Adenovirus: Methods and Protocols

252 Pages·2014·3.509 MB·English

by  Rosa Menéndez-Conejero, Ana J. Pérez-Berná, Gabriela N. Condezo (auth.), Miguel Chillón, Assumpció Bosch (eds.)

Methods in
Molecular Biology 1089
Miguel Chillón
Assumpció Bosch Editors
Adenovirus
Methods and Protocols
Third 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:
http://www.springer.com/series/7651

Adenovirus
Methods and Protocols
Third Edition
Edited by
Miguel Chillón
Institució Catalana de Recerca i Estudis Avançats (ICREA) and CBATEG-Department of Biochemistry
and Molecular Biology, Universitat Autonoma Barcelona, Bellaterra, Barcelona, Spain
Assumpció Bosch
Department of Biochemistry and Molecular Biology, Center of Animal Biotechnology and Gene Therapy

(CBATEG), Universitat Autonoma Barcelona, Bellaterra, Barcelona, Spain
Editors
Miguel Chillón Assumpció Bosch
Institució Catalana de Recerca i Estudis Avançats Department of Biochemistry and Molecular
(ICREA) and CBATEG-Department of Biology
Biochemistry and Molecular Biology Center of Animal Biotechnology and Gene
Universitat Autonoma Barcelona Therapy (CBATEG)
Bellaterra, B arcelona, Spain Universitat Autonoma Barcelona
Bellaterra, Barcelona, Spain
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-62703-678-8 ISBN 978-1-62703-679-5 (eBook)
DOI 10.1007/978-1-62703-679-5
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2013947923
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Pref ace
Since the fi rst reports in the mid-1950s, adenoviruses have been extensively studied in
virology research, with over 43,000 publications listed in Pubmed (more than 1,700 in
2012 alone). Moreover, their effi ciency as gene therapy tools has resulted in over 450 pro-
tocols approved for clinical trials. Initially, the majority of the techniques employed were
commonly used in basic virology, such as small-scale production and purifi cation, cell infec-
tion, and in vivo tropism. However, in recent years, advances in molecular biology, genom-
ics and proteomics, imaging, and bioinformatics have allowed the development of powerful
new tools and high-throughput methods to analyze adenoviral particles and their interac-
tions with host cells, many of which are described in this book.
The A denovirus: Methods and Protocols (3rd edition) book is intended for both the
novice as well as the experienced investigators in the fi eld. For this reason, despite it being
impossible to cover all aspects of adenovirus research, we have aimed to compile a vast array
of techniques as well as to review the most recent updates and new methodological devel-
opments in the fi eld. Briefl y, this third edition of A denovirus: Methods and Protocols consists
of 16 chapters covering state-of-the-art techniques. It includes cryoelectron microscopy,
atomic force microscopy, and mass spectrometry for a high-resolution image and character-
ization of the virion (Chapters 1 and 2 ), capsid modifi cations and viral-like particles as
promising alternatives to classical adenovirus vectors (Chapters 3 and 4 ), the study of ade-
novirus: host interactions in vitro at cellular level as well as in vivo in animal models
(Chapters 5 – 10 ), and fi nally, an update of the most effi cient protocols to generate, amplify,
and/or purify at small- and large-scale, standard human Ad5 as well as nonhuman, chime-
ric, and helper-dependent adenovirus vectors (Chapters 11 – 16 ) . More importantly, since
this is a comprehensive methods book written by top scientists who are well aware of the
pitfalls of the experiments, at the end of each chapter there is a helpful Notes section pro-
viding valuable troubleshooting guides and alternative procedures.
Adenovirus: Methods and Protocols (3rd edition) is the product of the hard work of a
large number of scientists, all experts in various aspects of adenovirus research. We are
indebted to all of them for their dedication and cooperation as well as for their patience
during the editing process. We are also very grateful to the series editor, John Walker, as
well as to David Casey and the editorial staff at Humana Press, for all the advice and assis-
tance they have provided, and also to Rosemary Thwaite for her valuable assistance in
proofreading. Without them, this book would not have been possible in its current form.
Finally, we would like to highlight that, as editors, it has been a privilege to participate
in the development of the Adenovirus book. On behalf of all the authors, we hope you will
fi nd the book useful and informative.
Bellaterra, Barcelona, Spain Miguel C hillón
Assumpció Bosch
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Biophysical Methods to Monitor Structural Aspects
of the Adenovirus Infectious Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Rosa Menéndez-Conejero, Ana J. Pérez-Berná, Gabriela N. Condezo,
Alvaro Ortega-Esteban, Marta del Alamo, Pedro J. de Pablo,
and C armen San Martín
2 Proteome Analysis of Adenovirus Using Mass Spectrometry . . . . . . . . . . . . . . 2 5
Sara Bergström Lind, Konstantin A. Artemenko, and Ulf Pettersson
3 Capsid Modification Strategies for Detargeting Adenoviral Vectors . . . . . . . . . 4 5
Alan L. Parker, Angela C. Bradshaw, Raul Alba, Stuart A. Nicklin,
and A ndrew H. Baker
4 Use of Dodecahedron “VLPs” as an Alternative to the
Whole Adenovirus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1
Pascal Fender
5 Study of Adenovirus and CAR Axonal Transport in Primary Neurons . . . . . . . 7 1
Charleine Zussy and Sara Salinas
6 The Use of Chromatin Immunoprecipitation (ChIP) to Study
the Binding of Viral Proteins to the Adenovirus Genome In Vivo . . . . . . . . . . 79
Yueting Zheng and Patrick Hearing
7 DNA Microarray to Analyze Adenovirus–Host Interactions. . . . . . . . . . . . . . . 8 9
Stefania Piersanti, Enrico Tagliafico, and Isabella Saggio
8 Determination of the Transforming Activities of Adenovirus Oncogenes. . . . . 1 05
Thomas Speiseder, Michael Nevels, and Thomas Dobner
9 Oncolytic Adenovirus Characterization: Activity and Immune Responses. . . . . 1 17
Raul Gil-Hoyos, Juan M iguel-Camacho, and Ramon Alemany
10 The Analysis of Innate Immune Response to Adenovirus
Using Antibody Arrays. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Nelson C. Di Paolo and Dmitry M. Shayakhmetov
11 Engineering Adenovirus Genome by Bacterial Artificial
Chromosome (BAC) Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 43
Zsolt Ruzsics, Frederic Lemnitzer, and Christian Thirion
12 Construction, Production, and Purification
of Recombinant Adenovirus Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 59
Susana Miravet, Maria Ontiveros, Jose Piedra, Cristina Penalva,
Mercè Monfar, and Miguel Chillón
vii
viii Contents
13 Scalable Production of Adenovirus Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 75
Ana Carina Silva, Paulo Fernandes, Marcos F. Q. Sousa,
and P aula M. Alves
14 Canine Adenovirus Downstream Processing Protocol . . . . . . . . . . . . . . . . . . . 1 97
Meritxell Puig, Jose Piedra, Susana Miravet,
and M aría Mercedes Segura
15 Production of High-Capacity Adenovirus Vectors . . . . . . . . . . . . . . . . . . . . . . 2 11
Florian Kreppel
16 Production of Chimeric Adenovirus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 31
Marta Miralles, Marc Garcia, Marcos Tejero,
Assumpció Bosch, and Miguel Chillón
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Contributors
RAUL ALBA • British Heart Foundation Glasgow Cardiovascular Research , Glasgow, UK ;
Nanotherapix S.L. , Sant Cugat del Vallès, Spain
RAMON ALEMANY • Institut Catala d´Oncologia, Institut d´Investigació Biomèdica de
Bellvitge, L´Hospitalet de Llobregat , Barcelona, Spain
PAULA M. ALVES • iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras,
Portugal; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa ,
Oeiras , Portugal
KONSTANTIN A. ARTEMENKO • Department of Chemistry-BMC , Uppsala University ,
Uppsala , Sweden
ANDREW H. BAKER • British Heart Foundation Glasgow Cardiovascular Research ,
Glasgow , UK
ASSUMPCIÓ BOSCH • Department of Biochemistry and Molecular Biology, Center of Animal
Biotechnology and Gene Therapy (CBATEG) , Universitat Autonoma Barcelona ,
Bellaterra, Barcelona, Spain
ANGELA C. BRADSHAW • British Heart Foundation Glasgow Cardiovascular Research ,
Glasgow , UK
MIGUEL CHILLÓN • Institut Català de Recerca i Estudis Avançats (ICREA) and
CBATEG-Department of Biochemistry and Molecular Biology, Universitat Autonoma
Barcelona , Bellaterra, Barcelona, Spain
GABRIELA N. CONDEZO • Department of Macromolecular Structure , Centro Nacional de
Biotecnología (CNB-CSIC) , Cantoblanco, Spain
PEDRO J. D E PABLO • Department of Physics of the Condensed Matter , Universidad
Autónoma de Madrid , Madrid , Spain
MARTA DEL ALAMO • Department of Macromolecular Structure , Centro Nacional de
Biotecnología (CNB-CSIC) , Cantoblanco, Spain
NELSON C. DI PAOLO • Department of Medicine, Division of Medical Genetics, U niversity
of Washington , Seattle , WA , USA
THOMAS DOBNER • Department of Viral Transformation, Heinrich Pette Institute, Leibniz
Institute for Experimental Virology , Hamburg, Germany
PASCAL FENDER • Unit of Virus Host Cell Interactions (UMI-3265:CNRS/UJF/EMBL) ,
Grenoble, France
PAULO FERNANDES • Animal Cell Technology Unit, Instituto de Tecnologia Química e
Biológica, Universidade Nova de Lisboa (ITQB-UNL) , Oeiras , Portugal ; Animal Cell
Technology Unit, Instituto de Biologia Experimental e Tecnologica (IBET) , Oeiras , Portugal
MARC GARCIA • Department of Biochemistry and Molecular Biology, Center of Animal
Biotechnology and Gene Therapy (CBATEG) , Universitat Autonoma Barcelona ,
Bellaterra, Spain
RAUL GIL-HOYOS • Institut Catala d´Oncologia, Institut d´Investigació Biomèdica de
Bellvitge, L´Hospitalet de Llobregat , Barcelona, Spain
PATRICK HEARING • Department of Molecular Genetics and Microbiology, School of
Medicine, Stony Brook University , Stony Brook, NY , USA
ix