RNA Technologies in Cardiovascular Medicine and Research Volker A. Erdmann • Wolfgang Poller Jan Barciszewski Editors RNA Technologies in Cardiovascular Medicine and Research Prof. Dr. rer.nat Volker A. Erdmann Prof. Dr. med Wolfgang Poller Institute for Chemistry/Biochemistry Clinic for Cardiology and Pneumology Free University of Berlin, Campus Benjamin Franklin Thielallee 63 Charite University Medicine Berlin 14195 Berlin, Germany Hindenburgdamm 30 [email protected] 12200 Berlin, Germany [email protected] Prof. Dr. hab. Jan Barciszewski Institute of Bioorganic Chemistry of the Polish Academy of Sciences Noskowskiego 12 61-704 Poznan Poland [email protected] ISBN 978-3-540-78708-2 e-ISBN 978-3-540-78709-9 DOI: 10.1007/978-3-540-78709-9 Library of Congress Control Number: 2008923849 © 2008 Springer-Verlag Berlin Heidelberg This work is subject to copyright. 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In every individual case the user must check such information by consulting the relevant literature. Cover Design: WMX Design GmbH, Heidelberg, Germany Printed on acid-free paper 5 4 3 2 1 springer.com Preface The heart may respond to chronic and acute injury by hypertrophic growth and pathological remodeling. Cardiomyocyte hypertrophy is a dominant cellular response to all kinds of hemodynamic overload, inherited mutations in many structural and contractile proteins, and other factors and may be compensatory or maladaptive. In the latter case pathological remodeling may result from diverse molecular patho- mechanisms which are still incompletely understood. Small deviations in a mechanism controlling cardiac morphology and function may lead to enormous negative effects including loss of function and, in severe cases, even death. Despite great progress in understanding various aspects of heart development, cardiovascular diseases remain a major problem for medicine. Therefore, there is a need for new diagnostic and therapeutic strategies to detect, classify and cure heart diseases. Ribonucleic acid (RNA) in its many facets of structure and function is more and more understood, and therefore it is possible to design and use RNAs as valu- able tools in molecular biology and medicine. An understanding of the role of RNAs within the cell has changed dramatically in recent years (Fig. 1). Its status expanded with reports on catalytic RNAs (ribozymes) 25 years ago, of endog- enous RNA interference 15 years later, and other noncoding RNA very recently. Today, it is obvious that RNAs are not merely the intermediary molecules between DNA and proteins, but that they can also be functional end products. Large stretches of genomic DNA do not contain protein-coding sequences and have, therefore, been considered as ‘junk’. However, a significant fraction of this noncoding DNA have actually been found to hold the information for some of these functional noncoding RNAs. Diverse eukaryotic organisms harbor a class of noncoding small RNAs which are thought to function as regulators of gene expression. Thus, RNAs can be the transmitters (mRNAs) of genetic information to the ribosome for proteins to be synthesized, and also the regulators in protein synthesis. The conclusion to be drawn is that RNA is much more than solely a messenger RNA, and therefore this class of molecules are truly renaissance mol- ecules. Most of the noncoding DNA is occupied by various units of repeats, satel- lite sequences and transposons. These sequences have been sought to be epigenetic elements that control stability of gene expression programs, and organ- ize heterochromatic domains at centromers and telomers. Their role appears to be mainly regulatory. Although the effects of antisense RNAs on the corresponding v vi Preface mRNA noncoding RNA DNA proteins Fig. 1 Genetic information from DNA is transcribed into mRNA containing instruction for pro- tein synthesis and regulatory RNAs which take part in systems controlling expression of genes sense RNAs have not been clearly established, a number of examples indicate that they may exert control at various levels of gene expression, such as transcription, mRNA processing, splicing, stability, transport, and translation. RNA has become a focus of investigations into novel therapeutic schemes. Ribozymes, antisense RNAs, RNA decoys, aptamers, micro RNAs and small interfer- ing (siRNAs) have been used to down regulate undesired gene expression (Fig. 2). Multiple challenges, such as optimization of selectivity, stability, delivery and long term safety, have to be addressed in order for RNA drugs to become successful therapeutic agents. Not all RNA classes (e.g., ribozymes or RNA decoys) have been so far success- fully developed as drugs. The recognition of the biological roles of small molecular weight RNAs have been one of the most significant discoveries in molecular biology. These RNA molecules influence the translation of messenger RNAs (mRNAs) in post- transcriptional manner that makes the regulation of RNAs even more complex. The use of RNA-mediated interference (RNAi) for gene silencing has provided a powerful tool for loss-of-function studies in a variety of metazoans. SiRNA mediated gene silencing by degradation of target messenger RNAs have been widely used in gene function characterizations. Compared with the laborious, time-consuming, and very costly gene knockout mod- els, siRNA provides an efficient, specific and cheap solution for inhibiting expression of target genes. Efficient siRNA delivery is essential for the success of specific gene silencing. As the popularity of RNAi technology grows, so does the frustration it still causes for many researchers. Direct measurement at the mRNA level is always needed for direct verification that RNA interference is decreasing the amount of mRNA. Because high doses of siRNAs may provoke an altered expression of many other genes, selections of optimal conditions are essential to minimize potential side effects. The most informative experiments in understanding the specificity of a siRNA would consider acquiring global gene expression of relevant genes, which unfortunately is lacking in many siRNA studies. These small RNAs of about 15–49 nucleotides in length guide the RNA-induced silencing complex (RISC). The beauty of the system lies in the application of short RNAs, which can be synthesized at reasonable cost and can evolve quickly, to regulate a large and complex protein synthesis. Preface vii Fig. 2 The potentials of the different RNA technologies which can be applied to inhibit protein biosynthesis on RNA levels (antisense oligonucleotides,ribozymes,short interference RNAs and microRNAs) or protein functional level (aptamers) In several recent studies, microarray analyses were performed to determine whether miRNAs are deregulated in hyperthrophic and failing hearts. The results implicate that miRNAs function as negative regulators of cell growth or as regulators of prosurvival pathways such that their downregulation predisposes the heart to pathological remodeling. A major challenge for the future will be to identify the mRNA targets of RNAs that participate in cardiac remodeling and to understand the functions of their target mRNAs. Finally, the recent application of advanced vector technologies developed initially in the gene therapy field has had an enormous impact on the efficacy by which RNAi and microRNAs can be employed for therapeutic purposes in vivo. These most recent devel- opments have brought clinical translation of certain RNA-based therapies within reach. Berlin, Germany Volker A. Erdmann Berlin, Germany Wolfgang Poller Poznan, Poland Jan Barciszewski February 2008 Contents Part I MicroRNA......................................................................................... 1 An Overview of MicroRNA ........................................................................... 3 E. Wang MicroRNAs and Their Potential ................................................................... 17 M. Abdellatif miRNAs and Their Emerging Role in Cardiac Hypertrophy .................... 35 T.E. Callis, M. Tatsuguchi, and D.-Z. Wang MicroRNAs and the Control of Heart Pathophysiology............................. 53 D. Catalucci, M.V.G. Latronico, and G. Condorelli MicroRNA Systems Biology .......................................................................... 69 E. Wang Part II RNA Interference ........................................................................... 87 Targeting Viral Heart Disease by RNA Interference .................................. 89 S. Merl and R. Wessely Design of siRNAs and shRNAs for RNA Interference: Possible Clinical Applications ....................................................................... 109 V. Pekarik RNA Interference and MicroRNA Modulation for the Treatment of Cardiac Disorders: Status and Challenges .............................................. 131 W. Poller, L. Suckau, S. Pinkert, and H. Fechner Cardiac Delivery of Nucleic Acids by Transcriptional and Transductional Targeting of Adeno-Associated Viral Vectors ........... 167 O.J. Müller and H.A. Katus ix x Contents Part III Ribozymes ....................................................................................... 183 Characterization of Hammerhead Ribozymes Potentially Suitable for the Treatment of Hyper-Proliferative Vascular Diseases ..................... 185 G. Grassi and M. Grassi Applications of Ribozymes and Pyrrole–Imidazole Polyamides for Cardiovascular and Renal Diseases........................................................ 209 E.-H. Yao and N. Fukuda Part IV Noncoding, Aptamer and Antisense RNAs ................................. 233 Noncoding RNAs in Human Diseases........................................................... 235 M. Szyman´ski and J. Barciszewski Aptamers and siRNAs in Cardiovascular Disease ...................................... 255 C.M. Blake, S. Oney, S.M. Nimjee, and B.A. Sullenger Nucleic Acid Aptamers for Cardiovascular Therapeutics ......................... 289 P.S. Pendergrast, K.M. Thompson, and R.G. Schaub NFkB Decoy Oligodeoxynucleotide-Based Therapy in Cardiovascular Diseases ............................................................................ 299 H. Nakagami, M.K. Osako, N. Tomita, and R. Morishita Antisense Therapy for Restenosis Following Percutaneous Coronary Interventions ................................................................................. 311 N. Kipshidze Toxic RNA in Pathogenesis of Human Neuromuscular Disorders ............................................................................. 325 D. Napierala and M. Napierala Index ................................................................................................................ 355 Contributors Maha Abdellatif Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, University of Medicine and Dentistry of New Jersey, 185 S Orange Ave, Newark, NJ 07103, USA [email protected] Jan Barciszewski Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland [email protected] Charlene M. Blake Duke Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, NC 27710, USA [email protected] Thomas E. Callis Carolina Cardiovascular Biology Center, Department of Cell and Developmental Biology, 8340C Medical Biomolecular Research Building (MBRB), CB #7126, University of North Carolina, Chapel Hill, NC 27599-7126, USA Daniele Catalucci Division of Cardiology, Department of Medicine, University of California San Diego, 9500 Gilman Drive, BSB 5022, LaJolla, San Diego, CA 92093-0613, USA Scientific and Technology Pole, IRCCS MultiMedica, Via G. Fantoli 16/15, 20138 Milan, Italy [email protected] Gianluigi Condorelli Division of Cardiology, Department of Medicine, University of California San Diego, 9500 Gilman Drive, BSB 5022, LaJolla, San Diego, CA 92093-0613, USA Scientific and Technology Pole, IRCCS MultiMedica, Via G. Fantoli 16/15, 20138 Milan, Italy [email protected] xi xii Contributors Volker A. Erdmann Institut für Chemie/Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany [email protected] Henry Fechner Department of Cardiology and Pneumology, Campus-Benjamin Franklin, Charite University Medicine, Berlin, Germany Noboru Fukuda Division of Nephrology and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan Advanced Research Institute of Science and Humanities, Nihon University School of Medicine, Tokyo, Japan [email protected] Gabriele Grassi Department of Internal Medicine, University Hospital of Trieste, Cattinara 34149, Trieste, Italy Department of Molecular Pathology, University Hospital of Tübingen, Liebermeisterstr. 8, 72076 Tübingen, Germany [email protected] Mario Grassi Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, Trieste 34127, Italy Hugo A. Katus Innere Medizin III, Universitatsklinikum Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany Nicholas Kipshidze Lenox Hill Hospital, Department of Interventional Cardiac & Vascular Services, 30 East 77th Street, New York, NY 10021, USA [email protected] Michael V.G. Latronico Scientific and Technology Pole, IRCCS MultiMedica, Via G. Fantoli 16/15, 20138 Milan, Italy Osako Kiomy Mariana Division of Clinical Gene Therapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan Sabine Merl Deutsches Herzzentrum and 1 Medizinische Klinik, Technische Universität, Lazarettstrasse 36, 80636 München, Germany Ryuichi Morishita Division of Clinical Gene Therapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan