RNA Imaging: Methods and Protocols

231 Pages·2015·8.654 MB·English

by  Zdravka Medarova

Methods in
Molecular Biology 1372
Zdravka Medarova Editor
RNA Imaging
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

RNA Imaging
Methods and Protocols
Edited by
Zdravka Medarova
Molecular Imaging Laboratory, MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA; Department of
Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
Editor
Zdravka Medarova
Molecular Imaging Laboratory, MGH/MIT/HMS
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
and Harvard Medical School
Charlestown, MA, USA
Department of Radiology
Massachusetts General Hospital
and Harvard Medical School
Charlestown, MA, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-3147-7 ISBN 978-1-4939-3148-4 (eBook)
DOI 10.1007/978-1-4939-3148-4
Library of Congress Control Number: 2015955553
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Prefa ce
This book is intended for physicians, scientists, and graduate students who are either new
to the fi eld of RNA-based imaging and its associated therapeutic applications or who wish
to be apprised of recent advances in the state of the art.
This volume will focus on the phenomenon of RNA interference. RNA interference
(RNAi) is a normal endogenous cellular mechanism for posttranscriptional regulation of gene
expression in which double-stranded ribonucleic acid inhibits the expression of genes with
complementary nucleotide sequences. Its potential as a tool for therapy is unlimited, consid-
ering that one can use this mechanism to modulate the expression of virtually any gene.
RNAi is mediated by small noncoding RNA molecules that are either endogenous to
the cell (microRNA, miRNA) or introduced exogenously (small interfering RNA, siRNA ).
miRNA is positioned at the center of gene regulatory networks. A single miRNA can infl u-
ence the expression of multiple gene targets. Consequently, miRNA reprogramming using
inhibitory oligonucleotides or miRNA mimics can be a very powerful tool for the “normal-
ization” of cellular phenotype and eliminating pathology. By contrast, siRNA can be
designed to inhibit a given gene with single-nucleotide specifi city. As such, siRNA delivers
the capability of “correcting” the levels of individual proteins that predispose to disease.
An essential element in the development and optimization of these therapies is the abil-
ity to measure the bioavailability and functionality of the RNA/oligonucleotide molecule
after administration into the body. Noninvasive imaging provides the necessary set of tools
to accomplish this in authentic physiologic environments and across time. This book focuses
on providing comprehensive coverage of various techniques for in vivo micro/s iRNA imag-
ing including the design and synthesis of specifi c imaging agents and tools, the develop-
ment of imaging methodologies, and their interpretation.
Charlestown, MA, USA Zdravka Medarova
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Imaging Functional Nucleic Acid Delivery to Skin. . . . . . . . . . . . . . . . . . . . . . 1
Roger L. Kaspar , Robyn P . Hickerson , Emilio González-González ,
Manuel A. Flores , T ycho P . S peaker , Faye A . Rogers , Leonard M. Milstone ,
and C hristopher H . C ontag
2 I n Vivo Magnetic Resonance Imaging of Small Interfering RNA
Nanodelivery to Pancreatic Islets. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Ping Wang and Anna M oore
3 M agnetic Resonance Spectroscopy of siRNA-Based Cancer Therapy . . . . . . . . 3 7
Marie-France P enet , Zhihang C hen , N oriko Mori ,
B alaji K rishnamachary , and Zaver M . B hujwalla
4 Targeted Delivery with Imaging Assessment of siRNA Expressing
Nanocassettes into Cancer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Wei C hen and L ily Y ang
5 Analyses of Tumor Burden In Vivo and Metastasis Ex Vivo
Using Luciferase-Expressing Cancer Cells in an Orthotopic Mouse
Model of Neuroblastoma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Frances L. Byrne , Joshua A . McCarroll , and M aria Kavallaris
6 I ndium-Labeling of siRNA for Small Animal SPECT Imaging. . . . . . . . . . . . . 7 9
Steven J ones and O livia M erkel
7 I maging of Electrotransferred siRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 9
Muriel G olzio and Justin T eissié
8 W hole-Body Scanning PCR, a Tool for the Visualization
of the In Vivo Biodistribution Pattern of Endogenous and Exogenous
Oligonucleotides in Rodents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Julien A. B oos and Iwan B euvink
9 s iRNA Nanoparticles for Ultra-Long Gene Silencing In Vivo . . . . . . . . . . . . . 1 13
Seung Koo L ee and Ching-Hsuan T ung
10 Sensing miRNA: Signal Amplification by Cognate RISC
for Intracellular Detection of miRNA in Live Cells . . . . . . . . . . . . . . . . . . . . . 1 21
Amol Kavishwar and Zdravka Medarova
11 Molecular Beacon-Based MicroRNA Imaging During Neurogenesis . . . . . . . . 129
Jonghwan L ee and Soonhag Kim
12 Hypoxia-Responsive Copolymer for siRNA Delivery. . . . . . . . . . . . . . . . . . . . 1 39
Federico P erche , Swati B iswas , N iravkumar R . Patel ,
and Vladimir P. T orchilin
vii
viii Contents
13 Controlling RNA Expression in Cancer Using Iron Oxide
Nanoparticles Detectable by MRI and In Vivo Optical Imaging . . . . . . . . . . . 163
Zdravka Medarova , M ustafa B alcioglu , and Mehmet V. Yigit
14 M icrovesicles: Isolation, Characterization for In Vitro
and In Vivo Procedures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Karmele Valencia and Fernando L ecanda
15 Positive Bioluminescence Imaging of MicroRNA Expression
in Small Animal Models Using an Engineered Genetic-
Switch Expression System, RILES. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Patrick Baril and C hantal P ichon
16 MicroRNA Imaging in Combination with Diagnostic Ultrasound
and Bubble Liposomes for MicroRNA Delivery. . . . . . . . . . . . . . . . . . . . . . . . 209
Yoko Endo-Takahashi , Yoichi N egishi , Ryo Suzuki , K azuo Maruyama ,
and Yukihiko A ramaki
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 15
Contributors
YUKIHIKO ARAMAKI • Department of Drug Delivery and Molecular Biopharmaceutics,
School of Pharmacy, Tokyo University of Pharmacy and Life Sciences , T okyo , J apan
MUSTAFA BALCIOGLU • Department of Chemistry , University at Albany, SUNY , A lbany,
NY , U SA
PATRICK BARIL • Centre de Biophysique Moléculaire, CNRS UPR4301 , U niversité
d’Orléans France , Orléans, France
IWAN BEUVINK • Novartis Institutes for Biomedical Research (NIBR) , Novartis Pharma
AG , B asel , S witzerland
ZAVER M. B HUJWALLA • Division of Cancer Imaging Research, The Russell H. Morgan
Department of Radiology and Radiological Science, T he Johns Hopkins University
School of Medicine , B altimore , MD, USA ; Sidney Kimmel Comprehensive Cancer Center,
The Johns Hopkins University School of Medicine , Baltimore , M D , U SA
SWATI BISWAS • Center for Pharmaceutical Biotechnology and Nanomedicine, School of
Pharmacy, B ouve College of Health Sciences, Northeastern University , Boston, M A, USA ;
Department of Pharmaceutical Sciences, School of Pharmacy, B ouve College of Health
Sciences, Northeastern University , Boston, MA , U SA
JULIEN A. BOOS • Novartis Institutes for Biomedical Research (NIBR) , Novartis Pharma
AG , B asel , S witzerland
FRANCES L. B YRNE • School of Biotechnology and Biomolecular Sciences, U niversity of New
South Wales , S ydney, N SW , A ustralia
WEI C HEN • Department of Surgery , Emory University School of Medicine , A tlanta, GA ,
USA ; D epartment of Gastrointestinal Surgery , First Affi liated Hospital of Sun Yat-Sen
University , G uangzhou, China
ZHIHANG C HEN • Division of Cancer Imaging Research, The Russell H. Morgan
Department of Radiology and Radiological Science, T he Johns Hopkins University School
of Medicine , B altimore, MD, USA
CHRISTOPHER H. CONTAG • Molecular Imaging Program at Stanford (MIPS) , S tanford
University School of Medicine , Stanford , C A , USA ; D epartment of Pediatrics, Stanford
University School of Medicine , Stanford , C A , U SA ; D epartment of Radiology, Stanford
University School of Medicine , Stanford, CA , USA ; D epartment of Microbiology
and Immunology , Stanford University School of Medicine , S tanford , C A , USA
YOKO ENDO-TAKAHASHI • Department of Drug Delivery and Molecular Biopharmaceutics,
School of Pharmacy, T okyo University of Pharmacy and Life Sciences , T okyo , J apan
MANUEL A. FLORES • TransDerm Inc. , Santa Cruz, CA , U SA
MURIEL GOLZIO • IPBS (Institut de Pharmacologie et de Biologie Structurale), CNRS ,
Toulouse, F rance ; IPBS (Institut de Pharmacologie et de Biologie Structurale), Université
de Toulouse and UPS (Université Paul Sabatier) , T oulouse , F rance
EMILIO G ONZÁLEZ-GONZÁLEZ • Canvax Biotech S.L. , C ordoba , S pain
ROBYN P. HICKERSON • Centre for Dermatology and Genetic Medicine, U niversity
of Dundee , D undee, U K
STEVEN J ONES • Department of Oncology, Wayne State University School of Medicine ,
Detroit, M I , U SA
ix