1
|
Umurzakova A, Ayaganov D, Nurgaliyeva R. Results of a genetic study of children with Duchenne myodystrophy in Kazakhstan. J Neurosci Rural Pract 2023; 14:389-390. [PMID: 37181168 PMCID: PMC10174136 DOI: 10.25259/jnrp_55_2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/25/2023] [Indexed: 05/16/2023] Open
|
2
|
Abstract
Muscular dystrophies are a group of genetic disorders characterized by varying degrees of progressive muscle weakness and degeneration. They are clinically and genetically heterogeneous but share the common histological features of dystrophic muscle. There is currently no cure for muscular dystrophies, which is of particular concern for the more disabling and/or lethal forms of the disease. Through the years, several therapies have encouragingly been developed for muscular dystrophies and include genetic, cellular, and pharmacological approaches. In this chapter, we undertake a comprehensive exploration of muscular dystrophy therapeutics under current development. Our review includes antisense therapy, CRISPR, gene replacement, cell therapy, nonsense suppression, and disease-modifying small molecule compounds.
Collapse
|
3
|
Pattan V, Kashyap R, Bansal V, Candula N, Koritala T, Surani S. Genomics in medicine: A new era in medicine. World J Methodol 2021; 11:231-242. [PMID: 34631481 PMCID: PMC8472545 DOI: 10.5662/wjm.v11.i5.231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
The sequencing of complete human genome revolutionized the genomic medicine. However, the complex interplay of gene-environment-lifestyle and influence of non-coding genomic regions on human health remain largely unexplored. Genomic medicine has great potential for diagnoses or disease prediction, disease prevention and, targeted treatment. However, many of the promising tools of genomic medicine are still in their infancy and their application may be limited because of the limited knowledge we have that precludes its use in many clinical settings. In this review article, we have reviewed the evolution of genomic methodologies/tools, their limitations, and scope, for current and future clinical application.
Collapse
Affiliation(s)
- Vishwanath Pattan
- Division of Endocrinology, Wyoming Medical Center, Casper, WY 82601, United States
| | - Rahul Kashyap
- Department of Anesthesiology and Peri-operative Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Vikas Bansal
- Department of Anesthesiology and Peri-operative Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Narsimha Candula
- Hospital Medicine, University Florida Health, Jacksonville, FL 32209, United States
| | - Thoyaja Koritala
- Hospital Medicine, Mayo Clinic Health System, Mankato, MN 56001, United States
| | - Salim Surani
- Department of Internal Medicine, Texas A&M University, Corpus Christi, TX 78405, United States
| |
Collapse
|
4
|
Chiba S, Lim KRQ, Sheri N, Anwar S, Erkut E, Shah MNA, Aslesh T, Woo S, Sheikh O, Maruyama R, Takano H, Kunitake K, Duddy W, Okuno Y, Aoki Y, Yokota T. eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping. Nucleic Acids Res 2021; 49:W193-W198. [PMID: 34104972 PMCID: PMC8265194 DOI: 10.1093/nar/gkab442] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/18/2021] [Accepted: 05/12/2021] [Indexed: 01/13/2023] Open
Abstract
Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the difficulty in selecting an optimal sequence for exon skipping. The efficacy of ASOs is often unpredictable, because of the numerous factors involved in exon skipping. To address this gap, we have developed a computational method using machine-learning algorithms that factors in many parameters as well as experimental data to design highly effective ASOs for exon skipping. eSkip-Finder (https://eskip-finder.org) is the first web-based resource for helping researchers identify effective exon skipping ASOs. eSkip-Finder features two sections: (i) a predictor of the exon skipping efficacy of novel ASOs and (ii) a database of exon skipping ASOs. The predictor facilitates rapid analysis of a given set of exon/intron sequences and ASO lengths to identify effective ASOs for exon skipping based on a machine learning model trained by experimental data. We confirmed that predictions correlated well with in vitro skipping efficacy of sequences that were not included in the training data. The database enables users to search for ASOs using queries such as gene name, species, and exon number.
Collapse
Affiliation(s)
- Shuntaro Chiba
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Kenji Rowel Q Lim
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Narin Sheri
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Saeed Anwar
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Esra Erkut
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Md Nur Ahad Shah
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Tejal Aslesh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Stanley Woo
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Omar Sheikh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Rika Maruyama
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Hiroaki Takano
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - William Duddy
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, C-TRIC, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK
| | - Yasushi Okuno
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan.,Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| |
Collapse
|
5
|
Choy J, Kan Y, Cifelli S, Johnson J, Chen M, Shiao LL, Zhou H, Previs S, Lei Y, Johnstone R, Liaw A, Saigal A, Hu L, Ramos R, Visconti R, McElroy WT, Kreamer A, Wildey MJ, Peier A, Shin MK, Imbriglio J, Ren Z, Hoek M, Weinglass A, Ai X. High-Throughput Screening to Identify Small Molecules That Selectively Inhibit APOL1 Protein Level in Podocytes. SLAS DISCOVERY 2021; 26:1225-1237. [PMID: 34218698 DOI: 10.1177/24725552211026245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
High-throughput phenotypic screening is a key driver for the identification of novel chemical matter in drug discovery for challenging targets, especially for those with an unclear mechanism of pathology. For toxic or gain-of-function proteins, small-molecule suppressors are a targeting/therapeutic strategy that has been successfully applied. As with other high-throughput screens, the screening strategy and proper assays are critical for successfully identifying selective suppressors of the target of interest. We executed a small-molecule suppressor screen to identify compounds that specifically reduce apolipoprotein L1 (APOL1) protein levels, a genetically validated target associated with increased risk of chronic kidney disease. To enable this study, we developed homogeneous time-resolved fluorescence (HTRF) assays to measure intracellular APOL1 and apolipoprotein L2 (APOL2) protein levels and miniaturized them to 1536-well format. The APOL1 HTRF assay served as the primary assay, and the APOL2 and a commercially available p53 HTRF assay were applied as counterscreens. Cell viability was also measured with CellTiter-Glo to assess the cytotoxicity of compounds. From a 310,000-compound screening library, we identified 1490 confirmed primary hits with 12 different profiles. One hundred fifty-three hits selectively reduced APOL1 in 786-O, a renal cell adenocarcinoma cell line. Thirty-one of these selective suppressors also reduced APOL1 levels in conditionally immortalized human podocytes. The activity and specificity of seven resynthesized compounds were validated in both 786-O and podocytes.
Collapse
Affiliation(s)
- Jonathan Choy
- Cardio-Metabolic Diseases, Merck & Co., Inc., South San Francisco, CA, USA.,Maze Therapeutics, South San Francisco, CA, USA
| | - Yanqing Kan
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Steve Cifelli
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Josephine Johnson
- Cardio-Metabolic Diseases, Merck & Co., Inc., South San Francisco, CA, USA
| | - Michelle Chen
- Cardio-Metabolic Diseases, Merck & Co., Inc., South San Francisco, CA, USA
| | - Lin-Lin Shiao
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Haihong Zhou
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Stephen Previs
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ying Lei
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Richard Johnstone
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Andy Liaw
- Biometrics Research, Merck & Co., Inc., Rahway, NJ, USA
| | - Ashmita Saigal
- Cardio-Metabolic Diseases, Merck & Co., Inc., South San Francisco, CA, USA
| | - Lufei Hu
- Cardio-Metabolic Diseases, Merck & Co., Inc., South San Francisco, CA, USA
| | - Robert Ramos
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Richard Visconti
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA.,Bristol Myers Squibb, New York, NY, USA
| | - William T McElroy
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA.,Constellation Pharmaceuticals, Cambridge, MA, USA
| | - Anthony Kreamer
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Mary-Jo Wildey
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Andrea Peier
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Myung K Shin
- Genetics and Pharmacogenomics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Jason Imbriglio
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Zhao Ren
- Cardio-Metabolic Diseases, Merck & Co., Inc., South San Francisco, CA, USA
| | - Maarten Hoek
- Cardio-Metabolic Diseases, Merck & Co., Inc., South San Francisco, CA, USA.,Maze Therapeutics, South San Francisco, CA, USA
| | - Adam Weinglass
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Xi Ai
- Screening, Target and Compound Profiling, Merck & Co., Inc., Kenilworth, NJ, USA
| |
Collapse
|
6
|
From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies. Biomedicines 2021; 9:biomedicines9050550. [PMID: 34068948 PMCID: PMC8156014 DOI: 10.3390/biomedicines9050550] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023] Open
Abstract
Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siRNAs). These antisense-based mechanisms can tackle several genetic disorders in a gene-specific manner, primarily by gene downregulation (gapmers and siRNAs) or splicing defects correction (exon-skipping oligos). Still, the challenge remains for the repair at the single-nucleotide level. The emerging field of epitranscriptomics and RNA modifications shows the enormous possibilities for recoding the transcriptome and repairing genetic mutations with high specificity while harnessing endogenously expressed RNA processing machinery. Some of these techniques have been proposed as alternatives to CRISPR-based technologies, where the exogenous gene-editing machinery needs to be delivered and expressed in the human cells to generate permanent (DNA) changes with unknown consequences. Here, we review the current FDA-approved antisense MoA (emphasizing some enabling technologies that contributed to their success) and three novel modalities based on post-transcriptional RNA modifications with therapeutic potential, including ADAR (Adenosine deaminases acting on RNA)-mediated RNA editing, targeted pseudouridylation, and 2′-O-methylation.
Collapse
|
7
|
Lim KRQ, Nguyen Q, Yokota T. Detection of Locked Nucleic Acid Gapmers from Mouse Muscle Samples Using ELISA. Methods Mol Biol 2021; 2176:233-239. [PMID: 32865795 DOI: 10.1007/978-1-0716-0771-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Antisense oligonucleotide (ASO)-mediated therapy is promising for the treatment of a variety of genetic disorders, such as Duchenne muscular dystrophy. As more ASOs advance in therapeutic development and enter clinical trials, it becomes necessary to have a means of quantifying their amounts in biological samples post-treatment. This information will be valuable for evaluating the safety and pharmacokinetic profiles of ASOs, and in deciding how the efficacy of these drugs can be improved. Gapmers are a class of ASOs characterized by having a central DNA portion that is surrounded by chemically modified nucleotides on both ends. While relatively simple and accessible methods to quantify other ASOs such as phosphorodiamidate morpholino oligomers (PMOs) using enzyme-linked immunosorbent assay (ELISA)-based techniques are available and have been used for in vivo studies, no such method is available for gapmers to our knowledge. Here, we describe a sensitive ELISA protocol that can be used to quantify the levels of locked nucleic acid (LNA) gapmers in mouse muscle tissue.
Collapse
Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Quynh Nguyen
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
| |
Collapse
|
8
|
Lim KRQ, Yokota T. Genetic Approaches for the Treatment of Facioscapulohumeral Muscular Dystrophy. Front Pharmacol 2021; 12:642858. [PMID: 33776777 PMCID: PMC7996372 DOI: 10.3389/fphar.2021.642858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant disorder characterized by progressive, asymmetric muscle weakness at the face, shoulders, and upper limbs, which spreads to the lower body with age. It is the third most common inherited muscular disorder worldwide. Around 20% of patients are wheelchair-bound, and some present with extramuscular manifestations. FSHD is caused by aberrant expression of the double homeobox protein 4 (DUX4) gene in muscle. DUX4 codes for a transcription factor which, in skeletal muscle, dysregulates numerous signaling activities that culminate in cytotoxicity. Potential treatments for FSHD therefore aim to reduce the expression of DUX4 or the activity of its toxic protein product. In this article, we review how genetic approaches such as those based on oligonucleotide and genome editing technologies have been developed to achieve these goals. We also outline the challenges these therapies are facing on the road to translation, and discuss possible solutions and future directions.
Collapse
Affiliation(s)
- Kenji Rowel Q. Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada, HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada
| |
Collapse
|
9
|
Morais P, Adachi H, Yu YT. Spliceosomal snRNA Epitranscriptomics. Front Genet 2021; 12:652129. [PMID: 33737950 PMCID: PMC7960923 DOI: 10.3389/fgene.2021.652129] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
Small nuclear RNAs (snRNAs) are critical components of the spliceosome that catalyze the splicing of pre-mRNA. snRNAs are each complexed with many proteins to form RNA-protein complexes, termed as small nuclear ribonucleoproteins (snRNPs), in the cell nucleus. snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes. The recognition is achieved primarily by base-pairing interactions (or nucleotide-nucleotide contact) between snRNAs and pre-mRNA. Notably, snRNAs are extensively modified with different RNA modifications, which confer unique properties to the RNAs. Here, we review the current knowledge of the mechanisms and functions of snRNA modifications and their biological relevance in the splicing process.
Collapse
Affiliation(s)
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
| |
Collapse
|
10
|
Lim KRQ, Maruyama R, Echigoya Y, Nguyen Q, Zhang A, Khawaja H, Sen Chandra S, Jones T, Jones P, Chen YW, Yokota T. Inhibition of DUX4 expression with antisense LNA gapmers as a therapy for facioscapulohumeral muscular dystrophy. Proc Natl Acad Sci U S A 2020; 117:16509-16515. [PMID: 32601200 PMCID: PMC7368245 DOI: 10.1073/pnas.1909649117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), characterized by progressive muscle weakness and deterioration, is genetically linked to aberrant expression of DUX4 in muscle. DUX4, in its full-length form, is cytotoxic in nongermline tissues. Here, we designed locked nucleic acid (LNA) gapmer antisense oligonucleotides (AOs) to knock down DUX4 in immortalized FSHD myoblasts and the FLExDUX4 FSHD mouse model. Using a screening method capable of reliably evaluating the knockdown efficiency of LNA gapmers against endogenous DUX4 messenger RNA in vitro, we demonstrate that several designed LNA gapmers selectively and effectively reduced DUX4 expression with nearly complete knockdown. We also found potential functional benefits of AOs on muscle fusion and structure in vitro. Finally, we show that one of the LNA gapmers was taken up and induced effective silencing of DUX4 upon local treatment in vivo. The LNA gapmers developed here will help facilitate the development of FSHD therapies.
Collapse
Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Rika Maruyama
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Yusuke Echigoya
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Quynh Nguyen
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Aiping Zhang
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010
- Department of Integrative Systems Biology, George Washington University, Washington, DC 20052
| | - Hunain Khawaja
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010
- Department of Integrative Systems Biology, George Washington University, Washington, DC 20052
| | - Sreetama Sen Chandra
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010
- Department of Integrative Systems Biology, George Washington University, Washington, DC 20052
| | - Takako Jones
- Department of Pharmacology, University of Nevada Reno School of Medicine, Reno, NV 89557-0318
| | - Peter Jones
- Department of Pharmacology, University of Nevada Reno School of Medicine, Reno, NV 89557-0318
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010;
- Department of Genomics and Precision Medicine, School of Medicine and Health Science, George Washington University, Washington, DC 20052
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada;
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB T6G2H7, Canada
| |
Collapse
|
11
|
Inoue T, Nagano C, Matsuo M, Yamamura T, Sakakibara N, Horinouchi T, Shibagaki Y, Ichikawa D, Aoto Y, Ishiko S, Ishimori S, Rossanti R, Iijima K, Nozu K. Functional analysis of suspected splicing variants in CLCN5 gene in Dent disease 1. Clin Exp Nephrol 2020; 24:606-612. [PMID: 32201916 PMCID: PMC7935734 DOI: 10.1007/s10157-020-01876-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023]
Abstract
Background In recent years, the elucidation of splicing abnormalities as a cause of hereditary diseases has progressed. However, there are no comprehensive reports of suspected splicing variants in the CLCN5 gene in Dent disease cases. We reproduced gene mutations by mutagenesis, inserted the mutated genes into minigene vectors, and investigated the pathogenicity and onset mechanisms of these variants. Methods We conducted functional splicing assays using a hybrid minigene for six suspected splicing variants (c.105G>A, c.105+5G>C, c.106−17T>G, c.393+4A>G, c.517−8A>G, c.517−3C>A) in CLCN5. We extracted information on these variants from the Human Gene Mutation Database. We reproduced minigene vectors with the insertion of relevant exons with suspected splicing variants. We then transfected these minigene vectors into cultured cells and extracted and analyzed the mRNA. In addition, we conducted in silico analysis to confirm our minigene assay results. Results We successfully determined that five of these six variants are pathogenic via the production of splicing abnormalities. One showed only normal transcript production and was thus suspected of not being pathogenic (c.106−17T>G). Conclusion We found that five CLCN5 variants disrupted the original splice site, resulting in aberrant splicing. It is sometimes difficult to obtain mRNA from patient samples because of the fragility of mRNA or its low expression level in peripheral leukocytes. Our in vitro system can be used as an alternative to in vivo assays to determine the pathogenicity of suspected splicing variants. Electronic supplementary material The online version of this article (10.1007/s10157-020-01876-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tomohiko Inoue
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.,Division of Nephrology and Hypertension, St. Marianna University Graduate School of Medicine, 2-16-1 Sugao, Kawasaki City, Kanagawa, 216-8511, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe, Hyogo, 651-2180, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Yugo Shibagaki
- Division of Nephrology and Hypertension, St. Marianna University Graduate School of Medicine, 2-16-1 Sugao, Kawasaki City, Kanagawa, 216-8511, Japan
| | - Daisuke Ichikawa
- Division of Nephrology and Hypertension, St. Marianna University Graduate School of Medicine, 2-16-1 Sugao, Kawasaki City, Kanagawa, 216-8511, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| |
Collapse
|
12
|
Abstract
Gapmers are antisense oligonucleotides composed of a central DNA segment flanked by nucleotides of modified chemistry. Hybridizing with transcripts by sequence complementarity, gapmers recruit ribonuclease H and induce target RNA degradation. Since its concept first emerged in the 1980s, much work has gone into developing gapmers for use in basic research and therapy. These include improvements in gapmer chemistry, delivery, and therapeutic safety. Gapmers have also successfully entered clinical trials for various genetic disorders, with two already approved by the U.S. Food and Drug Administration for the treatment of familial hypercholesterolemia and transthyretin amyloidosis-associated polyneuropathy. Here, we review the events surrounding the early development of gapmers, from conception to their maturity, and briefly conclude with perspectives on their use in therapy.
Collapse
Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
| |
Collapse
|
13
|
Tiek DM, Khatib SA, Trepicchio CJ, Heckler MM, Divekar SD, Sarkaria JN, Glasgow E, Riggins RB. Estrogen-related receptor β activation and isoform shifting by cdc2-like kinase inhibition restricts migration and intracranial tumor growth in glioblastoma. FASEB J 2019; 33:13476-13491. [PMID: 31570001 PMCID: PMC6894094 DOI: 10.1096/fj.201901075r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/26/2019] [Indexed: 11/11/2022]
Abstract
Glioblastoma (GBM; grade 4 glioma) is a highly aggressive and incurable tumor. GBM has recently been characterized as highly dependent on alternative splicing, a critical driver of tumor heterogeneity and plasticity. Estrogen-related receptor β (ERR-β) is an orphan nuclear receptor expressed in the brain, where alternative splicing of the 3' end of the pre-mRNA leads to the production of 3 validated ERR-β protein products: ERR-β short form (ERR-βsf), ERR-β2, and ERR-β exon 10 deleted. Our prior studies have shown the ERR-β2 isoform to play a role in G2/M cell cycle arrest and induction of apoptosis, in contrast to the function of the shorter ERR-βsf isoform in senescence and G1 cell cycle arrest. In this study, we sought to better define the role of the proapoptotic ERR-β2 isoform in GBM. We show that the ERR-β2 isoform is located not only in the nucleus but also in the cytoplasm. ERR-β2 suppresses GBM cell migration and interacts with the actin nucleation-promoting factor cortactin, and an ERR-β agonist is able to remodel the actin cytoskeleton and similarly suppress GBM cell migration. We further show that inhibition of the splicing regulatory cdc2-like kinases in combination with an ERR-β agonist shifts isoform expression in favor of ERR-β2 and potentiates inhibition of growth and migration in GBM cells and intracranial tumors.-Tiek, D. M., Khatib, S. A., Trepicchio, C. J., Heckler, M. M., Divekar, S. D., Sarkaria, J. N., Glasgow, E., Riggins, R. B. Estrogen-related receptor β activation and isoform shifting by cdc2-like kinase inhibition restricts migration and intracranial tumor growth in glioblastoma.
Collapse
Affiliation(s)
- Deanna M. Tiek
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Subreen A. Khatib
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland, USA; and
| | - Colin J. Trepicchio
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Mary M. Heckler
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Shailaja D. Divekar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Jann N. Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric Glasgow
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rebecca B. Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| |
Collapse
|
14
|
Nguyen Q, Lim KRQ, Yokota T. Current understanding and treatment of cardiac and skeletal muscle pathology in laminin-α2 chain-deficient congenital muscular dystrophy. APPLICATION OF CLINICAL GENETICS 2019; 12:113-130. [PMID: 31308722 PMCID: PMC6618038 DOI: 10.2147/tacg.s187481] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/08/2019] [Indexed: 01/04/2023]
Abstract
Congenital muscular dystrophy (CMD) is a class of severe early-onset muscular dystrophies affecting skeletal/cardiac muscles as well as the central nervous system (CNS). Laminin-α2 chain-deficient congenital muscular dystrophy (LAMA2 MD), also known as merosin-deficient congenital muscular dystrophy type 1A (MDC1A), is an autosomal recessive CMD characterized by severe muscle weakness and degeneration apparent at birth or in the first 6 months of life. LAMA2 MD is the most common congenital muscular dystrophy, affecting approximately 4 in 500,000 children. The most common cause of death in early-onset LAMA2 MD is respiratory tract infection, with 30% of them dying within the first decade of life. LAMA2 MD is caused by loss-of-function mutations in the LAMA2 gene encoding for the laminin-α2 chain, one of the subunits of laminin-211. Laminin-211 is an extracellular matrix protein that functions to stabilize the basement membrane and muscle fibers during contraction. Since laminin-α2 is expressed in many tissue types including skeletal muscle, cardiac muscle, Schwann cells, and trophoblasts, patients with LAMA2 MD experience a multi-systemic clinical presentation depending on the extent of laminin-α2 chain deficiency. Cardiac manifestations are typically associated with a complete absence of laminin-α2; however, recent case reports highlight cardiac involvement in partial laminin-α2 chain deficiency. Laminin-211 is also expressed in the brain, and many patients have abnormalities on brain imaging; however, mental retardation and/or seizures are rarely seen. Currently, there is no cure for LAMA2 MD, but various therapies are being investigated in an effort to lessen the severity of LAMA2 MD. For example, antisense oligonucleotide-mediated exon skipping and CRISPR-Cas9 genome editing have efficiently restored the laminin-α2 chain in mouse models in vivo. This review consolidates information on the clinical presentation, genetic basis, pathology, and current treatment approaches for LAMA2 MD.
Collapse
Affiliation(s)
- Quynh Nguyen
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,The Friends of Garrett Cumming Research & Muscular Dystrophy Canada, HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada
| |
Collapse
|
15
|
Applications of CRISPR/Cas9 for the Treatment of Duchenne Muscular Dystrophy. J Pers Med 2018; 8:jpm8040038. [PMID: 30477208 PMCID: PMC6313657 DOI: 10.3390/jpm8040038] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 12/29/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive neuromuscular disease prevalent in 1 in 3500 to 5000 males worldwide. As a result of mutations that interrupt the reading frame of the dystrophin gene (DMD), DMD is characterized by a loss of dystrophin protein that leads to decreased muscle membrane integrity, which increases susceptibility to degeneration. CRISPR/Cas9 technology has garnered interest as an avenue for DMD therapy due to its potential for permanent exon skipping, which can restore the disrupted DMD reading frame in DMD and lead to dystrophin restoration. An RNA-guided DNA endonuclease system, CRISPR/Cas9 allows for the targeted editing of specific sequences in the genome. The efficacy and safety of CRISPR/Cas9 as a therapy for DMD has been evaluated by numerous studies in vitro and in vivo, with varying rates of success. Despite the potential of CRISPR/Cas9-mediated gene editing for the long-term treatment of DMD, its translation into the clinic is currently challenged by issues such as off-targeting, immune response activation, and sub-optimal in vivo delivery. Its nature as being mostly a personalized form of therapy also limits applicability to DMD patients, who exhibit a wide spectrum of mutations. This review summarizes the various CRISPR/Cas9 strategies that have been tested in vitro and in vivo for the treatment of DMD. Perspectives on the approach will be provided, and the challenges faced by CRISPR/Cas9 in its road to the clinic will be briefly discussed.
Collapse
|