Eukaryotic Initiation Factor 4E Binding Protein Family of Proteins: Sentinels at a Translational Control Checkpoint in Lung Tumor Defense
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Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Accumulation of Dephosphorylated 4EBP After Mtor Inhibition with Rapamycin Is Sufficient to Disrupt Paracrine Transformation By
Oncogene (2014) 33, 2405–2412 & 2014 Macmillan Publishers Limited All rights reserved 0950-9232/14 www.nature.com/onc SHORT COMMUNICATION Accumulation of dephosphorylated 4EBP after mTOR inhibition with rapamycin is sufficient to disrupt paracrine transformation by the KSHV vGPCR oncogene D Martin, Q Nguyen, A Molinolo and JS Gutkind Dysregulation of the PI3K/Akt/mTOR pathway is one of the most frequent events in human cancer. However, the clinical benefits of PI3K/Akt/mTOR inhibitors have not yet achieved their predicted potential in many of the most prevalent human cancers. Of interest, treatment of Kaposi’s sarcoma (KS) patients with rapamycin provided the first evidence of the antineoplastic activity of mTOR inhibitors in humans, becoming the standard of care for KS arising in renal transplant patients. Thus, the study of KS may provide a unique opportunity to dissect the contribution of specific mTOR downstream targets to cancer development. The KS- associated herpesvirus (KSHV) is the etiological agent for KS, and the KSHV-encoded oncogene viral-G protein-coupled receptor (vGPCR) promotes the potent activation of the PI3K-Akt-mTOR pathway by both direct and paracrine mechanisms. We focused on a direct target of mTOR, EIF4EBP1/2/3 (4EBP), which inhibits the translation of eukaryotic initiation factor 4E (eiF4E)-bound mRNAs. 4EBP phosphorylation by mTOR relieves its inhibitory activity, hence resulting in increased eiF4E-dependent mRNA translation. We developed a paracrine transformation model, recapitulating the cellular composition of KS lesions, in which vGPCR-expressing cells promote the rapid proliferation of endothelial cells, thus expressing KSHV-latent genes by the release of growth factors. -
4E-BP2 / EIF4EBP2 Antibody (Aa99-120) Rabbit Polyclonal Antibody Catalog # ALS12947
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 4E-BP2 / EIF4EBP2 Antibody (aa99-120) Rabbit Polyclonal Antibody Catalog # ALS12947 Specification 4E-BP2 / EIF4EBP2 Antibody (aa99-120) - Product Information Application IHC Primary Accession Q13542 Reactivity Human, Mouse, Rat, Pig, Bovine, Dog Host Rabbit Clonality Polyclonal Calculated MW 13kDa KDa 4E-BP2 / EIF4EBP2 Antibody (aa99-120) - Additional Information Anti-EIF4EBP2 / 4EBP2 antibody IHC of Gene ID 1979 human pancreas. Other Names Eukaryotic translation initiation factor 4E-BP2 / EIF4EBP2 Antibody (aa99-120) - 4E-binding protein 2, 4E-BP2, eIF4E-binding Background protein 2, EIF4EBP2 Regulates eIF4E activity by preventing its Target/Specificity assembly into the eIF4F complex. Mediates the Detects 17 and 20 kD proteins, regulation of protein translation by hormones, corresponding to the apparent molecular growth factors and other stimuli that signal mass of PHAS-II and its phosphorylated through the MAP kinase pathway. state on SDS-PAGE immunoblots. 4E-BP2 / EIF4EBP2 Antibody (aa99-120) - Reconstitution & Storage References Short term 4°C, long term aliquot and store at -20°C, avoid freeze thaw cycles. For Pause A.,et al.Nature 371:762-767(1994). maximum product recovery, after thawing, Kalnine N.,et al.Submitted (MAY-2003) to the centrifuge the product vial before removing cap. EMBL/GenBank/DDBJ databases. Dephoure N.,et al.Proc. Natl. Acad. Sci. U.S.A. Precautions 105:10762-10767(2008). 4E-BP2 / EIF4EBP2 Antibody (aa99-120) is Gauci S.,et al.Anal. Chem. for research use only and not for use in 81:4493-4501(2009). diagnostic or therapeutic procedures. -
Adaptive Capabilities of the Pi3k/Akt/Mtor Pathway in Acute Myeloid Leukemia Revealed by the Use of Selective Inhibitors
Alma Mater Studiorum – Università di Bologna SCIENZE BIOMEDICHE: PROGETTO 5 “SCIENZE MORFOLOGICHE UMANE E MOLECOLARI” Ciclo XXV SSD : BIO 16, SETTORE CONCORSUALE :05H1 ADAPTIVE CAPABILITIES OF THE PI3K/AKT/MTOR PATHWAY IN ACUTE MYELOID LEUKEMIA REVEALED BY THE USE OF SELECTIVE INHIBITORS Presentata da Jessika Bertacchini Relatori Prof.ssa Lucia Manzoli Prof.ssa Sandra Marmiroli Coordinatore Chiar. mo Prof. Lucio Cocco TABLE OF CONTENTS o ABSTRACT o INTRODUCTION o ACUTE MYELOID LEUKEMIA o PROGNOSIS AND GENETICS o DEREGULATED SIGNAL TRANSDUCTION PATHWAYS IN ACUTE MYELOID LEUKEMIA o PI3K/AKT/MTOR SIGNAL TRANSDUCTION PATHWAY IN ACUTE MYELOID LEUKEMIA o PI3K o AKT/PKB o Mtor o NEGATIVE REGULATION OF PI3K/AKT/mTOR PATHWAY o PI3K/AKT/mTOR PATHWAY AND SURVIVAL o PI3K/AKT/mTOR PATHWAY AND CELL CYCLE o PI3K/AKT/mTOR PATHWAY AND METABOLISM o PI3K/AKT/mTOR INHIBITORS o PI3K INHIBITORS o AKT INHIBITORS o mTOR INHIBITORS o TYROSINE KINASE RECEPTOR o TYROSINE KINASE RECEPTOR IN ACUTE MYELOID LEUKEMIA o AIMS o MATERIALS AND METHODS o PATIENTS DEMOGRAPHICS o CELL CULTURE AND DRUG TREATMENTS o ARRAY ASSEMBLY o RESULTS o RESULTS o DISCUSSION o BIBLIOGRA 1.ABSTRACT The objective of the study was to investigate the sensitivity of primary blasts from AML patients to PI3K/Akt/mTor inhibitors through reverse-phase protein microarray. Reverse-phase microarray assays using phosphospecific antibodies (RPPA) can directly measure levels of phosphorylated protein isoforms. Mapping of deregulated kinases and protein signaling networks within tumors can provide a means to stratify patients with shared biological characteristics to the most optimal treatment, and identify drug targets. In particular, the PI3K/AKT/mTOR signaling pathways are frequently activated in blast cells from patients with acute myelogenous leukemia (AML), a neoplastic disorder characterized by the accumulation of genetically altered myelogenous cells displaying deregulated intracellular signalling pathways and aggressive clinical behavior with poor prognosis. -
Comparative Mapping of Bovine Chromosome 27 with Human Chromosome 8 Near a Dairy Form QTL in Cattle
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Agriculture: Agricultural Publications from USDA-ARS / UNL Faculty Research Service, Lincoln, Nebraska 2006 Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle E. E. Connor USDA-ARS M. S. Ashwell North Carolina State University at Raleigh R. Schnabel University of Missouri-Columbia J. L. Williams Roslin Institute (Edinburgh) Follow this and additional works at: https://digitalcommons.unl.edu/usdaarsfacpub Part of the Agricultural Science Commons Connor, E. E.; Ashwell, M. S.; Schnabel, R.; and Williams, J. L., "Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle" (2006). Publications from USDA-ARS / UNL Faculty. 698. https://digitalcommons.unl.edu/usdaarsfacpub/698 This Article is brought to you for free and open access by the U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications from USDA-ARS / UNL Faculty by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Original Article Cytogenet Genome Res 112:98–102 (2006) DOI: 10.1159/000087519 Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle E.E. Connor,a M.S. Ashwell,a,b R. Schnabel,c J.L. Williamsd a Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD; b North Carolina State University, Department of Animal Science, Raleigh, NC; c University of Missouri-Columbia, Animal Sciences Unit, Columbia, MO (USA); d Roslin Institute (Edinburgh), Roslin, Midlothian, Scotland (UK) Manuscript received 30 December 2004; accepted in revised form for publication by T. -
Protein.Spotlight a Question of Perspective
Issue 168, April 2015 www.proteinspotlight.org Issue 168 Protein.Spotlight e838 a question of perspective Vivienne Baillie Gerritsen Paradigms are meant to be broken. In the 1980s, biology students were taught “the one gene = one protein” dogma which has since stepped down from its pedestal, as we now know that one gene, by way of any number of post-translational modifications on the protein sequence, can actually give rise to more than one protein. Or what would be more correct: to more than one function. In the same way, structural biologists are beginning to realise that proteins are not always stable bu t that a significant amount exist in particularly unstable forms – which has given them the name “disordered proteins”. Until recently, proteins were thought to fold up into thermodynamically stable forms before getting on with what they had to do. Now we know that it is not necessarily the case. Eukaryotic translation initiation factor 4E- binding protein 2, for instance, is one such disordered protein whose lack of stability gives rise to a new kind of biological regulation. But it took a further 20 years for such a notion to become popular. This is because of the angle from which structural biologists have been observing proteins. It is not an easy task to predict the kinetics and thermodynamics underlying the conformational states of a protein – not to mention those driving its catalytic reactions and binding properties. So, as is the case in scientific research, biologists set a basis from which they can make powerful correlations. In this case, low energy states and a limited number of combinations of macromolecules which provided links between the 3D conformation of proteins and by Jodee Knowles their functions. -
B Inhibition in a Mouse Model of Chronic Colitis1
The Journal of Immunology Differential Expression of Inflammatory and Fibrogenic Genes and Their Regulation by NF-B Inhibition in a Mouse Model of Chronic Colitis1 Feng Wu and Shukti Chakravarti2 Fibrosis is a major complication of chronic inflammation, as seen in Crohn’s disease and ulcerative colitis, two forms of inflam- matory bowel diseases. To elucidate inflammatory signals that regulate fibrosis, we investigated gene expression changes under- lying chronic inflammation and fibrosis in trinitrobenzene sulfonic acid-induced murine colitis. Six weekly 2,4,6-trinitrobenzene sulfonic acid enemas were given to establish colitis and temporal gene expression patterns were obtained at 6-, 8-, 10-, and 12-wk time points. The 6-wk point, TNBS-w6, was the active, chronic inflammatory stage of the model marked by macrophage, neu- trophil, and CD3؉ and CD4؉ T cell infiltrates in the colon, consistent with the idea that this model is T cell immune response driven. Proinflammatory genes Cxcl1, Ccl2, Il1b, Lcn2, Pla2g2a, Saa3, S100a9, Nos2, Reg2, and Reg3g, and profibrogenic extra- cellular matrix genes Col1a1, Col1a2, Col3a1, and Lum (lumican), encoding a collagen-associated proteoglycan, were up-regulated at the active/chronic inflammatory stages. Rectal administration of the NF-B p65 antisense oligonucleotide reduced but did not abrogate inflammation and fibrosis completely. The antisense oligonucleotide treatment reduced total NF-B by 60% and down- regulated most proinflammatory genes. However, Ccl2, a proinflammatory chemokine known to promote fibrosis, was not down- regulated. Among extracellular matrix gene expressions Lum was suppressed while Col1a1 and Col3a1 were not. Thus, effective treatment of fibrosis in inflammatory bowel disease may require early and complete blockade of NF-B with particular attention to specific proinflammatory and profibrogenic genes that remain active at low levels of NF-B. -
Human 4E-BP1 / EIF4EBP1 Protein (His Tag)
Human 4E-BP1 / EIF4EBP1 Protein (His Tag) Catalog Number: 10022-H07E General Information SDS-PAGE: Gene Name Synonym: 4E-BP1; 4EBP1; BP-1; PHAS-I Protein Construction: A DNA sequence encoding the human 4EBP1 (NP_004086.1) (Ser 2-Ile 118) with a N-terminal polyhistidine tag was expressed. Source: Human Expression Host: E. coli QC Testing Purity: > 90 % as determined by SDS-PAGE Endotoxin: Protein Description Please contact us for more information. The translational suppressor eIF4E binding protein-1, 4E-BP1 functions as Stability: a key regulator in cellular growth, differentiation, apoptosis and survival. The Eif4ebp1 gene, encoding 4E-BP1, is a direct target of a transcription Samples are stable for up to twelve months from date of receipt at -70 ℃ factor activating transcription factor-4 (ATF4), a master regulator of gene expression in stress responses. 4E-BP1 is characterized by its capacity to Predicted N terminal: Met bind specifically to eIF4E and inhibit its interaction with eIF4G. Molecular Mass: Phosphorylation of 4E-BP1 regulates eIF4E availability, and therefore, cap- dependent translation, in cell stress. Binding of eIF4E to eIF4G is inhibited The secreted recombinant human 4EBP1 comprises 124 amino acids with in a competitive manner by 4E-BP1. Phosphorylation of 4E-BP1 decreases a predicted molecular mass of 13.4 kDa. It migrates as an approximately the affinity of this protein for eIF4E, thus favouring the binding of eIF4G 19 kDa band in SDS-PAGE under reducing conditions. and enhancing translation. 4E-BP1 is important for beta-cell survival under endoplasmic reticulum (ER) stress. 4E-BP1 mediates the regulation of Formulation: protein translation by hormones, growth factors and other stimuli that signal through the MAP kinase and mTORC1 pathways. -
Copy Number Variants in Ebstein Anomaly
RESEARCH ARTICLE Copy number variants in Ebstein anomaly Andreas Giannakou1, Robert J. Sicko2, Wei Zhang1, Paul Romitti3, Marilyn L. Browne4, Michele Caggana2, Lawrence C. Brody5, Laura Jelliffe-Pawlowski6, Gary M. Shaw7, Denise M. Kay2, James L. Mills1* 1 Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America, 2 Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America, 3 Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America, 4 Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, New York, United States of America, 5 Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America, 6 California University of California a1111111111 San Francisco School of Medicine, San Francisco, California, United States of America, 7 Department of a1111111111 Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America a1111111111 a1111111111 * [email protected] a1111111111 Abstract OPEN ACCESS Citation: Giannakou A, Sicko RJ, Zhang W, Romitti Background P, Browne ML, Caggana M, et al. (2017) Copy Ebstein anomaly (EA) is a rare congenital defect characterized by apical displacement of number variants in Ebstein anomaly. PLoS ONE 12 (12): e0188168. https://doi.org/10.1371/journal. the septal tricuspid leaflets and atrialization of the right ventricle. The etiology of EA is pone.0188168 unclear; however, recurrence in families and the association of EA with genetic syndromes Editor: Diego Fraidenraich, Rutgers University and copy number variants (CNVs) suggest a genetic component. -
Relevance of Translation Initiation in Diffuse Glioma Biology and Its
cells Review Relevance of Translation Initiation in Diffuse Glioma Biology and its Therapeutic Potential Digregorio Marina 1, Lombard Arnaud 1,2, Lumapat Paul Noel 1, Scholtes Felix 1,2, Rogister Bernard 1,3 and Coppieters Natacha 1,* 1 Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; [email protected] (D.M.); [email protected] (L.A.); [email protected] (L.P.N.); [email protected] (S.F.); [email protected] (R.B.) 2 Department of Neurosurgery, CHU of Liège, 4000 Liège, Belgium 3 Department of Neurology, CHU of Liège, 4000 Liège, Belgium * Correspondence: [email protected] Received: 18 October 2019; Accepted: 26 November 2019; Published: 29 November 2019 Abstract: Cancer cells are continually exposed to environmental stressors forcing them to adapt their protein production to survive. The translational machinery can be recruited by malignant cells to synthesize proteins required to promote their survival, even in times of high physiological and pathological stress. This phenomenon has been described in several cancers including in gliomas. Abnormal regulation of translation has encouraged the development of new therapeutics targeting the protein synthesis pathway. This approach could be meaningful for glioma given the fact that the median survival following diagnosis of the highest grade of glioma remains short despite current therapy. The identification of new targets for the development of novel therapeutics is therefore needed in order to improve this devastating overall survival rate. This review discusses current literature on translation in gliomas with a focus on the initiation step covering both the cap-dependent and cap-independent modes of initiation. -
DATASHEET Eukaryotic Translation Initiation Factor 4E-Binding
DATASHEET Abbexa Ltd, Innovation Centre, Cambridge Science Park, Cambridge, CB4 0EY, UK Telephone: +44 (0) 1223 755950 - Fax: +44 (0) 1223 755951 - E-Mail: [email protected] Eukaryotic Translation Initiation Factor 4E-Binding Protein 1 (4EBP1) Antibody Catalogue No.:abx015717 Western blot analysis using 4E-BP1 antibody against truncated 4E-BP1 recombinant protein (1) and A431 cell lysate (2). Immunohistochemical analysis of paraffin-embedded human pancreas carcinoma (A), esophagus carcinoma tissue (B) and ovary tumor tissue (C), showing cytoplasmic and membrane localization using 4E-BP1 antibody with DAB staining. 4E-BP1 (eukaryotic translation Initiation Factor 4E Binding Protein 1),also called ELF4EBP1/BP-1/PHAS-I,which is located on chromosome 8p12, with 118-amino acid protein (about 13kDa).Binding of eIF4EBP1 to eIF4E is reversible and is dependent on the phosphorylation status of eIF4EBP1.Non phosphorylated eIF4EBP1 will bind strongly to eIF4E while (24kDa), the phosphorylated form will not.Akt, TOR, MAP kinase, S6 kinase, and Cdc2 are known kinases capable of inactivating eIF4EBP1 binding to eIF4E by phosphorylating either threonines 35, 45, 69 or serine 64.Although, not all phosphorylation events equally block the eIF4EBP1-eIF4E interaction. Target: 4EBP1 Reactivity: Human Host: Mouse Clonality: Monoclonal Tested Applications: ELISA, WB, IHC Recommended dilutions: ELISA: 1/10000, WB: 1/500 - 1/2000, IHC: 1/200 - 1/1000. Optimal dilutions/concentrations should be determined by the end user. Immunogen: Purified recombinant fragment of 4E-BP1 expressed in E. coli. Purification: Unpurified Ascites. Registered in England: 8475531 - VAT Reg No: GB 167 9240 79 Page 1 DATASHEET Abbexa Ltd, Innovation Centre, Cambridge Science Park, Cambridge, CB4 0EY, UK Telephone: +44 (0) 1223 755950 - Fax: +44 (0) 1223 755951 - E-Mail: [email protected] Isotype: IgG1 Conjugation: Unconjugated Storage: Aliquot and store at -20 °C. -
4E-BP1 Antibody [9E12D9] Cat
4E-BP1 Antibody [9E12D9] Cat. No.: 32-101 4E-BP1 Antibody [9E12D9] Specifications HOST SPECIES: Mouse SPECIES REACTIVITY: Human IMMUNOGEN: Ni-NTA purified truncated recombinant 4EBP1 expressed in E. Coli strain BL21 (DE3). TESTED APPLICATIONS: ELISA, WB Western Blot:1:500 - 1:1,000. APPLICATIONS: ELISA:Propose dilution 1:10,000. Determining optimal working dilutions by titration test. Properties CLONALITY: Monoclonal ISOTYPE: IgG1 CONJUGATE: Unconjugated BUFFER: Ascitic fluid containing 0.03% sodium azide. 4E-BP1 monoclonal antibody can be stored at -20˚C, stable for one year. As with all STORAGE CONDITIONS: antibodies care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. September 25, 2021 1 https://www.prosci-inc.com/4e-bp1-antibody-9e12d9-32-101.html Additional Info OFFICIAL SYMBOL: EIF4EBP1 Phosphorylated heat- and acid-stable protein regulated by insulin 1, 4E-BP1, BP-1, 4EBP1, ALTERNATE NAMES: PHAS-I ACCESSION NO.: Q13541 PROTEIN GI NO.: 34921508 GENE ID: 1978 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References 4E-BP1(eukaryotic translation Initiation Factor 4E Binding Protein 1),also called ELF4EBP1/BP-1/PHAS-I ,which is located on chromosome 8p12, with 118-amino acid protein (about 13 kDa). Binding of eIF4EBP1 to eIF4E is reversible and is dependent on the phosphorylation status of eIF4EBP1. Non phosphorylated eIF4EBP1 will bind strongly to BACKGROUND: eIF4E while(24 kDa), the phosphorylated form will not. Akt, TOR, MAP kinase, S6 kinase, and Cdc2 are known kinases capable of inactivating eIF4EBP1 binding to eIF4E by phosphorylating either threonines 35, 45, 69 or serine 64.