Arthritis Research: Volume 2: Methods and Protocols (Methods in Molecular Medicine)

438 Pages·2007·5.1 MB·English

by  Andrew P. Cope

Arthritis Research
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 E™
John M. Walker, SERIES EDITOR
139.Vascular Biology Protocols, edited by 117.Fibrosis Research: Methods and Protocols,
Nair Sreejayan and Jun Ren, 2007 edited by John Varga, David A. Brenner,
138.Allergy Methods and Protocols, edited by and Sem H. Phan, 2005
Meinir G. Jones and Penny Lympany, 2007 116.Inteferon Methods and Protocols,edited by
137.Microtubule Protocols,edited by Jun Zhou, 2007 Daniel J. J. Carr, 2005
136.Arthritis Research: Methods and Protocols, 115.Lymphoma: Methods and Protocols, edited by
Vol. 2,edited by Andrew P. Cope, 2007 Timothy Illidge and Peter W. M. Johnson, 2005
135.Arthritis Research: Methods and Protocols, 114.Microarrays in Clinical Diagnostics,edited by
Vol. 1,edited by Andrew P. Cope, 2007 Thomas O. Joos and Paolo Fortina, 2005
134.Bone Marrow and Stem Cell Transplantation, 113.Multiple Myeloma: Methods andProtocols,
edited by Meral Beksac, 2007 edited by Ross D. Brown and P. Joy Ho, 2005
133.Cancer Radiotherapy,edited by Robert A. 112.Molecular Cardiology: Methods andProtocols,
Huddart and Vedang Murthy, 2007 edited by Zhongjie Sun, 2005
132.Single Cell Diagnostics: Methods and 111.Chemosensitivity: Volume 2, In Vivo Mod-
Protocols,edited by Alan Thornhill, 2007 els, Imaging, and Molecular Regulators, edited
131. Adenovirus Methods and Protocols, Second byRosalyn D. Blumethal, 2005
Edition, Vol. 2: Ad Proteins, RNA, Lifecycle, 110.Chemosensitivity: Volume 1, In Vitro Assays,
Host Interactions, and Phylogenetics,edited by edited by Rosalyn D. Blumethal, 2005
William S. M. Wold and Ann E. Tollefson,
109.Adoptive Immunotherapy: Methods and
2007
Protocols, edited by Burkhard Ludewig and
130.Adenovirus Methods and Protocols, Second
Matthias W. Hoffman, 2005
Edition, Vol. 1: Adenoviruses, Ad Vectors,
108.Hypertension: Methods and Protocols,
Quantitation, and Animal Models,edited by
edited by Jérôme P. Fennell and Andrew
William S. M. Wold and Ann E. Tollefson, 2007
H. Baker, 2005
129. Cardiovascular Disease: Methods and Protocols,
Volume 2: Molecular Medicine, edited by 107.Human Cell Culture Protocols, Second
Qing K.Wang, 2006 Edition, edited by Joanna Picot, 2005
128. Cardiovascular Disease: Methods and Protocols, 106.Antisense Therapeutics, Second Edition,
Volume 1: Genetics, edited by Qing K. Wang, edited by M. Ian Phillips, 2005
2006 105.Developmental Hematopoiesis: Methods and
127. DNA Vaccines: Methods and Protocols,Second Protocols, edited by Margaret H. Baron, 2005
Edition, edited by Mark W. Saltzman, Hong 104. Stroke Genomics: Methods and Reviews, edited
Shen, and Janet L. Brandsma, 2006 bySimon J. Read and David Virley, 2004
126. Congenital Heart Disease: Molecular Diagnostics, 103.Pancreatic Cancer: Methods and Protocols,
edited by Mary Kearns-Jonker, 2006 edited by Gloria H. Su, 2004
125.Myeloid Leukemia:Methods and Protocols, ed- 102.Autoimmunity: Methods and Protocols,
ited by Harry Iland, Mark Hertzberg, edited by Andras Perl, 2004
and Paula Marlton, 2006 101.Cartilage and Osteoarthritis: Volume 2,
124.Magnetic Resonance Imaging:Methods and Structure and In Vivo Analysis, edited by
Biologic Applications, edited by Pottumarthi V. Frédéric De Ceuninck, Massimo Sabatini,
Prasad, 2006 and Philippe Pastoureau, 2004
123.Marijuana and Cannabinoid Research: 100.Cartilage and Osteoarthritis: Volume 1,
Methods and Protocols, edited by Emmanuel S. Cellular and Molecular Tools, edited by
Onaivi, 2006 Massimo Sabatini, Philippe Pastoureau,
122.Placenta Research Methods and Protocols: and Frédéric De Ceuninck, 2004
Volume 2, edited by Michael J. Soares and 99.Pain Research: Methods and Protocols,
Joan S. Hunt, 2006 edited by David Z. Luo, 2004
121.Placenta Research Methods and Protocols: 98.Tumor Necrosis Factor: Methods and
Volume 1, edited by Michael J. Soares and Protocols, edited by Angelo Corti and Pietro
Joan S. Hunt, 2006 Ghezzi, 2004
120.Breast Cancer Research Protocols,edited by 97.Molecular Diagnosis of Cancer: Methods
Susan A. Brooks and Adrian Harris, 2006 and Protocols, Second Edition, edited by
119.Human Papillomaviruses: Methods and Joseph E. Roulston and John M. S. Bartlett,
Protocols,edited by Clare Davy and John 2004
Doorbar, 2005 96.Hepatitis B and D Protocols: Volume 2,
118.Antifungal Agents: Methods and Protocols, Immunology, Model Systems, and Clinical
edited by Erika J. Ernst and P. David Rogers, Studies, edited by Robert K. Hamatake and
2005 Johnson Y. N. Lau, 2004
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 E™
Arthritis Research
Methods and Protocols
Volume 2
Edited by
Andrew P. Cope
The Kennedy Institute of Rheumatology
Imperial College London, London UK
© 2007 Humana Press Inc.
999 Riverview Drive, Suite 208
Totowa, New Jersey 07512
www.humanapress.com
All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in
any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise
without written permission from the Publisher. Methods in Molecular BiologyTMis a trademark of The
Humana Press Inc.
All papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not
necessarily reflect the views of the publisher.
This publication is printed on acid-free paper. ∞
ANSI Z39.48-1984 (American Standards Institute)
Permanence of Paper for Printed Library Materials.
Cover design by Nancy K. Fallatt.
Cover illustration: (Background)Figure 1 from Chapter 24 from volume 1. (Inset) Figure 2 from Chapter 15
from volume 1.
For additional copies, pricing for bulk purchases, and/or information about other Humana titles, contact
Humana at the above address or at any of the following numbers: Tel.: [phone]; Fax: [phone];
E-mail: [email protected]; or visit our Website: www.humanapress.com
Photocopy Authorization Policy:
Authorization to photocopy items for internal or personal use, or the internal or personal use of specific
clients, is granted by Humana Press Inc., provided that the base fee of US $30.00 per copy is paid directly
to the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA 01923. For those organizations
that have been granted a photocopy license from the CCC, a separate system of payment has been arranged
and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is:
[978-1-58829-918-5/07 $30.00 ].
Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1
eISBN: 978-1-59745-402-5
Library of Congress Cataloging in Publication Data
Arthritis research : methods and protocols / edited by Andrew P. Cope.
p. ; cm. — (Methods in molecular biology ; v. 135-136)
Includes bibliographical references and index.
ISBN 1-58829-344-0 (v. 1 : alk. paper) — ISBN 1-58829-918-X (v. 2 : alk. paper)
1. Arthritis—Laboratory manuals. 2. Arthritis—Molecular aspects. I. Cope, Andrew P. II. Series:
Methods in molecular biology (Clifton, N.J.) ; v. 135-136.
[DNLM: 1. Arthritis—Laboratory Manuals. 2. Laboratory Techniques and Procedures—Laboratory
Manuals. W1 ME9616J v.135-136 2007 / WE 25 A787 2007]
RC933.A665245 2007
616.7’220072—dc22 2006019975
Preface
“……………… do not go where the path may lead,
go instead where there is no path and leave a trail”
Ralph Waldo Emerson
The postgenomic era is upon us and with it comes a growing need to under-
stand the function of every gene and its contribution to physiological and patho-
logical processes. Such advances will underpin our understanding of the
molecular basis of common chronic inflammatory and degenerative diseases
and inspire the development of targeted therapy. Any postgenomic approach
for exploring gene function must necessarily address gene expression and regu-
lation, localization of gene products in diseased tissue, manipulation of expres-
sion by transgenesis or knockdown technology, and combine these studies with
appropriate manipulations in relevant in vivo models. To validate potential
therapeutic targets in any depth requires a growing repertoire of assays and
disease models that underpin key pathogenic pathways. The same repertoire of
tools must be employed to rigorously evaluate process specific biomarkers,
which may be of diagnostic and prognostic value. Indeed, measuring the im-
pact of our interventions remains a major challenge for the future.
The rheumatic diseases encompass prototypic chronic inflammatory and
degenerative diseases. It would be true to say that experimental procedures
adapted for investigating the pathogenesis of diseases such as rheumatoid arthri-
tis have contributed greatly to recent advances in biological therapy. Arthritis
Research: Methods and Protocols seeks to crystallize methods and protocols
that have contributed to such advances in molecular medicine.These volumes are
timely because the tools are now accessible to most laboratories. Also included
are newer technologies, some of which are still evolving and whose impact are
yet to be realized. It is important to note that in these volumes there is something
for everyone—basic scientists, clinician scientists, and clinicians alike—with
contributions from leaders in their field covering imaging and immunobiology,
animal models, and new technologies. Combine volumes 1 and 2 and the end
product is a concise set of protocols condensing decades of experience and
expertise. From the outset of this project it was always the intention that this
compendium should provide a unique resource at the bench that would be used
in ways that will facilitate the endeavors of clinicians at the bedside in the
future.
v
Acknowledgments
I wish to thank many friends and colleagues for their enthusiasm, support,
and invaluable contributions toward this project. I am also very grateful to
Mandy Wilcox for her dedicated secretarial assistance in compiling the fin-
ished product. The research carried out by the Editor’s laboratory at the
Kennedy Institute is supported by grants from the Wellcome Trust and the
Arthritis Research Campaign, UK.
Andrew P. Cope
vii
Contents
Preface ..............................................................................................................v
Ackowlegments................................................................................................vi
Contributors .................................................................................................. xiii
Color Plate .....................................................................................................xix
Contents for Volume 1...................................................................................xxi
PART I IMMUNOBIOLOGY
1 Phenotypic Analysis of B-Cells and Plasma Cells
Henrik E. Mei, Taketoshi Yoshida, Gwendolin Muehlinghaus,
Falk Hiepe, Thomas Dörner, Andreas Radbruch,
and Bimba F. Hoyer..........................................................................3
2 Detection of Antigen Specific B-Cells in Tissues
Marie Wahren-Herlenius and Stina Salomonsson..............................19
3 Single Cell Analysis of Synovial Tissue B-Cells
Hye-Jung Kim and Claudia Berek.......................................................25
4 Tracking Antigen Specific CD4+ T-Cells with Soluble
MHC Molecules
John A. Gebe and William W. Kwok..................................................39
5 Analysis of Antigen Reactive T-Cells
Clare Alexander, Richard C. Duggleby, Jane C. Goodall,
Malgosia K. Matyszak, Natasha Telyatnikova,
and J. S. Hill Gaston.......................................................................51
6 Identification and Manipulation of Antigen Specific T-Cells
with Artificial Antigen Presenting Cells
Eva Koffeman, Elissa Keogh, Mark Klein, Berent Prakken,
andSalvatore Albani.......................................................................69
7 Analysis of Th1/Th2 T-Cell Subsets
Alla Skapenko and Hendrik Schulze-Koops........................................87
8 Analysis of the T-Cell Receptor Repertoire of Synovial T-Cells
Lucy R. Wedderburn and Douglas J. King..........................................97
9 The Assessment of T-Cell Apoptosis in Synovial Fluid
Karim Raza, Dagmar Scheel-Toellner, Janet M. Lord,
Arne N. Akbar, Christopher D. Buckley,
and Mike Salmon..........................................................................117
ix
x Contents
10 Assay of T-Cell Contact Dependent Monocyte-Macrophage
Functions
Danielle Burger and Jean-Michel Dayer...........................................139
11 Phenotypic and Functional Analysis of Synovial
Natural Killer Cells
Nicola Dalbeth and Margaret F. C. Callan.......................................149
12 Identification and Isolation and Synovial Dendritic Cells
Allison R. Pettit, Lois Cavanagh, Amanda Boyce,
Jagadish Padmanabha, Judy Peng,
and Ranjeny Thomas.....................................................................165
PART II ANIMAL MODELS OF ARTHRITIS
13 The Use of Animal Models for Rheumatoid Arthritis
Rikard Holmdahl...............................................................................185
14 Collagen-Induced Arthritis in Mice
Richard O. Williams.........................................................................191
15 Collagen-Induced Arthritis in Rats
Marie M. Griffiths, Grant W. Cannon, Tim Corsi, Van Reese,
and Kandie Kunzler......................................................................201
16 Collagen Antibody Induced Arthritis
Kutty Selva Nandakumar and Rikard Holmdahl...............................215
17 Arthritis Induced with Minor Cartilage Proteins
Stefan Carlsen, Shemin Lu, and Rikard Holmdahl............................225
18 Murine Antigen-Induced Arthritis
Wim van den Berg, Leo A. B. Joosten,
and Peter L. E. M. van Lent...........................................................243
19 Pristane-Induced Arthritis in the Rat
Peter Olofsson and Rikard Holmdahl...............................................255
20 The K/BxN Mouse Model of Inflammatory Arthritis:
Theory and Practice
Paul Monach, Kimie Hattori, Haochu Huang,
Elzbieta Hyatt, Jody Morse, Linh Nguyen,
Adriana Ortiz-Lopez, Hsin-Jung Wu,
Diane Mathis, and Christophe Benoist.........................................269
21 Analysis of Arthritic Lesions in the Del1 Mouse:
A Model for Osteoarthritis
Anna-Marja Säämänen, Mika Hyttinen,
and Eero Vuorio............................................................................283
Contents xi
PART III APPLICATION OF NEW TECHNOLOGIES TO DEFINE NOVEL
THERAPEUTIC TARGETS
22 Gene Expression Profiling in Rheumatology
Tineke C. T. M. van der Pouw Kraan, Lisa G. M. van Baarsen,
François Rustenburg, Belinda Baltus, Mike Fero,
and Cornelis L. Verweij................................................................305
23 Differential Display Reverse Transcription-Polymerase Chain
Reaction to Identify Novel Biomolecules in Arthritis Research
Manir Ali and John D. Isaacs............................................................329
24 Two-Dimensional Electrophoresis of Proteins Secreted
from Articular Cartilage
Monika Hermansson, Jeremy Saklatvala, and Robin Wait...............349
25 Mapping Lymphocyte Plasma Membrane Proteins:
A Proteomic Approach
Matthew J. Peirce, Jeremy Saklatvala, Andrew P. Cope,
and Robin Wait.............................................................................361
26 In Vivo Phage Display Selection in the Human/SCID Mouse
Chimera Model for Defining Synovial Specific Determinants
Lewis Lee, Toby Garrood, and Costantino Pitzalis...........................369
27 Adenoviral Targeting of Signal Transduction Pathways
in Synovial Cell Cultures
Alison Davis, Corinne Taylor, Kate Willetts,
Clive Smith, and Brian M. J. Foxwell...........................................395
Index ............................................................................................................421