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Applying Genomic, Proteomic Microarray Tech in Drug Discovery - R. Matson (CRC, 2005) WW PDF

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Preview Applying Genomic, Proteomic Microarray Tech in Drug Discovery - R. Matson (CRC, 2005) WW

APPLYING GENOMIC AND PROTEOMIC MICROARRAY TECHNOLOGY IN DRUG DISCOVERY Copyright 2005 by CRC Press CRC PR ESS Boca Raton London New York Washington, D.C. APPLYING GENOMIC AND PROTEOMIC MICROARRAY TECHNOLOGY IN DRUG DISCOVERY Robert S. Matson Copyright 2005 by CRC Press This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and recording, or by any information storage or retrieval system, without prior permission in writing from the publisher. The consent of CRC Press does not extend to copying for general distribution, for promotion, for creating new works, or for resale. Specific permission must be obtained in writing from CRC Press for such copying. Direct all inquiries to CRC Press, 2000 N.W. Corporate Blvd., Boca Raton, Florida 33431. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation, without intent to infringe. Visit the CRC Presss Web site at www.crcpress.com © 2005 by CRC Press No claim to original U.S. Government works International Standard Book Number 0-8493-1469-0 Library of Congress Card Number 2004057042 Printed in the United States of America 1 2 3 4 5 6 7 8 9 0 Printed on acid-free paper Library of Congress Cataloging-in-Publication Data Matson, Robert S. Applying genomic and proteomic microarray technology in drug discovery / Robert S. Matson. p. ; cm. Includes bibliographical references. ISBN 0-8493-1469-0 1. High throughput screening (Drug development) 2. DNA microarrays. 3. Protein microarrays. 4. Pharmacogenomics. 5. Proteomics. [DNLM: 1. Drug Design. 2. Genomics--methods. 3. Oligonucleotide Array Sequence Analysis--methods. 4. Proteomics--methods. QV 744 M434a 2004] I. Title. RS419.5.M38 2004 615'.19--dc22 2004057042 1469_book.fm Page iv Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press Preface Array technology, much like polymerase chain reaction (PCR) technique, was created to satisfy an existing need in molecular biology. PCR provided a means to amplify enough DNA to sequence genes. The first applications for arrays involved gene sequencing by hybridization (SBH) and genotyping. However, gel-based sequencing quickly supplanted the emerging SBH approach, while genotyping and mutation analysis have been slow in devel- opment. The challenge for those involved in array technology then became finding that elusive application niche, one that would demonstrate a clear, unmitigated, and thereby sustained need for the technology. This book picks up the array technology journey from the mid-1990s with the introduction of microarray-based gene expression analysis. The global analysis of genes by microarrays has provided a fresh and exciting view of the cellular process. More importantly, it enabled others to consider similar utility in various “omic” fields. Hence, we have witnessed the emer- gence of protein arrays to address proteomics. In writing this book, my aim was first to provide a detailed description and offer insight into present and future utilities for microarray technology. While arguably array-based technologies are now being adopted in diverse fields, I have placed emphasis on applications related to drug discovery. Microarrays continue to play significant and increasingly important roles in the drug discovery process. Chapter 1 considers the respective roles as well as the many issues surrounding the future adoption of gene expression and protein microarrays for pharmacogenomic and pharmacoproteomic applications. For acceptance by the pharmaceutical and diagnostic industries, commercially validated array technology is required. Chapter 2 details the commercial microarray landscape. Chapter 3 describes alternative substrates and the preparation of various surface chemistries along with their suitability for immobilization of nucleic acids and proteins. In Chapter 4, the mechanics of microarraying are described in detail including environmental conditions, printer and pin performance, and instructions for setting up a print run. Protocols for print- ing nucleic acids and proteins are provided along with in-depth discussion of other important parameters such as print buffers (inks) and factors influ- encing print quality. I also set out to discuss the importance and provide a critical assessment of studies that helped to define applications in genomics 1469_book.fm Page v Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press and proteomics. In Chapter 5, gene expression microarray applications are described; Chapter 6 examines the utility of protein microarrays. Finally, an understanding of the making of a microarray is fundamen- tally important to those interested in producing “spotted” arrays and prop- erly using them. While complementary (cDNA) microarray fabrication on glass slides has been well studied, we have less experience with the attach- ment of oligonucleotides and the preparation of protein arrays. Moreover, additional substrates and surface chemistries that may be better suited for printing proteins are now available. It is my hope that this book will provide you with the knowledge and confidence to embrace microarraying in your future. Robert S. Matson, Ph.D. Orange, California 1469_book.fm Page vi Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press Author Robert (Bob) Matson, Ph.D., is a senior staff scientist in the Advanced Technology Center at Beckman Coulter, Inc., Fullerton, California. He has been involved in the devel- opment of both nucleic acid and protein array-based tech- nology for the past 13 years. His initial introduction to array technology began in collaboration with Sir Edwin Southern in developing an in situ oligonucleotide array synthesis platform for the corporation. Later work by Dr. Matson and his research team produced some of the first plastic microplate-based microarrays. Beckman Coulter recently launched the A 2 ™ plate based upon the microplate “array of arrays” concept. Prior to joining Beckman Coulter, he served in several technical man- agement roles including: R&D director at BioProbe International, R&D direc- tor at Costar-Nuclepore, and R&D group leader, chemistry, at BioRad Lab- oratories. Dr. Matson currently holds seven United States patents and has contrib- uted numerous papers in peer-reviewed journals as well as chapters in several books on microarrays. He has also made many presentations in the United States and abroad on the development of microarray technology. His current interest is in automated approaches to multiplexed assay development. Dr. Matson grew up in the San Juan Islands of Washington State and attended Western Washington University, Bellingham, where he earned his B.A. and M.S. in chemistry. He received his Ph.D. in biochemistry from Wayne State University. Following postdoctoral studies at the medical school of the University of California at Los Angeles, he served as a principal investigator with the Veterans Administration Medical Center and as an adjunct professor of biological chemistry at the medical school of the Uni- versity of California at Davis. Dr. Matson also held a faculty lectureship in the department of chemistry at University of Southern California and was an assistant professor of chemistry at the University of Southern Maine, Portland. He served on the editorial boards of Applied Biochemistry and Bio- technology and the Journal of Preparative Chromatography , and is a member of the Scientific Advisory and Organizing Board of International Business Com- munications’ “Chips to Hits” conferences. 1469_book.fm Page vii Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press Dr. Matson is a member of the Science Education Advisory Board of the University of California at Irvine. He also volunteers in numerous science education outreach programs including Project Tomorrow and the Orange County Science Fair. He is a past board member of the Orange County Science Education Association (OCSEA). 1469_book.fm Page viii Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press Contents Chapter 1 Quantitative biology: The “Omics” Era ....................................1 Introduction .............................................................................................................1 Microarray format...................................................................................................2 Terms and definitions....................................................................................2 General utility..........................................................................................................5 Biomedical testing..........................................................................................5 Biotechnology sector trends.........................................................................6 The Omics Era.........................................................................................................7 Role of gene expression microarrays in drug discovery ............................... 11 Toxicogenomic applications .......................................................................14 Proteomics today: The great challenge .............................................................14 Potential role for protein microarrays in drug discovery..............................15 Critical issues with protein microarrays...........................................................17 Stability and performance ..........................................................................17 Content ..........................................................................................................19 Detection........................................................................................................19 Micro-ELISA formats...................................................................................20 Protein profiling formats ............................................................................21 Near-term biomedical applications...........................................................22 Cytokines .............................................................................................22 Autoimmune diseases and allergies................................................22 Future medicine: Pharmacoproteomics or pharmacogenomics?..................23 References...............................................................................................................26 Chapter 2 Commercial microarrays .............................................................31 Introduction ...........................................................................................................31 In situ arrays ..........................................................................................................31 Ex situ or spotted arrays......................................................................................38 3D and 4D chips ...................................................................................................44 Flow-through biochips.........................................................................................45 Electronic biochips................................................................................................46 Future opportunities ............................................................................................50 DNA microarrays.........................................................................................50 Protein microarrays .....................................................................................51 Tissue and cell microarrays........................................................................52 References...............................................................................................................53 1469_book.fm Page ix Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press Chapter 3 Supports and surface chemistries.............................................57 Introduction ...........................................................................................................57 Substrates ...............................................................................................................57 Membrane substrates ..................................................................................59 Use with nucleic acids........................................................................59 Use with proteins................................................................................60 Glass substrates............................................................................................61 Use with nucleic acids........................................................................61 Use with proteins................................................................................66 Plastic substrates..........................................................................................68 Use with nucleic acids........................................................................68 Use with proteins................................................................................70 Physical features...........................................................................................71 Hydrogels.............................................................................................71 Surface chemistries ......................................................................................73 Linkers ..................................................................................................73 Reactive groups...................................................................................83 Preparation of glass substrates for derivatization..................................86 Beattie et al. (1995): Attachment of oligonucleotides by epoxide ...............................................................................86 Beier and Hoheisel (1999): Attachment of dendrimer linkers from amine.........................................................................86 Zammatteo et al. (2000): Preparation of carboxylic acid and aldehyde slides .........................................................86 Belosludtsev et al. (2001): Vacuum amine and epoxy silanization protocols .......................................................87 Benters et al. (2002): Preparation of carboxyl- and NHS-activated surfaces ...................................................87 Lee et al. (2002): Preparation of PEI-coated slides ........................88 Summary ................................................................................................................88 References...............................................................................................................89 Chapter 4 Arraying processes .......................................................................93 Introduction ...........................................................................................................93 Creating spotted microarrays .............................................................................94 Substrates ......................................................................................................94 Probe composition (print buffer)...............................................................95 Printing environment ..................................................................................96 Printing mechanics ......................................................................................97 Microarray pins .................................................................................104 Other approaches..............................................................................106 Printer performance.......................................................................... 112 Pin performance................................................................................ 113 Microarray design............................................................................. 115 Setting up a print run ............................................................................... 118 Printing parameters............................................................................................120 1469_book.fm Page x Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press Preparing probe ink...................................................................................122 Optimization of probe concentration .....................................................124 Protocols for printing nucleic acids.................................................................124 cDNA microarray.......................................................................................124 Oligonucleotides ........................................................................................125 Dimethyl sulfoxide ...........................................................................127 Betaine.................................................................................................127 Evaporation........................................................................................129 Print quality assessment...........................................................................132 Backgrounds ...............................................................................................136 Protocols for printing proteins .........................................................................138 Antibody arrays .........................................................................................139 Protocol of Haab et al. (2001)..........................................................139 Protocol of MacBeath and Schreiber (2000)..................................140 References.............................................................................................................144 Chapter 5 Gene expression: Microarray-based applications................147 Introduction .........................................................................................................147 Applications demonstrating DNA microarray utility ..................................147 Gene expression .........................................................................................147 Biomedical research applications.....................................................................159 Drug discovery...........................................................................................159 Drug toxicity...............................................................................................161 Cancer ..........................................................................................................164 Infectious disease.......................................................................................176 Other disease states ...................................................................................180 Hearing loss .......................................................................................181 Bone pathology..................................................................................181 Glaucoma ...........................................................................................182 Multiple sclerosis ..............................................................................182 References.............................................................................................................184 Chapter 6 Protein microarray applications ..............................................189 Introduction .........................................................................................................189 Spot theory...........................................................................................................189 Applications demonstrating protein microarray utility...............................196 Microtiter-based antibody arrays............................................................196 Membranes..................................................................................................198 Glass slides..................................................................................................201 Measuring microarray performance................................................................209 Sensitivity and dynamic range................................................................209 Other microarray formats useful for proteomic applications.....................217 mRNA–protein fusions .............................................................................217 Protein in situ array (PISA) ......................................................................219 Aptamers.....................................................................................................220 Universal protein array.............................................................................223 1469_book.fm Page xi Wednesday, November 17, 2004 11:01 AM Copyright 2005 by CRC Press

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