Molecular Diagnostics and Treatment of Pancreatic Cancer. Systems and Network Biology Approaches PDF
Preview Molecular Diagnostics and Treatment of Pancreatic Cancer. Systems and Network Biology Approaches
MOLECULAR DIAGNOSTICS AND TREATMENT OF PANCREATIC CANCER: SYSTEMS AND NETWORK BIOLOGY APPROACHES Edited by ASFAR S. AZMI Amsterdam • Boston • Heidelberg • London New York • Oxford • Paris • San Diego San Francisco • Singapore • Sydney • Tokyo Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 32 Jamestown Road, London NW1 7BY, UK 225 Wyman Street, Waltham, MA 02451, USA 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA 2014 Elsevier Inc. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone (+44) (0) 1865 843830; fax (+44) (0) 1865 853333; email: [email protected]. Alternatively, visit the Science and Technology Books website at www.elsevierdirect.com/rights for further information Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress ISBN: 978-0-12-408103-1 For information on all Academic Press publications visit our website at elsevierdirect.com Typeset by TNQ Books and Journals www.tnq.co.in Printed and bound in the United States of America 14 15 16 17 18 10 9 8 7 6 5 4 3 2 1 DEDICATION This book is dedicated to my Father, Dr. Sohail Ahmad Azmi, a tireless physician who instilled in me the right values, work ethics, and scientific temperament. PREFACE Pancreatic cancer remains a deadly disease that is receiving more and more attention nowadays. Its diagnosis is still considered a death sentence and sadly every two minutes a patient dies from the disease somewhere in the world (∼300,000 annual deaths). It is quite unfortunate to note that unlike other cancers that have witnessed major progress in early diagnostics, better management and some success in the identification of molecularly targeted drugs, the field of pancreatic cancer research lags behind on all these fronts. There is an urgent need for the identification of diagnostic and prognostic markers and a dire need for effective drugs to tame the disease. A major reason for such poor progress is due to the reductionism in approaches that for the past few decades have focused on studying single or few pathways and searching for magic bullet drugs. Being a heterogeneous disease, there is a need for interdisciplinary strategies that take a holistic view at the whole system instead of individual components. The scale of the complexity of pancreatic cancer calls for equally com- plex solutions and holistic computational technologies, especially systems biology, are expected to play pivotal roles in current and future research. The depth and breadth of opportunities provided by systems sciences are endless and researchers are increasingly relying on these interdisciplinary areas to enhance the understanding of this invariably terminal disease of the pan- creas. Although the cross talk between different scientific disciplines has increased, a wide gap still exists between basic biologist and computational experts; the former hesitant to dwell into unchartered bioinformatics terri- tory and the later unable to obtain opportunities to test and validate their powerful analytical tools in actual biological systems. The literature on pancreas cancer systems biology is sparsely distributed in the web of knowledge and no previous work has satisfactorily integrated this new interdisciplinary subject area. Unlike prior works, this book brings together wide-ranging modern topics and for the first time, showcases the recent advancement in systems approaches to pancreatic cancer under one comprehensive volume. The 18 chapters presented here are from leading pancreas cancer experts who have been using many novel computational tools to get new information by reaching to previously unfathomable depths. Many of these experts are founders in their own fields. They have discussed a wide range of topics such as pancreatic cancer bioinformatics, xiii xiv Preface expression analysis, and proteomics. Other topics highlight the use of sys- tems sciences in unraveling the complexities of pancreas cancer signaling, understanding disease metabolomics, the role of microRNAs, overcoming therapy resistance, resolving the pancreatic cancer stem cell debate, under- standing the cross talk between different components that make up the microenvironment, pursuing patient stratification for tailored treatments, and many more. These chapters carry more than a thousand updated refer- ences and numerous web resources and detailed illustrations. They should be very helpful for the researchers that are seriously engaged in the area of translational pancreatic cancer research. It is anticipated that this book will bridge the gap among basic researchers, clinicians, and computational biolo- gists, all of whom have a common goal—to defeat pancreatic cancer. Asfar S. Azmi, PhD. ACKNOWLEDGMENTS First of all I would like to thank Elsevier Academic Press for appreciating the value of this concept and allowing me to edit this book. Special thanks to Nisbet Graham for entertaining the idea of this volume. I am extremely grateful to the constant support provided by Catherine Van Der Laan (Cassie) and her editorial team during the various stages of this project. Her help in setting up the submission website and cover design is deeply appre- ciated. I would like to especially thank Professor Ramzi Mohammad, Divi- sion Head, Hamad Medical Corporation, Doha, Qatar for giving his unending support in my editorial ventures. The scholarly guidance from Professor Fazlul Sarkar (Distinguished Professor), Wayne State University is deeply acknowledged. I am highly grateful to the entire Gastrointestinal Cancer Research Team at Karmanos Cancer Institute, especially our team leader Dr Philip A. Philip for developing in me the enthusiasm to work in the area of pancreatic cancer. xv CONTRIBUTORS Amir Abdollahi German Cancer Consortium (DKTK), Heidelberg, Germany; Molecular & Translational Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany Baltazar D. Aguda DiseasePathways LLC, Bethesda, MD, USA Shadan Ali Department of Oncology, Karmanos Cancer Institute, Detroit, MI, USA Osama M. Alian Department of Oncology, Karmanos Cancer Institute, Detroit, MI, USA Laufey T. Amundadottir Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA Asfar S. Azmi Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA Ginny F. Bao Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA Oliver F. Bathe Departments of Surgery and Oncology, University of Calgary, Calgary, AB, Canada Charles E. Birse Department of Protein Therapeutics, Celera, Rockville, MD, USA; Celera, Alameda, CA, USA Teresa A. Brentnall Department of Medicine, University of Washington, Seattle, WA, USA Ru Chen Department of Medicine, University of Washington, Seattle, WA, USA Sara Chiblak German Cancer Consortium (DKTK), Heidelberg, Germany; Molecular & Translational Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany Edmund Clarke Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA Bruno Domon Department of Protein Therapeutics, Celera, Rockville, MD, USA; Luxembourg Clinical Proteomics Center, CRP-Sante, Luxembourg xvii xviii Contributors Niccola Funel Department of Surgical, Molecular and Medical Pathology, University of Pisa, Pisa, Italy Jiankun Gao Department of Basic Medical Sciences, Sichuan College of Traditional Chinese Medicine, Mianyang, Sichuan, China Haijun Gong Department of Mathematics and Computer Science, Saint Louis University, St. Louis, MO, USA Robert Grützmann Department of General, Thoracic, and Vascular Surgery, University Hospital “Carl Gustav Carus”, Dresden University of Technology, Dresden, Germany Tao He Department of Protein Therapeutics, Celera, Rockville, MD, USA; Pfizer, Cambridge, MA, USA Jason Hoskins Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA Sun-Il Hwang Proteomics and Mass Spectrometry Research Laboratory, Carolinas HealthCare System, Charlotte, NC, USA Jinping Jia Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA Amin I. Kassis Department of Radiology, Harvard Medical School, Boston, MA, USA Jin-Gyun Lee Proteomics and Mass Spectrometry Research Laboratory, Carolinas HealthCare System, Charlotte, NC, USA Candy N. Lee Department of Protein Therapeutics, Celera, Rockville, MD, USA; Pfizer, South San Francisco, CA, USA Lance A. Liotta Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA Kenneth E. Lipson FibroGen, Inc., San Francisco, CA, USA Ian McCaffrey Department of Protein Therapeutics, Celera, Rockville, MD, USA; Genentech, South San Francisco, CA, USA Contributors xix Kimberly Q. McKinney Proteomics and Mass Spectrometry Research Laboratory, Carolinas HealthCare System, Charlotte, NC, USA Katherine McKinnon Department of Protein Therapeutics, Celera, Rockville, MD, USA; NCI, Bethesda, MD, USA Lucio Miele University of Mississippi Cancer Institute, Jackson, MS, USA Ramzi M. Mohammad Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA; Hamad Medical Corporation, Doha, Qatar Paul A. Moore Department of Protein Therapeutics, Celera, Rockville, MD, USA; MacroGenics Inc., Rockville, MD, USA Irfana Muqbil Department of Biochemistry, Faculty of Life Sciences, AMU, Aligarh, UP, India Sheng Pan Department of Medicine, University of Washington, Seattle, WA, USA Emanuel F. Petricoin III Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA Philip A. Philip Department of Oncology, Karmanos Cancer Institute, Detroit, MI, USA Mariaelena Pierobon Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA Christian Pilarsky Department of V isceral-, Thoracic- and Vascular Surgery, Medizinische Universität Carl Gustav Carus, TU Dresden, Dresden, Germany Pavel Pospisil Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland Francisco X. Real Spanish National Cancer Research Center (CNIO), Madrid, Spain Steven M. Ruben Department of Protein Therapeutics, Celera, Rockville, MD, USA Enrique Carrillo-de Santa Pau Spanish National Cancer Research Center (CNIO), Madrid, Spain Fazlul H. Sarkar Department of Pathology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA xx Contributors Alfonso Valencia Spanish National Cancer Research Center (CNIO), Madrid, Spain Zhiwei Wang The Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, the First, Affiliated Hospital, Soochow University, Suzhou, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA Tong Tong Wu Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA Julie Wulfkuhle Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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