M e t h o d s i n M o l e c u l a r B i o l o g y ™

Series EditorJohn M. Walker

School of Life SciencesUniversity of Hertfordshire

Hatfield, Hertfordshire, AL10 9AB, UK

For other titles published in this series, go to www.springer.com/series/7651

MicroRNA and Cancer

Methods and Protocols

Edited by

Wei Wu

Institute for Biocomplexity and Informatics, Department of Biological Science, University of Calgary, Calgary, AB, Canada

EditorWei WuInstitute for Biocomplexity and InformaticsDepartment of Biological ScienceUniversity of CalgaryCalgary, ABCanadawwu65@yahoo.com; wuwei@ucalgary.ca

ISSN 1064-3745 e-ISSN 1940-6029ISBN 978-1-60761-862-1 e-ISBN 978-1-60761-863-8DOI 10.1007/978-1-60761-863-8Springer New York Dordrecht Heidelberg London

Library of Congress Control Number: 2010934277

© Springer Science+Business Media, LLC 2011All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden.The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.

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v

Preface

The discovery of microRNAs (miRNAs or miRs) heralded a new and an exciting era in biology and started a new chapter in human gene regulation. The miRNAs, a class of small endogenous noncoding RNAs (~22 nt), fine tune the gene expression at the posttran-scriptional level through mainly binding 3′-UTR of mRNAs. They are involved in stem cell self-renewal, cellular development, differentiation, proliferation, and apoptosis.

Small miRNAs have big impacts in cancer development. Among the many miRNAs, a subset of miRNAs were identified as regulators of neoplastic transformation, tumor pro-gression, invasion, and metastasis as well as tumor-initiating cells (cancer stem cells). The widespread deregulation of miRNomes in diverse cancers when compared to normal tis-sues have been unveiled. The oncomirs (oncogenic miRNAs), TSmiRs (tumor suppressive miRNAs), and MetastamiRs (miRNAs associated to cancer metastasis) comprise an impor-tant part of the cancer genome and confer pivotal diagnostic and prognostic significance. Moreover, cancer-associated miRNAs are proving worthwhile for developing effective cancer biomarkers for individualized medicine and potential therapeutic targets.

This book provides the latest and foremost miRNAs knowledge of cancer research applications from scientists all over the world. It is organized in two parts: the first part begins with a general introduction of miRNA biogenesis which is followed by chapters on the computational prediction of new microRNAs in cancer, the innovative technologies for modulating miRNAs of interests, and an overview of miRNA-based therapeutic approaches for cancer treatment. The second part of the book provides experimental and computational procedures in miRNA detection with diverse techniques, miRNA library construction, epigenetic regulation of miNRAs, microRNA::mRNA regulatory networks predicted with computational analysis in cancer cells or tissues, and the principle of design-ing the miRNA-mimics for miRNA activation. These chapters have been written for prac-tical use in laboratories for graduate students, postdoctoral fellows, and scientists in cancer research. The contributors have shared their most valuable experiences in the translation of miRNA knowledge into cancer research.

MicroRNA is a fast growing field, and microRNA knowledge is a pivotal element of cancer biology. An individual miRNA interferes with a broad range of mRNAs; conversely, a single mRNA could be targeted by a variety of miRNAs. The complexity of miRNA::mRNA interac-tion is far-reaching and a bit beyond our understanding to date. This book is expected to provide the basic principles of experimental and computational methods for microRNA study in cancer research and provide a firm grounding for those who wish to develop further applications.

I am especially indebted to Prof. Shu Zheng and Dr. Suzanne D. Conzen for giving me the opportunity to gain substantial experience in cancer research. I would like to thank Dr. Gunglin Li for his kind support. Without their confidence and continuous support, many things would not have been possible. I also thank Prof. John Walker for his encour-agement. Finally, I am grateful to all of the contributing authors for providing such high quality manuscripts. Additional thanks go to Zineb Elkadiri and the Humana Press for their excellent assistance.

Wei Wu Calgary, AB, Canada

vii

Contents

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vContributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

Part I revIews

1 MicroRNA Biogenesis and Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3Julia Winter and Sven Diederichs

2 Computational Identification of miRNAs Involved in Cancer . . . . . . . . . . . . . 23Anastasis Oulas, Nestoras Karathanasis, and Panayiota Poirazi

3 The Principles of MiRNA-Masking Antisense Oligonucleotides Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Zhiguo Wang

4 The Concept of Multiple-Target Anti-miRNA Antisense Oligonucleotide Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Zhiguo Wang

5 Modulation of MicroRNAs for Potential Cancer Therapeutics . . . . . . . . . . . . 59Wei Wu

Part II Protocols

6 Detection of MicroRNAs in Cultured Cells and Paraffin-Embedded Tissue Specimens by In Situ Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . 73Ashim Gupta and Yin-Yuan Mo

7 MicroRNA Northern Blotting, Precursor Cloning, and Ago2-Improved RNA Interference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85Julia Winter and Sven Diederichs

8 miRNA Profiling on High-Throughput OpenArray™ System . . . . . . . . . . . . . 101Elena V. Grigorenko, Elen Ortenberg, James Hurley, Andrew Bond, and Kevin Munnelly

9 Silicon Nanowire Biosensor for Ultrasensitive and Label-Free Direct Detection of miRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111Guo-Jun Zhang

10 High-Throughput and Reliable Protocols for Animal MicroRNA Library Cloning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123Caide Xiao

11 MicroRNA Regulation of Growth Factor Receptor Signaling in Human Cancer Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147Keith M. Giles, Andrew Barker, Priscilla M. Zhang, Michael R. Epis, and Peter J. Leedman

viii Contents

12 Epigenetic Regulation of MicroRNA Expression in Cancer . . . . . . . . . . . . . . . 165Hani Choudhry and James W.F. Catto

13 In Vitro Functional Study of miR-126 in Leukemia . . . . . . . . . . . . . . . . . . . . 185Zejuan Li and Jianjun Chen

14 Prediction of the Biological Effect of Polymorphisms Within MicroRNA Binding Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197Debora Landi, Roberto Barale, Federica Gemignani, and Stefano Landi

15 The Guideline of the Design and Validation of MiRNA Mimics . . . . . . . . . . . 211Zhiguo Wang

16 Analysis of Targets and Functions Coregulated by MicroRNAs . . . . . . . . . . . . 225Shu-Jen Chen and Hua-Chien Chen

17 Utilization of SSCprofiler to Predict a New miRNA Gene . . . . . . . . . . . . . . . 243Anastasis Oulas and Panayiota Poirazi

18 MicroRNA Profiling Using Fluorescence-Labeled Beads: Data Acquisition and Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253Thomas Streichert, Benjamin Otto, and Ulrich Lehmann

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269

ix

Contributors

roberto barale • Genetics, Department of Biology, University of Pisa, Pisa, Italyandrew barker • Laboratory for Cancer Medicine, Centre for Medical Research,

Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia

andrew bond • BioTrove Inc, Woburn, MA, USAJames w. F. catto • Academic Urology Unit, Division of Clinical Sciences,

Royal Hallamshire Hospital, University of Sheffield, Sheffield, UKHua-cHIen cHen • Department of Life Science, Molecular Medicine Research Center,

Change Gung University, Taiwan, ChinaJIanJun cHen • Department of Medicine, The University of Chicago, Chicago, IL, USAsHu-Jen cHen • Department of Life Science, Molecular Medicine Research Center,

Change Gung University, Taiwan, ChinaHanI cHoudHry • Faculty of Science, Academic Urology Unit, Division of Clinical

Sciences, Royal Hallamshire Hospital, University of Sheffield, Sheffield, UK; Biochemistry Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia

sven dIederIcHs • Helmholtz-University-Group “Molecular RNA Biology & Cancer,” German Cancer Research Center (DKFZ), Institute of Pathology, University of Heidelberg, Heidelberg, Germany

mIcHael r. ePIs • Laboratory for Cancer Medicine, Centre for Medical Research, Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia

FederIca GemIGnanI • Genetics, Department of Biology, University of Pisa, Pisa, ItalykeItH m. GIles • Laboratory for Cancer Medicine, Centre for Medical Research,

Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia

elena v. GrIGorenko • BioTrove Inc, Woburn, MA, USAasHIm GuPta • Immunology and Cell Biology, Department of Medical Microbiology,

School of Medicine, Southern Illinois University, Springfield, IL, USAJames Hurley • BioTrove Inc, Woburn, MA, USAnestoras karatHanasIs • Institute for Molecular Biology and Biotechnology (IMBB),

Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece

debora landI • Genetics, Department of Biology, University of Pisa, Pisa, ItalysteFano landI • Genetics, Department of Biology, University of Pisa, Pisa, ItalyPeter J. leedman • Laboratory for Cancer Medicine, Centre for Medical Research,

School of Medicine and Pharmacologcxxy, Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia

x Contributors

ulrIcH leHmann • Institute of Pathology Medizinische Hochschule Hannover, Hannover, Germany

ZeJuan lI • Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA

yIn-yuan mo • Immunology and Cell Biology, Department of Medical Microbiology, School of Medicine, Southern Illinois University, Springfield, IL, USA

kevIn munnelly • BioTrove Inc, Woburn, MA, USAelen ortenberG • BioTrove Inc, Woburn, MA, USAbenJamIn otto • Department of Clinical Chemistry/Central Laboratories,

Universitätsklinikum Hamburg-Eppendorf, Hamburg, GermanyanastasIs oulas • Institute for Molecular Biology and Biotechnology (IMBB),

Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece

PanayIota PoIraZI • Computational Biology Laboratory, Institute for Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece

tHomas streIcHert • Department of Clinical Chemistry/Central Laboratories, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany

ZHIGuo wanG • Department of Medicine, Montreal Heart Institute, University of Montreal, Montreal, QC, Canada

JulIa wInter • Helmholtz-University-Group “Molecular RNA Biology & Cancer,” German Cancer Research Center (DKFZ) & Institute of Pathology, University of Heidelberg, Heidelberg, Germany

weI wu • Institute for Biocomplexity and Informatics, Department of Biological Science, University of Calgary, Calgary, AB, Canada

caIde XIao • Institute for Biocomplexity and Informatics, Department of Biological Science, University of Calgary, Calgary, AB, Canada

Guo-Jun ZHanG • Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore

PrIscIlla m. ZHanG • Laboratory for Cancer Medicine, Centre for Medical Research, Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia