Arthritis Research: Methods and Protocols

209 Pages·2014·11.92 MB·English

by  Shunichi Shiozawa (eds.)

Methods in
Molecular Biology 1142
Shunichi Shiozawa Editor
Arthritis
Research
Methods and Protocols
Second Edition
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire

Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
h ttp://www.springer.com/series/7651

Arthritis Research
Methods and Protocols
Second Edition
Edited by
Shunichi Shiozawa
Department of Rheumatology, Kyushu University, Beppu, Japan
Editor
Shunichi S hiozawa
Department of Rheumatology
Kyushu University
Beppu , Japan
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-0403-7 ISBN 978-1-4939-0404-4 (eBook)
DOI 10.1007/978-1-4939-0404-4
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2014934695
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Prefa ce
It is my pleasure to provide the readers a new volume of the Methods in Molecular Biology,
which deals with current techniques for the research of arthritis and related conditions.
Nowadays, information can be easily shared by anyone in the world so quickly without
boundary, and so are the techniques for experimental medicine. Further, the results obtained
from medical research have increasingly become accurate, quantitative, and reliable.
Accordingly, the experimental techniques described here should be brand new, but, at the
same time, one should also note that even such techniques are based on chemistry and
biochemistry. In this regard, therefore, I must fi rst thank all the authors, because they real-
ized what the methods in molecular biology sought to be and did not hesitate to share their
state-of-the-art techniques with us.
In this book, intravital multiphoton microscopy technique is introduced to visualize
bone resorption of mature osteoclasts in living bone marrow and joints, which is a novel
technique enabling the study of dynamical movements of cells in vivo not only for bone
resorption but also for arthritis and systemic autoimmunity. The techniques for evaluating
exhausted CD8 T cell and for studying nucleic acid sensors and their effects are also intro-
duced. Also described are the techniques for in vivo tetracycline-controlled transgenic mice
and T cell receptor transgenic mice. The former is described in an overview form because
how to select respective techniques is often keen to the success of experiments technique.
The techniques to detect V(D)J recombination products and microRNA are described.
Current techniques for isolating, making cell lines, and assaying the activity of iNKT cell
and MAIT cell are also described. Since we have succeeded in inducing autoimmunity akin
to systemic lupus erythematosus (SLE) in mice not prone to autoimmune diseases with
almost 100 % effi ciency, we describe this technique and how to isolate the particular T cell
responsible for inducing autoimmunity. As a model of systemic sclerosis (scleroderma), the
technique to make bleomycin-induced dermal fi brosis is described. Quantitative proteomic
techniques are also available for screening novel biomarkers in sera, and this is described in
relation to the biomarkers found in rheumatoid arthritis (RA). The method for genome-
wide study is also overviewed and detailed from practical viewpoint. Then, from a view-
point of data synthesis of the genetic data obtained in high-throughput genotyping era, the
method using Bayesian-based genetic association analysis is described in a form of
hypothesis-d riven candidate gene association studies, which enables solid evaluation of the
results. Finally, seemingly somewhat abrupt but novel techniques including time-of-fl ight
secondary ion mass spectrometry assaying cartilage surface components and a label-free
imaging technique using coherent anti-Stokes Raman scattering microscopy taking adipose
tissue as an example are described. The latter enables visualization of unlabeled samples by
using the novel microscopy.
Beppu, J apan S hunichi S hiozawa
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Intravital Multiphoton Microscopy for Dissecting Cellular Dynamics
in Arthritic Inflammation and Bone Destruction. . . . . . . . . . . . . . . . . . . . . . . 1
Junichi Kikuta and Masaru Ishii
2 M onitoring Multifunctionality of Immune-Exhausted CD8
T Cells in Cancer Patients. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Shingo Eikawa, S husaku M izukami, and Heiichiro Udono
3 Characterization of Innate Immune Signalings Stimulated
by Ligands for Pattern Recognition Receptors. . . . . . . . . . . . . . . . . . . . . . . . . 19
Takeshi K ameyama and Akinori Takaoka
4 Principles for the Use of In Vivo Transgene Techniques: Overview
and an Introductory Practical Guide for the Selection
of Tetracycline-Controlled Transgenic Mice . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3
Norio Sakai
5 Unraveling Autoimmunity with the Adoptive Transfer of T Cells
from TCR-Transgenic Mice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1
Huard B ertrand
6 In Vivo Cell Transfer Assay to Detect Autoreactive T Cell Subsets. . . . . . . . . . 4 9
Yumi M iyazaki and Shunichi S hiozawa
7 Characterization of MicroRNAs and Their Targets . . . . . . . . . . . . . . . . . . . . . 5 5
Ghada Alsaleh and J acques-Eric G ottenberg
8 S tudies on the T Cell Receptor (TCR) Revision
of Autoantibody-Inducing CD4 T (aiCD4 T) Cell . . . . . . . . . . . . . . . . . . . . . 6 5
Shunichi S hiozawa and Kenichi U to
9 B asic Techniques for Studies of iNKT Cells and MAIT Cells. . . . . . . . . . . . . . 7 5
Asako Chiba and Sachiko Miyake
10 I nduction of De Novo Autoimmune Disease in Normal Mice
upon Repeated Immunization with Antigen . . . . . . . . . . . . . . . . . . . . . . . . . . 8 5
Ken Tsumiyama and Shunichi S hiozawa
11 M ouse Model of Experimental Dermal Fibrosis:
The Bleomycin-Induced Dermal Fibrosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Jérôme A vouac
12 S creening for Novel Serum Biomarker for Monitoring
Disease Activity in Rheumatoid Arthritis Using iTRAQ
Technology-Based Quantitative Proteomic Approach . . . . . . . . . . . . . . . . . . . 9 9
Satoshi S erada and Tetsuji N aka
vii
viii Contents
13 Genome-Wide Genetic Study in Autoimmune Disease-Prone Mice . . . . . . . . . 1 11
Masaomi Obata, M areki O htsuji, Y ukiyasu Iida, T oshikazu Shirai,
Sachiko Hirose, and H ioroyuki Nishimura
14 B ayesian Systems-Based Genetic Association Analysis
with Effect Strength Estimation and Omic Wide Interpretation:
A Case Study in Rheumatoid Arthritis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Gábor H ullám, András G ézsi, A ndrás M illinghoffer,
Péter S árközy, B ence B olgár, S anjeev K . S rivastava, Z suzsanna Pál,
Edit I. B uzás, and Péter Antal
15 S ample Processing, Protocol, and Statistical Analysis
of the Time-of-Flight Secondary Ion Mass Spectrometry (ToF-S IMS)
of Protein, Cell, and Tissue Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 77
Goncalo B arreto, A ntti S oininen, T arvo Sillat, Yrjö T . K onttinen,
and Emilia K aivosoja
16 L abel-Free Imaging of Adipogenesis by Coherent
Anti- Stokes Raman Scattering Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Antti Isomäki, Tarvo S illat, M ari A inola, Mikko L iljeström,
Yrjö T. Konttinen, and M ika H ukkanen
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 03
Contributors
MARI AINOLA • Department of Medicine/Invärtes medicin , H elsinki University Hospital ,
Helsinki, F inland ; Department of Medicine, I nstitute of Clinical Medicine, University of
Helsinki , H elsinki, Finland
GHADA ALSALEH • University of Strasbourg , Strasbourg , F rance
PÉTER ANTAL • Department of Measurement and Information Systems , B udapest University
of Technology and Economics (BME) , Budapest, H ungary
JÉRÔME A VOUAC • Université Paris Descartes, Service de Rhumatologie A et INSERM
U1016, Hôpital, Cochin, Paris, France
GONCALO B ARRETO • Institute of Clinical Medicine, University of Helsinki ,
Helsinki, F inland
HUARD BERTRAND • Team 8, Institut Albert Bonniot, L a Tronche , F rance
BENCE B OLGÁR • Department of Measurement and Information Systems, Budapest University
of Technology and Economics (BME) , Budapest, Hungary
EDIT I. BUZÁS • Department of Genetics, Cell and Immunobiology , S emmelweis University ,
Budapest, H ungary
ASAKO CHIBA • Department of Immunology , J untendo University School of Medicine ,
Tokyo, Japan
SHINGO E IKAWA • Okayama University, Shikata , O kayama , J apan
ANDRÁS GEZSI • Department of Genetics, Cell and Immunobiology , Semmelweis University ,
Budapest, H ungary
JACQUES - E RIC G OTTENBERG • University of Strasbourg , Strasbourg, F rance
SACHIKO H IROSE • Department of Pathology, Juntendo University School of Medicine ,
Tokyo, J apan
MIKA HUKKANEN • Institute of Biomedicine, Anatomy, University of Helsinki , H elsinki, F inland
GÁBOR H ULLÁM • Department of Measurement and Information Systems , B udapest
University of Technology and Economics , B udapest, H ungary
YUKIYASU IIDA • Toin Human Science and Technology Center, Toin University of Yokohama ,
Yokohama, J apan
MASARU I SHII • Department of Immunology and Cell Biology, Graduate School of Medicine
and Frontier Biosciences, Osaka University , Suita, O saka, Japan
ANTTI I SOMÄKI • Institute of Biomedicine, Anatomy, University of Helsinki , Helsinki, Finland
EMILIA KAIVOSOJA • Institute of Clinical Medicine, University of Helsinki , H elsinki, Finland
TAKESHI KAMEYAMA • Hokkaido University , Sapporo, J apan
JUNICHI KIKUTA • Department of Immunology and Cell Biology, Graduate School of
Medicine and Frontier Biosciences, Osaka University, S uita, O saka, Japan
YRJÖ T. K ONTTINEN • Department of Medicine, Institute of Clinical Medicine, University of
Helsinki , H elsinki, Finland
MIKKO LILJESTRÖM • Institute of Biomedicine, Anatomy, University of Helsinki ,
Helsinki, F inland
ANDRÁS MILLINGHOFFER • Department of Measurement and Information Systems , B udapest
University of Technology and Economics , Budapest, H ungary
ix