RNA Interference: From Biology to Clinical Applications / Edition 1

by Wei-Ping Min, Thomas Ichim

Overview

From the early days when RNA interference was a strange artifact in worms to the 2006 Noble Prize received by Fire and Mello and the current clinical trials, the field of RNA interference has grown at a breakneck pace. In RNA Interference: From Biology to Clinical Applications, expert contributors provide an overview of the most current science and prools that span the biological disciplines from detailed nucleic acid chemistry, to pharmacology, to the manipulation of signal transduction pathways. Divided into three distinct sections, this volume delves into the physiology of RNA interference, RNA interference in the laboratory and siRNA delivery, and preclinical and clinical issues associated with the use of RNAi-inducing agents as drugs in order to stimulate new questions and offer the tools necessary to start addressing those questions. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory prools, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and inspiring, RNA Interference: From Biology to Clinical Applications aims to promote and motivate innovation by reviewing what has been done, providing details of how it has been done, and encouraging speculation on what the future may hold.

Product Details

ISBN-13:	9781607615873
Publisher:	Springer-Verlag New York, LLC
Publication date:	03/18/2010
Series:	Methods in Molecular Biology , #623
Edition description:	2010
Pages:	450
Product dimensions:	7.10(w) x 10.10(h) x 1.30(d)

Table of Contents

Preface v

Contributors xiii

Part I Physiology of RNA Interference

1 Endogenous Antiviral Mechanisms of RNA Interference: A Comparative Biology Perspective Abubaker M.E. Sidahmed Bruce Wilkie 3

2 Monitoring Innate Immune Recruitment by siRNAs in Mammalian Cells Michael P. Gantier Bryan R.G. Williams 21

3 Current Knowledge of MicroRNAs and Noncoding RNAs in Virus-Infected Cells Dominique L. Ouellet Patrick Provost 35

4 Allele-Specific Silencing by RNA Interference Hirohiko Hohjoh 67

5 Computational siRNA Design Considering Alternative Splicing Young J. Kim 81

6 Bioinformatic Approaches to siRNA Selection and Optimization Pirkko Muhonen Harry Holthofer 93

7 Optimized Gene Silencing by Co-expression of Multiple shRNAs in a Single Vector Yasuhito Ishigaki Akihiro Nagao Tsukasa Matsunaga 109

8 Strategies in Designing Multigene Expression Units to Downregulate HTV-1 Jane Zhang John J. Rossi 123

9 Designing Optimal siRNA Based on Target Site Accessibility Ivo L. Hofacker Hakim Tafer 137

10 Chemical Synthesis of 2'-O-Alkylated siRNAs Joachim W. Engels Dalibor Odadzic Romualdas Smicius Jens Haas 155

Part II RNA Interference in the Laboratory and siRNA Delivery

11 siRNA Specific Delivery System for Targeting Dendritic Cells Xiufen Zheng Costin Vladau Aminah Shunner Wei-Ping Min 173

12 Hydrodynamic Delivery Protocols Piotr G. Rychahou B. Mark Evers 189

13 New Methods for Reverse Transfection with siRNA from a Solid Surface Satoshi Fujita Kota Takano Eiji Ota Takuma Sano Tomohiro Yoshikawa Masato Miyake Jun Miyake 197

14 Nonviral siRNA Delivery for Gene Silencing in Neurodegenerative Diseases Satya Prakash Meenakshi Malhotra Venkatesh Rengaswamy 211

15 Using siRNA to Uncover Novel Oncogenic Signaling Pathways Jin-Mei Lai Chi-Ying F. Huang Chang-Han Chen 231

16 Biodegradable Polymer-Mediated sh/siRNA Delivery for Cancer Studies Dhananjay J. Jere Chong-Su Cho 243

17 Cellular siRNA Delivery Using TatU1A and Photo-Induced RNA Interference Tamaki Endoh Takashi Ohtsuki 271

18 Polyethylenimine (PEI)/siRNA-Mediated Gene Knockdown In Vitro and In Vivo Sabrina Höbel Achim Aigner 283

19 Transfection of siRNAs in Multiple Myeloma Cell Lines Jose L.R. Brito Nicola Brown Gareth J. Morgan 299

Part III Clinical Implementation

20 A New Approach for Therapeutic Use by RNA Interference in the Brain Yukio Akaneya 313

21 Inhibitory RNA Molecules in Immunotherapy for Cancer Chih-Ping Mao T.-C. Wu 325

22 Preventing Tissue Injury Using siRNA Zhu-Xu Zhang Marianne E. Beduhn Xiufen Zheng Wei-Ping Min Anthony M. Jevnikar 341

23 Preventing Immune Rejection Through Gene Silencing Xusheng Zhang Mu Li Wei-Ping Min 357

24 Topical Application of siRNA Targeting Cutaneous Dendritic Cells in Allergic Skin Disease Miyuki Azuma Patcharee Ritprajak Masaaki Hashiguchi 373

25 Direct Application of siRNA for In Vivo Pain Research Philippe Sarret Louis Doré-Savard Nicolas Beaudet 383

26 A Potential Therapeutic for Pandemic Influenza Using RNA Interference Shaguna Seth Michael V. Templin Gregory Severson Oleksandr Baturevych 397

27 Evaluation of Targets for Ovarian Cancer Gene Silencing Therapy: In Vitro and In Vivo Approaches Anastasia Malek Oleg Tchernitsa 423

Index 437

Editorial Reviews

Reviewer: Marion C. Cohen, PhD (SUNY Downstate Medical Center)
Description: RNA interference (RNAi)-mediated silencing of specific genes is a powerful tool for the analysis of protein function. It also has enormous potential application in the development of therapeutics. RNA interference began as an observation in worms and today is being used to unravel basic biological processes as well as to find tools to treat diseases. This book discusses the physiology of RNA interference, RNA interference in the laboratory and siRNA delivery, and the issues associated with the use of RNAi-inducing agents as drugs. It uses the standard format of the Methods in Molecular Biology books.
Purpose: The purpose is to provide an overview of the ways in which RNAi may be used to answer a variety of biological questions. The editors seized upon the potential of the technique shortly after the first paper describing RNAi appeared and have used it successfully as a method to investigate both suppressive and immune stimulatory genes. Based on their own experiences, they recognize the power of the methodology and show how RNAi can be used successfully in a variety of systems. They have succeeded in their presentation. Although there are other books available, the standardized style of presentation makes this a worthwhile addition to the laboratory library.
Audience: This is written primarily for the research community at all levels from student to laboratory director. Certainly it could also be useful to clinicians interested in translational research as there is a section on its potential use in clinical implementation. The editors are well known for their use of RNAi for research. They have assembled contributors who describe their own specific uses of the technique.
Features: Although the book my not address a specific application of interest to a user, there are enough techniques that make it likely that at least one of them can be easily adapted for the desired use. There is some background information, but most sections are devoted to a cookbook approach to the technique being described. This means that the protocols are quite detailed and include notes on troubleshooting and avoiding known pitfalls.
Assessment: One might find sections in other books that might be of particular use to a researcher interested in using RNAi, but this book is a good starting point for a neophyte. Because of the detailed protocols that it provides, it is a useful lab manual. Furthermore, the references are a helpful source of technical information. It would be a good addition to the library of any laboratory that is considering using RNAi in its research projects.

Doody's Review Service

From the reviews:

“The book provides a broad overview of RNA chemistry, the pharmacology and the manipulation of signaling pathways by using RNA interference. … This book is very well written and will be an asset to any researcher who uses RNA interference as a tool to study gene function. … and will probably mainly be of use to researcher already working in the field and familiar with different techniques of siRNA delivery.” (Anna Vossenkaemper, Immunology News, November, 2010)

From the Publisher

Reviewer:One might find sections in other books that might be of particular use to a researcher interested in using RNAi, but this book is a good starting point for a neophyte. Because of the detailed protocols that it provides, it is a useful lab manual. Furthermore, the references are a helpful source of technical information. It would be a good addition to the library of any laboratory that is considering using RNAi in its research projects.
Description:
Purpose:RNA interference (RNAi)-mediated silencing of specific genes is a powerful tool for the analysis of protein function. It also has enormous potential application in the development of therapeutics. RNA interference began as an observation in worms and today is being used to unravel basic biological processes as well as to find tools to treat diseases. This book discusses the physiology of RNA interference, RNA interference in the laboratory and siRNA delivery, and the issues associated with the use of RNAi-inducing agents as drugs. It uses the standard format of the Methods in Molecular Biology books.
Audience:The purpose is to provide an overview of the ways in which RNAi may be used to answer a variety of biological questions. The editors seized upon the potential of the technique shortly after the first paper describing RNAi appeared and have used it successfully as a method to investigate both suppressive and immune stimulatory genes. Based on their own experiences, they recognize the power of the methodology and show how RNAi can be used successfully in a variety of systems. They have succeeded in their presentation. Although there are other books available, the standardized style of presentation makes this a worthwhile addition to the laboratory library.
Features:This is written primarily for the research community at all levels from student to laboratory director. Certainly it could also be useful to clinicians interested in translational research as there is a section on its potential use in clinical implementation. The editors are well known for their use of RNAi for research. They have assembled contributors who describe their own specific uses of the technique.
Assessment:"Although the book my not address a specific application of interest to a user, there are enough techniques that make it likely that at least one of them can be easily adapted for the desired use. There is some background information, but most sections are devoted to a cookbook approach to the technique being described. This means that the protocols are quite detailed and include notes on troubleshooting and avoiding known pitfalls. "

Reviewer: Marion C. Cohen, PhD (SUNY Downstate Medical Center)
Description: RNA interference (RNAi) -mediated silencing of specific genes is a powerful tool for the analysis of protein function. It also has enormous potential application in the development of therapeutics. RNA interference began as an observation in worms and today is being used to unravel basic biological processes as well as to find tools to treat diseases. This book discusses the physiology of RNA interference, RNA interference in the laboratory and siRNA delivery, and the issues associated with the use of RNAi-inducing agents as drugs. It uses the standard format of the Methods in Molecular Biology books.
Purpose: The purpose is to provide an overview of the ways in which RNAi may be used to answer a variety of biological questions. The editors seized upon the potential of the technique shortly after the first paper describing RNAi appeared and have used it successfully as a method to investigate both suppressive and immune stimulatory genes. Based on their own experiences, they recognize the power of the methodology and show how RNAi can be used successfully in a variety of systems. They have succeeded in their presentation. Although there are other books available, the standardized style of presentation makes this a worthwhile addition to the laboratory library.
Audience: This is written primarily for the research community at all levels from student to laboratory director. Certainly it could also be useful to clinicians interested in translational research as there is a section on its potential use in clinical implementation. The editors are well known for their use of RNAi for research. They have assembled contributors who describe their own specific uses of the technique.
Features: Although the book my not address a specific application of interest to a user, there are enough techniques that make it likely that at least one of them can be easily adapted for the desired use. There is some background information, but most sections are devoted to a cookbook approach to the technique being described. This means that the protocols are quite detailed and include notes on troubleshooting and avoiding known pitfalls.
Assessment: One might find sections in other books that might be of particular use to a researcher interested in using RNAi, but this book is a good starting point for a neophyte. Because of the detailed protocols that it provides, it is a useful lab manual. Furthermore, the references are a helpful source of technical information. It would be a good addition to the library of any laboratory that is considering using RNAi in its research projects.

Doody Reviews