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M E T H O D S I N M O L E C U L A R B I O L O G Y TM

Tumor Suppressor Genes

Volume 2 Regulation, Function, and Medicinal Applications

Edited by

Wafik S. El-Deiry, MD, PhD Departments of Medicine, Genetics, and Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA

Humana Press Totowa, New Jersey iv

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Tumor suppressor genes / edited by Wafik S. El-Deiry. p. ; cm. -- (Methods in molecular biology ; v. 223) Includes bibliographical references and index. Contents: v. 1. Pathways and isolate strategies -- v. 2. Regulation, function, and medicinal application. ISBN 0-89603-986-2 (v. 1 : alk. paper); 1-59259-328-3 (v. 1 : e-book) -- ISBN 0-89603-987-0 (v. 2 : alk. paper);1-59259-329-1 (v. 2 : e-book) 1. Antioncogenes--Laboratory manuals. I. El-Deiry, Wafik S. II. Methods in molecular biology (Clifton, N.J.) ; v. 222-223. [DNLM: 1. Genes, Tumor Suppressor--physiology--Laboratory Manuals. 2. Neoplasms--genetics--Laboratory Manuals. 3. Neoplasms--therapy--Laboratory Manuals. 4. Signal Transduction--physiology--Laboratory Manuals. 5. Tumor Suppressor Proteins--physiology--Laboratory Manuals. QZ 25 T925 2003] RC268.43 .T82 2003 616.99'4042--dc21 2002027501 v

Preface

It has become clear that tumors result from excessive cell proliferation and a corresponding reduction in cell death caused by the successive accumulation of mutations in key regulatory target genes over time. During the 1980s, a number of oncogenes were characterized, whereas from the 1990s to the present, the empha- sis has shifted to tumor suppressor genes (TSGs). It has become clear that oncogenes and TSGs function in the same pathways, providing positive and negative growth regulatory activities. The signaling pathways controlled by these genes involve virtually every process in cell biology, including nuclear events, cell cycle, cell death, cytoskeletal, cell membrane, angiogenesis, and cell adhesion effects. Muta- tions in tumor suppressor genes have been identified in familial cancer syndromes, and the same genes in many cases have been found to be mutationally inactivated in sporadically occurring cancers. In their normal state, TSGs control cancer development and progression, as well as contribute to the sensitivity of cancers to a variety of therapeutics. Understanding the classes of TSGs, the biochemical pathways they function in, and how they are regulated provides an essential lesson in cancer biology. We cannot hope to advance our current knowledge and to develop new and more effective therapies without understanding the relevant pathways and how they influence the present approaches to therapy. Moreover, it is important to be able to access not only the powerful tools now available to discover these genes, but also their links to cell biology and growth control. The scope of this two volume work, Tumor Suppressor Genes, Volume 1: Path- ways and Isolation Strategies and Volume 2: Regulation, Function, and Medicinal Applications, is broad in the sense that it covers all the known tumor suppressor pathways and provides key information on the road to their discovery, analysis, and uses in cancer therapeutics. The aim of the first volume, Pathways and Isolation Strategies, is to educate the reader about known TSGs and the relevance of the biochemical pathways they regulate to human cancer. The reader has an opportunity in Volume 1 to access state-of-the-art protocols that have been successful in the identification of TSGs in the past, and that can be applied to isolate novel TSGs. With a novel TSG in hand, the reader has an opportunity in Volume 2, Regulation, Function, and Medicinal Applications, to explore the cell biology and biochemical function of the encoded protein, as well as its physiological role in vivo. Finally, in Volume 2, the reader is exposed to strategies for the use of information on TSGs to develop diagnostic and therapeutic strategies for cancer. The two volumes of Tumor Suppressor Genes bring together many of the world’s experts in the identification and characterization of TSGs. The work is thus intended to become the core reference and compilation of the emerging path-

v vivi Preface ways and the growing number of molecules that suppress cancer. Importantly, it should also serve as a wide-ranging source of protocols useful in understanding and charac- terizing the function of TSGs. One of the challenges facing cancer researchers and clinicians is to bring forward and develop active therapeutics. This book, by example, puts forward highly useful paradigms for rational drug design, based on our dramatic new understanding of molecular pathogenesis. Tumor Suppressor Genes thus lays down a firm and timely foundation for understanding cancer. In this age of expression profiling and proteomics, there has already been revealed a remarkable complexity and interrelatedness of seemingly diverse pro- cesses and signal transduction pathways. For the student, this book provides a reference to the basics concerning the identity of the major TSGs and the signaling pathways they use to inhibit tumors. For the investigator, it provides not only a critical update, but also an extremely useful compendium of newly assembled research protocols, including both classical methods and state-of-the-art techniques. For the translational scientist, the book provides fertile ground for the development of therapeutic strategies based on understanding the mechanisms of action and appreciating the existing preclinical data. One of the criticisms of an effort leading to such a book is that the field is moving very quickly and material is likely to be outdated. However, with many of the world’s leading experts providing a comprehensive overview of all tumor suppressing pathways, along with their detailed protocols, we believe we have provided an invaluable resource for continued learning and discovery. Finally, Tumor Suppressor Genes provides a bridge to those interested in translational research by giving examples of the rationale for many of the most promising manipulations that may lead to novel therapeutic agents. Tumor Suppressor Genes is targeted at a broad audience including medical and graduate students, postdoctoral fellows, physician scientists, academics, and principal investigators. The text provides the critical information needed to rapidly gain appre- ciation of important TSGs in human cancer, as well as modern methods for their discovery, analysis, and clinical application. The reader is enabled to learn the background and then access the literature in which studies designed to define the biology and biochemistry of known TSGs have been performed. Details of protocols with examples of their previous uses allow the researcher to apply current technologies to novel or known genes whose role has not yet been defined. In summary, Tumor Suppressor Genes is a comprehensive compilation of the known tumor suppressing pathways, and the key molecular approaches to their discovery, analysis, and clinical applications. It should be of enduring value to students at all levels of experimental biology and medicine, as well as those clinicians who want to better understand the molecular biology of cancer.

Wafik S. El-Deiry, MD, PhD vii

Contents

Preface ...... v Contents of Companion Volume ...... xi Contributors ...... xiii

PART I. UNDERSTANDING THE FUNCTION AND REGULATION OF TUMOR SUPPRESSOR GENES 1 Utilizing NMR to Study the Structure of Growth-Inhibitory Proteins Francesca M. Marassi ...... 3 2 Generation and Application of Phospho-Specific Antibodies for p53 and pRB Yoichi Taya, Kiichiro Nakajima, Kumiko Yoshizawa-Kumagaye, and Katsuyuki Tamai ...... 17 3 Stability and Ubiquitination of the Tumor Suppressor Protein p53 Lesley J. Jardine and Carl G. Maki ...... 27 4 Role of Tumor Suppressors in DNA Damage Response Bin-Bing S. Zhou, Michael R. Mattern, and Kum Kum Khanna ...... 39 5 In Situ Hybridization in Cancer and Normal Tissue Shrihari Kadkol, Jeremy Juang, and Tzyy-choou Wu ...... 51 6 Genetic Strategies in Saccharomyces cerevisiae to Study Human Tumor Suppressor Genes Takahiko Kobayashi, Ting Wang, Hua Qian, and Rainer K. Brachmann ...... 73 7 Electrophoretic Mobility Shift Analysis of the DNA Binding of Tumor Suppressor Gene Products Edward C. Thornborrow, Matthew Maurer, and James J. Manfredi...... 87 8 Analysis of Gene Promoter Regulation by Tumor Suppressor Genes Kumaravel Somasundaram, Sanjeev Das, Smita Lakhotia, and Narendra Wajapeyee ...... 101 9 DNA Footprinting M. Stacey Ricci and Wafik S. El-Deiry...... 117 10 Identification of DNA-Binding of Tumor Suppressor Genes by Chromatin Immunoprecipitation Timothy K. MacLachlan and Wafik S. El-Deiry ...... 129 11 Co-immunoprecipitation of Tumor Suppressor Protein-Interacting Proteins Li-Kuo Su ...... 135

vii viii Contents

12 Microarray Approaches for Analysis of Tumor Suppressor Gene Function Sally A. Amundson and Albert J. Fornace, Jr...... 141 13 Analysis of Tumor Suppressor Gene-Induced Senescence Judith Campisi ...... 155 14 Yeast Two-Hybrid Screening as a Means of Deciphering Tumor Suppressor Pathways E. Robert McDonald III and Wafik S. El-Deiry ...... 173 15 Somatic Cell Knockouts of Tumor Suppressor Genes Ruth Hemmer, Wenyi Wei, Annie Dutriaux, and John M. Sedivy ...... 187 16 Colony Growth Suppression by Tumor Suppressor Genes Gen Sheng Wu ...... 207 17 Flow Cytometric Analysis of Cell Cycle Control by Tumor Suppressor Genes David T. Dicker and Wafik S. El-Deiry ...... 211 18 Analysis of Cyclin-Dependent Kinase Activity Timothy K. MacLachlan and Wafik S. El-Deiry ...... 217 19 Tumor Suppressor Gene-Inducible Cell Lines Michael Dohn, Susan Nozell, Amy Willis, and Xinbin Chen ...... 221 20 In Vitro Models of Early Neoplastic Transformation of Human Mammary Epithelial Cells Vimla Band...... 237 21 Tumor Suppression Through Angiogenesis Inhibition Andrew M. Arsham and M. Celeste Simon ...... 249 22 Flow Cytometric Analysis of Tumor Suppressor Gene-Induced Apoptosis David T. Dicker and Wafik S. El-Deiry ...... 271 23 Functional Analysis of Tumor Suppressor Genes in Mice Stephen N. Jones and Lawrence A. Donehower ...... 283 24 The Tissue Microenvironment as an Epigenetic Tumor Modifier Meredith Unger and Valerie M. Weaver ...... 315 25 Analyzing the Function of Tumor Suppressor Genes Using a Drosophila Model Raymond A. Pagliarini, Ana T. Quiñones, and Tian Xu ...... 349 26 Assembling a Tumor Progression Model Mark Redston ...... 383 27 Conformation-Sensitive Gel Electrophoresis for Detecting BRCA1 Mutations Smita Lakhotia and Kumaravel Somasundaram ...... 403 PART II. MEDICINAL APPLICATIONS OF TUMOR SUPPRESSORS 28 Conversion Technology and Cancer Predispositions Nickolas Papadopoulos ...... 415 Contents ix

29 Discovering Novel Anticancer Drugs: Practical Aspects and Recent Advances Cristina T. Lewis and Patrick M. O’Connor ...... 425 30 Targets in Apoptosis Signaling: Promise of Selective Anticancer Therapy Ramadevi Nimmanapalli and Kapil Bhalla ...... 465 31 Tumor Deprivation of Oxygen and Tumor Suppressor Gene Function Zhong Yun and Amato J. Giaccia ...... 485 32 Hormonal and Differentiation Agents in Cancer Growth Suppression Mikhail V. Blagosklonny ...... 505 33 Regulation of NF-gB by Oncoproteins and Tumor Suppressor Proteins Lee V. Madrid and Albert S. Baldwin, Jr...... 523 34 Blocking Survivin to Kill Cancer Cells Dario C. Altieri ...... 533 35 Targeting the Mitochondria to Enhance Tumor Suppression Eyal Gottlieb and Craig B. Thompson ...... 543 36 Novel Approaches to Screen for Anticancer Drugs Using Saccharomyces cerevisiae Julian A. Simon and Timothy J. Yen ...... 555 37 Tumor Suppressor Gene Therapy Jack A. Roth and Susan F. Grammer ...... 577 38 Therapeutic Strategies Using Inhibitors of Angiogenesis Michael S. O’Reilly ...... 599 39 Isolation of p53 Inhibitors by Screening Chemical Libraries in Cell-Based Readout System Andrei Gudkov and Elena Komarova...... 635 Index ...... 649 xi

CONTENTS OF THE COMPANION VOLUME Volume 1: Pathways and Isolation Strategies

PART I. KNOWN TUMOR SUPPRESSOR GENES AND PATHWAYS 1 Growth Control by the Retinoblastoma Gene Family Marco G. Paggi, Armando Felsani, and Antonio Giordano 2 The APC Tumor Suppressor Pathway Patrice J. Morin and Ashani T. Weeraratna 3 Hereditary Breast and Ovarian Cancer Genes Ralph Scully and Nadine Puget 4 Hereditary Colon Cancer Genes William M. Grady and Sanford D. Markowitz 5 Patched, Hedgehog, and Skin Cancer Anthony G. Quinn and Ervin Epstein, Jr. 6 Tumor Suppressor Genes in Lung Cancer Arvind K. Virmani and Adi F. Gazdar 7 TP53, hChk2, and the Li-Fraumeni Syndrome Jenny Varley 8 Genetic Alterations in Esophageal Cancer Jun-ichi Okano, Lorraine Snyder, and Anil K. Rustgi 9 PTEN and Cancer Ramon Parsons and Laura Simpson 10 VHL and Kidney Cancer Michael Ohh and William G. Kaelin, Jr. 11 p16INK4A and Familial Melanoma Kapaettu Satyamoorthy and Meenhard Herlyn 12 The INK4a/ARF Locus and Human Cancer Greg H. Enders 13 Progression Model of Prostate Cancer Teresa Acosta Almeida and Nickolas Papadopoulos 14 Neurofibromatosis Type 1 Margaret E. McLaughlin and Tyler Jacks 15 Wilms’ Tumor as a Model for Cancer Biology Andrew P. Feinberg and Bryan R. G. Williams 16 Inadequate “Caretaker” Gene Function and Human Cancer Development Theodore L. DeWeese and William G. Nelson 17 Regulation of Tumor Suppressor Genes by Oncogenes Paul Dent, Liang Qiao, Donna Gilfor, Michael Birrer, Steven Grant, and Paul B. Fisher

xi xii Contents of Companion Volume

PART II. IDENTIFICATION OF TUMOR SUPPRESSOR GENES 18 Determination of Cancer Allelotype Jennifer J. Ascaño and Steven M. Powell 19 Epidemiologic Approaches to the Identification of Cancer Predisposition Genes Timothy R. Rebbeck 20 Characterization of Translocations in Human Cancer Keri Fair and Michelle M. Le Beau 21 Positional Approaches to Cancer Genetics Gavin P. Robertson, Linda Sargent, and Mark A. Nelson 22 Hybrid Capture of Putative Tumor Suppressor Genes Bryan L. Betz and Bernard E. Weissman 23 Approaches to Proteomic Analysis of Human Tumors Mamoun Ahram and Michael R. Emmert-Buck 24 Representational Difference Analysis of Gene Expression James M. Bugni and Norman R. Drinkwater 25 Antisense Libraries to Isolate Tumor Suppressor Genes Adi Kimchi 26 Genetic Suppressor Elements in the Characterization and Identification of Tumor Suppressor Genes Igor B. Roninson and Andrei V. Gudkov 27 Cross-Linking Subtractive Hybridization to Identify Tumor Suppressor Genes Gen Sheng Wu 28 Suppression Subtractive Hybridization for Identification and Functional Analysis of Tumor Suppressor Genes Iuri D. Louro, Evans C. Bailey, and J. Michael Ruppert 29 SAGE as a Strategy to Isolate Cancer-Related Genes Kathy Boon and Gregory J. Riggins 30 Differential Display Techniques to Identify Tumor Suppressor Gene Pathways Siham Biade and Maureen E. Murphy 31 Detection of Mismatch Repair Gene Expression in Urologic Malignancies Fredrick S. Leach xiii

Contributors

MAMOUN AHRAM • Molecular Biosciences, Pacific Northwest National Laboratory, Battelle, Richland, WA TERESA ACOSTA ALMEIDA • Institute of Cancer Genetics, Department of Pathology, Columbia University, New York, NY DARIO C. ALTIERI • Department of Cancer Biology and the Cancer Center, University of Massachusetts Medical School, Worcester, MA SALLY A. AMUNDSON • National Cancer Institute, National Institutes of Health, Bethesda, MD ANDREW M. ARSHAM • Abramson Family Cancer Research Institute and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA JENNIFER J. ASCAÑO • Division of Gastroenterology, University of Virginia Health System, Charlottesville, VA EVANS C. BAILEY • Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL ALBERT S. BALDWIN, JR. • Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC VIMLA BAND • Department of Radiation Oncology, New England Medical Center, Boston, MA BRYAN L. BETZ • Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC KAPIL BHALLA • Department of Interdisciplinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL SIHAM BIADE • Department of Pharmacology, Fox Chase Cancer Center, Philadelphia, PA MICHAEL BIRRER • Biomarkers Branch, Division of Clinical Sciences, National Cancer Institute, Rockville, MD MIKHAIL V. BLAGOSKLONNY • Medicine Branch, National Institutes of Health, Bethesda, MD KATHY BOON • Duke University Medical Center, Durham, NC RAINER K. BRACHMANN • Departments of Medicine and Biological Chemistry, University of California at Irvine, Irvine, CA JAMES M. BUGNI • McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, WI JUDITH CAMPISI • Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, and Buck Institute for Age Research, Novato, CA

xiii xiv Contributors

XINBIN CHEN • Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL SANJEEV DAS • Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India PAUL DENT • Department of Radiation Oncology, Virginia Commonwealth University, Medical College of Virginia, Richmond, VA THEODORE L. DEWEESE • Johns Hopkins Oncology Center, Baltimore, MD DAVID T. DICKER • Howard Hughes Medical Institute, Departments of Medicine, Genetics, and Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA MICHAEL DOHN • Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL LAWRENCE A. DONEHOWER • Division of Molecular Virology, Baylor College of Medicine, Houston, TX NORMAN R. DRINKWATER • McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, WI ANNIE DUTRIAUX • Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI WAFIK S. EL-DEIRY • Departments of Medicine, Genetics, and Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA MICHAEL R. EMMERT-BUCK • Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD GREG H. ENDERS • Departments of Medicine and Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA ERVIN EPSTEIN, JR. • Department of Dermatology, UCSF Medical Center, San Francisco, CA KERI FAIR • Section of Hematology/Oncology, University of Chicago, Chicago, IL ANDREW P. FEINBERG • Johns Hopkins University School of Medicine, Baltimore, MD ARMANDO FELSANI • CNR, Istituto di Neurobiologia e Medicina Molecolare, Rome, Italy PAUL B. FISHER • Department of Urology and Pathology, College of Physicians and Surgeons, Columbia University, New York, NY ALBERT J. FORNACE, JR. • National Cancer Institute, National Institutes of Health, Bethesda, MD ADI F. GAZDAR • Hamon Cancer Center, UT Southwestern Medical Center, Dallas, TX AMATO J. GIACCIA • Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA DONNA GILFOR • Department of Radiation Oncology, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA ANTONIO GIORDANO • Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA Contributors xv

EYAL GOTTLIEB • Abramson Family Cancer Research Institute, Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA WILLIAM M. GRADY • Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN SUSAN F. GRAMMER • Biotechwrite: Biomedical and Science Communications, Kalamazoo, MI STEPHEN GRANT • Department of Medicine/Hematology, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA ANDREI V. GUDKOV • Lerner Research Institute, Department of Molecular Biology, Cleveland Clinic Foundation, Cleveland, OH RUTH HEMMER • Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI MEENHARD HERLYN • The Wistar Institute, Philadelphia, PA TYLER JACKS • Center for Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA LESLEY J. JARDINE • Department of Cancer Cell Biology, Harvard School of Public Health, Boston, MA STEPHEN N. JONES • Department of Cell Biology, University of Massachusetts Medical Center, Worcester, MA JEREMY JUANG • Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD SHRIHARI KADKOL • Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD WILLIAM G. KAELIN, JR.•Dana-Farber Cancer Institute, Boston, MA KUM KUM KHANNA • Queensland Institute of Medical Research, Brisbane, Queensland, Australia ADI KIMCHI • Department of Molecular Genetics and Virology, The Weizmann Institute of Science, Rehovot, Israel TAKAHIKO KOBAYASHI • Hokkaido University Medical Hospital, Sapporo, Japan ELENA KOMAROVA • Lerner Research Institute, Department of Molecular Biology, Cleveland Clinic Foundation, Cleveland, OH SMITA LAKHOTIA • Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India FREDRICK S. LEACH • Departments of Urology and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX MICHELLE M. LE BEAU • Section of Hematology/Oncology, University of Chicago, Chicago, IL CRISTINA T. LEWIS • Pfizer Global Research and Development, San Diego, CA IURI D. LOURO • Division of Hematology/Oncology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL TIMOTHY K. MACLACHLAN • CuraGen Corporation, Branford, CT LEE V. MADRID • Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC xvi Contributors

CARL G. MAKI • Department of Cancer Cell Biology, Harvard School of Public Health, Boston, MA JAMES J. MANFREDI • Derald H. Ruttenberg Cancer Center, Mount Sinai School of Medicine, New York, NY FRANCESCA M. MARASSI • The Burnham Institute, La Jolla, CA SANFORD D. MARKOWITZ • Howard Hughes Medical Institute, and Department of Medicine and Ireland Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH MICHAEL R. MATTERN • Department of Oncology Research, GlaxoSmithKline, King of Prussia, PA MATTHEW MAURER • Derald H. Ruttenberg Cancer Center, Mount Sinai School of Medicine, New York, NY E. ROBERT MCDONALD III • Howard Hughes Medical Institute, Departments of Medicine, Genetics, and Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA MARGARET E. MCLAUGHLIN • Center for Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA; Department of Pathology, Brigham and Women's Hospital, Boston, MA PATRICE J. MORIN • Laboratory of Biological Chemistry, National Institute on Aging, National Institutes of Health, Baltimore, MD MAUREEN E. MURPHY • Department of Pharmacology, The Fox Chase Cancer Center, Philadelphia, PA KIICHIRO NAKAJIMA • Peptide Institute Co. Ltd., Osaka, Japan MARK A. NELSON • Department of Pathology, College of Medicine, University of Arizona, Tucson, AZ WILLIAM G. NELSON • Johns Hopkins Oncology Center, Baltimore, MD RAMADEVI NIMMANAPALLI • Department of Interdisciplinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL SUSAN NOZELL • Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL PATRICK M. O’CONNOR • Pfizer Global Research and Development, San Diego, CA MICHAEL OHH • Dana-Farber Cancer Institute, Boston, MA JUN-ICHI OKANO • Division of Gastroenterology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA MICHAEL S. O’REILLY • Department of Radiation Oncology and Cancer Biology, M. D. Anderson Cancer Center, University of Texas, Houston, TX MARCO G. PAGGI • Center for Experimental Research, Regina Elena Cancer Institute, Rome, Italy RAYMOND A. PAGLIARINI • Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, CT NICKOLAS PAPADOPOULOS • Department of Pathology, Institute of Cancer Genetics, Columbia University, New York, NY; Present address: GMP Genetics, Waltham, MA Contributors xvii

RAMON PARSONS • Department of Pathology, Columbia University, New York, NY STEVEN M. POWELL • Division of Gastroenterology and Hepatology, University of Virginia Health System, Charlottesville, VA NADINE PUGET • Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA HUA QIAN • Department of Surgery, Shanghai Second Medical University, Shangai, P. R. China LIANG QIAO • Department of Radiation Oncology, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA ANTHONY G. QUINN • Experimental Medicine, AstraZeneca R&D Charnwood, Leicestershire, UK ANA T. QUIÑONES • Yale University School of Medicine, New Haven, CT TIMOTHY R. REBBECK • Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA MARK REDSTON • Department of Pathology, Brigham and Women’s Hospital, Boston, MA M. STACEY RICCI • Howard Hughes Medical Institute, Departments of Medicine, Genetics, and Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA GREGORY J. RIGGINS • Duke University Medical Center, Durham, NC GAVIN P. ROBERTSON • Department of Pharmacology, Penn State College of Medicine, Hershey, PA IGOR B. RONINSON • Department of Molecular Genetics, University of Illinois, Chicago, IL JACK A. ROTH • Department of Thoracic and Cardiovascular Surgery, University of Texas M. D. Anderson Cancer Center, Houston, TX J. MICHAEL RUPPERT • Department of Medicine, University of Alabama at Birmingham, Birmingham, AL ANIL K. RUSTGI • Division of Gastroenterology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA LINDA SARGENT • Genetic Susceptibility Team, Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, NIOSH, Morgantown, WV KAPAETTU SATYAMOORTHY • The Wistar Institute, Philadelphia, PA RALPH SCULLY • Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA JOHN M. SEDIVY • Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI JULIAN A. SIMON • Program in Molecular Pharmacology, Fred Hutchinson Cancer Research Center, Seattle, WA M. CELESTE SIMON • Abramson Family Cancer Research Institute and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA LAURA SIMPSON • Institute of Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY xviii Contributors

LORRAINE SNYDER • Division of Gastroenterology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA KUMARAVEL SOMASUNDARAM • Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India LI-KUO SU • Department of Molecular and Cellular Oncology, M.D. Anderson Cancer Center, The University of Texas, Houston, TX KATSUYUKI TAMAI • Cyclex Co. Ltd., Nagano, Japan YOICHI TAYA • National Cancer Center Research Institute, Tokyo, Japan CRAIG B. THOMPSON • Abramson Family Cancer Research Institute, Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA EDWARD C. THORNBORROW • Derald H. Ruttenberg Cancer Center, Mount Sinai School of Medicine, New York, NY MEREDITH UNGER • Abramson Family Cancer Research Institute, University of Pennsylvania Cancer Center, Philadelphia PA JENNY VARLEY • CR-UK Department of Cancer Genetics, Paterson Institute of Cancer Research, Manchester, UK ARVIND K. VIRMANI • Hamon Cancer Center, UT Southwestern Medical Center, Dallas, TX NARENDRA WAJAPEYEE • Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India TING WANG • Department of Genetics, Washington University School of Medicine, St. Louis, MO VALERIE M. WEAVER • Department of Pathology, The Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA ASHANI T. WEERARATNA • Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD WENYI WEI • Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI BERNARD E. WEISSMAN • Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC BRYAN R. G. WILLIAMS • Lerner Research Institute, Department of Cancer Biology, The Cleveland Clinic Foundation, Cleveland, OH AMY WILLIS • Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL GEN SHENG WU • Karmanos Cancer Institute, Department of Pathology, Wayne State University School of Medicine, Detroit, MI TZYY-CHOOU WU • Department of Pathology, The Johns Hopkins Medical Institution, Baltimore, MD TIAN XU • Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, CT TIMOTHY J. YEN • Fox Chase Cancer Center, Philadelphia, PA KUMIKO YOSHIZAWA-KUMAGAYE • Peptide Institute Co. Ltd., Osaka, Japan xix

ZHONG YUN • Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA BIN-BING S. ZHOU • Incyte Genomics, Newark, DE