Table Of ContentAPPLYING 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
