Novel Anticancer Drug Protocols M E T H O D S I N M O L E C U L A R M E D I C I N ETM John M. Walker, SERIES EDITOR 89. The Blood–Brain Barrier: Biology and 72. Malaria Methods and Protocols, edited by Research Protocols, edited by Sukriti Nag, Denise L. Doolan, 2002 2003 71. Haemophilus influenzae Protocols, edited 88. Cancer Cell Culture: Methods and Protocols, byMark A. Herbert, Derek Hood, and E. edited bySimon P. Langdon, 2003 Richard Moxon, 2002 87. Vaccine Protocols, Second Edition, edited 70. Cystic Fibrosis Methods and Protocols, byAndrew Robinson, Martin P. Cranage, edited by William R. Skach, 2002 and Michael Hudson, 2003 69. Gene Therapy Protocols, 2nd ed., edited 86. Renal Disease: Techniques and Protocols, byJeffrey R. Morgan, 2002 edited by Michael S. Goligorsky, 2003 68. Molecular Analysis of Cancer, edited by 85. Novel Anticancer Drug Protocols, edited Jacqueline Boultwood and Carrie Fidler, 2002 byJohn K. Buolamwini and Alex A. Adjei, 67. 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Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 Library of Congress Cataloging in Publication Data Novel anticancer drug protocols / edited by John K. Buolamwini and Alex A. Adjei. p. cm. -- (Methods in molecular medicine) Includes bibliographical references and index. ISBN 0-89603-963-3 (alk. paper) e-ISBN 1-59259-380-1 1. Antineoplastic agents--Research--Methodology. I. Buolamwini, John K. II. Adjei, Alex A. III. Series RC271.C5 N476 2003 616.99’4061--dc21 2002038702 Preface Weare in an exciting era in the war against cancer, with real prospects for novel anticancer drugs that are cancer cell-specific without the toxicities that have been the hallmark of conventional cytotoxic cancer chemotherapy. Advances in cancer cell biology fueled by the molecular biology revolution have resulted in the uncovering of many novel potential molecular targets for cancer therapy. New anticancer drug discovery and development is now largely focused on exploiting these new molecular targets, which encompass oncogenes, tumor sup- pressor genes, and their gene products, as well as targets involved in tumor angiogenesis, metastasis, survival, and longevity mechanisms. Exploitation of some of these targets has already yielded fruits and introduced new paradigms of molecularly targeted cancer therapy into the clinic, namely, protein kinase inhi- bition by antibodies or small molecules, exemplified by Herceptin® (trastuzumab), a humanized antibody targeted against the HER-2 growth factor receptor tyrosine kinase for the treatment of metastatic breast cancer; and Gleevec, a small molecule bcr-abl kinase inhibitor for the treatment of chronic myelog- enous leukemia. With many potential molecular targets having already been identified, and many more yet to be discovered, we face challenges in their validation, the use of relevant assays for successful drug discovery, and efficient pre- clinical and clinical development strategies to enable the translation of the discoveries into effective clinical regimens for cancer patients. To meet these challenges, novel tools in the form of basic and clinical research and testing protocols are required. In this volume on Novel Anticancer Drug Protocols, we have provided not only a broad overview of the whole arena of novel anticancer drug targets, but also a wide-ranging selection of cutting-edge tech- niques that are being applied to novel anticancer drug discovery and develop- ment. These comprise protocols involving, or applied to, growth factors, receptor/nonreceptor tyrosine kinases and their downstream signal transduc- tion targets, serine/threonine kinases, angiogenesis, metastasis, apoptosis, cell longevity, protein chaperoning and degradation, functional genomics, antibody methods, antisense oligonucleotide strategies, protein–protein and protein–DNA interactions, and miscellaneous pertinent methods. With the exception of the introductory chapter on novel anticancer drug targets and a v vi Preface review chapter on assays for in vitro and in vivo synergy, each methodologi- cal chapter begins with background information, followed by a detailed description of the experimental protocols in easy-to-follow reproducible reci- pes, and notes to ensure their successful use by other investigators. We hope that Novel Anticancer Drug Protocolswill serve its purpose of making available, in a user-friendly format, a broad range of the cutting-edge methodologies now being used in the discovery and development of novel anticancer drugs, to basic scientists and clinical researchers in academia, in- dustry, and government laboratories, as well as cancer research institutions. Our gratitude goes to all the authors who have contributed chapters to the book. John K. Buolamwini, PhD Alex A. Adjei, MD, PhD Contents Preface .............................................................................................................v Contributors.....................................................................................................xi PART I. INTRODUCTION 1 Overview of Novel Anticancer Drug Targets John K. Buolamwini and Haregewein Assefa....................................3 PART II. KINASE INHIBITOR DISCOVERY PROTOCOLS 2 Biomarker Assays for Phosphorylated MAP Kinase: Their Utility for Measurement of MEK Inhibition Judith S. Sebolt-Leopold, Keri Van Becelaere, Kenneth Hook, and Roman Herrera.........................................................................31 3 Assays for Cyclin-Dependent Kinase Inhibitors Adrian M. Senderowicz and Tyler Lahusen.....................................39 4 Identifying Inhibitors of ATM and ATR Kinase Activities Jann N. Sarkaria...................................................................................49 PART III. ANGIOGENESIS AND METASTASIS PROTOCOLS 5 The Rat Aortic Ring Assay for In Vitro Study of Angiogenesis Ronald S. Go and Whyte G. Owen.....................................................59 6 Real Time In Vivo Quantitation of Tumor Angiogenesis Gregory I. Frost and Per Borgström.................................................65 7 Use of Tumor-Activated Hepatic Stellate Cell as a Target for the Preclinical Testing of Anti-Angiogenic Drugs Against Hepatic Tumor Development Elvira Olaso and Fernando Vidal-Vanaclocha.................................79 8 Cell Motility, Adhesion, Homing, and Migration Assays in the Studies of Tyrosine Kinases Martin Sattler, Elizabeth Quackenbush, and Ravi Salgia...............87 9 Inflammatory Response of Tumor-Activated Hepatic Sinusoidal Endothelium as a Target for the Screening of Metastasis Chemopreventive Drugs Lorea Mendoza and Fernando Vidal-Vanaclocha..........................107 vii viii Contents 10 Binding Assay for Selectins Jianing Zhang and Michiko N. Fukuda...........................................117 11 Determination of Peak Serum Levels and Immune Response to the Humanized Anti-Ganglioside Antibody–Interleukin-2 Immunocytokine Jacquelyn A. Hank, Jean E. Surfus, Jacek Gan, Amy Ostendorf, Stephen D. Gillies, and Paul M. Sondel.........123 PART IV. IMMUNOHISTOCHEMICAL ASSAYS IN THE CLINICAL SETTING 12 Immunohistochemical Determination of EGFR-Tyrosine Kinase Inhibition in Clinical Samples Shazli N. Malik, Roble G. Bedolla, Manuel Hidalgo, Michael G. Brattain, and Jeffrey I. Kreisberg............................135 13 Immunohistochemical Assays of Farnesyltransferase Inhibition in Patient Samples Alex A. Adjei.......................................................................................141 PART V. PROTEIN CHAPERONING/DEGRADATION PROTOCOLS 14 Assays for HSP90 and Inhibitors Wynne Aherne, Alison Maloney, Chris Prodromou, Martin G. Rowlands, Anthea Hardcastle, Katherine Boxall, Paul Clarke, Michael I. Walton, Laurence Pearl, and Paul Workman........................................................................149 15 Assays for Proteasome Inhibition Peter J. Elliott, Teresa A. Soucy, Christine S. Pien, Julian Adams, and Eric S. Lightcap............................................163 PART VI. PROTEIN–PROTEIN AND PROTEIN–DNA INTERACTIONS 16 The Mammalian Two-Hybrid Assay for Detection of Coactivator-Nuclear Receptor Interactions Curtis M. Tyree and Kay Klausing...................................................175 17 Preparation of DNA-Protein Complexes Suitable for Spectroscopic Analysis Nouri Neamati, Manisha Murthy, and Yun-Xing Wang.................185 PART VII. ANTISENSE 18 Antisense Oligonucleotide Inhibitors of MDM2 Oncogene Expression Ruiwen Zhang and Hui Wang...........................................................205 PART VIII. GENOMICS 19 Pharmacogenetic Analysis of Clinically Relevant Genetic Polymorphisms Christine M. Rose, Sharon Marsh, Margaret-Mary Ameyaw, and Howard L. McLeod.................................................................225 Contents ix 20 Gene Expression Microarrays Christopher P. Kolbert, William R. Taylor, Kelly L. Krajnik, and Dennis J. O’Kane...................................................................239 21 Methods for Isolation and Genetic Analysis of Circulating Tumor DNA in Patient Plasma Tomoya Kawaguchi, Will S. Holland, and Paul H. Gumerlock.....257 PART IX. CELL LIFESPAN/LONGEVITY 22 The Use of Early Sea Urchin Embryos in Anticancer Drug Testing David Nishioka, Vanessa Marcell, Meghan Cunningham, Merium Khan, Daniel D. Von Hoff, and Elzbieta Izbicka..........265 PART X. IN VIVO IMAGING 23 PET Screening of Anticancer Drugs: A Faster Route to Drug/Target Evaluations In Vivo Anna Fredriksson and Sharon Stone-Elander...............................279 PART XI. MISCELLANEOUS PROTOCOLS 24 Assays for In Vitro and In Vivo Synergy Beverly A. Teicher.............................................................................297 25 Flow Cytometric Methods for Detection and Quantification of Apoptosis David P. Steensma, Michael Timm, and Thomas E. Witzig..........323 26 Assays for Neoplastic Cell Enrichment in Bone Marrow Samples Rafael Fonseca and Gregory J. Ahmann........................................333 Index.....................................................................................................343 Contributors JULIAN ADAMS • Millennium Pharmaceuticals Inc., Cambridge, MA ALEXA. ADJEI•Department of Oncology, Mayo Clinic and Foundation, Rochester, MN WYNNE AHERNE • CRC Centre for Cancer Therapeutics, Institute of Cancer Research, Surrey, UK GREGORY J. AHMANN•Department of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN MARGARET-MARY AMEYAW•Washington University School of Medicine, St. Louis, MO HAREGEWEIN ASSEFA•Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN ROBLE G. BEDOLLA•Department of Surgery, University of Texas Health Science Center, San Antonio, TX PER BORGSTRÖM • Sidney Kimmel Cancer Center, San Diego, CA KATHERINE BOXALL • CRC Centre for Cancer Therapeutics, Institute of Cancer Research, Surrey, UK MICHAEL G. BRATTAIN•Department of Pharmacology and Therapeutic, Roswell Park Cancer Institute, Buffalo, NY JOHN K. BUOLAMWINI•Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN PAUL CLARKE • CRC Centre for Cancer Therapeutics, Institute of Cancer Research, Surrey, UK MEGHAN CUNNINGHAM • Department of Biology, Georgetown University, Washington, DC PETER J. ELLIOTT • CombinatorRx Inc., Boston, MA RAFAEL FONSECA•Department of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN ANNA FREDRIKSSON • Karolinska Pharmacy, Karolinska Hospital, Stockholm, Sweden GREGORY I. FROST • Sidney Kimmel Cancer Center, San Diego, CA MICHIKO N. FUKUDA • Glycobiology Program, The Burnham Institute, La Jolla, CA xi