labeled RNA from 18 hr control versus SpRunt-1 morphant embryos. For an 8x15k chip the 8 arrays were 4 biological replicates and a dye swap of the same 4. Biological Replicates - Four separate embryo cultures, each from a different mating pair were initiated and divided into a control group and a treatment group. All of the embryos in the treatment group were micoinjected with a splice-blocking morpholino antisense oligonucleotide (MASO) targeted to SpRunt-1. All control and sample embryos were developed to hatched blastula stage (18 hours post-fertilization) in filtered seawater at 15Â°C. Total RNA was extracted from each of the four separate samples (3,600 embryos in each sample) with an RNA yield near 5 micro grams per sample. Total RNA was also extracted from the untreated embryos of each separate culture pooled together (about 14,400) with an RNA yield near 20 micro grams. Technical (dye swap) Replicates - Control derived Cy3 (green) labeled aRNA was mixed with sample derived Cy5 (red) labeled aRNA in one biological replicate set of 4 samples and using half of the extracted RNA amount. The other half of the RNA was reciprocally labeled with control derived aRNA Cy5 labeled and sample derived aRNA Cy3 labeled.

2010-05-16 | E-GEOD-19751 | biostudies-arrayexpress

PEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress

Project description:Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.

2023-10-24 | PXD042395 | Pride

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