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: http://www.springer.com/series/7651 Autoimmunity Methods and Protocols Second Edition Edited by Andras Perl Departments of Medicine, Microbiology and Immunology, Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, College of Medicine, Syracuse, NY, USA Editor Andras Perl Departments of Medicine Microbiology and Immunology Biochemistry and Molecular Biology State University of New York Upstate Medical University College of Medicine Syracuse, NY, USA ISSN 1064-3745 ISSN 1940-6029 (electronic) ISBN 978-1-60761-719-8 ISBN 978-1-60761-720-4 (eBook) DOI 10.1007/978-1-60761-720-4 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2012943612 © Springer Science+Business Media New York 2012 This work is subject to copyright. 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Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (www.springer.com) Dedication To my parents, Ibolya and Miklos, and family, Katalin, Annmarie, Marcel, and Daniel, for their inspiration, support, and love in my pursuit of medicine and science. Preface “Research is to see what everybody else has seen, and to think what nobody else has thought” —Albert Szentgyörgyi The fi rst edition of Autoimmunity: Methods and Protocols, published in 2005, has been initiated to provide a ready-to-use guide to establish and interrogate human and animal models of autoimmune diseases. The second edition contains several updated chapters and many new ones. Due to continued refi nement of and widespread access to transgenic tech- nology, perhaps hundreds of new animal models have been developed that exhibit features of autoimmune disease. Alternatively, the increasing resolution of whole genome typing oligonucleotide chips and full genome sequencing identifi ed many new pathways that can lead to autoimmunity. The fi rst chapter, Pathogenesis and Spectrum of Autoimmunity , discusses major hypoth- eses driving this most tantalizing area of research since the concept of autoimmunity has been proposed by Paul Ehrlich in 1900. Considering the great diversity and ever-changing spectrum of autoimmunity, it has not been possible to include models and experimental protocols for each known clinical disorder. Rather, several chapters have been devoted to the most prevalent and complex diseases, such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), insulin-dependent diabetes mellitus (IDDM), scleroderma or progressive systemic sclerosis (PSS), and multiple sclerosis (MS). The chapters are contrib- uted by laboratories actively using the presented models. Each chapter contains an intro- ductory section that discusses relevance of the model for a particular disease and autoimmunity in general. The fi rst set of eight chapters contains methods and protocols used to assess immuno- logical and biochemical pathways of diseases’ pathogenesis in human samples. Chapters in this section focus on methods to identify susceptibility genes, intercellular signaling via cytokines, intracellular signaling through the T-cell receptor and signal processing via pro- tein kinases, identifi cation and enumeration of autoantigen-specifi c T cells and autoanti- bodies, dysregulation of apoptosis and its role in modifi cation of self antigens, and epigenetic control of gene expression via DNA methylation. The second section, Chapters 9 – 23 , con- tains protocols to establish, to investigate, and to treat infl ammatory arthritis, experimental allergic encephalomyelitis (EAE), IDDM, scleroderma, and uveitis in animal models. The methods focus on assessment of genetic, immunological, and biochemical parameters underlying spontaneous or exogenous antigen-induced diseases. Although the individual protocols focus on a specifi c disease, they can be adapted to investigate additional signaling pathways or pathogenic autoantigens. This book does not replace laboratory manuals with recipes for standard cell and molec- ular biology and immunology techniques, such as cell culture, gene cloning, sequencing, and amplifi cation by polymerase chain reaction, vector design for generation of transgenic and knockout animals, fl ow cytometry, fl uorescence microscopy, electrophoresis, and gene vii viii Preface and protein microarray and sequencing methods. Although these general methods are not described in detail, they are appropriately referenced in each section. With both my col- leagues in the fi eld and newcomers in mind, step-by-step protocols and detailed trouble- shooting guides supplement all chapters. I am thankful to Professor John Walker for inviting me to organize the 2nd edition and Dr. Paul Phillips for continued encouragement and support. I am grateful to the distin- guished authors for their time, expertise, and devotion that made this book possible. If the reader feels that a particularly relevant disease or model is missing, I should be held respon- sible. Re fi ning and extracting new meaning of old models and developing new ones is a constantly ongoing process. Therefore, we invite our readers to approach the authors with questions and comments or offer new models and protocols for a future volume of this endeavor. Syracuse, NY, USA Andras Perl Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi 1 Pathogenesis and Spectrum of Autoimmunity. . . . . . . . . . . . . . . . . . . . . . . . . 1 Andras Perl 2 Mapping Susceptibility Gene in Systemic Lupus Erythematosus. . . . . . . . . . . . 11 R. Hal Scofield and Kenneth M. Kaufman 3 Methods and Protocols to Study T Cell Signaling Abnormalities in Human Systemic Lupus Erythematosus. . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Vaishali R. Moulton, Mindy S. Lo, and George C. Tsokos 4 Assessment of Mitochondrial Dysfunction in Lymphocytes of Patients with Systemic Lupus Erythematosus. . . . . . . . . . . . . . . . . . . . . . . . 61 Andras Perl, Robert Hanczko, and Edward Doherty 5 The Role of Endocytic Recycling in Autoimmunity. . . . . . . . . . . . . . . . . . . . . 91 Tiffany Telarico and Andras Perl 6 Multiparameter Flow Cytometry and Bioanalytics for B Cell Profiling in Systemic Lupus Erythematosus. . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Denise A. Kaminski, Chungwen Wei, Alexander F. Rosenberg, F. Eun-Hung Lee, and Ignacio Sanz 7 Experimental Use of Mouse Models of Systemic Lupus Erythematosus. . . . . . 135 Stanford L. Peng 8 Murine Models of Lupus Induced by Hypomethylated T Cells (DNA Hypomethylation and Lupus…). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 Bruce Richardson, Amr H. Sawalha, Donna Ray, and Raymond Yung 9 Aspects of CNS Lupus: Mouse Models of Anti-NMDA Receptor Antibody Mediated Reactivity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 Czeslawa Kowal and Betty Diamond 10 Analysis of Renal Mononuclear Phagocytes in Murine Models of SLE. . . . . . . 207 Ramalingam Bethunaickan, Ranjit Sahu, and Anne Davidson 11 A Murine Autoimmune Model of Rheumatoid Arthritis and Systemic Lupus Erythematosus Associated with Deregulated Production of IL-17 and IL-21. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233 Partha S. Biswas, Kyuho Kang, Sanjay Gupta, Govind Bhagat, and Alessandra B. Pernis ix x Contents 12 The Parent-into-F1 Murine Model in the Study of Lupus-Like Autoimmunity and CD8 Cytotoxic T Lymphocyte Function. . . . . . . . . . . . . . 253 Kateryna Soloviova, Maksym Puliaiev, Anthony Foster, and Charles S. Via 13 Genetic Approach to Study Lupus Glomerulonephritis . . . . . . . . . . . . . . . . . . 271 Yan Ge, Michael G. Brown, Hongyang Wang, and Shu Man Fu 14 Animal Models of Primary Biliary Cirrhosis: Materials and Methods . . . . . . . . 291 Patrick S.C. Leung, Guo Xiang Yang, Amy Dhirapong, Koichi Tsuneyama, William M. Ridgway, and M. Eric Gershwin 15 Modeling Innate Immunity in Murine Skin: Utilization of Subcutaneous Osmotic Pumps for Inflammatory and Fibrotic Skin Disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317 Michael Dimarzio, Giuseppina Farina, and Robert Lafyatis 16 Flow Cytometric Identification of Fibrocytes in Scleroderma Lung Disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327 Thomas M. Russell, Erica L. Herzog, and Richard Bucala 17 Oxidative Stress and Beta Cell Dysfunction. . . . . . . . . . . . . . . . . . . . . . . . . . . 347 Yaíma L. Lightfoot, Jing Chen, and Clayton E. Mathews 18 Experimental Autoimmune Encephalomyelitis. . . . . . . . . . . . . . . . . . . . . . . . . 363 Praveen Rao and Benjamin M. Segal 19 Mouse Models of Multiple Sclerosis: Experimental Autoimmune Encephalomyelitis and Theiler’s Virus-Induced Demyelinating Disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381 Derrick P. McCarthy, Maureen H. Richards, and Stephen D. Miller 20 Pathogenesis of Multiple Sclerosis: What Can We Learn from the Cuprizone Model. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403 Peter Acs and Bernadette Kalman 21 Assessing Inflammatory Disease at Mucosal Surfaces in Murine Genetic Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433 R.W. Engelman and William G. Kerr 22 Rodent Models of Experimental Autoimmune Uveitis. . . . . . . . . . . . . . . . . . . 443 Rajeev K. Agarwal, Phyllis B. Silver, and Rachel R. Caspi 23 Tolerance Induction via B-Cell Delivered Gene Therapy . . . . . . . . . . . . . . . . . 471 Robert J. Rossi, Belinda M. Jackson, Ai-Hong Zhang, and David W. Scott Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489