Ephrin-B1 Forward Signaling Regulates Craniofacial Morphogenesis by Controlling Cell Proliferation Across Eph–Ephrin Boundaries
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The Proximal Signaling Network of the BCR-ABL1 Oncogene Shows a Modular Organization
Oncogene (2010) 29, 5895–5910 & 2010 Macmillan Publishers Limited All rights reserved 0950-9232/10 www.nature.com/onc ORIGINAL ARTICLE The proximal signaling network of the BCR-ABL1 oncogene shows a modular organization B Titz, T Low, E Komisopoulou, SS Chen, L Rubbi and TG Graeber Crump Institute for Molecular Imaging, Institute for Molecular Medicine, Jonsson Comprehensive Cancer Center, California NanoSystems Institute, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA BCR-ABL1 is a fusion tyrosine kinase, which causes signaling effects of BCR-ABL1 toward leukemic multiple types of leukemia. We used an integrated transformation. proteomic approach that includes label-free quantitative Oncogene (2010) 29, 5895–5910; doi:10.1038/onc.2010.331; protein complex and phosphorylation profiling by mass published online 9 August 2010 spectrometry to systematically characterize the proximal signaling network of this oncogenic kinase. The proximal Keywords: adaptor protein; BCR-ABL1; phospho- BCR-ABL1 signaling network shows a modular and complex; quantitative mass spectrometry; signaling layered organization with an inner core of three leukemia network; systems biology transformation-relevant adaptor protein complexes (Grb2/Gab2/Shc1 complex, CrkI complex and Dok1/ Dok2 complex). We introduced an ‘interaction direction- ality’ analysis, which annotates static protein networks Introduction with information on the directionality of phosphorylation- dependent interactions. In this analysis, the observed BCR-ABL1 is a constitutively active oncogenic fusion network structure was consistent with a step-wise kinase that arises through a chromosomal translocation phosphorylation-dependent assembly of the Grb2/Gab2/ and causes multiple types of leukemia. It is found in Shc1 and the Dok1/Dok2 complexes on the BCR-ABL1 many cases (B25%) of adult acute lymphoblastic core. -
Mutation-Specific and Common Phosphotyrosine Signatures of KRAS G12D and G13D Alleles Anticipated Graduation August 1St, 2018
MUTATION-SPECIFIC AND COMMON PHOSPHOTYROSINE SIGNATURES OF KRAS G12D AND G13D ALLELES by Raiha Tahir A dissertation submitted to The Johns Hopkins University in conformity with the requirement of the degree of Doctor of Philosophy Baltimore, MD August 2018 © 2018 Raiha Tahir All Rights Reserved ABSTRACT KRAS is one of the most frequently mutated genes across all cancer subtypes. Two of the most frequent oncogenic KRAS mutations observed in patients result in glycine to aspartic acid substitution at either codon 12 (G12D) or 13 (G13D). Although the biochemical differences between these two predominant mutations are not fully understood, distinct clinical features of the resulting tumors suggest involvement of disparate signaling mechanisms. When we compared the global phosphotyrosine proteomic profiles of isogenic colorectal cancer cell lines bearing either G12D or G13D KRAS mutations, we observed both shared as well as unique signaling events induced by the two KRAS mutations. Remarkably, while the G12D mutation led to an increase in membrane proximal and adherens junction signaling, the G13D mutation led to activation of signaling molecules such as non-receptor tyrosine kinases, MAPK kinases and regulators of metabolic processes. The importance of one of the cell surface molecules, MPZL1, which found to be hyperphosphorylated in G12D cells, was confirmed by cellular assays as its knockdown led to a decrease in proliferation of G12D but not G13D expressing cells. Overall, our study reveals important signaling differences across two common KRAS mutations and highlights the utility of our approach to systematically dissect the subtle differences between related oncogenic mutants and potentially lead to individualized treatments. -
Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
Host-Pathogen Systems Biology: Logical Modelling of Hepatocyte
BMC Systems Biology BioMed Central Research article Open Access Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction Raimo Franke†1, Melanie Müller†1, Nicole Wundrack1, Ernst-Dieter Gilles2, Steffen Klamt2, Thilo Kähne1 and Michael Naumann*1 Address: 1Institute of Experimental Internal Medicine, Otto von Guericke University, Leipziger Str. 44, 39120 Magdeburg, Germany and 2Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany Email: Raimo Franke - [email protected]; Melanie Müller - [email protected]; Nicole Wundrack - [email protected]; Ernst-Dieter Gilles - [email protected]; Steffen Klamt - Klamt@mpi- magdeburg.mpg.de; Thilo Kähne - [email protected]; Michael Naumann* - [email protected] * Corresponding author †Equal contributors Published: 14 January 2008 Received: 3 October 2007 Accepted: 14 January 2008 BMC Systems Biology 2008, 2:4 doi:10.1186/1752-0509-2-4 This article is available from: http://www.biomedcentral.com/1752-0509/2/4 © 2008 Franke et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The hepatocyte growth factor (HGF) stimulates mitogenesis, motogenesis, and morphogenesis in a wide range of tissues, including epithelial cells, on binding to the receptor tyrosine kinase c-Met. Abnormal c-Met signalling contributes to tumour genesis, in particular to the development of invasive and metastatic phenotypes. -
CD93 and Dystroglycan Cooperation in Human Endothelial Cell Adhesion and Migration
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 9 CD93 and dystroglycan cooperation in human endothelial cell adhesion and migration Federico Galvagni1,*, Federica Nardi1,*, Marco Maida1, Giulia Bernardini1, Silvia Vannuccini2, Felice Petraglia2, Annalisa Santucci1, Maurizio Orlandini1 1 Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 2-53100 Siena, Italy 2 Department of Molecular and Developmental Medicine, Obstetrics and Gynecology, University of Siena, 53100 Siena, Italy *These authors contributed equally to this work Correspondence to: Maurizio Orlandini, e-mail: [email protected] Keywords: angiogenesis, signal transduction, C1qRp, Src, Cbl Received: June 29, 2015 Accepted: January 22, 2016 Published: February 02, 2016 ABSTRACT CD93 is a transmembrane glycoprotein predominantly expressed in endothelial cells. Although CD93 displays proangiogenic activity, its molecular function in angiogenesis still needs to be clarified. To get molecular insight into the biological role of CD93 in the endothelium, we performed proteomic analyses to examine changes in the protein profile of endothelial cells after CD93 silencing. Among differentially expressed proteins, we identified dystroglycan, a laminin-binding protein involved in angiogenesis, whose expression is increased in vascular endothelial cells within malignant tumors. Using immunofluorescence, FRET, and proximity ligation analyses, we observed a close interaction between CD93 and β-dystroglycan. Moreover, silencing experiments showed that CD93 and dystroglycan promoted endothelial cell migration and organization into capillary-like structures. CD93 proved to be phosphorylated on tyrosine 628 and 644 following cell adhesion on laminin through dystroglycan. This phosphorylation was shown to be necessary for a proper endothelial migratory phenotype. Moreover, we showed that during cell spreading phosphorylated CD93 recruited the signaling protein Cbl, which in turn was phosphorylated on tyrosine 774. -
RET Gene Fusions in Malignancies of the Thyroid and Other Tissues
G C A T T A C G G C A T genes Review RET Gene Fusions in Malignancies of the Thyroid and Other Tissues Massimo Santoro 1,*, Marialuisa Moccia 1, Giorgia Federico 1 and Francesca Carlomagno 1,2 1 Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy; [email protected] (M.M.); [email protected] (G.F.); [email protected] (F.C.) 2 Institute of Endocrinology and Experimental Oncology of the CNR, 80131 Naples, Italy * Correspondence: [email protected] Received: 10 March 2020; Accepted: 12 April 2020; Published: 15 April 2020 Abstract: Following the identification of the BCR-ABL1 (Breakpoint Cluster Region-ABelson murine Leukemia) fusion in chronic myelogenous leukemia, gene fusions generating chimeric oncoproteins have been recognized as common genomic structural variations in human malignancies. This is, in particular, a frequent mechanism in the oncogenic conversion of protein kinases. Gene fusion was the first mechanism identified for the oncogenic activation of the receptor tyrosine kinase RET (REarranged during Transfection), initially discovered in papillary thyroid carcinoma (PTC). More recently, the advent of highly sensitive massive parallel (next generation sequencing, NGS) sequencing of tumor DNA or cell-free (cfDNA) circulating tumor DNA, allowed for the detection of RET fusions in many other solid and hematopoietic malignancies. This review summarizes the role of RET fusions in the pathogenesis of human cancer. Keywords: kinase; tyrosine kinase inhibitor; targeted therapy; thyroid cancer 1. The RET Receptor RET (REarranged during Transfection) was initially isolated as a rearranged oncoprotein upon the transfection of a human lymphoma DNA [1]. -
Imatinib Dependent Tyrosine Phosphorylation Profiling of Bcr-Abl
Provided by the author(s) and University College Dublin Library in accordance with publisher policies. Please cite the published version when available. Title Imatinib-dependent tyrosine phosphorylation profiling of Bcr-Abl-positive chronic myeloid leukemia cells Authors(s) Preisinger, C.; Schwarz, J. P.; Bleijerveld, O. B.; et al. Publication date 2012-08-27 Publication information Leukemia, 27 (3): 743-746 Publisher Nature Publishing Group Item record/more information http://hdl.handle.net/10197/5078 Publisher's version (DOI) 10.1038/leu.2012.243 Downloaded 2021-09-25T14:43:28Z The UCD community has made this article openly available. Please share how this access benefits you. Your story matters! (@ucd_oa) © Some rights reserved. For more information, please see the item record link above. 1 Imatinib dependent tyrosine phosphorylation profiling of Bcr-Abl 2 positive chronic myeloid leukemia cells 3 Bcr-Abl is the major cause and pathogenetic principle of chronic myeloid leukemia (CML). 4 Bcr-Abl results from a chromosomal translocation that fuses the bcr and the abl genes, 5 thereby generating a constitutively active tyrosine kinase, which stimulates several signaling 6 networks required for proliferation and survival. Bcr-Abl’s oncogenic properties comprise 7 both functions as a kinase and as a scaffold protein 1. A number of Bcr-Abl interaction 8 partners and downstream effectors have been described, improving our understanding of the 9 signaling networks deranged in CML. Brehme et al. recently defined the “core-interactome of 10 Bcr-Abl”, identifying seven major interaction partners of Bcr-Abl (GRB2, Shc1, Crk, c-Cbl, 11 p85, Sts-1, and SHIP-2) 2. -
NCK1 Antibody (Monoclonal) (M01) Mouse Monoclonal Antibody Raised Against a Partial Recombinant NCK1
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 NCK1 Antibody (monoclonal) (M01) Mouse monoclonal antibody raised against a partial recombinant NCK1. Catalog # AT2980a Specification NCK1 Antibody (monoclonal) (M01) - Product Information Application WB, E Primary Accession P16333 Other Accession BC006403 Reactivity Human Host mouse Clonality Monoclonal Isotype IgG1 Kappa Calculated MW 42864 NCK1 Antibody (monoclonal) (M01) - Additional Information Antibody Reactive Against Recombinant Protein.Western Blot detection against Gene ID 4690 Immunogen (37.73 KDa) . Other Names Cytoplasmic protein NCK1, NCK adaptor protein 1, Nck-1, SH2/SH3 adaptor protein NCK-alpha, NCK1, NCK Target/Specificity NCK1 (AAH06403, 185 a.a. ~ 294 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Dilution WB~~1:500~1000 Format Clear, colorless solution in phosphate NCK1 monoclonal antibody (M01), clone 1A1 buffered saline, pH 7.2 . Western Blot analysis of NCK1 expression in Hela S3 NE ( (Cat # AT2980a ) Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Precautions NCK1 Antibody (monoclonal) (M01) is for research use only and not for use in diagnostic or therapeutic procedures. NCK1 Antibody (monoclonal) (M01) - Protocols Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Provided below are standard protocols that you may find useful for product applications. • Western Blot • Blocking Peptides • Dot Blot • Immunohistochemistry • Immunofluorescence • Immunoprecipitation • Flow Cytomety • Cell Culture Western Blot analysis of NCK1 expression in transfected 293T cell line by NCK1 monoclonal antibody (M01), clone 1A1. -
Detection of a Rare BCR–ABL Tyrosine Kinase Fusion Protein in H929 Multiple Myeloma Cells Using Immunoprecipitation (IP)-Tandem Mass Spectrometry (MS/MS)
Detection of a rare BCR–ABL tyrosine kinase fusion protein in H929 multiple myeloma cells using immunoprecipitation (IP)-tandem mass spectrometry (MS/MS) Susanne B. Breitkopfa,b, Min Yuana, German A. Pihanc, and John M. Asaraa,b,1 aDivision of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115; bDepartment of Medicine, Harvard Medical School, Boston, MA 02115; and cDepartment of Hematopathology, Beth Israel Deaconess Medical Center, Boston, MA 02115 Edited by Peter K. Vogt, The Scripps Research Institute, La Jolla, CA, and approved August 23, 2012 (received for review July 26, 2012) Hypothesis directed proteomics offers higher throughput over Here, we focused on a hypothesis-directed approach to identify global analyses. We show that immunoprecipitation (IP)–tandem the active signaling pathways that drive cancers. To this end, we mass spectrometry (LC-MS/MS) in H929 multiple myeloma (MM) immunoprecipitated proteins that have clinical significance in cell cancer cells led to the discovery of a rare and unexpected BCR– proliferation such as the central nodes in the AKT and ERK sig- ABL fusion, informing a therapeutic intervention using imatinib naling pathways. The p85 regulatory subunit of phosphoinositide- (Gleevec). BCR–ABL is the driving mutation in chronic myeloid leu- 3-kinase (PI3K) binds pYXXM motif-containing proteins to the kemia (CML) and is uncommon to other cancers. Three different IP– SRC homology 2 (SH2) domains of p85, thus recruiting the p110 MS experiments central to cell signaling pathways were sufficient to catalytic subunit to the plasma membrane for activation (5, 17). Activated p110 phosphorylates its lipid substrate phosphatidyli- discover a BCR–ABL fusion in H929 cells: phosphotyrosine (pY) pep- nositol-4,5-bisphosphate (PIP2) to phosphatidylinositol-3,4,5-tri- tide IP, p85 regulatory subunit of phosphoinositide-3-kinase (PI3K) phosphate (PIP3) and binds to the pleckstrin homology (PH) IP, and the GRB2 adaptor IP. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Supp Table 6.Pdf
Supplementary Table 6. Processes associated to the 2037 SCL candidate target genes ID Symbol Entrez Gene Name Process NM_178114 AMIGO2 adhesion molecule with Ig-like domain 2 adhesion NM_033474 ARVCF armadillo repeat gene deletes in velocardiofacial syndrome adhesion NM_027060 BTBD9 BTB (POZ) domain containing 9 adhesion NM_001039149 CD226 CD226 molecule adhesion NM_010581 CD47 CD47 molecule adhesion NM_023370 CDH23 cadherin-like 23 adhesion NM_207298 CERCAM cerebral endothelial cell adhesion molecule adhesion NM_021719 CLDN15 claudin 15 adhesion NM_009902 CLDN3 claudin 3 adhesion NM_008779 CNTN3 contactin 3 (plasmacytoma associated) adhesion NM_015734 COL5A1 collagen, type V, alpha 1 adhesion NM_007803 CTTN cortactin adhesion NM_009142 CX3CL1 chemokine (C-X3-C motif) ligand 1 adhesion NM_031174 DSCAM Down syndrome cell adhesion molecule adhesion NM_145158 EMILIN2 elastin microfibril interfacer 2 adhesion NM_001081286 FAT1 FAT tumor suppressor homolog 1 (Drosophila) adhesion NM_001080814 FAT3 FAT tumor suppressor homolog 3 (Drosophila) adhesion NM_153795 FERMT3 fermitin family homolog 3 (Drosophila) adhesion NM_010494 ICAM2 intercellular adhesion molecule 2 adhesion NM_023892 ICAM4 (includes EG:3386) intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)adhesion NM_001001979 MEGF10 multiple EGF-like-domains 10 adhesion NM_172522 MEGF11 multiple EGF-like-domains 11 adhesion NM_010739 MUC13 mucin 13, cell surface associated adhesion NM_013610 NINJ1 ninjurin 1 adhesion NM_016718 NINJ2 ninjurin 2 adhesion NM_172932 NLGN3 neuroligin -
Anti-VEGFR2 Phospho (Tyr1214) Antibody (ARG51588)
Product datasheet [email protected] ARG51588 Package: 100 μl, 50 μl anti-VEGFR2 phospho (Tyr1214) antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes VEGFR2 phospho (Tyr1214) Tested Reactivity Hu, Ms Tested Application ICC/IF, IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name VEGFR2 Antigen Species Human Immunogen Peptide sequence around phosphorylation site of tyrosine 1214 (F-H-Y(p)-D-N) derived from Human VEGFR2. Conjugation Un-conjugated Alternate Names FLK1; VEGFR; CD antigen CD309; FLK-1; Fetal liver kinase 1; VEGFR2; Vascular endothelial growth factor receptor 2; VEGFR-2; CD309; Kinase insert domain receptor; EC 2.7.10.1; Protein-tyrosine kinase receptor flk-1; KDR Application Instructions Application table Application Dilution ICC/IF 1:100 - 1:200 IHC-P 1:50 - 1:100 WB 1:500 - 1:1000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 152 kDa Properties Form Liquid Purification Antibodies were produced by immunizing rabbits with KLH-conjugated synthetic phosphopeptide. Antibodies were purified by affinity-chromatography using epitope-specific phosphopeptide. In addition, non-phospho specific antibodies were removed by chromatogramphy using non- phosphopeptide. Buffer PBS (without Mg2+ and Ca2+, pH 7.4), 150mM NaCl, 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol www.arigobio.com 1/3 Concentration 1 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C.