Books
Muscular dystrophy therapeutics: Methods and Protocols Hardcover – Nov. 19 2022
by Rika Maruyama (Editor) Toshifumi Yokota (Editor),
This detailed book presents a comprehensive collection of state-of-the-art protocols on muscular dystrophy therapeutics, covering therapeutics using antisense oligonucleotides, gene replacement, genome editing, small molecules, stem cells, and antibodies. Written by leaders in the field, the volume explores techniques that are currently in use and are starting an exciting therapeutic revolution in muscular dystrophy. As a part of the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Muscular Dystrophy Therapeutics: Methods and Protocols serves as an ideal resource to inspire readers and provide tips, strategies, and advice to develop new therapeutic technologies for this group of diseases.
Table of contents
Basics and Introduction
Front Matter
Pages 1-1
Chapter 1
Current Strategies of Muscular Dystrophy Therapeutics: An Overview
Kenji Rowel Q. Lim, Toshifumi Yokota
Pages 3-30
Chapter 2
Viltolarsen: From Preclinical Studies to FDA Approval
Rohini Roy Roshmi, Toshifumi Yokota
Pages 31-41
Animal Models, Sample Preparation, and Assessment
Front Matter
Pages 43-43
Chapter 3
Rapid Freezing of Skeletal and Cardiac Muscles Using Isopentane Cooled with Liquid Nitrogen and Tragacanth Gum for Histological, Genetic, and Protein Expression Studies
Saeed Anwar, Toshifumi Yokota
Pages 45-53
Chapter 4
Cardiac and Skeletal Muscle Pathology in the D2/mdx Mouse Model and Caveats Associated with the Quantification of Utrophin
Tahnee L. Kennedy, Hannah F. Dugdale
Pages 55-66
Chapter 5
Physiological Assessment of Muscle, Heart, and Whole Body Function in the Canine Model of Duchenne Muscular Dystrophy
Chady H. Hakim, James Teixeira, Stacy B. Leach, Dongsheng Duan
Pages 67-103
Chapter 6
Antisense Oligonucleotides and Gene Replacement Therapies
Front Matter
Pages 105-105
Chapter 7
Restoring Dystrophin Expression by Skipping Exons 6 and 8 in Neonatal Dystrophic Dogs
Md Nur Ahad Shah, Toshifumi Yokota
Pages 107-124
Chapter 8
Restoring Dystrophin Expression with Exon 44 and 53 Skipping in the DMD Gene in Immortalized Myotubes
Yusuke Echigoya, Toshifumi Yokota
Pages 125-139
Chapter 9
Restoring Dystrophin Expression with Duchenne Muscular Dystrophy Exon 45 Skipping in Induced Pluripotent Stem Cell-Derived Cardiomyocytes
Mitsuto Sato, Naoko Shiba, Daigo Miyazaki, Yuji Shiba, Akinori Nakamura
Pages 141-151
Chapter 10
Quantitative Evaluation of Exon Skipping in Urine-Derived Cells for Duchenne Muscular Dystrophy
Katsuhiko Kunitake, Chaitra Sathyaprakash, Norio Motohashi, Yoshitsugu Aoki
Pages 153-164
Chapter 11
Use of Glycine to Augment Exon Skipping and Cell Therapies for Duchenne Muscular Dystrophy
Gang Han, Caorui Lin, HaiFang Yin
Pages 165-182
Chapter 12
Morpholino-Mediated Exons 28–29 Skipping of Dysferlin and Characterization of Multiexon-skipped Dysferlin using RT-PCR, Immunoblotting, and Membrane Wounding Assay
Saeed Anwar, Toshifumi Yokota
Pages 183-196
Chapter 13
Knocking Down DUX4 in Immortalized Facioscapulohumeral Muscular Dystrophy Patient-Derived Muscle Cells
Kenji Rowel Q. Lim, Toshifumi Yokota
Pages 197-208
Chapter 14
Peptide-Conjugated PMOs for the Treatment of Myotonic Dystrophy
Jessica Stoodley, David Seoane Miraz, Yahya Jad, Mathieu Fischer, Matthew J. A. Wood, Miguel A. Varela
Pages 209-237
Chapter 15
Developing Therapeutic Splice-Correcting Antisense Oligomers for Adult-Onset Pompe Disease with c.-32-13T>G Mutation
Kristin A. Ham, Russell D. Johnsen, Michel Tchan, Steve D. Wilton, May T. Aung-Htut
Pages 239-251
Gene Replacement Therapies
Front Matter
Pages 253-253
Chapter 16
Molecular and Biochemical Assessment of Gene Therapy in the Canine Model of Duchenne Muscular Dystrophy
Chady H. Hakim, Dennis Pérez-López, Matthew J. Burke, James Teixeira, Dongsheng Duan
Pages 255-301
Gene Replacement Therapies
Chapter 17
Histological Assessment of Gene Therapy in the Canine DMD Model
Chady H. Hakim, Matthhew J. Burke, James Teixeira, Dongsheng Duan
Pages 303-338
Chapter 18
MRI Evaluation of Gene Therapy in the Canine Model of Duchenne Muscular Dystrophy
Amy R. Zalcman, Chady H. Hakim, Jimmy C. Lattimer, James R. Holland, John R. Dodam, Dongsheng Duan
Pages 339-352
Assessment of the Gene Therapy Immune Response in the Canine Muscular Dystrophy Model
Chady H. Hakim, Sandeep R. P. Kumar, Dennis Pérez-López, James Teixeira, Roland W. Herzog, Dongsheng Duan
Pages 353-375
Chapter 19
Use of Mesenchymal Stem Cells to Enhance the Efficacy of Gene Therapy
Hiromi Hayashita-Kinoh, Takashi Okada
Pages 377-386
Chapter 19
Exon-Skipping for a Pathogenic COL6A1 Variant in Ullrich Congenital Muscular Dystrophy
Sara Aguti, Fady Guirguis, Carsten Bönnemann, Francesco Muntoni, Véronique Bolduc, Haiyan Zhou
Pages 387-407
Genome Editing/CRISPR
Front Matter
Pages 409-409
Chapter 20
CRISPR-Cas9 Correction of Duchenne Muscular Dystrophy in Mice by a Self-Complementary AAV Delivery System
Yu Zhang, Rhonda Bassel-Duby, Eric N. Olson
Pages 411-425
Chapter 21
Preparation of NanoMEDIC Extracellular Vesicles to Deliver CRISPR-Cas9 Ribonucleoproteins for Genomic Exon Skipping
Kei Watanabe, Peter Gee, Akitsu Hotta
Pages 427-453
Chapter 22
Restoration of Dystrophin Expression in Mdx-Derived Muscle Progenitor Cells Using CRISPR/Cas9 System and Homology-Directed Repair Technology
Yue Jin, Yan Shen, Il-man Kim, Neal L. Weintraub, Mark Hamrick, Yaoliang Tang
Pages 455-464
Small Molecules
Front Matter
Pages 465-465
Chapter 23
Effects of Glucocorticoids in Murine Models of Duchenne and Limb-Girdle Muscular Dystrophy
Michelle Wintzinger, Karen Miz, Allen York, Alexis R. Demonbreun, Jeffery D. Molkentin, Elizabeth M. McNally et al.
Pages 467-478
Chapter 24
High-Throughput Screening to Identify Modulators of Sarcospan
Cynthia Shu, Ekaterina Mokhonova, Rachelle H. Crosbie
Pages 479-493
Chapter 25
Identifying FDA-Approved Drugs that Upregulate Utrophin A as a Therapeutic Strategy for Duchenne Muscular Dystrophy
Christine Péladeau, Bernard J. Jasmin
Pages 495-510
Chapter 26
Cell Models and Stem Cells
Front Matter
Pages 511-511
Chapter 27
Monitoring Plasma Membrane Injury-Triggered Endocytosis at Single-Cell and Single-Vesicle Resolution
Daniel C. Bittel, Jyoti K. Jaiswal
Pages 513-526
Chapter 28
Evaluation of hiPSC-Derived Muscle Progenitor Cell Transplantation in a Mouse Duchenne Muscular Dystrophy Model
Minas Nalbandian, Mingming Zhao, Hidetoshi Sakurai
Pages 527-536
Chapter 29
Quantification of Muscle Satellite Stem Cell Divisions by High-Content Analysis
William Chen, Theodore J. Perkins, Michael A. Rudnicki
Pages 537-553
Antibody
Front Matter
Pages 555-555
Chapter 30
Systemic Delivery of a Monoclonal Antibody to Immunologically Block Myostatin in the A17 Mouse Model of OPMD
Alberto Malerba, Pradeep Harish, Linda Popplewell
Pages 557-568
Back Matter
Pages 569-575
Cover Image: Muscle cells with facioscapulohumeral muscular dystrophy (FSHD) after gapmer treatment against DUX4.
Gapmers: Methods and Protocols Hardcover – Oct. 10 2020
by Toshifumi Yokota (Editor), Rika Maruyama (Editor)
This volume presents a comprehensive collection of detailed state-of-the-art protocols for gapmer-mediated RNA knockdown from leaders in the field. Chapters detail a historical and contemporary perspective of RNase H-inducing antisense oligonucleotides called gapmers and gapmer-mediated RNA knockdown for basic research and therapies. 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 protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Gapmers: Methods and Protocols aims to provide diverse applications of gapmers along with protocols that will assist readers in moving the frontier.
Table of contents
Basics and Introduction
Front Matter
Pages 1-1
Chapter 1
Invention and Early History of Gapmers
Kenji Rowel Q. Lim, Toshifumi Yokota
Pages 3-19
Chapter 2
Development and Clinical Applications of Antisense Oligonucleotide Gapmers
Leanna Chan, Toshifumi Yokota
Pages 21-47
Chapter 3
Knocking Down Long Noncoding RNAs Using Antisense Oligonucleotide Gapmers
Rika Maruyama, Toshifumi Yokota
Pages 49-56
Chapter 4
Development of Antisense Oligonucleotide Gapmers for the Treatment of Huntington’s Disease
Tejal Aslesh, Toshifumi Yokota
Pages 57-67
Chapter 5
Development of Antisense Oligonucleotide Gapmers for the Treatment of Dyslipidemia and Lipodystrophy
Tejal Aslesh, Toshifumi Yokota
Pages 69-85
Chapter 6
Inotersen for the Treatment of Hereditary Transthyretin Amyloidosis
Maria Mahfouz, Rika Maruyama, Toshifumi Yokota
Pages 87-98
Chapter 7
Degradation of Toxic RNA in Myotonic Dystrophy Using Gapmer Antisense Oligonucleotides
Quynh Nguyen, Toshifumi Yokota
Pages 99-109
Design of Gapmers and Strategies
Chapter 8
DNA–RNA Heteroduplex Oligonucleotide for Highly Efficient Gene Silencing
Rintaro Iwata Hara, Kotaro Yoshioka, Takanori Yokota
Pages 113-119
Chapter 9
Tips for Successful lncRNA Knockdown Using Gapmers
Kim A. Lennox, Mark A. Behlke
Pages 121-140
Chapter 10
Calcium-Mediated In Vitro Transfection Technique of Oligonucleotides with Broad Chemical Modification Compatibility
Fumito Wada, Shin-ichiro Hori, Satoshi Obika, Tsuyoshi Yamamoto
Pages 141-154
Chapter 11
Evaluating the Knockdown Activity of MALAT1 ENA Gapmers In Vitro
Shinzo Iwashita, Takao Shoji, Makoto Koizumi
Pages 155-161
Chapter 12
Albumin-Binding Fatty Acid–Modified Gapmer Antisense Oligonucleotides for Modulation of Pharmacokinetics
Yunpeng Cai, Chenguang Lou, Jesper Wengel, Kenneth A. Howard
Pages 163-174
In Vitro/In Vivo Evaluation of Gapmers
Front Matter
Pages 175-175
Chapter 13
The Use of Gapmers for In Vivo Suppression of Hepatic mRNA Targets
David S. Greenberg, Yonat Tzur, Hermona Soreq
Pages 177-184
Chapter 14
Development of LNA Gapmer Oligonucleotide-Based Therapy for ALS/FTD Caused by the C9orf72 Repeat Expansion
Chaitra Sathyaprakash, Raquel Manzano, Miguel A. Varela, Yasumasa Hashimoto, Matthew J. A. Wood, Kevin Talbot et al.
Pages 185-208
Chapter 15
Targeted Gene Silencing in Malignant Hematolymphoid Cells Using GapmeR
Atish Kizhakeyil, Mobashar Hussain Urf Turabe Fazil, Navin Kumar Verma
Pages 209-219
Chapter 16
Gapmer Antisense Oligonucleotides to Selectively Suppress the Mutant Allele in COL6A Genes in Dominant Ullrich Congenital Muscular Dystrophy
Sara Aguti, Elena Marrosu, Francesco Muntoni, Haiyan Zhou
Pages 221-230
Detection of Gapmers
Front Matter
Pages 231-231
Chapter 17
Detection of Locked Nucleic Acid Gapmers from Mouse Muscle Samples Using ELISA
Kenji Rowel Q. Lim, Quynh Nguyen, Toshifumi Yokota
Pages 233-239
Back Matter
Pages 241-247
Cover Image: Restoration of dystrophin expression with morpholino-mediated multiple exon skipping in the Canine X-linked Muscular Dystrophy.
Exon Skipping and Inclusion Therapies: Methods and Protocols (Methods in Molecular Biology (1828)) 1st ed. 2018 Edition
by Toshifumi Yokota (Editor), Rika Maruyama (Editor)
This book presents a comprehensive collection of detailed state-of-the-art exon skipping and splices modulation protocols. Chapters detail 14 genetic diseases, AON-mediated therapies, and CRISPR/Cas9-mediated gene editing therapies. 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 protocols, and tips on troubleshooting and avoiding known pitfalls.
Table of contents (37 protocols)
Front Matter
Pages i-xv
Basics and Introductions
Front Matter
Pages 1-1
Chapter 1
Invention and Early History of Exon Skipping and Splice Modulation
Kenji Rowel Q. Lim, Toshifumi Yokota
Pages 3-30
Chapter 2
An Overview of Recent Advances and Clinical Applications of Exon Skipping and Splice Modulation for Muscular Dystrophy and Various Genetic Diseases
Merryl Rodrigues, Toshifumi Yokota
Pages 31-55
Chapter 3
Recent Advances and Clinical Applications of Exon Inclusion for Spinal Muscular Atrophy
Hae-Won Son, Toshifumi Yokota
Pages 57-68
Chapter 4
Nusinersen in the Treatment of Spinal Muscular Atrophy
Kara Goodkey, Tejal Aslesh, Rika Maruyama, Toshifumi Yokota
Pages 69-76
Chapter 5
Design of AONs and Strategy
Front Matter
Pages 77-77
Chapter 6
Tips to Design Effective Splice-Switching Antisense Oligonucleotides for Exon Skipping and Exon Inclusion
Rika Maruyama, Toshifumi Yokota
Pages 79-90
Chapter 7
Antisense Oligonucleotide Targeting of 3’-UTR of mRNA for Expression Knockdown
Golnoush Golshirazi, Lukasz Ciszewski, Ngoc Lu-Nguyen, Linda Popplewell
Pages 91-124
In Vitro Evaluation of Exon Skipping for DMD
Front Matter
Pages 125-125
Chapter 8
Quantitative Evaluation of Exon Skipping in Immortalized Muscle Cells In Vitro
Kenji Rowel Q. Lim, Toshifumi Yokota
Pages 127-139
Chapter 9
Direct Reprogramming of Human DMD Fibroblasts into Myotubes for In Vitro Evaluation of Antisense-Mediated Exon Skipping and Exons 45–55 Skipping Accompanied by Rescue of Dystrophin Expression
Joshua J. A. Lee, Takashi Saito, William Duddy, Shin’ichi Takeda, Toshifumi Yokota
Pages 141-150
Chapter 10
In Vitro Multiexon Skipping by Antisense PMOs in Dystrophic Dog and Exon 7-Deleted DMD Patient
Akinori Nakamura, Yoshitsugu Aoki, Maria Tsoumpra, Toshifumi Yokota, Shin’ichi Takeda
Pages 151-163
Chapter 11
Creation of DMD Muscle Cell Model Using CRISPR-Cas9 Genome Editing to Test the Efficacy of Antisense-Mediated Exon Skipping
Rika Maruyama, Toshifumi Yokota
Pages 165-171
Chapter 12
In Vitro Evaluation of Exon Skipping in Disease-Specific iPSC-Derived Myocytes
Mingming Zhao, Emi Shoji, Hidetoshi Sakurai
Pages 173-189
Chapter 13
Restoration of Dystrophin Protein Expression by Exon Skipping Utilizing CRISPR-Cas9 in Myoblasts Derived from DMD Patient iPS Cells
Masataka Ifuku, Kumiko A. Iwabuchi, Masami Tanaka, Mandy Siu Yu Lung, Akitsu Hotta
Pages 191-217
Chapter 14
Skipping of Duplicated Dystrophin Exons: In Vitro Induction and Assessment
Kane Greer, Sue Fletcher, Steve D. Wilton
Pages 219-228
In Vivo Evaluation of Exon Skipping for DMD
Front Matter
Pages 229-229
Chapter 15
In Vivo Evaluation of Dystrophin Exon Skipping in mdx Mice
Bo Wu, Mingxing Wang, Sapana Shah, Qi Long Lu
Pages 231-247
Chapter 16
Exon 51 Skipping Quantification by Digital Droplet PCR in del52hDMD/mdx Mice
Monika Hiller, Pietro Spitali, Nicole Datson, Annemieke Aartsma-Rus
Pages 249-262
In Vivo Evaluation of Exon Skipping for DMD
Chapter 17
Systemic Injection of Peptide-PMOs into Humanized DMD Mice and Evaluation by RT-PCR and ELISA
Dyanna Melo, Rika Maruyama, Toshifumi Yokota
Pages 263-273
Chapter 18
In Vivo Evaluation of Single-Exon and Multiexon Skipping in mdx52 Mice
Yoshitaka Mizobe, Shouta Miyatake, Hotake Takizawa, Yuko Hara, Toshifumi Yokota, Akinori Nakamura et al.
Pages 275-292
Chapter 19
A Novel Zebrafish Model for Assessing In Vivo Delivery of Morpholino Oligomers
Joseph Kim, Karl Clark, Carrie Barton, Robert Tanguay, Hong Moulton
Pages 293-306
Enhancing the Efficacy
Front Matter
Pages 307-307
Chapter 20
Validation and Detection of Exon Skipping Boosters in DMD Patient Cell Models and mdx Mouse
Florian Barthelemy, Dereck Wang, Stanley F. Nelson, M. Carrie Miceli
Pages 309-326
Chapter 21
Use of Glucose–Fructose to Enhance the Exon Skipping Efficacy
Gang Han, Xianjun Gao, Haifang Yin
Pages 327-342
Chapter 22
Systemic Intravenous Administration of Antisense Therapeutics for Combinatorial Dystrophin and Myostatin Exon Splice Modulation
Ngoc Lu-Nguyen, George Dickson, Alberto Malerba
Pages 343-354
Chapter 23
The Assembly of Fluorescently Labeled Peptide–Oligonucleotide Conjugates via Orthogonal Ligation Strategies
John Karas, Bradley J. Turner, Fazel Shabanpoor
Pages 355-363
Chapter 24
In Vivo Evaluation of Multiple Exon Skipping with Peptide-PMOs in Cardiac and Skeletal Muscles in Dystrophic Dogs
Rika Maruyama, Yoshitsugu Aoki, Shin’ichi Takeda, Toshifumi Yokota
Pages 365-379
Chapter 25
Use of Tricyclo-DNA Antisense Oligonucleotides for Exon Skipping
Karima Relizani, Aurelie Goyenvalle
Pages 381-394
Chapter 26
Optimization of 2′,4′-BNA/LNA-Based Oligonucleotides for Splicing Modulation In Vitro
Takenori Shimo, Satoshi Obika
Pages 395-411
Exon Inclusion for SMA
Front Matter
Pages 413-413
Chapter 27
Pre-mRNA Splicing Modulation by Antisense Oligonucleotides
Natalia N. Singh, Diou Luo, Ravindra N. Singh
Pages 415-437
Chapter 28
In Vitro Evaluation of Antisense-Mediated Exon Inclusion for Spinal Muscular Atrophy
Aleksander Touznik, Rika Maruyama, Toshifumi Yokota
Pages 439-454
Chapter 29
Systemic and ICV Injections of Antisense Oligos into SMA Mice and Evaluation
Tejal Aslesh, Rika Maruyama, Toshifumi Yokota
Pages 455-465
Chapter 30
Morpholino-Mediated Exon Inclusion for SMA
Haiyan Zhou, Francesco Muntoni
Pages 467-477
Exon Skipping and Splice Modulation for Various Diseases
Front Matter
Pages 479-479
Chapter 31
Exon Skipping by Ultrasound-Enhanced Delivery of Morpholino with Bubble Liposomes for Myotonic Dystrophy Model Mice
Yoichi Negishi, Yoko Endo-Takahashi, Shoichi Ishiura
Pages 481-487
Chapter 32
Dysferlin Exon 32 Skipping in Patient Cells
Florian Barthélémy, Sébastien Courrier, Nicolas Lévy, Martin Krahn, Marc Bartoli
Pages 489-496
Chapter 33
Morpholino-Mediated Exon Skipping Targeting Human ACVR1/ALK2 for Fibrodysplasia Ossificans Progressiva
Rika Maruyama, Toshifumi Yokota
Pages 497-502
Chapter 34
Exon Skipping and Splice Modulation for Various Diseases
Exon Skipping of FcεRIβ for Allergic Diseases
Greer K. Arthur, Glenn Cruse
Pages 503-518
Chapter 35
Antisense Oligonucleotide Design and Evaluation of Splice-Modulating Properties Using Cell-Based Assays
Ralph Slijkerman, Hannie Kremer, Erwin van Wijk
Pages 519-530
Chapter 36
Antisense-Mediated Splice Modulation to Reframe Transcripts
Matthias Titeux, Sandrina Turczynski, Nathalie Pironon, Alain Hovnanian
Pages 531-552
Chapter 37
Exon Skipping Using Antisense Oligonucleotides for Laminin-Alpha2-Deficient Muscular Dystrophy
Yuko Hara, Yoshitaka Mizobe, Shouta Miyatake, Hotake Takizawa, Tetsuya Nagata, Toshifumi Yokota et al.
Pages 553-564
Correction to: Antisense-Mediated Splice Modulation to Reframe Transcripts
Matthias Titeux, Sandrina Turczynski, Nathalie Pironon, Alain Hovnanian
Pages E1-E1
Back Matter
Pages 565-569
Last updated: 21 March 2023
