201
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Yang SJ, Lipnick SL, Makhortova NR, Venugopalan S, Fan M, Armstrong Z, Schlaeger TM, Deng L, Chung WK, O'Callaghan L, Geraschenko A, Whye D, Berndl M, Hazard J, Williams B, Narayanaswamy A, Ando DM, Nelson P, Rubin LL. Applying Deep Neural Network Analysis to High-Content Image-Based Assays. SLAS DISCOVERY 2019; 24:829-841. [PMID: 31284814 PMCID: PMC6710615 DOI: 10.1177/2472555219857715] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The etiological underpinnings of many CNS disorders are not well understood. This is likely due to the fact that individual diseases aggregate numerous pathological subtypes, each associated with a complex landscape of genetic risk factors. To overcome these challenges, researchers are integrating novel data types from numerous patients, including imaging studies capturing broadly applicable features from patient-derived materials. These datasets, when combined with machine learning, potentially hold the power to elucidate the subtle patterns that stratify patients by shared pathology. In this study, we interrogated whether high-content imaging of primary skin fibroblasts, using the Cell Painting method, could reveal disease-relevant information among patients. First, we showed that technical features such as batch/plate type, plate, and location within a plate lead to detectable nuisance signals, as revealed by a pre-trained deep neural network and analysis with deep image embeddings. Using a plate design and image acquisition strategy that accounts for these variables, we performed a pilot study with 12 healthy controls and 12 subjects affected by the severe genetic neurological disorder spinal muscular atrophy (SMA), and evaluated whether a convolutional neural network (CNN) generated using a subset of the cells could distinguish disease states on cells from the remaining unseen control–SMA pair. Our results indicate that these two populations could effectively be differentiated from one another and that model selectivity is insensitive to batch/plate type. One caveat is that the samples were also largely separated by source. These findings lay a foundation for how to conduct future studies exploring diseases with more complex genetic contributions and unknown subtypes.
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Affiliation(s)
| | - Scott L Lipnick
- 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,3 Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,4 Center for Assessment Technology & Continuous Health (CATCH), Massachusetts General Hospital, Boston, MA, USA
| | - Nina R Makhortova
- 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,5 Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | | | | | | | | | - Liyong Deng
- 6 Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Wendy K Chung
- 6 Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | | | | | - Dosh Whye
- 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | | | | | | | | | | | - Lee L Rubin
- 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,7 Harvard Stem Cell Institute, Cambridge, MA, USA
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202
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NCALD Antisense Oligonucleotide Therapy in Addition to Nusinersen further Ameliorates Spinal Muscular Atrophy in Mice. Am J Hum Genet 2019; 105:221-230. [PMID: 31230718 DOI: 10.1016/j.ajhg.2019.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease causing the most frequent genetic childhood lethality. Recently, nusinersen, an antisense oligonucleotide (ASO) that corrects SMN2 splicing and thereby increases full-length SMN protein, has been approved by the FDA and EMA for SMA therapy. However, the administration of nusinersen in severe and/or post-symptomatic SMA-affected individuals is insufficient to counteract the disease. Therefore, additional SMN-independent therapies are needed to support the function of motoneurons and neuromuscular junctions. We recently identified asymptomatic SMN1-deleted individuals who were protected against SMA by reduced expression of neurocalcin delta (NCALD). NCALD reduction is proven to be a protective modifier of SMA across species, including worm, zebrafish, and mice. Here, we identified Ncald-ASO3-out of 450 developed Ncald ASOs-as the most efficient and non-toxic ASO for the CNS, by applying a stepwise screening strategy in cortical neurons and adult and neonatal mice. In a randomized-blinded preclinical study, a single subcutaneous low-dose SMN-ASO and a single intracerebroventricular Ncald-ASO3 or control-ASO injection were presymptomatically administered in a severe SMA mouse model. NCALD reduction of >70% persisted for about 1 month. While low-dose SMN-ASO rescues multiorgan impairment, additional NCALD reduction significantly ameliorated SMA pathology including electrophysiological and histological properties of neuromuscular junctions and muscle at P21 and motoric deficits at 3 months. The present study shows the additional benefit of a combinatorial SMN-dependent and SMN-independent ASO-based therapy for SMA. This work illustrates how a modifying gene, identified in some asymptomatic individuals, helps to develop a therapy for all SMA-affected individuals.
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203
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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204
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Osman EY, Bolding MR, Villalón E, Kaifer KA, Lorson ZC, Tisdale S, Hao Y, Conant GC, Pires JC, Pellizzoni L, Lorson CL. Functional characterization of SMN evolution in mouse models of SMA. Sci Rep 2019; 9:9472. [PMID: 31263170 PMCID: PMC6603021 DOI: 10.1038/s41598-019-45822-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a monogenic neurodegenerative disorder and the leading genetic cause of infantile mortality. While several functions have been ascribed to the SMN (survival motor neuron) protein, their specific contribution to the disease has yet to be fully elucidated. We hypothesized that some, but not all, SMN homologues would rescue the SMA phenotype in mouse models, thereby identifying disease-relevant domains. Using AAV9 to deliver Smn homologs to SMA mice, we identified a conservation threshold that marks the boundary at which homologs can rescue the SMA phenotype. Smn from Danio rerio and Xenopus laevis significantly prevent disease, whereas Smn from Drosophila melanogaster, Caenorhabditis elegans, and Schizosaccharomyces pombe was significantly less efficacious. This phenotypic rescue correlated with correction of RNA processing defects induced by SMN deficiency and neuromuscular junction pathology. Based upon the sequence conservation in the rescuing homologs, a minimal SMN construct was designed consisting of exons 2, 3, and 6, which showed a partial rescue of the SMA phenotype. While a significant extension in survival was observed, the absence of a complete rescue suggests that while the core conserved region is essential, additional sequences contribute to the overall ability of the SMN protein to rescue disease pathology.
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Affiliation(s)
- Erkan Y Osman
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Madeline R Bolding
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Eric Villalón
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Kevin A Kaifer
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Zachary C Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sarah Tisdale
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Division of Biological Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - J Chris Pires
- Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Christian L Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA. .,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
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205
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Taladriz-Sender A, Campbell E, Burley GA. Splice-switching small molecules: A new therapeutic approach to modulate gene expression. Methods 2019; 167:134-142. [PMID: 31203161 DOI: 10.1016/j.ymeth.2019.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
Manipulating alternative RNA splicing events with small molecules is emerging as a viable mechanism for the development of therapeutics. A salient challenge in the field is understanding the molecular determinants defining the selectivity of splice-switching events and their mechanisms of action. In this review, the current state-of-the-art in splice-switching small molecules is described. Three examples of splice-switching small molecules are presented, and the differences in their modes of action compared.
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Affiliation(s)
- Andrea Taladriz-Sender
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Emma Campbell
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom.
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206
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Nerve sprouting capacity in a pharmacologically induced mouse model of spinal muscular atrophy. Sci Rep 2019; 9:7799. [PMID: 31127156 PMCID: PMC6534600 DOI: 10.1038/s41598-019-44222-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/10/2019] [Indexed: 11/18/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by loss-of-function mutations in the survival of motoneuron gene 1 (SMN1). SMA is characterized by motoneuron death, skeletal muscle denervation and atrophy. Disease severity inversely correlates with copy number of a second gene (SMN2), which harbors a splicing defect that causes the production of inadequate levels of functional SMN protein. Small molecules that modify SMN2 splicing towards increased production of functional SMN significantly ameliorate SMA phenotypes in mouse models of severe SMA. At suboptimal doses, splicing modifiers, such as SMN-C1, have served to generate mice that model milder SMA, referred to as pharmacological SMA mice, which survive into early adulthood. Nerve sprouting at endplates, known as terminal sprouting, is key to normal muscle fiber reinnervation following nerve injury and its promotion might mitigate neuromuscular symptoms in mild SMA. Sprouting has been difficult to study in severe SMA mice due to their short lifespan. Here, we show that pharmacological SMA mice are capable of terminal sprouting following reinnervation that is largely SMN-C1 dose-independent, but that they display a reinnervation delay that is critically SMN-C1 dose-dependent. Data also suggest that SMN-C1 can induce by itself a limited terminal sprouting response in SMA and wild-type normally-innervated endplates.
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207
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Abstract
PURPOSE OF REVIEW In this review, we discuss the clinical and genetic features of 5q spinal muscular atrophy and highlight approved and upcoming therapies. RECENT FINDINGS We emphasize that multidisciplinary care has been a key component of the improved quality and length of life seen in these individuals in the past decade. We discuss the evidence leading to the approval of nusinersen and the evidence leading to the anticipated approval of onasemnogene abeparvovec-xioi. Additional clinical therapies that are on the horizon are discussed and the importance of continued multidisciplinary care even after treatment is emphasized. The pursuit of therapies for spinal muscular atrophy is becoming a success story and continued development of biomarkers will allow for more informed therapeutic decision making and eventual cost-effective utilization of available therapies.
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Affiliation(s)
- Megan A Waldrop
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA.,Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Stephen J Kolb
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA. .,Department of Biological Chemistry & Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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208
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Disney MD. Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine. J Am Chem Soc 2019; 141:6776-6790. [PMID: 30896935 DOI: 10.1021/jacs.8b13419] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The biology of healthy and disease-affected cells is often mediated by RNA structures, desirable targets for small molecule chemical probes and lead medicines. Although structured regions are found throughout the transcriptome, some even with demonstrated functionality, human RNAs are considered recalcitrant to small molecule targeting. However, targeting structured regions with small molecules provides an important alternative to oligonucleotides that target sequence. In this Perspective, we describe challenges and progress in developing small molecules interacting with RNA (SMIRNAs) to capture their significant opportunities at the intersection of chemistry, biology, and medicine. Key to establishing a new paradigm in chemical biology and medicine is the development of methods to obtain, preferably by design, bioactive compounds that modulate RNA targets and companion methods that validate their direct effects in cells and pre-clinical models. While difficult, demonstration of direct target engagement in the complex cellular milieu, along with methods to establish modes of action, is required to push this field forward. We also describe frameworks for accelerated advancements in this burgeoning area, their implications, key new technologies for development of SMIRNAs, and milestones that have led to broader acceptance of RNA as a small molecule druggable target.
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Affiliation(s)
- Matthew D Disney
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
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209
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ELP1 Splicing Correction Reverses Proprioceptive Sensory Loss in Familial Dysautonomia. Am J Hum Genet 2019; 104:638-650. [PMID: 30905397 DOI: 10.1016/j.ajhg.2019.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/08/2019] [Indexed: 12/14/2022] Open
Abstract
Familial dysautonomia (FD) is a recessive neurodegenerative disease caused by a splice mutation in Elongator complex protein 1 (ELP1, also known as IKBKAP); this mutation leads to variable skipping of exon 20 and to a drastic reduction of ELP1 in the nervous system. Clinically, many of the debilitating aspects of the disease are related to a progressive loss of proprioception; this loss leads to severe gait ataxia, spinal deformities, and respiratory insufficiency due to neuromuscular incoordination. There is currently no effective treatment for FD, and the disease is ultimately fatal. The development of a drug that targets the underlying molecular defect provides hope that the drastic peripheral neurodegeneration characteristic of FD can be halted. We demonstrate herein that the FD mouse TgFD9;IkbkapΔ20/flox recapitulates the proprioceptive impairment observed in individuals with FD, and we provide the in vivo evidence that postnatal correction, promoted by the small molecule kinetin, of the mutant ELP1 splicing can rescue neurological phenotypes in FD. Daily administration of kinetin starting at birth improves sensory-motor coordination and prevents the onset of spinal abnormalities by stopping the loss of proprioceptive neurons. These phenotypic improvements correlate with increased amounts of full-length ELP1 mRNA and protein in multiple tissues, including in the peripheral nervous system (PNS). Our results show that postnatal correction of the underlying ELP1 splicing defect can rescue devastating disease phenotypes and is therefore a viable therapeutic approach for persons with FD.
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210
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Shorrock HK, Gillingwater TH, Groen EJN. Overview of Current Drugs and Molecules in Development for Spinal Muscular Atrophy Therapy. Drugs 2019; 78:293-305. [PMID: 29380287 PMCID: PMC5829132 DOI: 10.1007/s40265-018-0868-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease primarily characterized by a loss of spinal motor neurons, leading to progressive paralysis and premature death in the most severe cases. SMA is caused by homozygous deletion of the survival motor neuron 1 (SMN1) gene, leading to low levels of SMN protein. However, a second SMN gene (SMN2) exists, which can be therapeutically targeted to increase SMN levels. This has recently led to the first disease-modifying therapy for SMA gaining formal approval from the US Food and Drug Administration (FDA) and European Medicines Agency (EMA). Spinraza (nusinersen) is a modified antisense oligonucleotide that targets the splicing of SMN2, leading to increased SMN protein levels, capable of improving clinical phenotypes in many patients. In addition to Spinraza, several other therapeutic approaches are currently in various stages of clinical development. These include SMN-dependent small molecule and gene therapy approaches along with SMN-independent strategies, such as general neuroprotective factors and muscle strength-enhancing compounds. For each therapy, we provide detailed information on clinical trial design and pharmacological/safety data where available. Previous clinical studies are also discussed to provide context on SMA clinical trial development and the insights these provided for the design of current studies.
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Affiliation(s)
- Hannah K Shorrock
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK
| | - Thomas H Gillingwater
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK
| | - Ewout J N Groen
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK. .,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK.
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211
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Velagapudi SP, Li Y, Disney MD. A cross-linking approach to map small molecule-RNA binding sites in cells. Bioorg Med Chem Lett 2019; 29:1532-1536. [PMID: 30987892 DOI: 10.1016/j.bmcl.2019.04.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 10/27/2022]
Abstract
Methods to identify RNAs bound by small molecules in cells are sparse. Herein, an advance to identify the direct RNA targets of small molecules in cells is described. The approach, dubbed Chemical Cross-Linking and Isolation by Pull-down to Map Small Molecule-RNA Binding Sites (Chem-CLIP-Map-Seq), appends a cross-linker and a purification tag onto a small molecule. In cells, the compound binds to RNA and undergoes a proximity-based reaction. The cross-linked RNA is purified and then amplified using a universal reverse transcription (RT) primer and gene-specific PCR primers. At nucleotides proximal to the binding site, RT "stops" are observed. This approach has broad utility in identifying and validating the RNA targets and binding sites of small molecules in the context of a complex cellular system.
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Affiliation(s)
| | - Yue Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
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212
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Long KK, O’Shea KM, Khairallah RJ, Howell K, Paushkin S, Chen KS, Cote SM, Webster MT, Stains JP, Treece E, Buckler A, Donovan A. Specific inhibition of myostatin activation is beneficial in mouse models of SMA therapy. Hum Mol Genet 2019; 28:1076-1089. [PMID: 30481286 PMCID: PMC6423420 DOI: 10.1093/hmg/ddy382] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease characterized by loss of α-motor neurons, leading to profound skeletal muscle atrophy. Patients also suffer from decreased bone mineral density and increased fracture risk. The majority of treatments for SMA, approved or in clinic trials, focus on addressing the underlying cause of disease, insufficient production of full-length SMN protein. While restoration of SMN has resulted in improvements in functional measures, significant deficits remain in both mice and SMA patients following treatment. Motor function in SMA patients may be additionally improved by targeting skeletal muscle to reduce atrophy and improve muscle strength. Inhibition of myostatin, a negative regulator of muscle mass, offers a promising approach to increase muscle function in SMA patients. Here we demonstrate that muSRK-015P, a monoclonal antibody which specifically inhibits myostatin activation, effectively increases muscle mass and function in two variants of the pharmacological mouse model of SMA in which pharmacologic restoration of SMN has taken place either 1 or 24 days after birth to reflect early or later therapeutic intervention. Additionally, muSRK-015P treatment improves the cortical and trabecular bone phenotypes in these mice. These data indicate that preventing myostatin activation has therapeutic potential in addressing muscle and bone deficiencies in SMA patients. An optimized variant of SRK-015P, SRK-015, is currently in clinical development for treatment of SMA.
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Affiliation(s)
| | | | | | - Kelly Howell
- SMA Foundation, 888 7th Avenue #400, New York, NY
| | | | - Karen S Chen
- SMA Foundation, 888 7th Avenue #400, New York, NY
| | - Shaun M Cote
- Scholar Rock Inc., 620 Memorial Drive, Cambridge, MA
| | | | - Joseph P Stains
- Department of Orthopedics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Erin Treece
- Scholar Rock Inc., 620 Memorial Drive, Cambridge, MA
| | - Alan Buckler
- Scholar Rock Inc., 620 Memorial Drive, Cambridge, MA
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213
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Wang Y, Xu C, Ma L, Mou Y, Zhang B, Zhou S, Tian Y, Trinh J, Zhang X, Li XJ. Drug screening with human SMN2 reporter identifies SMN protein stabilizers to correct SMA pathology. Life Sci Alliance 2019; 2:2/2/e201800268. [PMID: 30910806 PMCID: PMC6435041 DOI: 10.26508/lsa.201800268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 01/14/2023] Open
Abstract
Spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, is caused by reduced levels of functional survival motor neuron (SMN) protein. To identify therapeutic agents for SMA, we established a versatile SMN2-GFP reporter line by targeting the human SMN2 gene. We then screened a compound library and identified Z-FA-FMK as a potent candidate. Z-FA-FMK, a cysteine protease inhibitor, increased functional SMN through inhibiting the protease-mediated degradation of both full-length and exon 7-deleted forms of SMN. Further studies reveal that CAPN1, CAPN7, CTSB, and CTSL mediate the degradation of SMN proteins, providing novel targets for SMA. Notably, Z-FA-FMK mitigated mitochondriopathy and neuropathy in SMA patient-derived motor neurons and showed protective effects in SMA animal model after intracerebroventricular injection. E64d, another cysteine protease inhibitor which can pass through the blood-brain barrier, showed even more potent therapeutic effects after subcutaneous delivery to SMA mice. Taken together, we have successfully established a human SMN2 reporter for future drug discovery and identified the potential therapeutic value of cysteine protease inhibitors in treating SMA via stabilizing SMN proteins.
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Affiliation(s)
- Yiran Wang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chongchong Xu
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Lin Ma
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai, China.,Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University, School of Medicine, Shanghai, China
| | - Yongchao Mou
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Bowen Zhang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shanshan Zhou
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yue Tian
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jessica Trinh
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA
| | - Xiaoqing Zhang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China .,Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai, China.,Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University, School of Medicine, Shanghai, China.,Tsingtao Advanced Research Institute, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China.,Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xue-Jun Li
- Department of Biomedical Sciences, University of Illinois College of Medicine Rockford, Rockford, IL, USA .,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
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214
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Chauhan K, Kalam H, Dutt R, Kumar D. RNA Splicing: A New Paradigm in Host-Pathogen Interactions. J Mol Biol 2019; 431:1565-1575. [PMID: 30857970 DOI: 10.1016/j.jmb.2019.03.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/21/2022]
Abstract
RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pathologies including cancer. Emerging evidence suggests precise regulation of splicing as fundamental to normal well-being. In this context, infection-induced alternative splicing has emerged as a new pivot of host function, which pathogenic microbes can alter-directly or indirectly-to tweak the host immune responses against the pathogen. The implications of these findings are vast, and although not explored much in the case of pathogenic infections, we present here examples from splicing mediated regulation of immune responses across a variety of conditions and explore how this fascinating finding brings a new paradigm to host-pathogen interactions.
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Affiliation(s)
- Komal Chauhan
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Haroon Kalam
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ravi Dutt
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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215
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Tabrizi SJ, Ghosh R, Leavitt BR. Huntingtin Lowering Strategies for Disease Modification in Huntington's Disease. Neuron 2019; 101:801-819. [PMID: 30844400 DOI: 10.1016/j.neuron.2019.01.039] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/21/2018] [Accepted: 01/17/2019] [Indexed: 12/24/2022]
Abstract
Huntington's disease is caused by an abnormally expanded CAG repeat expansion in the HTT gene, which confers a predominant toxic gain of function in the mutant huntingtin (mHTT) protein. There are currently no disease-modifying therapies available, but approaches that target proximally in disease pathogenesis hold great promise. These include DNA-targeting techniques such as zinc-finger proteins, transcription activator-like effector nucleases, and CRISPR/Cas9; post-transcriptional huntingtin-lowering approaches such as RNAi, antisense oligonucleotides, and small-molecule splicing modulators; and novel methods to clear the mHTT protein, such as proteolysis-targeting chimeras. Improvements in the delivery and distribution of such agents as well as the development of objective biomarkers of disease and of HTT lowering pharmacodynamic outcomes have brought these potential therapies to the forefront of Huntington's disease research, with clinical trials in patients already underway.
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Affiliation(s)
- Sarah J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute (DRI) at UCL, London, UK.
| | - Rhia Ghosh
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Blair R Leavitt
- UBC Centre for Huntington's Disease, Department of Medical Genetics and Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
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216
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Boemer F, Caberg JH, Dideberg V, Dardenne D, Bours V, Hiligsmann M, Dangouloff T, Servais L. Newborn screening for SMA in Southern Belgium. Neuromuscul Disord 2019; 29:343-349. [PMID: 31030938 DOI: 10.1016/j.nmd.2019.02.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 11/29/2022]
Abstract
Approval was recently granted for a new treatment for spinal muscular atrophy (SMA). Given that the treatment is effective when administered early and the societal burden of SMA-related disability, the implementation of a newborn screening program is warranted. We describe the stepwise process that led us to launch a newborn screening program for SMA in Southern Belgium. Different political, ethical, and clinical partners were informed about this project and were involved in its governance, as were genetic and screening labs. We developed and validated a newborn screening method to specifically recognize homozygous deletions of exon 7 in the SMN1 gene. Subsequently, a 3-year pilot study has been recently initiated in one Belgian neonatal screening laboratory to cover 17.000 neonates per year. Coverage extension to all of Southern Belgium to screen 55.000 babies each year is underway.
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Affiliation(s)
- François Boemer
- Biochemical Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege 4000, Belgium.
| | - Jean-Hubert Caberg
- Molecular Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Vinciane Dideberg
- Molecular Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Domien Dardenne
- Molecular Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Vincent Bours
- Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Mickaël Hiligsmann
- Department of Health Services Research, CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
| | - Tamara Dangouloff
- I-Motion, Platform for Pediatric Clinical Trials, Arnold Trousseau Hospital, Paris, France; Neuromuscular Center, CHR Citadelle, University of Liege, Liege, Belgium
| | - Laurent Servais
- I-Motion, Platform for Pediatric Clinical Trials, Arnold Trousseau Hospital, Paris, France; Neuromuscular Center, CHR Citadelle, University of Liege, Liege, Belgium
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217
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Abulwerdi FA, Xu W, Ageeli AA, Yonkunas MJ, Arun G, Nam H, Schneekloth JS, Dayie TK, Spector D, Baird N, Le Grice SFJ. Selective Small-Molecule Targeting of a Triple Helix Encoded by the Long Noncoding RNA, MALAT1. ACS Chem Biol 2019; 14:223-235. [PMID: 30620551 DOI: 10.1021/acschembio.8b00807] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 ( Malat1/ MALAT1, mouse/human), a highly conserved long noncoding (lnc) RNA, has been linked with several physiological processes, including the alternative splicing, nuclear organization, and epigenetic modulation of gene expression. MALAT1 has also been implicated in metastasis and tumor proliferation in multiple cancer types. The 3' terminal stability element for nuclear expression (ENE) assumes a triple-helical configuration that promotes its nuclear accumulation and persistent function. Utilizing a novel small molecule microarray strategy, we identified multiple Malat1 ENE triplex-binding chemotypes, among which compounds 5 and 16 reduced Malat1 RNA levels and branching morphogenesis in a mammary tumor organoid model. Computational modeling and Förster resonance energy transfer experiments demonstrate distinct binding modes for each chemotype, conferring opposing structural changes to the triplex. Compound 5 modulates Malat1 downstream genes without affecting Neat1, a nuclear lncRNA encoded in the same chromosomal region as Malat1 with a structurally similar ENE triplex. Supporting this observation, the specificity of compound 5 for Malat1 over Neat1 and a virus-coded ENE was demonstrated by nuclear magnetic resonance spectroscopy. Small molecules specifically targeting the MALAT1 ENE triplex lay the foundation for new classes of anticancer therapeutics and molecular probes for the treatment and investigation of MALAT1-driven cancers.
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Affiliation(s)
- Fardokht A. Abulwerdi
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wenbo Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, United States
- Stony Brook University, Molecular and Cellular Biology Program, Stony Brook, New York 11794, United States
| | - Abeer A. Ageeli
- University of the Sciences, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Michael J. Yonkunas
- University of the Sciences, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Gayatri Arun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, United States
| | - Hyeyeon Nam
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Theodore Kwaku Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - David Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, United States
| | - Nathan Baird
- University of the Sciences, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Stuart F. J. Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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218
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DeNicola AB, Tang Y. Therapeutic approaches to treat human spliceosomal diseases. Curr Opin Biotechnol 2019; 60:72-81. [PMID: 30772756 DOI: 10.1016/j.copbio.2019.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
Mutated RNA splicing machinery drives many human diseases and is a promising therapeutic target for engineering and small molecule therapy. In the case of mutations in individual genes that cause them to be incorrectly spliced, engineered splicing factors can be introduced to correct splicing of these aberrant transcripts and reduce the effects of the disease phenotype. Mutations that occur in certain splicing factor genes themselves have been implicated in many cancers, particularly myelodysplastic syndromes. Small molecules that target splicing factors have been developed as therapies to preferentially induce apoptosis in these cancer cells. Specifically, drugs targeting the splicing factor SF3B1 have led to recent clinical trials. Here, we review the role of alternative splicing in disease, approaches to rescue incorrect splicing using engineered splicing factors, and small molecule splicing inhibitors developed to treat hematological cancers.
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Affiliation(s)
- Anthony B DeNicola
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States.
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
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219
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Intraperitoneal delivery of a novel drug-like compound improves disease severity in severe and intermediate mouse models of Spinal Muscular Atrophy. Sci Rep 2019; 9:1633. [PMID: 30733501 PMCID: PMC6367425 DOI: 10.1038/s41598-018-38208-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder that causes progressive muscle weakness and is the leading genetic cause of infant mortality worldwide. SMA is caused by the loss of survival motor neuron 1 (SMN1). In humans, a nearly identical copy gene is present, called SMN2. Although SMN2 maintains the same coding sequence, this gene cannot compensate for the loss of SMN1 because of a single silent nucleotide difference in SMN2 exon 7. SMN2 primarily produces an alternatively spliced isoform lacking exon 7, which is critical for protein function. SMN2 is an important disease modifier that makes for an excellent target for therapeutic intervention because all SMA patients retain SMN2. Therefore, compounds and small molecules that can increase SMN2 exon 7 inclusion, transcription and SMN protein stability have great potential for SMA therapeutics. Previously, we performed a high throughput screen and established a class of compounds that increase SMN protein in various cellular contexts. In this study, a novel compound was identified that increased SMN protein levels in vivo and ameliorated the disease phenotype in severe and intermediate mouse models of SMA.
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220
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Ratni H, Mueller L, Ebeling M. Rewriting the (tran)script: Application to spinal muscular atrophy. PROGRESS IN MEDICINAL CHEMISTRY 2019; 58:119-156. [PMID: 30879473 DOI: 10.1016/bs.pmch.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Targeting RNA drastically expands our target space to therapeutically modulate numerous cellular processes implicated in human diseases. Of particular interest, drugging pre-mRNA splicing appears a very viable strategy; to control levels of splicing product by promoting the inclusion or exclusion of exons. After describing the concept of "splicing modulation", this chapter will cover the outstanding progress achieved in this field, by highlighting the breakthrough accomplished recently for the treatment of spinal muscular atrophy using two therapeutic modalities: splice switching oligonucleotides and small molecules. This review discusses the vital but feasible requirement for such drugs to deliver selectivity, and critical safety aspects are highlighted. Transformational medicines such as those developed to treat SMA are likely just the beginning of this story.
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Affiliation(s)
- Hasane Ratni
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Lutz Mueller
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Martin Ebeling
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
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221
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The power of combining phenotypic and target-focused drug discovery. Drug Discov Today 2019; 24:526-532. [DOI: 10.1016/j.drudis.2018.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/10/2018] [Accepted: 10/16/2018] [Indexed: 01/09/2023]
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222
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Application of induced pluripotent stem cells to primary immunodeficiency diseases. Exp Hematol 2019; 71:43-50. [PMID: 30664903 DOI: 10.1016/j.exphem.2019.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/12/2022]
Abstract
Primary immunodeficiency diseases (PIDs) are a heterogeneous group of rare immune disorders with genetic causes. Effective treatments using hematopoietic stem cells or pharmaceutical agents have been around for decades. However, for many patients, these treatment options are ineffective, partly because the rarity of these PIDs complicates the diagnosis and therapy. Induced pluripotent stem cells (iPSCs) offer a potential solution to these problems. The proliferative capacity of iPSCs allows for the preparation of a large, stable supply of hematopoietic cells with the same genome as the patient, allowing for new human cell models that can trace cellular abnormalities during the pathogenesis and lead to new drug discovery. PID models using patient iPSCs have been instrumental in identifying deviations in the development or function of several types of immune cells, revealing new molecular targets for experimental therapies. These models are only in their early stages and for the most part have recapitulated results from existing models using animals or primary cells. However, iPSC-based models are being used to study complex diseases of other organs, including those with multigenic causes, suggesting that advances in differentiation processes will expand iPSC-based models to complex PIDs as well.
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223
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Hinkle ER, Wiedner HJ, Black AJ, Giudice J. RNA processing in skeletal muscle biology and disease. Transcription 2019; 10:1-20. [PMID: 30556762 DOI: 10.1080/21541264.2018.1558677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.
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Affiliation(s)
- Emma R Hinkle
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Hannah J Wiedner
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Adam J Black
- b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Jimena Giudice
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA.,c McAllister Heart Institute , University of North Carolina , Chapel Hill , USA
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224
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Garner AL, Lorenz DA, Gallagher EE. A click chemistry assay to identify natural product ligands for pre-microRNAs. Methods Enzymol 2019; 623:85-99. [PMID: 31239059 PMCID: PMC6631307 DOI: 10.1016/bs.mie.2019.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite the great diversity of structure and function and relevance to human health, RNA remains an underexploited area of drug discovery. A major bottleneck toward this goal has been the identification of probes and drug leads that are specific for select RNAs and methods that will facilitate such discovery efforts. Our laboratory has recently developed an innovative approach for assaying RNA-small molecule interactions, catalytic enzyme-linked click chemistry assay or cat-ELCCA, which is a functional assay that takes advantage of the power of catalytic signal amplification combined with the selectivity and bioorthogonality of click chemistry. Importantly, through application of this platform assay technology to the challenging problem of identifying selective inhibitors of pre-microRNA maturation, we identified natural products as a potential source of such compounds. Herein we describe this methodology in addition to the downstream pipeline toward the discovery of natural product ligands for pre-microRNAs. Through cat-ELCCA, our goal is to discover novel ligands to facilitate our investigation of RNA recognition by small molecules.
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Affiliation(s)
- Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States.
| | - Daniel A Lorenz
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States
| | - Erin E Gallagher
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
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225
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Lin H, Li Q, Du Q, Wang O, Wang Z, Akert L, Carlson MA, Zhang C, Subramanian A, Zhang C, Lunning M, Li M, Lei Y. Integrated generation of induced pluripotent stem cells in a low-cost device. Biomaterials 2019; 189:23-36. [DOI: 10.1016/j.biomaterials.2018.10.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022]
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226
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Gidaro T, Servais L. Nusinersen treatment of spinal muscular atrophy: current knowledge and existing gaps. Dev Med Child Neurol 2019; 61:19-24. [PMID: 30221755 DOI: 10.1111/dmcn.14027] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/25/2018] [Indexed: 01/08/2023]
Abstract
Spinal muscular atrophy (SMA) is a recessive disorder caused by a mutation in the survival motor neuron 1 gene (SMN1); it affects 1 in 11 000 newborn infants. The most severe and most common form, type 1 SMA, is associated with early mortality in most cases and severe disability in survivors. Nusinersen, an antisense oligonucleotide, promotes production of full-length protein from the pseudogene SMN2. Nusinersen treatment prolongs survival of patients with type 1 SMA and allows motor milestone acquisition. Patients with type 2 SMA also show progress on different motor scales after nusinersen treatment. Nusinersen was recently approved by the European Medicines Agency and the US Food and Drug Administration; it is now reimbursed in several European countries and in the USA. In Australia, the transition from expanded access programme to commercial availability is coming soon. In New Zealand, an expanded access programme is opened, and in Canada price negotiation for the treatment is in progress. In this review we exemplify the clinical benefit of nusinersen in subgroups of patients with SMA. Nusinersen represents the first efficacious marked approved drug in type 1 and type 2 SMA. Different knowledge gaps, such as results in older patients, in patients with permanent ventilation, in patients with neonatal forms, or in patients after spinal fusion, still need to be addressed. WHAT THIS PAPER ADDS: Identifies gaps in knowledge about the efficacy of nusinersen in broader populations of patients with spinal muscular atrophy. Identifies open questions in populations of patients where proof of efficacy is available.
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Affiliation(s)
- Teresa Gidaro
- I-Motion - Pediatric Clinical Trials Department, Trousseau Hospital, Paris, France.,Institute of Myology, Pitié-Salpêtrière Hospital, Paris, France
| | - Laurent Servais
- I-Motion - Pediatric Clinical Trials Department, Trousseau Hospital, Paris, France.,Institute of Myology, Pitié-Salpêtrière Hospital, Paris, France.,CHU de Liège, Centre de référence des maladies Neuromusculaires, Liège, Belgium
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227
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Cheung AK, Hurley B, Kerrigan R, Shu L, Chin DN, Shen Y, O'Brien G, Sung MJ, Hou Y, Axford J, Cody E, Sun R, Fazal A, Fridrich C, Sanchez CC, Tomlinson RC, Jain M, Deng L, Hoffmaster K, Song C, Van Hoosear M, Shin Y, Servais R, Towler C, Hild M, Curtis D, Dietrich WF, Hamann LG, Briner K, Chen KS, Kobayashi D, Sivasankaran R, Dales NA. Discovery of Small Molecule Splicing Modulators of Survival Motor Neuron-2 (SMN2) for the Treatment of Spinal Muscular Atrophy (SMA). J Med Chem 2018; 61:11021-11036. [PMID: 30407821 DOI: 10.1021/acs.jmedchem.8b01291] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spinal muscular atrophy (SMA), a rare neuromuscular disorder, is the leading genetic cause of death in infants and toddlers. SMA is caused by the deletion or a loss of function mutation of the survival motor neuron 1 (SMN1) gene. In humans, a second closely related gene SMN2 exists; however it codes for a less stable SMN protein. In recent years, significant progress has been made toward disease modifying treatments for SMA by modulating SMN2 pre-mRNA splicing. Herein, we describe the discovery of LMI070/branaplam, a small molecule that stabilizes the interaction between the spliceosome and SMN2 pre-mRNA. Branaplam (1) originated from a high-throughput phenotypic screening hit, pyridazine 2, and evolved via multiparameter lead optimization. In a severe mouse SMA model, branaplam treatment increased full-length SMN RNA and protein levels, and extended survival. Currently, branaplam is in clinical studies for SMA.
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Affiliation(s)
- Atwood K Cheung
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Brian Hurley
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ryan Kerrigan
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lei Shu
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Donovan N Chin
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Yiping Shen
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Gary O'Brien
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Moo Je Sung
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ying Hou
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Jake Axford
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Emma Cody
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Robert Sun
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Aleem Fazal
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Cary Fridrich
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Carina C Sanchez
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ronald C Tomlinson
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Monish Jain
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lin Deng
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Keith Hoffmaster
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Cheng Song
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Mailin Van Hoosear
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Youngah Shin
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Rebecca Servais
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Christopher Towler
- Novartis Pharmaceuticals , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Marc Hild
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Daniel Curtis
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - William F Dietrich
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lawrence G Hamann
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Karin Briner
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Karen S Chen
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Dione Kobayashi
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Natalie A Dales
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
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228
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Poirier A, Weetall M, Heinig K, Bucheli F, Schoenlein K, Alsenz J, Bassett S, Ullah M, Senn C, Ratni H, Naryshkin N, Paushkin S, Mueller L. Risdiplam distributes and increases SMN protein in both the central nervous system and peripheral organs. Pharmacol Res Perspect 2018; 6:e00447. [PMID: 30519476 PMCID: PMC6262736 DOI: 10.1002/prp2.447] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/22/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a rare, inherited neuromuscular disease caused by deletion and/or mutation of the Survival of Motor Neuron 1 (SMN1) gene. A second gene, SMN2, produces low levels of functional SMN protein that are insufficient to fully compensate for the lack of SMN1. Risdiplam (RG7916; RO7034067) is an orally administered, small-molecule SMN2 pre-mRNA splicing modifier that distributes into the central nervous system (CNS) and peripheral tissues. To further explore risdiplam distribution, we assessed in vitro characteristics and in vivo drug levels and effect of risdiplam on SMN protein expression in different tissues in animal models. Total drug levels were similar in plasma, muscle, and brain of mice (n = 90), rats (n = 148), and monkeys (n = 24). As expected mechanistically based on its high passive permeability and not being a human multidrug resistance protein 1 substrate, risdiplam CSF levels reflected free compound concentration in plasma in monkeys. Tissue distribution remained unchanged when monkeys received risdiplam once daily for 39 weeks. A parallel dose-dependent increase in SMN protein levels was seen in CNS and peripheral tissues in two SMA mouse models dosed with risdiplam. These in vitro and in vivo preclinical data strongly suggest that functional SMN protein increases seen in patients' blood following risdiplam treatment should reflect similar increases in functional SMN protein in the CNS, muscle, and other peripheral tissues.
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Affiliation(s)
- Agnès Poirier
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | | | - Katja Heinig
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | - Franz Bucheli
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | - Kerstin Schoenlein
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | - Jochem Alsenz
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | - Simon Bassett
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | - Mohammed Ullah
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | - Claudia Senn
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | - Hasane Ratni
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
| | | | | | - Lutz Mueller
- Roche Pharma Research and Early DevelopmentRoche Innovation CenterBaselSwitzerland
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Li Y, Disney MD. Precise Small Molecule Degradation of a Noncoding RNA Identifies Cellular Binding Sites and Modulates an Oncogenic Phenotype. ACS Chem Biol 2018; 13:3065-3071. [PMID: 30375843 DOI: 10.1021/acschembio.8b00827] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we describe the precise cellular destruction of an oncogenic noncoding RNA with a small molecule-bleomycin A5 conjugate, affording reversal of phenotype and a facile method to map the cellular binding sites of a small molecule. In particular, bleomycin A5 was coupled to a small molecule that selectively binds the microRNA-96 hairpin precursor (pri-miR-96). By coupling of bleomycin A5's free amine to the RNA binder, its affinity for binding to pri-miR-96 is >100-fold stronger than to DNA and the compound selectively cleaves pri-miR-96 in triple negative breast cancer (TNBC) cells. Indeed, selective cleavage of pri-miR-96 enhanced expression of FOXO1 protein, a pro-apoptotic transcription factor that miR-96 silences, and triggered apoptosis in TNBC cells. No effects were observed in healthy breast epithelial cells. Thus, conjugation of a small molecule to bleomycin A5's free amine may provide programmable control over its cellular targets. Few approaches are available to define the binding sites of small molecules within cellular RNAs. Our targeted cleavage method provides such an approach that is straightforward to implement. That is, we determined experimentally the site cleaved within pri-miR-96 in vitro and in cells; these studies revealed that the site of cleavage is the precise site for which the small molecule cleaver was designed and in agreement with modeling. These studies demonstrate the potential of sequence-based design to provide bioactive compounds that precisely recognize and cleave RNA in cells.
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Affiliation(s)
- Yue Li
- The Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- The Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
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230
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Sturm S, Günther A, Jaber B, Jordan P, Al Kotbi N, Parkar N, Cleary Y, Frances N, Bergauer T, Heinig K, Kletzl H, Marquet A, Ratni H, Poirier A, Müller L, Czech C, Khwaja O. A phase 1 healthy male volunteer single escalating dose study of the pharmacokinetics and pharmacodynamics of risdiplam (RG7916, RO7034067), a SMN2 splicing modifier. Br J Clin Pharmacol 2018; 85:181-193. [PMID: 30302786 DOI: 10.1111/bcp.13786] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/29/2018] [Accepted: 09/09/2018] [Indexed: 12/22/2022] Open
Abstract
AIMS Risdiplam (RG7916, RO7034067) is an orally administered, centrally and peripherally distributed, survival of motor neuron 2 (SMN2) mRNA splicing modifier for the treatment of spinal muscular atrophy (SMA). The objectives of this entry-into-human study were to assess the safety, tolerability, pharmacokinetics (PK) and pharmacodynamics of risdiplam, and the effect of the strong CYP3A inhibitor itraconazole on the PK of risdiplam in healthy male volunteers. METHODS Part 1 had a randomized, double-blind, adaptive design with 25 subjects receiving single ascending oral doses of risdiplam (ranging from 0.6-18.0 mg, n = 18) or placebo (n = 7). A Bayesian framework was applied to estimate risdiplam's effect on SMN2 mRNA. The effect of multiple doses of itraconazole on the PK of risdiplam was also assessed using a two-period cross-over design (n = 8). RESULTS Risdiplam in the fasted or fed state was well tolerated. Risdiplam exhibited linear PK over the dose range with a multi-phasic decline with a mean terminal half-life of 40-69 h. Food had no relevant effect, and itraconazole had only a minor effect on plasma PK indicating a low fraction of risdiplam metabolized by CYP3A. The highest tested dose of 18.0 mg risdiplam led to approximately 41% (95% confidence interval 27-55%) of the estimated maximum increase in SMN2 mRNA. CONCLUSIONS Risdiplam was well tolerated and proof of mechanism was demonstrated by the intended shift in SMN2 splicing towards full-length SMN2 mRNA. Based on these data, Phase 2/3 studies of risdiplam in patients with SMA are now ongoing.
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231
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Tizzano EF, Zafeiriou D. Prenatal aspects in spinal muscular atrophy: From early detection to early presymptomatic intervention. Eur J Paediatr Neurol 2018; 22:944-950. [PMID: 30219357 DOI: 10.1016/j.ejpn.2018.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/23/2018] [Accepted: 08/29/2018] [Indexed: 01/22/2023]
Abstract
With the recent advances in spinal muscular atrophy therapies, the complete scenario of standard of care and following up is changing not only in the clinical field with new phenotypes emerging but also with new expectations for patients, caregivers and health providers. The actual evidence indicates that early intervention and treatment is crucial for better response and prognosis. Knowledge of the prenatal and pre-symptomatic postnatal stages of the disease are becoming essential to consider the opportunities of timely diagnosis and to decide the earliest therapeutic intervention.
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Affiliation(s)
- Eduardo F Tizzano
- Department of Clinical and Molecular Genetics and Rare Diseases Unit and Medicine Genetics Group, VHIR, Hospital Valle Hebron, Barcelona, Spain; CIBERER, Barcelona, Spain.
| | - Dimitrios Zafeiriou
- 1st Department of Pediatrics, "Hippokratio" General Hospital, Aristotle University, Thessaloniki, Greece.
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232
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Abstract
Although we live in the remnants of an RNA world, the world of drug discovery and chemical probes is firmly protein-centric. Developing highly selective small molecules targeting RNA is often considered to be an insurmountable challenge. Our goal is to demystify the design of such compounds. In this review, we describe various approaches to design small molecules that target RNA from sequence and the application of these compounds in RNA biology, with a focus on inhibition of human RNA-protein complexes. We have developed a library-versus-library screening approach to define selective RNA-small-molecule binding partners and applied them to disease-causing RNAs, in particular noncoding oncogenic RNAs and expanded RNA repeats, to modulate their biology in cells and animals. We also describe the design of new types of small-molecule probes that could broadly decipher the mysteries of RNA in cells.
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Affiliation(s)
- Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458
| | - Brendan G Dwyer
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458
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233
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Kletzl H, Marquet A, Günther A, Tang W, Heuberger J, Groeneveld GJ, Birkhoff W, Mercuri E, Lochmüller H, Wood C, Fischer D, Gerlach I, Heinig K, Bugawan T, Dziadek S, Kinch R, Czech C, Khwaja O. The oral splicing modifier RG7800 increases full length survival of motor neuron 2 mRNA and survival of motor neuron protein: Results from trials in healthy adults and patients with spinal muscular atrophy. Neuromuscul Disord 2018; 29:21-29. [PMID: 30553700 DOI: 10.1016/j.nmd.2018.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 11/15/2022]
Abstract
Spinal muscular atrophy (SMA) is a rare genetic and progressively debilitating neuromuscular disease. It is the leading genetic cause of death among infants. In SMA, low levels of survival of motor neuron (SMN) protein lead to motor neuron death and muscle atrophy as the SMN protein is critical to motor neuron survival. SMA is caused by mutations in, or deletion of, the SMN1 gene. A second SMN gene, SMN2, produces only low levels of functional SMN protein due to alternative splicing which excludes exon 7 from most transcripts, generating truncated, rapidly degraded SMN protein. Patients with SMA rely on limited expression of functional SMN full-length protein from the SMN2 gene, but insufficient levels are generated. RG7800 is an oral, selective SMN2 splicing modifier designed to modulate alternative splicing of SMN2 to increase the levels of functional SMN protein. In two trials, oral administration of RG7800 increased in blood full-length SMN2 mRNA expression in healthy adults and SMN protein levels in SMA patients by up to two-fold, which is expected to provide clinical benefit.
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Affiliation(s)
- Heidemarie Kletzl
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland.
| | - Anne Marquet
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Andreas Günther
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Wakana Tang
- Research, Genomics & Oncology, Roche Molecular Systems, Inc., Pleasanton, USA
| | | | | | | | | | - Hanns Lochmüller
- Medical Center-University of Freiburg, Freiburg, Germany; Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK; Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada and Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Claire Wood
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Dirk Fischer
- Universitäts-Kinderspital beider Basel, Basel, Switzerland; University Clinic of Internal Medicine, Kantonsspital Baselland, Bruderholz, Switzerland
| | - Irene Gerlach
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Katja Heinig
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Teodorica Bugawan
- Research, Genomics & Oncology, Roche Molecular Systems, Inc., Pleasanton, USA
| | - Sebastian Dziadek
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Russell Kinch
- Roche Innovation Center, Hoffmann-La Roche Ltd., Welwyn, UK
| | - Christian Czech
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Omar Khwaja
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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234
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Soldner F, Jaenisch R. Stem Cells, Genome Editing, and the Path to Translational Medicine. Cell 2018; 175:615-632. [PMID: 30340033 PMCID: PMC6461399 DOI: 10.1016/j.cell.2018.09.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/31/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
Abstract
The derivation of human embryonic stem cells (hESCs) and the stunning discovery that somatic cells can be reprogrammed into human induced pluripotent stem cells (hiPSCs) holds the promise to revolutionize biomedical research and regenerative medicine. In this Review, we focus on disorders of the central nervous system and explore how advances in human pluripotent stem cells (hPSCs) coincide with evolutions in genome engineering and genomic technologies to provide realistic opportunities to tackle some of the most devastating complex disorders.
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Affiliation(s)
- Frank Soldner
- The Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA.
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235
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Reed UC, Zanoteli E. Therapeutic advances in 5q-linked spinal muscular atrophy. ARQUIVOS DE NEURO-PSIQUIATRIA 2018; 76:265-272. [PMID: 29742241 DOI: 10.1590/0004-282x20180011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/15/2017] [Indexed: 12/18/2022]
Abstract
Spinal muscular atrophy (SMA) is a severe and clinically-heterogeneous motor neuron disease caused, in most cases, by a homozygous mutation in the SMN1 gene. Regarding the age of onset and motor involvement, at least four distinct clinical phenotypes have been recognized. This clinical variability is, in part, related to the SMN2 copy number. By now, only supportive therapies have been available. However, promising specific therapies are currently being developed based on different mechanisms to increase the level of SMN protein; in particular, intrathecal antisense oligonucleotides that prevent the skipping of exon 7 during SMN2 transcription, and intravenous SMN1 insertion using viral vector. These therapeutic perspectives open a new era in the natural history of the disease. In this review, we intend to discuss the most recent and promising therapeutic strategies, with special consideration to the pathogenesis of the disease and the mechanisms of action of such therapies.
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Affiliation(s)
- Umbertina Conti Reed
- Departamento de Neurologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Edmar Zanoteli
- Departamento de Neurologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
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236
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Granatosky EA, DiPrimio N, Pickering JR, Stevens DC, Perlstein EO, Taylor RE. GEX1A, a Polyketide from Streptomyces chromofuscus, Corrects the Cellular Defects Associated with Niemann-Pick Type C1 in Human Fibroblasts. JOURNAL OF NATURAL PRODUCTS 2018; 81:2018-2025. [PMID: 30188717 PMCID: PMC6868502 DOI: 10.1021/acs.jnatprod.8b00314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report the first evidence of GEX1A, a polyketide known to modulate alternative pre-mRNA splicing, as a potential treatment for Niemann-Pick type C disease. GEX1A was isolated from its producing organism, Streptomyces chromofuscus, and screened in NPC1 mutant cells alongside several semisynthetic analogues. We found that GEX1A and analogues are capable of restoring cholesterol trafficking in NPC1 mutant fibroblasts, as well as altering the expression of NPC1 isoforms detected by Western blot. These results, along with the compound's favorable pharmacokinetic properties, highlight the potential of spliceosome-targeting scaffolds such as GEX1A for the treatment of genetic diseases.
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Affiliation(s)
- Eve A. Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | | | - Jarred R.E. Pickering
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - D. Cole Stevens
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | | | - Richard E. Taylor
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
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237
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Kim H, Schaniel C. Modeling Hematological Diseases and Cancer With Patient-Specific Induced Pluripotent Stem Cells. Front Immunol 2018; 9:2243. [PMID: 30323816 PMCID: PMC6172418 DOI: 10.3389/fimmu.2018.02243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
The advent of induced pluripotent stem cells (iPSCs) together with recent advances in genome editing, microphysiological systems, tissue engineering and xenograft models present new opportunities for the investigation of hematological diseases and cancer in a patient-specific context. Here we review the progress in the field and discuss the advantages, limitations, and challenges of iPSC-based malignancy modeling. We will also discuss the use of iPSCs and its derivatives as cellular sources for drug target identification, drug development and evaluation of pharmacological responses.
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Affiliation(s)
- Huensuk Kim
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christoph Schaniel
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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238
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Neueder A, Dumas AA, Benjamin AC, Bates GP. Regulatory mechanisms of incomplete huntingtin mRNA splicing. Nat Commun 2018; 9:3955. [PMID: 30262848 PMCID: PMC6160442 DOI: 10.1038/s41467-018-06281-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/13/2018] [Indexed: 11/09/2022] Open
Abstract
Huntington’s disease is caused by a CAG repeat expansion in exon 1 of the HTT gene. We have previously shown that exon 1 HTT does not always splice to exon 2 producing a small transcript (HTTexon1) that encodes the highly pathogenic exon 1 HTT protein. The mechanisms by which this incomplete splicing occurs are unknown. Here, we have generated a minigene system that recapitulates the CAG repeat-length dependence of HTTexon1 production, and has allowed us to define the regions of intron 1 necessary for incomplete splicing. We show that manipulation of the expression levels of the splicing factor SRSF6, predicted to bind CAG repeats, modulates this aberrant splicing event and also demonstrate that RNA polymerase II transcription speed regulates the levels of HTTexon1 production. Understanding the mechanisms by which this pathogenic exon 1 HTT is generated may provide the basis for the development of strategies to prevent its production. Incomplete splicing of HTT results in the production of the highly pathogenic exon 1 HTT protein. Here the authors identify the necessary intronic regions and the underlying mechanisms that contribute to this process.
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Affiliation(s)
- Andreas Neueder
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease and Dementia Research Institute, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK. .,Department of Neurology, Ulm University, Ulm, 89081, Germany.
| | - Anaelle A Dumas
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease and Dementia Research Institute, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Agnesska C Benjamin
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease and Dementia Research Institute, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Gillian P Bates
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease and Dementia Research Institute, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK.
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240
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Biliouris K, Gaitonde P, Yin W, Norris DA, Wang Y, Henry S, Fey R, Nestorov I, Schmidt S, Rogge M, Lesko LJ, Trame MN. A Semi-Mechanistic Population Pharmacokinetic Model of Nusinersen: An Antisense Oligonucleotide for the Treatment of Spinal Muscular Atrophy. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2018; 7:581-592. [PMID: 30043511 PMCID: PMC6157691 DOI: 10.1002/psp4.12323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/06/2018] [Indexed: 01/21/2023]
Abstract
A pharmacokinetic (PK) model was developed for nusinersen, an antisense oligonucleotide (ASO) that is the first approved treatment for spinal muscular atrophy (SMA). The model was built with data from 92 nonhuman primates (NHPs) following intrathecal doses (0.3–7 mg) and characterized the PK in cerebrospinal fluid (CSF), plasma, total spinal cord, brain, and pons. The estimated volumes were 13.6, 937, 4.5, 53.8, and 2.11 mL, respectively. Global sensitivity analysis demonstrated that the CSF‐to‐plasma drug distribution rate (0.09 hour−1) is a major determinant of the maximum nusinersen concentration in central nervous system (CNS) tissues. Physiological age‐based and body weight‐based allometric scaling was implemented with exponent values of −0.08 and 1 for the rate constants and the volume of distribution, respectively. Simulations of the scaled model were in agreement with clinical observations from 52 pediatric phase I PK profiles. The developed model can be used to guide the design of clinical trials with ASOs.
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Affiliation(s)
- Konstantinos Biliouris
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Puneet Gaitonde
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Wei Yin
- Biogen Idec, Cambridge, Massachusetts, USA
| | | | - Yanfeng Wang
- Ionis Pharmaceuticals Inc., Carlsbad, California, USA
| | - Scott Henry
- Ionis Pharmaceuticals Inc., Carlsbad, California, USA
| | - Robert Fey
- Ionis Pharmaceuticals Inc., Carlsbad, California, USA
| | | | - Stephan Schmidt
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Mark Rogge
- Biogen Idec, Cambridge, Massachusetts, USA
| | - Lawrence J Lesko
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Mirjam N Trame
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, Florida, USA
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241
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A new biomarker candidate for spinal muscular atrophy: Identification of a peripheral blood cell population capable of monitoring the level of survival motor neuron protein. PLoS One 2018; 13:e0201764. [PMID: 30102724 PMCID: PMC6089418 DOI: 10.1371/journal.pone.0201764] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/20/2018] [Indexed: 01/01/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a severe genetic neuromuscular disorder caused by insufficiency of functional survival motor neuron (SMN) protein. Several clinical trials have been conducted with the aim of upregulating the expression of the SMN protein in SMA patients. In order to evaluate the efficiency of these SMN-targeted approaches, it has become necessary to verify SMN protein levels in the cells of SMA patients. Accordingly, we have developed a method allowing the evaluation of the functional SMN protein with < 1.5 mL of peripheral blood using imaging flow cytometry. The expression of SMN protein in CD3+, CD19+, and CD33++ cells obtained from SMA patients, was significantly reduced compared with that in cells from control subjects. In spot analysis of CD33++ cells, the intensities of SMN spots were significantly reduced in SMA subjects, when compared with that in controls. Therefore, SMN spots implied the presence of functional SMN protein in the cell nucleus. To our knowledge, our results are the first to demonstrate the presence of functional SMN protein in freshly isolated peripheral blood cells. We anticipate that SMN spot analysis will become the primary endpoint assay for the evaluation and monitoring of therapeutic intervention, with SMN serving as a reliable biomarker of therapeutic efficacy in SMA patients.
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Abstract
Autosomal-recessive proximal spinal muscular atrophy (Werdnig-Hoffmann, Kugelberg-Welander) is caused by mutation of the SMN1 gene, and the clinical severity correlates with the number of copies of a nearly identical gene, SMN2. The SMN protein plays a critical role in spliceosome assembly and may have other cellular functions, such as mRNA transport. Cell culture and animal models have helped to define the disease mechanism and to identify targets for therapeutic intervention. The main focus for developing treatment has been to increase SMN levels, and accomplishing this with small molecules, oligonucleotides, and gene replacement has been quite. An oligonucleotide, nusinersen, was recently approved for treatment in patients, and confirmatory studies of other agents are now under way.
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Affiliation(s)
- Eveline S Arnold
- Neurogenetics Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States.
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Maretina MA, Zheleznyakova GY, Lanko KM, Egorova AA, Baranov VS, Kiselev AV. Molecular Factors Involved in Spinal Muscular Atrophy Pathways as Possible Disease-modifying Candidates. Curr Genomics 2018; 19:339-355. [PMID: 30065610 PMCID: PMC6030859 DOI: 10.2174/1389202919666180101154916] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by mutations in the SMN1 gene. Being a monogenic disease, it is characterized by high clinical heterogeneity. Variations in penetrance and severity of symptoms, as well as clinical discrepancies between affected family members can result from modifier genes influence on disease manifestation. SMN2 gene copy number is known to be the main phenotype modifier and there is growing evidence of additional factors contributing to SMA severity. Potential modifiers of spinal muscular atrophy can be found among the wide variety of different factors, such as multiple proteins interacting with SMN or promoting motor neuron survival, epigenetic modifications, transcriptional or splicing factors influencing SMN2 expression. Study of these factors enables to reveal mechanisms underlying SMA pathology and can have pronounced clinical application.
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Affiliation(s)
- Marianna A. Maretina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
- Saint Petersburg State University, Universitetskaya emb. 7/9, 199034Saint Petersburg, Russia
| | - Galina Y. Zheleznyakova
- Department of Clinical Neuroscience, Karolinska Institutet, Karolinska Universitetssjukhuset, 171 76 Stockholm, Sweden
| | - Kristina M. Lanko
- Saint Petersburg State Institute of Technology, Moskovsky prospect, 26, Saint Petersburg190013, Russia
| | - Anna A. Egorova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
| | - Vladislav S. Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
- Saint Petersburg State University, Universitetskaya emb. 7/9, 199034Saint Petersburg, Russia
| | - Anton V. Kiselev
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
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Ratni H, Ebeling M, Baird J, Bendels S, Bylund J, Chen KS, Denk N, Feng Z, Green L, Guerard M, Jablonski P, Jacobsen B, Khwaja O, Kletzl H, Ko CP, Kustermann S, Marquet A, Metzger F, Mueller B, Naryshkin NA, Paushkin SV, Pinard E, Poirier A, Reutlinger M, Weetall M, Zeller A, Zhao X, Mueller L. Discovery of Risdiplam, a Selective Survival of Motor Neuron-2 ( SMN2) Gene Splicing Modifier for the Treatment of Spinal Muscular Atrophy (SMA). J Med Chem 2018; 61:6501-6517. [PMID: 30044619 DOI: 10.1021/acs.jmedchem.8b00741] [Citation(s) in RCA: 336] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SMA is an inherited disease that leads to loss of motor function and ambulation and a reduced life expectancy. We have been working to develop orally administrated, systemically distributed small molecules to increase levels of functional SMN protein. Compound 2 was the first SMN2 splicing modifier tested in clinical trials in healthy volunteers and SMA patients. It was safe and well tolerated and increased SMN protein levels up to 2-fold in patients. Nevertheless, its development was stopped as a precautionary measure because retinal toxicity was observed in cynomolgus monkeys after chronic daily oral dosing (39 weeks) at exposures in excess of those investigated in patients. Herein, we describe the discovery of 1 (risdiplam, RG7916, RO7034067) that focused on thorough pharmacology, DMPK and safety characterization and optimization. This compound is undergoing pivotal clinical trials and is a promising medicine for the treatment of patients in all ages and stages with SMA.
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Affiliation(s)
- Hasane Ratni
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Martin Ebeling
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - John Baird
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Stefanie Bendels
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Johan Bylund
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Karen S Chen
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Nora Denk
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Zhihua Feng
- Section of Neurobiology, Department of Biological Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Luke Green
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Melanie Guerard
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Philippe Jablonski
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Bjoern Jacobsen
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Omar Khwaja
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Heidemarie Kletzl
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Chien-Ping Ko
- Section of Neurobiology, Department of Biological Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Stefan Kustermann
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Anne Marquet
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Friedrich Metzger
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Barbara Mueller
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Nikolai A Naryshkin
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Sergey V Paushkin
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Emmanuel Pinard
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Agnès Poirier
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Michael Reutlinger
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Marla Weetall
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Andreas Zeller
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Xin Zhao
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Lutz Mueller
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development , Roche Innovation Center Basel , Grenzacherstrasse 124 , 4070 Basel , Switzerland
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245
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Furlanis E, Scheiffele P. Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing. Annu Rev Cell Dev Biol 2018; 34:451-469. [PMID: 30028642 DOI: 10.1146/annurev-cellbio-100617-062826] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Posttranscriptional mechanisms provide powerful means to expand the coding power of genomes. In nervous systems, alternative splicing has emerged as a fundamental mechanism not only for the diversification of protein isoforms but also for the spatiotemporal control of transcripts. Thus, alternative splicing programs play instructive roles in the development of neuronal cell type-specific properties, neuronal growth, self-recognition, synapse specification, and neuronal network function. Here we discuss the most recent genome-wide efforts on mapping RNA codes and RNA-binding proteins for neuronal alternative splicing regulation. We illustrate how alternative splicing shapes key steps of neuronal development, neuronal maturation, and synaptic properties. Finally, we highlight efforts to dissect the spatiotemporal dynamics of alternative splicing and their potential contribution to neuronal plasticity and the mature nervous system.
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246
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Chen KG, Mallon BS, Park K, Robey PG, McKay RDG, Gottesman MM, Zheng W. Pluripotent Stem Cell Platforms for Drug Discovery. Trends Mol Med 2018; 24:805-820. [PMID: 30006147 DOI: 10.1016/j.molmed.2018.06.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Use of human pluripotent stem cells (hPSCs) and their differentiated derivatives have led to recent proof-of-principle drug discoveries, defining a pathway to the implementation of hPSC-based drug discovery (hPDD). Current hPDD strategies, however, have inevitable conceptual biases and technological limitations, including the dimensionality of cell-culture methods, cell maturity and functionality, experimental variability, and data reproducibility. In this review, we dissect representative hPDD systems via analysis of hPSC-based 2D-monolayers, 3D culture, and organoids. We discuss mechanisms of drug discovery and drug repurposing, and roles of membrane drug transporters in tissue maturation and hPDD using the example of drugs that target various mutations of CFTR, the cystic fibrosis transmembrane conductance regulator gene, in patients with cystic fibrosis.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Barbara S Mallon
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyeyoon Park
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela G Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald D G McKay
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Michael M Gottesman
- The Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
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247
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Sumner CJ, Crawford TO. Two breakthrough gene-targeted treatments for spinal muscular atrophy: challenges remain. J Clin Invest 2018; 128:3219-3227. [PMID: 29985170 DOI: 10.1172/jci121658] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The motor neuron disease spinal muscular atrophy (SMA) is caused by recessive, loss-of-function mutations of the survival motor neuron 1 gene (SMN1). Alone, such mutations are embryonically lethal, but SMA patients retain a paralog gene, SMN2, that undergoes alternative pre-mRNA splicing, producing low levels of SMN protein. By mechanisms that are not well understood, reduced expression of the ubiquitously expressed SMN protein causes an early-onset motor neuron disease that often results in infantile or childhood mortality. Recently, striking clinical improvements have resulted from two novel treatment strategies to increase SMN protein by (a) modulating the splicing of existing SMN2 pre-mRNAs using antisense oligonucleotides, and (b) transducing motor neurons with self-complementary adeno-associated virus 9 (scAAV9) expressing exogenous SMN1 cDNA. We review the recently published clinical trial results and discuss the differing administration, tissue targeting, and potential toxicities of these two therapies. We also focus on the challenges that remain, emphasizing the many clinical and biologic questions that remain open. Answers to these questions will enable further optimization of these remarkable SMA treatments as well as provide insights that may well be useful in application of these therapeutic platforms to other diseases.
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Affiliation(s)
| | - Thomas O Crawford
- Department of Neurology.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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248
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Donlic A, Hargrove AE. Targeting RNA in mammalian systems with small molecules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1477. [PMID: 29726113 PMCID: PMC6002909 DOI: 10.1002/wrna.1477] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]
Abstract
The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina
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249
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Velagapudi SP, Costales MG, Vummidi BR, Nakai Y, Angelbello AJ, Tran T, Haniff HS, Matsumoto Y, Wang ZF, Chatterjee AK, Childs-Disney JL, Disney MD. Approved Anti-cancer Drugs Target Oncogenic Non-coding RNAs. Cell Chem Biol 2018; 25:1086-1094.e7. [PMID: 30251629 DOI: 10.1016/j.chembiol.2018.05.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/03/2018] [Accepted: 05/18/2018] [Indexed: 12/14/2022]
Abstract
Potential RNA drug targets for small molecules are found throughout the human transcriptome, yet small molecules known to elicit a pharmacological response by directly targeting RNA are limited to antibacterials. Herein, we describe AbsorbArray, a small molecule microarray-based approach that allows for unmodified compounds, including FDA-approved drugs, to be probed for binding to RNA motif libraries in a massively parallel format. Several drug classes bind RNA including kinase and topoisomerase inhibitors. The latter avidly bound the motif found in the Dicer site of oncogenic microRNA (miR)-21 and inhibited its processing both in vitro and in cells. The most potent compound de-repressed a downstream protein target and inhibited a miR-21-mediated invasive phenotype. The compound's activity was ablated upon overexpression of pre-miR-21. Target validation via chemical crosslinking and isolation by pull-down showed direct engagement of pre-miR-21 by the small molecule in cells, demonstrating that RNAs should indeed be considered druggable.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew G Costales
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Balayeshwanth R Vummidi
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yoshio Nakai
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Tuan Tran
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yasumasa Matsumoto
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Zi Fu Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Arnab K Chatterjee
- California Institute for Biomedical Research (CALIBR), 11119 North Torrey Pines Road, Suite 100, La Jolla, CA 92037, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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250
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Scoto M, Finkel R, Mercuri E, Muntoni F. Genetic therapies for inherited neuromuscular disorders. THE LANCET CHILD & ADOLESCENT HEALTH 2018; 2:600-609. [PMID: 30119719 DOI: 10.1016/s2352-4642(18)30140-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/15/2023]
Abstract
Inherited neuromuscular disorders encompass a broad group of genetic conditions, and the discovery of these underlying genes has expanded greatly in the past three decades. The discovery of such genes has enabled more precise diagnosis of these disorders and the development of specific therapeutic approaches that target the genetic basis and pathophysiological pathways. Such translational research has led to the approval of two genetic therapies by the US Food and Drug Administration: eteplirsen for Duchenne muscular dystrophy and nusinersen for spinal muscular atrophy, which are both antisense oligonucleotides that modify pre-mRNA splicing. In this Review we aim to discuss new genetic therapies and ongoing clinical trials for Duchenne muscular dystrophy, spinal muscular atrophy, and other less common childhood neuromuscular disorders.
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Affiliation(s)
- Mariacristina Scoto
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Richard Finkel
- Division of Pediatric Neurology, Nemours Children's Hospital, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Eugenio Mercuri
- Pediatric Neurology and Centro Nemo, IRCSS Fondazione Policlinico Gemelli, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, UK; National Institute for Health Research Great Ormond Street Hospital Biomedical Research Centre, London, UK.
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