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Dissertation DISSERTATION Titel der Dissertation Functional Proteomics of Bcr-Abl Signaling angestrebter akademischer Grad Doktor der Naturwissenschaften (Dr. rer.nat.) Verfasserin / Verfasser: Marc Jochen Brehme, M.Sc. Matrikel-Nummer: 0605249 Dissertationsgebiet (lt. 490 Molekulare Biologie Studienblatt): Betreuerin / Betreuer: Prof. Dr. Giulio Superti-Furga CeMM – Research Center for Molecular Medicine Austrian Academy of Sciences Wien, im Februar 2009 “In any case: The future looks bright, but let's talk about it!” Giulio Superti-Furga (July 2005) II III I am indebted to a number of people who contributed their time, expertise and passion during the pursuit of my PhD - thesis and I would like to express my gratitude to: Prof. Dr. Giulio Superti-Furga, for accepting me as his first PhD student in Vienna, for being my supervisor, for his memorable and bold leadership, his enthusiasm, for providing me with an innovative and inspiring working environment and for giving me the chance to work on this fascinating project. Oliver Hantschel, PhD, for his great and constructive supervision, his excellent assistance and incessant patience during the pursuit of my PhD - thesis. Prof. Junia V. Melo, MD, PhD and Univ.-Prof. Dr. Kristina Djinovic-Karugo, for being on my PhD thesis committee and for appraising this thesis. Anita Ender, for sharing evenings with me in the office and for her ingenious help with all administrative and organizational matters. Prof. Gerhard Schadler, for being the grey eminence in the background. The Austrian Academy of Sciences and the Austrian Science Fund (FWF), for funding the research project. I would like to thank all my past and present colleagues at CeMM, especially those who shared the laboratory with me during the last years, for contributing their valuable support, conversations, ideas and suggestions: Uwe Rix especially for the drugs, Lily Remsing-Rix, Nora Fernbach, Florian Grebien, Christoph Baumann, Alberto Calabro, Emanuel Gasser, Patricia Ganger, Evelyn Dixit, Gerhard Dürnberger, Thomas Stranzl, Florian Breitwieser, Thomas Burkard, Evren Karayel, Adrijana Stefanovic, Irene Aspalter, Hannah Jahn, Adriana Goncalves, Andreas Pichlmair, Roberto Giambruno, Georg Winter, Roberto Sacco, Ruth Scheicher, Stefan Blüml, Leopold Liechtenstein, Verena Lichtenegger and Michael Pilz for IT administration. Tilmann Bürckstümmer, for ʻtuningʼ the TAP protocol, for all his advice and for being such a great ʻlab citizenʼ. Keiryn Bennett, Melanie Planyavsky, André Müller, Norbert Venturini and Gregor Schütze, for world-class MS. Jacques Colinge, for his industrious computing. Ines Kaupe and Martin Krammer, for their excellent experimental support. Agnes Gstoettenbauer, for all the siRNA knockdowns. Edith Müller-Primeßnig, for her kind chocolate offers during the preparation of this thesis. Thomas Köcher and Karl Mechtler, for performing the iTRAQ analysis. Anne-Claude Gavin, for hosting me in her lab at the EMBL to purify yeast protein complexes. David Wisniewski, for supplying the excellent Ship2 antiserum that was indispensable for this work. Angela Bauch, for getting me in the door of Cellzome and the exciting world of proteomics. My girlfriend Heide, for her love, cheerfulness, music, food and the greatest time in Vienna and her parents for their support and encouragement. My parents and my brother Ralph, for their love and their cordial and never-ending care, support and encouragement. IV V Major parts of the results presented in this thesis are submitted for publication and currently under revision in the following manuscript: Brehme, M. *, Hantschel, O. *, Colinge, J., Kaupe, I., Planyavsky, M., Köcher, T., Mechtler, K., Bennett, K.L., Superti-Furga, G., “Charting the molecular network of the drug target Bcr-Abl”, PNAS, under revision * Equal contributions of Brehme, M. and Hantschel, O. VI Summary SUMMARY The constitutively active oncogenic fusion tyrosine kinase Bcr-Abl is the product of a reciprocal chromosomal translocation (t(9;22), ʻPhiladelphia Chromosomeʼ). The constitutive tyrosine kinase activity is central to Bcr-Ablʼs ability to cause chronic myeloid leukemia (CML) and is the target of tyrosine kinase inhibitors like imatinib (Gleevec®, Novartis). Despite the success of imatinib, many patients either develop resistance to the drugs and eventually relapse or they do not respond, when the treatment is initiated in advanced stages of the disease. However, the actual molecular setup of the endogenous drug target Bcr-Abl is still unknown. We have therefore charted the protein- protein interaction network of Bcr-Abl by a systematic two-pronged proteomics approach: Using a monoclonal antibody we have first purified endogenous Bcr-Abl protein complexes from the CML cell line K562 and characterized a set of eighteen most tightly associated interactors by mass spectrometry. Nine interactors were subsequently subjected to tandem affinity purification/mass spectrometry analysis to obtain a molecular interaction network. The resulting network revealed a high degree of interconnection of seven 'core' components around Bcr-Abl (Ship2, c-Cbl, p85, Sts-1, Shc1, Grb2 and Crk-I), as well as their links to the AP2 adaptor protein complex and different signaling pathways. Quantitative analysis of these Bcr-Abl ʻcoreʼ complex components showed that the absolute protein copy numbers range within one order of magnitude consistent with a stoichiometric complex of around 200,000 to 300,000 copies per cell and revealed the highest interaction stoichiometry for the 5-inositol phosphatase Ship2. Quantitative proteomics analysis showed that tyrosine kinase inhibitors disrupt this complex, while certain components still appear to interact with Bcr-Abl in a phospho-tyrosine-independent manner. The results of this study therefore motivate us to propose that Bcr-Abl and other drug targets, rather than being considered as single polypeptides, can be considered as complex protein assemblies that are disrupted or re-modeled upon drug action. VII Zusammenfassung ZUSAMMENFASSUNG Die konstitutiv aktive onkogene Fusions-Tyrosin-Kinase Bcr-Abl resultiert aus einer reziproken chromosomalen Translokation (t(9;22), ‚Philadelphia Chromosomʼ). Die konstitutive Tyrosin-Kinaseaktivität von Bcr-Abl ist Auslöser der Chronisch Myeloischen Leukämie (CML) und das Ziel von Tyrosin-Kinaseinhibitoren wie Imatinib (Gleevec®, Novartis). Trotz des Erfolges von Imatinib entwickeln Patienten Resistenzen und werden rückfällig oder sprechen nicht auf die Therapie an, wenn diese erst in fortgeschrittenen Krankheitsstadien initiiert wird. Dennoch ist die genaue Beschaffenheit des endogenen Arzneistoffziels Bcr-Abl noch unbekannt. Daher haben wir das Protein-Interaktionsnetzwerk um Bcr-Abl mit einer doppelten proteomischen Herangehensweise systematisch kartiert: Anhand eines monoklonalen Antikörpers haben wir zunächst endogene Bcr-Abl - Proteinkomplexe aus der CML-Zelllinie K562 gewonnen und massenspektrometrisch die achtzehn engsten Interaktoren charakterisiert. Nach ‚Tandem-Affinitätsreinigungʼ von neun dieser Kandidaten und massenspektrometrischer Analyse haben wir ein Interaktionsnetzwerk erstellt, das eine intensive Vernetzung der sieben ‚Kernkomponentenʼ (Ship2, c-Cbl, p85, Sts-1, Shc1, Grb2 und Crk-I) mit Bcr-Abl und deren Verknüpfung mit dem AP2-Adapterproteinkomplex und verschiedenen Signaltransduktionswegen offenbarte. Quantitative Analysen dieser sieben Komponenten zeigten, dass sich deren absolute Kopienzahl innerhalb einer Größenordnung bewegt und auf 200,000 - 300,000 stöchiometrische Komplexe pro Zelle schließen lässt, wobei die 5-Inositol-Phosphatase Ship2 die höchste Interaktionsstöchiometrie aufweist. Massenspektrometrische Quantifizierungen zeigten, dass Tyrosin- Kinaseinhibitoren den Bcr-Abl-ʼKernkomplexʼ zerstören, einige Komponenten aber in Phospho-Tyrosin-unabhängiger Weise mit Bcr-Abl verbunden bleiben. Wir kommen daher zu der Hypothese, dass Bcr-Abl und auch andere Arzneistoffziele nicht nur als einzelne Polypeptide, sondern vielmehr als komplexe Proteinverbände zu betrachten sind, die durch Arzneistoffe zerstört oder verändert werden. VIII IX Table of Contents TABLE OF CONTENTS SUMMARY VII ZUSAMMENFASSUNG VIII TABLE OF CONTENTS X 1 INTRODUCTION 2 1.1 Chronic myeloid leukemia (CML) 2 1.2 Expression of Bcr-Abl from the Philadelphia chromosome is sufficient to cause CML 5 1.3 Bcr-Abl protein architecture, domain structures and regulation 7 1.4 The Bcr-Abl phospho-tyrosine profile 12 1.5 Bcr-Abl, its interactors and affected signaling pathways 15 1.6 The human leukemia model cell line K562 18 1.7 “Oncogene addiction” 19 1.8 Targeted therapy by imatinib: the current front-line therapy for Ph-positive CML and ALL 21 1.9 Molecular determinants of CML patients relapse 24 1.10 Second generation tyrosine kinase inhibitors 25 1.11 Combination-therapies and alternative approaches 27 1.12 Signaling pathway mapping by Tandem Affinity Purification coupled to liquid chromatography and tandem mass spectrometry (TAP-LC-MSMS) 29 1.13 Quantitative proteomics 32 1.14 Aim of the thesis 35 2 MATERIALS AND METHODS 38 2.1 DNA constructs 38 2.2 Antibodies and epitopes 40 2.3 Cell culture, tyrosine kinase inhibitor treatment, immuno -precipitation and immunoblot assays 43 2.4 Large-scale immunoprecipitation of endogenous protein complexes of Bcr-Abl and its stoichiometric candidate ʻcoreʼ interactors 44 2.5 Generation of stable transgenic cell lines and Tandem Affinity Purification (TAP) 46 2.6 Mass Spectrometry and Bioinformatics 46 2.6.1 Sample preparation for mass
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