Effect of iron chelators on global gene expression pattern in SW480 cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Liliana Attisano
PROVIDER: E-GEOD-32369 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The molecular role of iron in gene expression remains poorly characterized. Moreover, the alterations in global gene expression after iron chelation remains unclear and are important to assess for understanding the molecular pathology of iron-depletion and the biological effects of iron chelators. We assessed the effect on whole genome gene expression of two iron chelators (desferrioxamine and Dp44mT). These studies are important for understanding the molecular and cellular effects of iron-depletion. The DMS-53 cells were incubated with either control medium or this medium containing DFO (250 µM) or Dp44mT (25 µM) for 24 h at 37oC. These concentrations were used since our previous studies demonstrated that under these conditions these chelators lead to up-regulation of iron-responsive genes such as the TfR1 after this incubation time. Moreover, the higher concentration of DFO was implemented due to its limited ability to permeate cell membranes. Total RNA was isolated from cells in 1 mL of TRIzol® reagent (Invitrogen). Samples were then prepared and hybridized to the Human Genome U133 Plus 2.0 430 2.0. The human GeneChip® U133 Plus 2.0 consists of greater than 47,000 transcripts and variants from over 38,500 well characterized human genes. On completion of hybridization and washing, microarray chips were scanned with the Affymetrix GeneChip® Scanner 3000 (Affymetrix).
2011-12-31 | E-GEOD-26920 | biostudies-arrayexpress
Project description:Iron is required as a cofactor for many critical cellular enzymes involved in energy metabolism and cell proliferation and is thus essential for all living cells. To facilitate the rapid replication, the neoplastic cells have significantly higher levels of ribonucleotide reductase and the transferrin receptor 1 (TfR1) and many in vitro and in vivo studies have demonstrated that, compared to normal cells, cancer cells are more sensitive to iron (Fe) deprivation because of their marked Fe requirements. The higher Fe utilization by cancer cells provides a rationale for the selective antitumor activity of chelators. To date, Deferoxamine (DFO) is one of the most widely used iron chelator. In addition, DFO also has some antitumor activity. Moreover, novel chelators based on the di-2-pyridylketone thiosemicarbazone (DpT) scaffold, such as di-2-pyridylketone 4,4-dimethyl-3-thiosemicarbazone (Dp44mT), induce iron sequestration and also form redox-active metal complexes that demonstrate potent and selective anti-tumor activity. Notably, Dp44mT and its analogs possess broad anti-cancer and anti-metastatic activity in vitro and in vivo against a variety of aggressive solid tumors. Understanding the mechanism of action of these ligands and their effect on the ER stress pathway will yield better clinical outcomes. It has been reported that iron depletion induced by Dp44mT and its metal complexes causes apoptosis by generating cytotoxic ROS and by inducing DNA strand breaks. The redox active complexes formed in lysosomes induce damages generating tumor cell cytotoxicity. The alterations in gene expression after iron depletion are complex. Moreover, in cultured cells Dp44mT resulted in marked up-regulation of the Fe-responsive tumor growth and metastasis suppressor Ndrg1 (N-myc downstream regulated gene-1). Therefore, Up-regulation of Ndrg1 may be another mechanism by which chelators inhibit cancer cell proliferation. Here we combine biochemistry, microscopy, flow cytometry and LC/MS-MS analyses to investigate cellular events induced by DFO and Dp44mT iron chelators on two human breast cancer cell lines, MDA-MB-231 and MDA-MB-157, in terms of proliferation, cell cycle, cytotoxicity and death. These experiments could potentially provide additional information in terms of the mechanism(s) of action of iron chelators in breast cancer cells.
2018-04-09 | PXD007595 | Pride
Project description:Gene expression analysis of SW480 cells treated with inhibitor compounds for 6 hours. Results provide insights into the role of iron in Wnt signalling and demonstrate that iron depletion is the primary mode of actions of these compounds on Wnt pathway.
2011-10-16 | GSE32369 | GEO
Project description:Iron-deficiency affects 500 million people, yet the molecular role of iron in gene expression remains poorly characterized. Moreover, the alterations in global gene expression after iron chelation remains unclear and are important to assess for understanding the molecular pathology of iron-deficiency and the biological effects of iron chelators. We assessed the effect on whole genome gene expression of two iron chelators (desferrioxamine and 2-hydroxy-1-napthylaldehyde isonicotinoyl hydrazone) that have markedly different permeability properties. Sixteen genes were significantly regulated by both chelators, while a further 50 genes were regulated by either ligand. Most of the genes identified in this study have not been previously described to be iron-regulated and are important for understanding the molecular and cellular effects of iron-deficiency. The MCF-7 cells were incubated with either control medium or this medium containing DFO (250 µM) or 311 (25 µM) for 24 h at 37oC. These concentrations were used since our previous studies demonstrated that under these conditions these chelators lead to up-regulation of iron-responsive genes such as the TfR1 after this incubation time.8 Moreover, the higher concentration of DFO was implemented due to its limited ability to permeate cell membranes. Total RNA was isolated from cells in 1 mL of TRIzol® reagent (Invitrogen). Samples were then prepared and hybridized to the Human Genome U133 Plus 2.0 430 2.0. The human GeneChip® U133 Plus 2.0 consists of greater than 47,000 transcripts and variants from over 38,500 well characterized human genes. On completion of hybridization and washing, microarray chips were scanned with the Affymetrix GeneChip® Scanner 3000 (Affymetrix).
2010-03-09 | E-GEOD-17832 | biostudies-arrayexpress
Project description:Transcription mediated by hypoxia inducible factor (HIF-1) contributes to tumor angiogenesis and metastasis but is also involved in the activation of cell-death pathways and normal physiological processes. Given the complexity of HIF-1 signaling it could be advantageous to target a subset of HIF-1 effectors rather than the entire pathway. We compared the genome-wide effects of three molecules that each interfere with the HIF-1-DNA interaction: a polyamide targeted to the hypoxia response element (HRE), siRNA targeted to HIF-1α, and echinomycin, a DNA binding natural product with a similar but less specific sequence preference to the polyamide. The polyamide affects a subset of hypoxia-induced genes that are consistent with the binding site preferences of the polyamide. For comparison, siRNA targeted to HIF-1α and echinomycin each affect the expression of nearly every gene induced by hypoxia. Remarkably, the total number of genes affected by either polyamide or HIF-1α siRNA over a range of thresholds is comparable. The data shows how polyamides can be used to affect a subset of a pathway regulated by a transcription factor. In addition, this study offers a unique comparison of three complementary approaches towards exogenous control of endogenous gene expression. Experiment Overall Design: Hypoxia-mimetic DFO (deferoxamine)-stimulated U251 cells that were treated with polyamide 1, HIF-1α siRNA, and echinomycin were compared to control cells that were also DFO-stimulated. Cells not stimulated with DFO were also compared to the DFO-stimulated controls. Three biological replicates were included for each treatment/condition.
2008-06-15 | E-GEOD-7835 | biostudies-arrayexpress
Project description:Mitochondria are centers of metabolism and signaling whose content and function must adapt to changing cellular environments. The biological signals that initiate mitochondrial restructuring and the cellular processes that drive this adaptive response are largely obscure. To better define these systems, we performed matched quantitative genomic and proteomic analyses of mouse muscle cells as they performed mitochondrial biogenesis. We find that proteins involved in cellular iron homeostasis are highly coordinated with this process, and that depletion of cellular iron results in a rapid, dose-dependent decrease of select mitochondrial protein levels and oxidative capacity. We further show that this process is universal across a broad range of cell types and fully reversed when iron is reintroduced. Collectively, our work reveals that cellular iron is a key regulator of mitochondrial biogenesis, and provides quantitative datasets that can be leveraged to explore post-transcriptional and post-translational processes that are essential for mitochondrial adaptation. C2C12 mouse myoblasts were differentiated into myotubes for 3 days, at which point they were infected with adenovirus expressing either green fluorescent protein (GFP) or GFP-tagged PGC-1M-NM-1 (GFP-PGC-1M-NM-1) M-BM-1 treatment with the iron chelator deferoxamine (DFO) (for 4 treatments total). The cells were grown for three more days, then RNA was extracted and applied to Affymetrix Mouse 430 2.0 arrays. Gene expression was measured in biological duplicate (4 treatments M-CM-^W 2 replicates = 8 arrays).
2012-12-10 | E-GEOD-42299 | biostudies-arrayexpress
Project description:Chronic obstructive pulmonary disease (COPD), the fourth leading cause of death globally, is influenced by both cigarette smoking and genetic determinants. We have previously identified iron-responsive element binding protein 2 (IRP2) as a candidate COPD susceptibility gene based on genetic association studies, with IRP2 increased in the lungs of COPD patients. Here we demonstrate that mice deficient in IRP2 are protected from cigarette smoke (CS)-induced COPD. Using RIP-Seq, RNA-Seq, gene expression and pathway analysis, we identify IRP2 as a regulator of mitochondrial function in the lung. We show that an increase in IRP2 results in a cytochrome c oxidase (COX)-dependent alteration in oxidative capacity and mitochondrial-iron dysfunction involving frataxin. We demonstrate that mice with impaired COX or frataxin activity have altered responses to CS and show that overexpressing IRP2 in vivo alters mitochondrial dynamics. These data suggest a critical role of the mitochondria-iron axis in mediating the pathogenesis of COPD. 1.5 X106 Beas2B cells (purchased from ATCC) with or without 10 μM DFO (16 h) (15 cm2 dishes) were washed with ice cold PBS and collected into 2 ml eppendorfs by scraping. RNA immunoprecipitation was carried out using the Magna RIP� RNA-Binding Protein Immunoprecipitation Kit (Millipore, Billerica, MA). 4 μg of Irp2 (7H6: sc-33682, Santa Cruz, Dallas, Texas) or 4 μg of IgG rabbit control antibody (sc-2749, Santa Cruz) were added to supernatants and incubated overnight at 4°C. RNA was extracted from Magna RIP� beads by Trizol extraction. Samples were prepared for RNA-Seq using the TruSeq RNA-Seq Lib Prep Reagent (Illumina, San Diego, CA) and performed on the Illumina HiSeq2000 platform.
2016-07-03 | E-GEOD-57073 | biostudies-arrayexpress
Project description:Neuroblastoma (NB) is the most frequent extracranial solid tumour of childhood. Clinical courses are highly variable, ranging from spontaneous regression/maturation to rapid progression despite intensive multimodal therapy. The estimation of 5-year event free survival in high-risk patients of only about 40 % stresses an importance of novel therapeutic strategies. A number of iron chelators have demonstrated marked in vitro and in vivo anti-tumor activity and are currently being developed as novel anti-cancer agents. Therefore, the potential antitumor effect of iron chelators in NB cancer was investigated. Among the compounds tested, ciclopirox olamine (CPX) was shown to be one of the most effective intracellular iron chelators in NB cells. To unveil the molecular mechanisms underlying the effects of CPX on viability of NB cells, microarray analysis was performed in CHP134 control cells and cells treated with 5 µM CPX for 90 minutes. Inclusion of both total RNA (reflecting transcriptional status of the cells) and polysomal RNA (approximating the proteomic representation of the cells) provided us with a deeper understanding of changes in the cells upon CPX treatment. Keywords: ciclopirox olamine, iron chelator, neuroblastoma, translatome profiling, transcriptome profiling. Keywords: ciclopirox olamine, iron chelator, neuroblastoma, translatome profiling, transcriptome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling
2015-02-04 | GSE60675 | GEO
Project description:Iron-deficiency affects 500 million people, yet the molecular role of iron in gene expression remains poorly characterized. Moreover, the alterations in global gene expression after iron chelation remains unclear and are important to assess for understanding the molecular pathology of iron-deficiency and the biological effects of iron chelators. We assessed the effect on whole genome gene expression of two iron chelators (desferrioxamine and 2-hydroxy-1-napthylaldehyde isonicotinoyl hydrazone) that have markedly different permeability properties. Sixteen genes were significantly regulated by both chelators, while a further 50 genes were regulated by either ligand. Most of the genes identified in this study have not been previously described to be iron-regulated and are important for understanding the molecular and cellular effects of iron-deficiency.
2010-02-28 | GSE17832 | GEO
Project description:The molecular role of iron in gene expression remains poorly characterized. Moreover, the alterations in global gene expression after iron chelation remains unclear and are important to assess for understanding the molecular pathology of iron-depletion and the biological effects of iron chelators. We assessed the effect on whole genome gene expression of two iron chelators (desferrioxamine and Dp44mT). These studies are important for understanding the molecular and cellular effects of iron-depletion.
2011-12-31 | GSE26920 | GEO