1
|
Ottesen EW, Singh NN, Seo J, Singh RN. U1 snRNA interactions with deep intronic sequences regulate splicing of multiple exons of spinal muscular atrophy genes. Front Neurosci 2024; 18:1412893. [PMID: 39086841 PMCID: PMC11289892 DOI: 10.3389/fnins.2024.1412893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction The U1 small nuclear RNA (snRNA) forms ribonucleoprotein particles (RNPs) such as U1 snRNP and U1-TAF15 snRNP. U1 snRNP is one of the most studied RNPs due to its critical role in pre-mRNA splicing in defining the 5' splice site (5'ss) of every exon through direct interactions with sequences at exon/intron junctions. Recent reports support the role of U1 snRNP in all steps of transcription, namely initiation, elongation, and termination. Functions of U1-TAF15 snRNP are less understood, though it associates with the transcription machinery and may modulate pre-mRNA splicing by interacting with the 5'ss and/or 5'ss-like sequences within the pre-mRNA. An anti-U1 antisense oligonucleotide (ASO) that sequesters the 5' end of U1 snRNA inhibits the functions of U1 snRNP, including transcription and splicing. However, it is not known if the inhibition of U1 snRNP influences post-transcriptional regulation of pre-mRNA splicing through deep intronic sequences. Methods We examined the effect of an anti-U1 ASO that sequesters the 5' end of U1 snRNA on transcription and splicing of all internal exons of the spinal muscular atrophy (SMA) genes, SMN1 and SMN2. Our study was enabled by the employment of a multi-exon-skipping detection assay (MESDA) that discriminates against prematurely terminated transcripts. We employed an SMN2 super minigene to determine if anti-U1 ASO differently affects splicing in the context of truncated introns. Results We observed substantial skipping of multiple internal exons of SMN1 and SMN2 triggered by anti-U1 treatment. Suggesting a role for U1 snRNP in interacting with deep intronic sequences, early exons of the SMN2 super minigene with truncated introns were resistant to anti-U1 induced skipping. Consistently, overexpression of engineered U1 snRNAs targeting the 5'ss of early SMN1 and SMN2 exons did not prevent exon skipping caused by anti-U1 treatment. Discussion Our results uncover a unique role of the U1 snRNA-associated RNPs in splicing regulation executed through deep intronic sequences. Findings are significant for developing novel therapies for SMA based on deep intronic targets.
Collapse
Affiliation(s)
| | | | | | - Ravindra N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| |
Collapse
|
2
|
Leckie J, Yokota T. Potential of Cell-Penetrating Peptide-Conjugated Antisense Oligonucleotides for the Treatment of SMA. Molecules 2024; 29:2658. [PMID: 38893532 PMCID: PMC11173757 DOI: 10.3390/molecules29112658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder that is caused by mutations in the survival motor neuron 1 (SMN1) gene, hindering the production of functional survival motor neuron (SMN) proteins. Antisense oligonucleotides (ASOs), a versatile DNA-like drug, are adept at binding to target RNA to prevent translation or promote alternative splicing. Nusinersen is an FDA-approved ASO for the treatment of SMA. It effectively promotes alternative splicing in pre-mRNA transcribed from the SMN2 gene, an analog of the SMN1 gene, to produce a greater amount of full-length SMN protein, to compensate for the loss of functional protein translated from SMN1. Despite its efficacy in ameliorating SMA symptoms, the cellular uptake of these ASOs is suboptimal, and their inability to penetrate the CNS necessitates invasive lumbar punctures. Cell-penetrating peptides (CPPs), which can be conjugated to ASOs, represent a promising approach to improve the efficiency of these treatments for SMA and have the potential to transverse the blood-brain barrier to circumvent the need for intrusive intrathecal injections and their associated adverse effects. This review provides a comprehensive analysis of ASO therapies, their application for the treatment of SMA, and the encouraging potential of CPPs as delivery systems to improve ASO uptake and overall efficiency.
Collapse
Affiliation(s)
- Jamie Leckie
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Sciences Research, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
3
|
Luo D, Ottesen EW, Lee JH, Singh RN. Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. Sci Rep 2024; 14:10442. [PMID: 38714739 PMCID: PMC11076517 DOI: 10.1038/s41598-024-60593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/25/2024] [Indexed: 05/10/2024] Open
Abstract
Spinal muscular atrophy (SMA) genes, SMN1 and SMN2 (hereinafter referred to as SMN1/2), produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. C2A-2B-3-4 is a universally and abundantly expressed circRNA of SMN1/2. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/2. These findings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, and expands our understanding of functions of SMN1/2 genes.
Collapse
Affiliation(s)
- Diou Luo
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Eric W Ottesen
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ji Heon Lee
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA.
| |
Collapse
|
4
|
Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements. Nat Commun 2024; 15:3839. [PMID: 38714659 PMCID: PMC11076525 DOI: 10.1038/s41467-024-47140-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/16/2024] [Indexed: 05/10/2024] Open
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is hampered by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically inactive CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identifies not only known SREs but also a previously unknown distal intronic SRE, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
Collapse
Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Flagship Pioneering, Cambridge, MA, 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Aperture Therapeutics, Inc., San Carlos, CA, 94070, USA
| | - Lekha V Yesantharao
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
| |
Collapse
|
5
|
Wang N, Jiao K, He J, Zhu B, Cheng N, Sun J, Chen L, Chen W, Gong L, Qiao K, Xi J, Wu Q, Zhao C, Zhu W. Diagnosis of Challenging Spinal Muscular Atrophy Cases with Long-Read Sequencing. J Mol Diagn 2024; 26:364-373. [PMID: 38490302 DOI: 10.1016/j.jmoldx.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/17/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder primarily caused by the deletion or mutation of the survival motor neuron 1 (SMN1) gene. This study assesses the diagnostic potential of long-read sequencing (LRS) in three patients with SMA. For Patient 1, who has a heterozygous SMN1 deletion, LRS unveiled a missense mutation in SMN1 exon 5. In Patient 2, an Alu/Alu-mediated rearrangement covering the SMN1 promoter and exon 1 was identified through a blend of multiplex ligation-dependent probe amplification, LRS, and PCR across the breakpoint. The third patient, born to a consanguineous family, bore four copies of hybrid SMN genes. LRS determined the genomic structures, indicating two distinct hybrids of SMN2 exon 7 and SMN1 exon 8. However, a discrepancy was found between the SMN1/SMN2 ratio interpretations by LRS (0:2) and multiplex ligation-dependent probe amplification (0:4), which suggested a limitation of LRS in SMA diagnosis. In conclusion, this newly adapted long PCR-based third-generation sequencing introduces an additional avenue for SMA diagnosis.
Collapse
Affiliation(s)
- Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Sun
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lan Chen
- Department of Neurology, Nantong First People's Hospital, Nantong, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Lingyun Gong
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kai Qiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qihan Wu
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, National Health Commission Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| |
Collapse
|
6
|
Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
Collapse
Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| |
Collapse
|
7
|
Ottesen EW, Seo J, Luo D, Singh NN, Singh RN. A super minigene with a short promoter and truncated introns recapitulates essential features of transcription and splicing regulation of the SMN1 and SMN2 genes. Nucleic Acids Res 2024; 52:3547-3571. [PMID: 38214229 DOI: 10.1093/nar/gkad1259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/19/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024] Open
Abstract
Here we report a Survival Motor Neuron 2 (SMN2) super minigene, SMN2Sup, encompassing its own promoter, all exons, their flanking intronic sequences and the entire 3'-untranslated region. We confirm that the pre-mRNA generated from SMN2Sup undergoes splicing to produce a translation-competent mRNA. We demonstrate that mRNA generated from SMN2Sup produces more SMN than an identical mRNA generated from a cDNA clone. We uncover that overexpression of SMN triggers skipping of exon 3 of SMN1/SMN2. We define the minimal promoter and regulatory elements associated with the initiation and elongation of transcription of SMN2. The shortened introns within SMN2Sup preserved the ability of camptothecin, a transcription elongation inhibitor, to induce skipping of exons 3 and 7 of SMN2. We show that intron 1-retained transcripts undergo nonsense-mediated decay. We demonstrate that splicing factor SRSF3 and DNA/RNA helicase DHX9 regulate splicing of multiple exons in the context of both SMN2Sup and endogenous SMN1/SMN2. Prevention of SMN2 exon 7 skipping has implications for the treatment of spinal muscular atrophy (SMA). We validate the utility of the super minigene in monitoring SMN levels upon splicing correction. Finally, we demonstrate how the super minigene could be employed to capture the cell type-specific effects of a pathogenic SMN1 mutation.
Collapse
Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Diou Luo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
8
|
Soufizadeh P, Mansouri V, Ahmadbeigi N. A review of animal models utilized in preclinical studies of approved gene therapy products: trends and insights. Lab Anim Res 2024; 40:17. [PMID: 38649954 PMCID: PMC11034049 DOI: 10.1186/s42826-024-00195-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 04/25/2024] Open
Abstract
Scientific progress heavily relies on rigorous research, adherence to scientific standards, and transparent reporting. Animal models play a crucial role in advancing biomedical research, especially in the field of gene therapy. Animal models are vital tools in preclinical research, allowing scientists to predict outcomes and understand complex biological processes. The selection of appropriate animal models is critical, considering factors such as physiological and pathophysiological similarities, availability, and ethical considerations. Animal models continue to be indispensable tools in preclinical gene therapy research. Advancements in genetic engineering and model selection have improved the fidelity and relevance of these models. As gene therapy research progresses, careful consideration of animal models and transparent reporting will contribute to the development of effective therapies for various genetic disorders and diseases. This comprehensive review explores the use of animal models in preclinical gene therapy studies for approved products up to September 2023. The study encompasses 47 approved gene therapy products, with a focus on preclinical trials. This comprehensive analysis serves as a valuable reference for researchers in the gene therapy field, aiding in the selection of suitable animal models for their preclinical investigations.
Collapse
Affiliation(s)
- Parham Soufizadeh
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Biomedical Research Institute, University of Tehran, Tehran, Iran
| | - Vahid Mansouri
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Naser Ahmadbeigi
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
9
|
Luo D, Ottesen E, Lee JH, Singh R. Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. RESEARCH SQUARE 2024:rs.3.rs-3818622. [PMID: 38464174 PMCID: PMC10925445 DOI: 10.21203/rs.3.rs-3818622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Spinal muscular atrophy (SMA) genes, SMN1 and SMN2, produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2. These fifindings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/SMN2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.
Collapse
|
10
|
Ottesen EW, Singh RN. Synergistic Effect of an Antisense Oligonucleotide and Small Molecule on Splicing Correction of the Spinal Muscular Atrophy Gene. Neurosci Insights 2024; 19:26331055241233596. [PMID: 38379891 PMCID: PMC10878212 DOI: 10.1177/26331055241233596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
Spinal muscular atrophy (SMA) is treated by increasing the level of Survival Motor Neuron (SMN) protein through correction of SMN2 exon 7 skipping or exogenous expression of SMN through gene therapy. Currently available therapies have multiple shortcomings, including poor body-wide distribution, invasive delivery, and potential negative consequences due to high doses needed for clinical efficacy. Here we test the effects of a combination treatment of a splice-correcting antisense oligonucleotide (ASO) Anti-N1 with the small compounds risdiplam and branaplam. We show that a low-dose treatment of Anti-N1 with either compound produces a synergistic effect on the inclusion of SMN2 exon 7 in SMA patient fibroblasts. Using RNA-Seq, we characterize the transcriptomes of cells treated with each compound as well as in combination. Although high doses of each individual treatment trigger widespread perturbations of the transcriptome, combination treatment of Anti-N1 with risdiplam and branaplam results in minimal disruption of gene expression. For individual genes targeted by the 3 compounds, we observe little to no additive effects of combination treatment. Overall, we conclude that the combination treatment of a splice-correcting ASO with small compounds represents a promising strategy for achieving a high level of SMN expression while minimizing the risk of off-target effects.
Collapse
Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| |
Collapse
|
11
|
Alves CRR, Ha LL, Yaworski R, Sutton ER, Lazzarotto CR, Christie KA, Reilly A, Beauvais A, Doll RM, de la Cruz D, Maguire CA, Swoboda KJ, Tsai SQ, Kothary R, Kleinstiver BP. Optimization of base editors for the functional correction of SMN2 as a treatment for spinal muscular atrophy. Nat Biomed Eng 2024; 8:118-131. [PMID: 38057426 PMCID: PMC10922509 DOI: 10.1038/s41551-023-01132-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 10/12/2023] [Indexed: 12/08/2023]
Abstract
Spinal muscular atrophy (SMA) is caused by mutations in SMN1. SMN2 is a paralogous gene with a C•G-to-T•A transition in exon 7, which causes this exon to be skipped in most SMN2 transcripts, and results in low levels of the protein survival motor neuron (SMN). Here we show, in fibroblasts derived from patients with SMA and in a mouse model of SMA that, irrespective of the mutations in SMN1, adenosine base editors can be optimized to target the SMN2 exon-7 mutation or nearby regulatory elements to restore the normal expression of SMN. After optimizing and testing more than 100 guide RNAs and base editors, and leveraging Cas9 variants with high editing fidelity that are tolerant of different protospacer-adjacent motifs, we achieved the reversion of the exon-7 mutation via an A•T-to-G•C edit in up to 99% of fibroblasts, with concomitant increases in the levels of the SMN2 exon-7 transcript and of SMN. Targeting the SMN2 exon-7 mutation via base editing or other CRISPR-based methods may provide long-lasting outcomes to patients with SMA.
Collapse
Affiliation(s)
- Christiano R R Alves
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Neurology, Harvard Medical School, Boston, MA, USA.
| | - Leillani L Ha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca Yaworski
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Emma R Sutton
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathleen A Christie
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Aoife Reilly
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Ariane Beauvais
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Roman M Doll
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Biosciences/Cancer Biology Program, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Demitri de la Cruz
- Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Casey A Maguire
- Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Kathryn J Swoboda
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rashmi Kothary
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
12
|
Schwartz S, Wu C, Kajitani N. RNA elements that control human papillomavirus mRNA splicing-targets for therapy? J Med Virol 2024; 96:e29473. [PMID: 38362929 DOI: 10.1002/jmv.29473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Human papillomaviruses (HPVs) cause more than 4.5% of all cancer in the world and more than half of these cases are attributed to human papillomavirus type 16 (HPV16). Prophylactic vaccines are available but antiviral drugs are not. Novel targets for therapy are urgently needed. Alternative RNA splicing is extensively used by HPVs to express all their genes and HPV16 is no exception. This process must function to perfection since mis-splicing could perturb the HPV gene expression program by altering mRNA levels or by generating dysfunctional mRNAs. Cis-acting RNA elements on the viral mRNAs and their cognate cellular trans-acting factors control papillomavirus RNA splicing. The precise but delicate nature of the splicing process renders splicing sensitive to interference. As such, papillomavirus RNA splicing is a potential target for therapy. Here we summarize our current understanding of cis-acting HPV16 RNA elements that control HPV16 mRNA splicing via cellular proteins and discuss how they may be exploited as targets for therapy to papillomavirus infections and cancer.
Collapse
Affiliation(s)
- Stefan Schwartz
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Chengjun Wu
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Naoko Kajitani
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
13
|
Olmos V, Thompson EN, Gogia N, Luttik K, Veeranki V, Ni L, Sim S, Chen K, Krause DS, Lim J. Dysregulation of alternative splicing in spinocerebellar ataxia type 1. Hum Mol Genet 2024; 33:138-149. [PMID: 37802886 PMCID: PMC10979408 DOI: 10.1093/hmg/ddad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
Spinocerebellar ataxia type 1 is caused by an expansion of the polyglutamine tract in ATAXIN-1. Ataxin-1 is broadly expressed throughout the brain and is involved in regulating gene expression. However, it is not yet known if mutant ataxin-1 can impact the regulation of alternative splicing events. We performed RNA sequencing in mouse models of spinocerebellar ataxia type 1 and identified that mutant ataxin-1 expression abnormally leads to diverse splicing events in the mouse cerebellum of spinocerebellar ataxia type 1. We found that the diverse splicing events occurred in a predominantly cell autonomous manner. A majority of the transcripts with misregulated alternative splicing events were previously unknown, thus allowing us to identify overall new biological pathways that are distinctive to those affected by differential gene expression in spinocerebellar ataxia type 1. We also provide evidence that the splicing factor Rbfox1 mediates the effect of mutant ataxin-1 on misregulated alternative splicing and that genetic manipulation of Rbfox1 expression modifies neurodegenerative phenotypes in a Drosophila model of spinocerebellar ataxia type 1 in vivo. Together, this study provides novel molecular mechanistic insight into the pathogenesis of spinocerebellar ataxia type 1 and identifies potential therapeutic strategies for spinocerebellar ataxia type 1.
Collapse
Affiliation(s)
- Victor Olmos
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Evrett N Thompson
- Department of Cell Biology, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Yale Stem Cell Center, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
| | - Neha Gogia
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Kimberly Luttik
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Vaishnavi Veeranki
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Luhan Ni
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Serena Sim
- Yale College, 433 Temple Street, New Haven, CT 06510, United States
| | - Kelly Chen
- Yale College, 433 Temple Street, New Haven, CT 06510, United States
| | - Diane S Krause
- Department of Cell Biology, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Yale Stem Cell Center, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Department of Pathology, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Department of Laboratory Medicine, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
| | - Janghoo Lim
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Yale Stem Cell Center, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Wu Tsai Institute, Yale School of Medicine, 100 College, New Haven, CT 06510, United States
| |
Collapse
|
14
|
Bhat MA, Dhaneshwar S. Neurodegenerative Diseases: New Hopes and Perspectives. Curr Mol Med 2024; 24:1004-1032. [PMID: 37691199 DOI: 10.2174/1566524023666230907093451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 09/12/2023]
Abstract
Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Huntington's disease, and Friedrich ataxia are all incurable neurodegenerative diseases defined by the continuous progressive loss of distinct neuronal subtypes. Despite their rising prevalence among the world's ageing population, fewer advances have been made in the concurrent massive efforts to develop newer drugs. Recently, there has been a shift in research focus towards the discovery of new therapeutic agents for neurodegenerative diseases. In this review, we have summarized the recently developed therapies and their status in the management of neurodegenerative diseases.
Collapse
Affiliation(s)
- Mohammad Aadil Bhat
- Amity Institute of Pharmacy, Lucknow, Amity University Uttar Pradesh, Noida, UP, India
| | - Suneela Dhaneshwar
- Amity Institute of Pharmacy, Amity University Maharashtra, Mumbai, Maharashtra, India
| |
Collapse
|
15
|
Nafchi NAM, Chilcott EM, Brown S, Fuller HR, Bowerman M, Yáñez-Muñoz RJ. Enhanced expression of the human Survival motor neuron 1 gene from a codon-optimised cDNA transgene in vitro and in vivo. Gene Ther 2023; 30:812-825. [PMID: 37322133 DOI: 10.1038/s41434-023-00406-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease particularly characterised by degeneration of ventral motor neurons. Survival motor neuron (SMN) 1 gene mutations cause SMA, and gene addition strategies to replace the faulty SMN1 copy are a therapeutic option. We have developed a novel, codon-optimised hSMN1 transgene and produced integration-proficient and integration-deficient lentiviral vectors with cytomegalovirus (CMV), human synapsin (hSYN) or human phosphoglycerate kinase (hPGK) promoters to determine the optimal expression cassette configuration. Integrating, CMV-driven and codon-optimised hSMN1 lentiviral vectors resulted in the highest production of functional SMN protein in vitro. Integration-deficient lentiviral vectors also led to significant expression of the optimised transgene and are expected to be safer than integrating vectors. Lentiviral delivery in culture led to activation of the DNA damage response, in particular elevating levels of phosphorylated ataxia telangiectasia mutated (pATM) and γH2AX, but the optimised hSMN1 transgene showed some protective effects. Neonatal delivery of adeno-associated viral vector (AAV9) vector encoding the optimised transgene to the Smn2B/- mouse model of SMA resulted in a significant increase of SMN protein levels in liver and spinal cord. This work shows the potential of a novel codon-optimised hSMN1 transgene as a therapeutic strategy for SMA.
Collapse
Affiliation(s)
- Neda A M Nafchi
- AGCTlab.org, Centre of Gene and Cell Therapy, Centre for Biomedical Sciences, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Ellie M Chilcott
- AGCTlab.org, Centre of Gene and Cell Therapy, Centre for Biomedical Sciences, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Sharon Brown
- School of Pharmacy and Bioengineering, Keele University, Staffordshire, ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, TORCH Building, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
| | - Heidi R Fuller
- School of Pharmacy and Bioengineering, Keele University, Staffordshire, ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, TORCH Building, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
| | - Melissa Bowerman
- Wolfson Centre for Inherited Neuromuscular Disease, TORCH Building, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
- School of Medicine, Keele University, Staffordshire, ST5 5BG, UK
| | - Rafael J Yáñez-Muñoz
- AGCTlab.org, Centre of Gene and Cell Therapy, Centre for Biomedical Sciences, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, UK.
| |
Collapse
|
16
|
Collotta D, Bertocchi I, Chiapello E, Collino M. Antisense oligonucleotides: a novel Frontier in pharmacological strategy. Front Pharmacol 2023; 14:1304342. [PMID: 38044945 PMCID: PMC10690781 DOI: 10.3389/fphar.2023.1304342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are short single stranded synthetic RNA or DNA molecules, whereas double-stranded RNA nucleotide sequences are called small interfering RNA (siRNA). ASOs bind to complementary nucleic acid sequences impacting the associated functions of the targeted nucleic acids. They represent an emerging class of drugs that, through a revolutionary mechanism of action, aim to directly regulate disease-causing genes and their variants, providing an alternative tool to traditional "protein-specific" therapies. The majority of the ASOs are designed to treat orphan genetic disorders that in most of the cases are seriously disabling and still lacking an adequate therapy. In order to translate ASOs into clinical success, constant technological advances have been instrumental in overcoming several pharmacological, toxicological and formulation limitations. Accordingly, chemical structures have been recently implemented and new bio-conjugation and nanocarriers formulation strategies explored. The aim of this work is to offer an overview of the antisense technology with a comparative analysis of the oligonucleotides approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA).
Collapse
Affiliation(s)
- D. Collotta
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
| | - I. Bertocchi
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi (NICO), University of Turin, Turin, Italy
| | - E. Chiapello
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
| | - M. Collino
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
| |
Collapse
|
17
|
Frezza V, Chellini L, Del Verme A, Paronetto MP. RNA Editing in Cancer Progression. Cancers (Basel) 2023; 15:5277. [PMID: 37958449 PMCID: PMC10648226 DOI: 10.3390/cancers15215277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Coding and noncoding RNA molecules play their roles in ensuring cell function and tissue homeostasis in an ordered and systematic fashion. RNA chemical modifications can occur both at bases and ribose sugar, and, similarly to DNA and histone modifications, can be written, erased, and recognized by the corresponding enzymes, thus modulating RNA activities and fine-tuning gene expression programs. RNA editing is one of the most prevalent and abundant forms of post-transcriptional RNA modification in normal physiological processes. By altering the sequences of mRNAs, it makes them different from the corresponding genomic template. Hence, edited mRNAs can produce protein isoforms that are functionally different from the corresponding genome-encoded variants. Abnormalities in regulatory enzymes and changes in RNA-modification patterns are closely associated with the occurrence and development of various human diseases, including cancer. To date, the roles played by RNA modifications in cancer are gathering increasing interest. In this review, we focus on the role of RNA editing in cancer transformation and provide a new perspective on its impact on tumorigenesis, by regulating cell proliferation, differentiation, invasion, migration, stemness, metabolism, and drug resistance.
Collapse
Affiliation(s)
- Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Arianna Del Verme
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| |
Collapse
|
18
|
Jiang T, Wang L, Tang L, Zeb A, Hou Y. Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 2023; 11:e16103. [PMID: 37744237 PMCID: PMC10512959 DOI: 10.7717/peerj.16103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
Collapse
Affiliation(s)
- Tao Jiang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University Army Medical University, Chongqing, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Liang Tang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Azhar Zeb
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Yanjun Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| |
Collapse
|
19
|
Huang J, Feng Y, Wang J, Huang S, Jin J, Xu L, Zhao C, Hua Y, Li X, Xu J, Li H, Zhang H, Zhang Y, Gao F, Mao S. Feasibility analysis of intrathecal administration strategy of nusinersen based on Cobb angle in children with spinal muscular atrophy. Eur J Paediatr Neurol 2023; 46:55-60. [PMID: 37453233 DOI: 10.1016/j.ejpn.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
AIM This retro-prospective observational study described the experience in lumbar puncture procedures in children with spinal muscular atrophy (SMA) with and without neuromuscular scoliosis in a single center. The technical feasibility of intrathecal nusinersen administration was the main limiting factor. STUDY DESIGN A total of 457 technically successful intrathecal injections based on a hierarchical strategy in Cobb angle were reviewed in 81 SMA children aged 0.75-13.5 years who were referred for nusinersen injections in our hospital from October 2019 to December 2022. RESULTS Under local anesthesia, conventional lumbar puncture was performed on 47 patients without spinal deformity (Cobb angle of 0-10°) and 20 patients with moderate scoliosis (Cobb angle of 10-50°). Ultrasound-assisted lumbar puncture was performed on 12 patients with moderate scoliosis but lordosis. A combination of ultrasound imaging and three-dimensional CT under sedation was performed in the remaining 14 patients with severe scoliosis (Cobb angle >50°). No severe complications were found. CONCLUSION Cobb angle is an important basis for intrathecal administration of nusinersen. It is feasible and suitable to carry out intrathecal nusinersen injection under ultrasound combined with three-dimensional CT imaging for children with severe scoliosis.
Collapse
Affiliation(s)
- Jinjin Huang
- Department of Anesthesiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yijie Feng
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Jia Wang
- Department of Pediatrics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Siyi Huang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Jianing Jin
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Lu Xu
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Congying Zhao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yi Hua
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Xiaoying Li
- Department of Ultrasonography, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Jingfang Xu
- Department of Orthopedics, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Haibing Li
- Department of Orthopedics, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Huan Zhang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yi Zhang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Feng Gao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Shanshan Mao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
| |
Collapse
|
20
|
Fortuna TR, Kour S, Chimata AV, Muiños-Bühl A, Anderson EN, Nelson Iv CH, Ward C, Chauhan O, O'Brien C, Rajasundaram D, Rajan DS, Wirth B, Singh A, Pandey UB. SMN regulates GEMIN5 expression and acts as a modifier of GEMIN5-mediated neurodegeneration. Acta Neuropathol 2023; 146:477-498. [PMID: 37369805 DOI: 10.1007/s00401-023-02607-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023]
Abstract
GEMIN5 is essential for core assembly of small nuclear Ribonucleoproteins (snRNPs), the building blocks of spliceosome formation. Loss-of-function mutations in GEMIN5 lead to a neurodevelopmental syndrome among patients presenting with developmental delay, motor dysfunction, and cerebellar atrophy by perturbing SMN complex protein expression and assembly. Currently, molecular determinants of GEMIN5-mediated disease have yet to be explored. Here, we identified SMN as a genetic suppressor of GEMIN5-mediated neurodegeneration in vivo. We discovered that an increase in SMN expression by either SMN gene therapy replacement or the antisense oligonucleotide (ASO), Nusinersen, significantly upregulated the endogenous levels of GEMIN5 in mammalian cells and mutant GEMIN5-derived iPSC neurons. Further, we identified a strong functional association between the expression patterns of SMN and GEMIN5 in patient Spinal Muscular Atrophy (SMA)-derived motor neurons harboring loss-of-function mutations in the SMN gene. Interestingly, SMN binds to the C-terminus of GEMIN5 and requires the Tudor domain for GEMIN5 binding and expression regulation. Finally, we show that SMN upregulation ameliorates defective snRNP biogenesis and alternative splicing defects caused by loss of GEMIN5 in iPSC neurons and in vivo. Collectively, these studies indicate that SMN acts as a regulator of GEMIN5 expression and neuropathologies.
Collapse
Affiliation(s)
- Tyler R Fortuna
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Anixa Muiños-Bühl
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Charlie H Nelson Iv
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caroline Ward
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Om Chauhan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Casey O'Brien
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Deepa S Rajan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
21
|
Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. Deep screening of proximal and distal splicing-regulatory elements in a native sequence context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554109. [PMID: 37662340 PMCID: PMC10473672 DOI: 10.1101/2023.08.21.554109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is impeded by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically dead CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identified not only known SREs, but also a novel distal intronic splicing enhancer, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
Collapse
Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Aperture Therapeutics, Inc., San Carlos, CA 94070, USA
| | - Lekha V. Yesantharao
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| |
Collapse
|
22
|
Nishio H, Niba ETE, Saito T, Okamoto K, Takeshima Y, Awano H. Spinal Muscular Atrophy: The Past, Present, and Future of Diagnosis and Treatment. Int J Mol Sci 2023; 24:11939. [PMID: 37569314 PMCID: PMC10418635 DOI: 10.3390/ijms241511939] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a lower motor neuron disease with autosomal recessive inheritance. The first cases of SMA were reported by Werdnig in 1891. Although the phenotypic variation of SMA led to controversy regarding the clinical entity of the disease, the genetic homogeneity of SMA was proved in 1990. Five years later, in 1995, the gene responsible for SMA, SMN1, was identified. Genetic testing of SMN1 has enabled precise epidemiological studies, revealing that SMA occurs in 1 of 10,000 to 20,000 live births and that more than 95% of affected patients are homozygous for SMN1 deletion. In 2016, nusinersen was the first drug approved for treatment of SMA in the United States. Two other drugs were subsequently approved: onasemnogene abeparvovec and risdiplam. Clinical trials with these drugs targeting patients with pre-symptomatic SMA (those who were diagnosed by genetic testing but showed no symptoms) revealed that such patients could achieve the milestones of independent sitting and/or walking. Following the great success of these trials, population-based newborn screening programs for SMA (more precisely, SMN1-deleted SMA) have been increasingly implemented worldwide. Early detection by newborn screening and early treatment with new drugs are expected to soon become the standards in the field of SMA.
Collapse
Affiliation(s)
- Hisahide Nishio
- Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan
| | - Emma Tabe Eko Niba
- Laboratory of Molecular and Biochemical Research, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Toshio Saito
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, 5-1-1 Toneyama, Toyonaka 560-8552, Japan;
| | - Kentaro Okamoto
- Department of Pediatrics, Ehime Prefectural Imabari Hospital, 4-5-5 Ishi-cho, Imabari 794-0006, Japan;
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo Medical University, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan;
| | - Hiroyuki Awano
- Organization for Research Initiative and Promotion, Research Initiative Center, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan;
| |
Collapse
|
23
|
Ottesen EW, Singh NN, Luo D, Kaas B, Gillette B, Seo J, Jorgensen H, Singh RN. Diverse targets of SMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy. Nucleic Acids Res 2023; 51:5948-5980. [PMID: 37026480 PMCID: PMC10325915 DOI: 10.1093/nar/gkad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Designing an RNA-interacting molecule that displays high therapeutic efficacy while retaining specificity within a broad concentration range remains a challenging task. Risdiplam is an FDA-approved small molecule for the treatment of spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. Branaplam is another small molecule which has undergone clinical trials. The therapeutic merit of both compounds is based on their ability to restore body-wide inclusion of Survival Motor Neuron 2 (SMN2) exon 7 upon oral administration. Here we compare the transcriptome-wide off-target effects of these compounds in SMA patient cells. We captured concentration-dependent compound-specific changes, including aberrant expression of genes associated with DNA replication, cell cycle, RNA metabolism, cell signaling and metabolic pathways. Both compounds triggered massive perturbations of splicing events, inducing off-target exon inclusion, exon skipping, intron retention, intron removal and alternative splice site usage. Our results of minigenes expressed in HeLa cells provide mechanistic insights into how these molecules targeted towards a single gene produce different off-target effects. We show the advantages of combined treatments with low doses of risdiplam and branaplam. Our findings are instructive for devising better dosing regimens as well as for developing the next generation of small molecule therapeutics aimed at splicing modulation.
Collapse
Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Diou Luo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Bailey Kaas
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Benjamin J Gillette
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Hannah J Jorgensen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
24
|
Lakhina Y, Boulis NM, Donsante A. Current and emerging targeted therapies for spinal muscular atrophy. Expert Rev Neurother 2023; 23:1189-1199. [PMID: 37843301 DOI: 10.1080/14737175.2023.2268276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION Spinal muscular atrophy (SMA) is a progressive neurodegenerative disorder caused by insufficiency or total absence of the survival motor neuron protein due to a mutation in the SMN1 gene. The copy number of its paralog, SMN2, influences disease onset and phenotype severity. Current therapeutic approaches include viral and non-viral modalities affecting gene expression. Regulatory-approved drugs Spinraza (Nusinersen), Zolgensma (Onasemnogene abeparvovec), and Evrysdi (Risdiplam) are still being investigated during clinical trials and show benefits in the long-term for symptomatic and pre-symptomatic patients. However, some ongoing interventions require repeated drug administration. AREAS COVERED In this review, the authors describe the existing therapy based on point of application, focusing on recent clinical trials of antisense oligonucleotides, viral gene therapy, and splice modulators and thepotential routes for correcting the mutation to provide therapeutic levels of SMN protein. EXPERT OPINION In the opinion of the authors, multiple treatment options for patients with SMA shifted the treatment paradigm from palliative supportive care to improvedmotor function, increased survival, and greater quality of life for such patients. They further believe that the future in SMA treatment development lies incombining existing treatment options, targeting aspects of the disease refractory to these treatments, and using gene editing technologies.
Collapse
Affiliation(s)
- Yuliya Lakhina
- Department of Neurosurgery, Emory University, Atlanta, USA
| | | | | |
Collapse
|
25
|
De Siqueira Carvalho AA, Tychon C, Servais L. Newborn screening for spinal muscular atrophy - what have we learned? Expert Rev Neurother 2023; 23:1005-1012. [PMID: 37635694 DOI: 10.1080/14737175.2023.2252179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
INTRODUCTION Over the last decade, the treatment of spinal muscular atrophy (SMA) has become a paradigm of the importance of early and accurate diagnosis and prompt treatment. Three different therapeutic approaches that aims to increase SMN protein are approved now by Food and Drug Administration (FDA) and European Medicines Agency (EMA) for treatment of SMA; their efficacies have been demonstrated in pivotal trials. AREAS COVERED The authors report on the two controlled studies and real-world evidence that have demonstrated that the treatment of patients pre-symptomatically ensures normal or only slightly sub-normal motor development in children who would otherwise develop a severe form of the disease. Furthermore, the authors highlight the several newborn screening (NBS) methods that are now available, all of which are based on real-time PCR, that reliably and robustly diagnose SMA except in subjects with disease caused by a point mutation. EXPERT OPINION Pre-symptomatic treatment of SMA has been clearly demonstrated to prevent the most severe forms of the disease. NBS constitutes more than a simple test and should be considered as a global process to accelerate treatment access and provide global management of patients and parents. Even though the cost of NBS is low and health economics studies have clearly demonstrated its value, the fear of identifying more patients than the system can treat is often reported in large middle-income countries.
Collapse
Affiliation(s)
| | - Cyril Tychon
- Neuromuscular Reference Center, Department of Paediatrics, University and University Hospital of Liege, Liege, Belgium
| | - Laurent Servais
- Neuromuscular Reference Center, Department of Paediatrics, University and University Hospital of Liege, Liege, Belgium
- MDUK Oxford Neuromuscular Centre & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| |
Collapse
|
26
|
Nakevska Z, Yokota T. Challenges and future perspective of antisense therapy for spinal muscular atrophy: A review. Eur J Cell Biol 2023; 102:151326. [PMID: 37295266 DOI: 10.1016/j.ejcb.2023.151326] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
Spinal muscular atrophy (SMA), the most common genetic cause of infantile death, is caused by a mutation in the survival of motor neuron 1 gene (SMN1), leading to the death of motor neurons and progressive muscle weakness. SMN1 normally produces an essential protein called SMN. Although humans possess a paralogous gene called SMN2, ∼90% of the SMN it produces is non-functional. This is due to a mutation in SMN2 that causes the skipping of a required exon during splicing of the pre-mRNA. The first treatment for SMA, nusinersen (brand name Spinraza), was approved by the FDA in 2016 and by the EMU in 2017. Nusinersen is an antisense oligonucleotide-based therapy that alters the splicing of SMN2 to make functional full-length SMN protein. Despite the recent advancements in antisense oligonucleotide therapy and SMA treatment development, nusinersen is faced with a multitude of challenges, such as intracellular and systemic delivery. In recent years, the use of peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs) in antisense therapy has gained interest. These are antisense oligonucleotides conjugated to cell-penetrating peptides such as Pips and DG9, and they have the potential to address the challenges associated with delivery. This review focuses on the historic milestones, development, current challenges, and future perspectives of antisense therapy for SMA.
Collapse
Affiliation(s)
- Zorica Nakevska
- Department of Biological Sciences, Faculty of Science, University of Alberta, 116 St. and 85 Ave., Edmonton AB T6G 2E1, Canada.
| | - Toshifumi Yokota
- Neuroscience and Mental Health Institute, Faculty of Medicine and Dentistry, University of Alberta, 116 St. and 85 Ave., Edmonton AB T6G 2E1, Canada; Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, 116 St. and 85 Ave., Edmonton AB T6G 2E1, Canada; The Friends of Garret Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, 8812 112 St., Edmonton AB T6G 2H7, Canada.
| |
Collapse
|
27
|
Ojala KS, Kaufhold CJ, Davey MR, Yang D, Liang M, Wipf P, Badawi Y, Meriney SD. Potentiation of neuromuscular transmission by a small molecule calcium channel gating modifier improves motor function in a severe spinal muscular atrophy mouse model. Hum Mol Genet 2023; 32:1901-1911. [PMID: 36757138 DOI: 10.1093/hmg/ddad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/03/2023] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a monogenic disease that clinically manifests as severe muscle weakness owing to neurotransmission defects and motoneuron degeneration. Individuals affected by SMA experience neuromuscular weakness that impacts functional activities of daily living. We have used a mouse model of severe SMA (SMNΔ7) to test whether a calcium channel gating modifier (GV-58), alone or in combination with a potassium channel antagonist (3,4-diaminopyridine; 3,4-DAP), can improve neuromuscular function in this mouse model. Bath application of GV-58 alone or in combination with 3,4-DAP significantly restored neuromuscular transmission to control levels in both a mildly vulnerable forearm muscle and a strongly vulnerable trunk muscle in SMNΔ7 mice at postnatal days 10-12. Similarly, acute subcutaneous administration of GV-58 to postnatal day 10 SMNΔ7 mice, alone or in combination with 3,4-DAP, significantly increased a behavioral measure of muscle strength. These data suggest that GV-58 may be a promising treatment candidate that could address deficits in neuromuscular function and strength and that the addition of 3,4-DAP to GV-58 treatment could aid in restoring function in SMA.
Collapse
Affiliation(s)
- Kristine S Ojala
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Cassandra J Kaufhold
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mykenzie R Davey
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Donggyun Yang
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mary Liang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Yomna Badawi
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Stephen D Meriney
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
28
|
Aartsma-Rus A, van Roon-Mom W, Lauffer M, Siezen C, Duijndam B, Coenen-de Roo T, Schüle R, Synofzik M, Graessner H. Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations. RNA (NEW YORK, N.Y.) 2023; 29:446-454. [PMID: 36669889 PMCID: PMC10019362 DOI: 10.1261/rna.079540.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/12/2023] [Indexed: 06/01/2023]
Abstract
Splice-modulating antisense oligonucleotides (ASOs) offer treatment options for rare neurological diseases, including those with very rare mutations, where patient-specific, individualized ASOs have to be developed. Inspired by the development of milasen, the 1 Mutation 1 Medicine (1M1M) and Dutch Center for RNA Therapeutics (DCRT) aim to develop patient-specific ASOs and treat eligible patients within Europe and the Netherlands, respectively. Treatment will be provided under a named patient setting. Our initiatives benefited from regulatory advice from the European Medicines Agency (EMA) with regard to preclinical proof-of-concept studies, safety studies, compounding and measuring benefit and safety in treated patients. We here outline the most important considerations from these interactions and how we implemented this advice into our plan to develop and treat eligible patients within Europe.
Collapse
Affiliation(s)
- Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics and Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- 1 Mutation 1 Medicine, 72076 Tübingen, Germany
| | - Willeke van Roon-Mom
- Dutch Center for RNA Therapeutics and Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- 1 Mutation 1 Medicine, 72076 Tübingen, Germany
| | - Marlen Lauffer
- Dutch Center for RNA Therapeutics and Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | | | - Britt Duijndam
- Medicines Evaluation Board, 3531 AH Utrecht, The Netherlands
| | - Tineke Coenen-de Roo
- Dutch Center for RNA Therapeutics and Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Animal and Transgenesis Facility, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Rebecca Schüle
- 1 Mutation 1 Medicine, 72076 Tübingen, Germany
- Division of Neurodegenerative Diseases, Department of Neurology, University of Heidelberg Medical Center, 69120 Heidelberg, Germany
- Center for Neurology and Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- European Reference Network for Rare Neurological Diseases
| | - Matthis Synofzik
- 1 Mutation 1 Medicine, 72076 Tübingen, Germany
- Center for Neurology and Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- Division of Translational Genomics of Neurodegenerative Diseases, Hertie-Institute of Clinical Brain Research & Center of Neurology, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- European Reference Network for Rare Neurological Diseases
| | - Holm Graessner
- 1 Mutation 1 Medicine, 72076 Tübingen, Germany
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Center for Rare Diseases, University Hospital Tübingen, 72076 Tübingen, Germany
- European Reference Network for Rare Neurological Diseases
| |
Collapse
|
29
|
Fernandez C, Giorgees I, Goss E, Desaulniers JP. Effective carrier-free gene-silencing activity of sphingosine-modified siRNAs. Org Biomol Chem 2023; 21:2107-2117. [PMID: 36645381 DOI: 10.1039/d2ob02099h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RNA interference (RNAi) is a natural cellular process that silences the expression of target genes in a sequence-specific way by mediating targeted mRNA degradation. One of the main challenges in RNAi research is developing an effective career-free delivery system and targeting cells in the central nervous system (CNS). Recently, lipid-conjugated systems involving fatty acids have shown promising potential as safe and effective delivery systems of oligonucleotides to CNS cells due to their hydrophobic tails and interactions with the cell's hydrophobic membrane. Therefore, in this study, we are interested in creating career-free siRNA therapeutics for potential applications in drug delivery to the CNS. Here we explore different synthetic pathways of conjugating sphingolipids containing long-carbon chains to siRNA and assess their effectiveness as career-free delivery systems. In this project, a library of sphingosine-modified siRNAs was created, and their gene-silencing effect was evaluated in both the presence and absence of a transfection carrier. siRNAs modified with one or two sphingosine moieties resulted in dose-dependent gene knockdown while demonstrating promising results for their use as carrier-free agents. The IC50 values of single-modified siRNAs ranged from 49.9 nM to 670.7 nM, whereas double-modified siRNAs had IC50 values in the range of 49.9 nM to 66.4 nM. In conclusion, sphingosine-modified siRNAs show promising results in advancing carrier-free siRNA therapeutics.
Collapse
Affiliation(s)
- Charlene Fernandez
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
| | - Ifrodet Giorgees
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
| | - Eva Goss
- Synthose Inc., 50 Viceroy Road Unit 7, Concord, Ontario, L4K 3A7 Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
| |
Collapse
|
30
|
Suzuki N, Nishiyama A, Warita H, Aoki M. Genetics of amyotrophic lateral sclerosis: seeking therapeutic targets in the era of gene therapy. J Hum Genet 2023; 68:131-152. [PMID: 35691950 PMCID: PMC9968660 DOI: 10.1038/s10038-022-01055-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/17/2022] [Accepted: 05/29/2022] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is an intractable disease that causes respiratory failure leading to mortality. The main locus of ALS is motor neurons. The success of antisense oligonucleotide (ASO) therapy in spinal muscular atrophy (SMA), a motor neuron disease, has triggered a paradigm shift in developing ALS therapies. The causative genes of ALS and disease-modifying genes, including those of sporadic ALS, have been identified one after another. Thus, the freedom of target choice for gene therapy has expanded by ASO strategy, leading to new avenues for therapeutic development. Tofersen for superoxide dismutase 1 (SOD1) was a pioneer in developing ASO for ALS. Improving protocols and devising early interventions for the disease are vital. In this review, we updated the knowledge of causative genes in ALS. We summarized the genetic mutations identified in familial ALS and their clinical features, focusing on SOD1, fused in sarcoma (FUS), and transacting response DNA-binding protein. The frequency of the C9ORF72 mutation is low in Japan, unlike in Europe and the United States, while SOD1 and FUS are more common, indicating that the target mutations for gene therapy vary by ethnicity. A genome-wide association study has revealed disease-modifying genes, which could be the novel target of gene therapy. The current status and prospects of gene therapy development were discussed, including ethical issues. Furthermore, we discussed the potential of axonal pathology as new therapeutic targets of ALS from the perspective of early intervention, including intra-axonal transcription factors, neuromuscular junction disconnection, dysregulated local translation, abnormal protein degradation, mitochondrial pathology, impaired axonal transport, aberrant cytoskeleton, and axon branching. We simultaneously discuss important pathological states of cell bodies: persistent stress granules, disrupted nucleocytoplasmic transport, and cryptic splicing. The development of gene therapy based on the elucidation of disease-modifying genes and early intervention in molecular pathology is expected to become an important therapeutic strategy in ALS.
Collapse
Affiliation(s)
- Naoki Suzuki
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
| | - Ayumi Nishiyama
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Hitoshi Warita
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
| |
Collapse
|
31
|
Velema WA, Lu Z. Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications. JACS AU 2023; 3:316-332. [PMID: 36873678 PMCID: PMC9975857 DOI: 10.1021/jacsau.2c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.
Collapse
Affiliation(s)
- Willem A. Velema
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6500 HC, The Netherlands
| | - Zhipeng Lu
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
| |
Collapse
|
32
|
Günther R. [Gene Therapies in Motor Neuron Diseases ALS and SMA]. FORTSCHRITTE DER NEUROLOGIE-PSYCHIATRIE 2023; 91:153-163. [PMID: 36822211 DOI: 10.1055/a-2002-5215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
In the past, the diagnosis of motor neuron diseases such as amyotrophic lateral sclerosis (ALS) and 5q-associated spinal muscular atrophy (SMA) meant powerlessness in the face of seemingly untreatable diseases with severe motor-functional limitations and sometimes fatal courses. Recent advances in an understanding of the genetic causalities of these diseases, combined with success in the development of targeted gene therapy strategies, spell hope for effective, innovative therapeutic approaches, pioneering the ability to treat neurodegenerative diseases. While gene therapies have been approved for SMA since a few years, gene therapy research in ALS is still in clinical trials with encouraging results. This article provides an overview of the genetic background of ALS and SMA known to date and gene therapy approaches to them with a focus on therapy candidates that are in clinical trials or have already gained market approval.
Collapse
Affiliation(s)
- René Günther
- Klinik und Poliklinik für Neurologie, University Hospital Carl Gustav Carus at Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
33
|
Ogiya D, Chyra Z, Verselis SJ, O'Keefe M, Cobb J, Abiatari I, Talluri S, Sithara AA, Hideshima T, Chu MP, Hájek R, Dorfman DM, Pilarski LM, Anderson KC, Adamia S. Identification of disease-related aberrantly spliced transcripts in myeloma and strategies to target these alterations by RNA-based therapeutics. Blood Cancer J 2023; 13:23. [PMID: 36737429 PMCID: PMC9898564 DOI: 10.1038/s41408-023-00791-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 12/17/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023] Open
Abstract
Novel drug discoveries have shifted the treatment paradigms of most hematological malignancies, including multiple myeloma (MM). However, this plasma cell malignancy remains incurable, and novel therapies are therefore urgently needed. Whole-genome transcriptome analyses in a large cohort of MM patients demonstrated that alterations in pre-mRNA splicing (AS) are frequent in MM. This manuscript describes approaches to identify disease-specific alterations in MM and proposes RNA-based therapeutic strategies to eradicate such alterations. As a "proof of concept", we examined the causes of aberrant HMMR (Hyaluronan-mediated motility receptor) splicing in MM. We identified clusters of single nucleotide variations (SNVs) in the HMMR transcript where the altered splicing took place. Using bioinformatics tools, we predicted SNVs and splicing factors that potentially contribute to aberrant HMMR splicing. Based on bioinformatic analyses and validation studies, we provided the rationale for RNA-based therapeutic strategies to selectively inhibit altered HMMR splicing in MM. Since splicing is a hallmark of many cancers, strategies described herein for target identification and the design of RNA-based therapeutics that inhibit gene splicing can be applied not only to other genes in MM but also more broadly to other hematological malignancies and solid tumors as well.
Collapse
Affiliation(s)
- Daisuke Ogiya
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Zuzana Chyra
- Department of Hemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic.,Department of Hemato-oncology, University of Ostrava, Ostrava, Czech Republic
| | - Sigitas J Verselis
- Molecular Diagnostic Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Morgan O'Keefe
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jacquelyn Cobb
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ivane Abiatari
- Institute of Medical and Public Health Research, School of Medicine, Ilia State University, Tbilisi, Georgia
| | - Srikanth Talluri
- Molecular Diagnostic Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Boston Healthcare System, West Roxbury, MA, USA
| | - Anjana Anilkumar Sithara
- Department of Hemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic.,Department of Hemato-oncology, University of Ostrava, Ostrava, Czech Republic
| | - Teru Hideshima
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Michael P Chu
- Department of Medicine, Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Roman Hájek
- Department of Hemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic.,Department of Hemato-oncology, University of Ostrava, Ostrava, Czech Republic
| | - David M Dorfman
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Linda M Pilarski
- Department of Medicine, Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Sophia Adamia
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Institute of Medical and Public Health Research, School of Medicine, Ilia State University, Tbilisi, Georgia. .,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
34
|
Reilly A, Chehade L, Kothary R. Curing SMA: Are we there yet? Gene Ther 2023; 30:8-17. [PMID: 35614235 DOI: 10.1038/s41434-022-00349-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/04/2022] [Accepted: 05/12/2022] [Indexed: 11/09/2022]
Abstract
Loss or deletion of survival motor neuron 1 gene (SMN1) is causative for a severe and devastating neuromuscular disease, Spinal Muscular Atrophy (SMA). SMN1 produces SMN, a ubiquitously expressed protein, that is essential for the development and survival of motor neurons. Major advances and developments in SMA therapeutics are shifting the natural history of the disease. With three relatively new available therapies, nusinersen (Spinraza), onasemnogene abeparvovec (Zolgensma), and risdiplam (Evrysdi), patients survive longer and have improved outcomes. However, patients and families continue to face many challenges associated with use of these therapies, including poor treatment response and a variability in the benefits to those that do respond, suggesting that the quest for the SMA cure is not over. In this review, we discuss the current therapies, their limitations, and highlight necessary gaps that need to be addressed to guarantee the best outcomes for SMA patients.
Collapse
Affiliation(s)
- Aoife Reilly
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Lucia Chehade
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Rashmi Kothary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada. .,Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada. .,Department of Medicine, University of Ottawa, Ottawa, ON, Canada.
| |
Collapse
|
35
|
Torroba B, Macabuag N, Haisma EM, O'Neill A, Herva ME, Redis RS, Templin MV, Black LE, Fischer DF. RNA-based drug discovery for spinal muscular atrophy: a story of small molecules and antisense oligonucleotides. Expert Opin Drug Discov 2023; 18:181-192. [PMID: 36408582 DOI: 10.1080/17460441.2022.2149733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Spinal Muscular Atrophy (SMA), the second most prevalent autosomal genetic disease affecting infants, is caused by the lack of SMN1, which encodes a neuron functioning vital protein, SMN. Improving exon 7 splicing in the paralogous gene SMN2, also coding for SMN protein, increases protein production efficiency from SMN2 to overcome the genetic deficit in SMN1. Several molecular mechanisms have been investigated to improve SMN2 functional splicing. AREAS COVERED This manuscript will cover two of the three mechanistically distinct available treatment options for SMA, both targeting the SMN2 splicing mechanism. The first therapeutic, nusinersen (Spinraza®, 2017), is an antisense oligonucleotide (ASO) targeting the splicing inhibitory sequence in the intron downstream of exon 7 from SMN2, thus increasing exon 7 inclusion. The second drug is a small molecule, risdiplam (Evrysdi®, 2021), that enhances the binding of splice factors and also promotes exon 7 inclusion. Both therapies, albeit through different mechanisms, increase full-length SMN protein expression. EXPERT OPINION Nusinersen and risdiplam have directly helped SMA patients and families, but they also herald a sea change in drug development for genetic diseases. This piece aims to draw parallels between both development histories; this may help chart the course for future targeted agents.
Collapse
Affiliation(s)
| | | | | | - Amy O'Neill
- Charles River Laboratories, Saffron Walden, UK
| | | | | | | | | | | |
Collapse
|
36
|
Alves CRR, Ha LL, Yaworski R, Lazzarotto CR, Christie KA, Reilly A, Beauvais A, Doll RM, de la Cruz D, Maguire CA, Swoboda KJ, Tsai SQ, Kothary R, Kleinstiver BP. Base editing as a genetic treatment for spinal muscular atrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524978. [PMID: 36711797 PMCID: PMC9882371 DOI: 10.1101/2023.01.20.524978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Spinal muscular atrophy (SMA) is a devastating neuromuscular disease caused by mutations in the SMN1 gene. Despite the development of various therapies, outcomes can remain suboptimal in SMA infants and the duration of such therapies are uncertain. SMN2 is a paralogous gene that mainly differs from SMN1 by a C•G-to-T•A transition in exon 7, resulting in the skipping of exon 7 in most SMN2 transcripts and production of only low levels of survival motor neuron (SMN) protein. Genome editing technologies targeted to the SMN2 exon 7 mutation could offer a therapeutic strategy to restore SMN protein expression to normal levels irrespective of the patient SMN1 mutation. Here, we optimized a base editing approach to precisely edit SMN2, reverting the exon 7 mutation via an A•T-to-G•C base edit. We tested a range of different adenosine base editors (ABEs) and Cas9 enzymes, resulting in up to 99% intended editing in SMA patient-derived fibroblasts with concomitant increases in SMN2 exon 7 transcript expression and SMN protein levels. We generated and characterized ABEs fused to high-fidelity Cas9 variants which reduced potential off-target editing. Delivery of these optimized ABEs via dual adeno-associated virus (AAV) vectors resulted in precise SMN2 editing in vivo in an SMA mouse model. This base editing approach to correct SMN2 should provide a long-lasting genetic treatment for SMA with advantages compared to current nucleic acid, small molecule, or exogenous gene replacement therapies. More broadly, our work highlights the potential of PAMless SpRY base editors to install edits efficiently and safely.
Collapse
Affiliation(s)
- Christiano R. R. Alves
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Leillani L. Ha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca Yaworski
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, ON, Canada
- Centre for Neuromuscular Disease, University of Ottawa, ON, Canada
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Kathleen A. Christie
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Aoife Reilly
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, ON, Canada
- Centre for Neuromuscular Disease, University of Ottawa, ON, Canada
| | - Ariane Beauvais
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, ON, Canada
- Centre for Neuromuscular Disease, University of Ottawa, ON, Canada
| | - Roman M. Doll
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Biosciences/Cancer Biology Program, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Demitri de la Cruz
- Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Casey A. Maguire
- Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Kathryn J. Swoboda
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Rashmi Kothary
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, ON, Canada
- Centre for Neuromuscular Disease, University of Ottawa, ON, Canada
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
37
|
Abstract
There are more than 7,000 paediatric genetic diseases (PGDs) but less than 5% have treatment options. Treatment strategies targeting different levels of the biological process of the disease have led to optimal health outcomes in a subset of patients with PGDs, where treatment is available. In the past 3 decades, there has been rapid advancement in the development of novel therapies, including gene therapy, for many PGDs. The therapeutic success of treatment relies heavily on knowledge of the genetic basis and the disease mechanism. Specifically, gene therapy has been shown to be effective in various clinical trials, and indeed, these trials have led to regulatory approvals, paving the way for gene therapies for other types of PGDs. In this review, we provide an overview of the treatment strategies and focus on some of the recent advancements in therapeutics for PGDs.
Collapse
Affiliation(s)
- Ai Ling Koh
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore,SingHealth Duke-NUS Genomic Medicine Centre, Nanyang Technological University, Singapore,Duke-NUS Medical School, Nanyang Technological University, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Saumya Shekhar Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore,SingHealth Duke-NUS Genomic Medicine Centre, Nanyang Technological University, Singapore,Duke-NUS Medical School, Nanyang Technological University, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore,SingHealth Duke-NUS Institute of Precision Medicine, Singapore,Correspondence: Dr. Saumya Shekhar Jamuar, Senior Consultant, Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, 100 Bukit Timah Road, 229899, Singapore. E-mail:
| |
Collapse
|
38
|
Aartsma-Rus A, Garanto A, van Roon-Mom W, McConnell EM, Suslovitch V, Yan WX, Watts JK, Yu TW. Consensus Guidelines for the Design and In Vitro Preclinical Efficacy Testing N-of-1 Exon Skipping Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:17-25. [PMID: 36516128 PMCID: PMC9940807 DOI: 10.1089/nat.2022.0060] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Antisense oligonucleotides (ASOs) can modulate pre-mRNA splicing. This offers therapeutic opportunities for numerous genetic diseases, often in a mutation-specific and sometimes even individual-specific manner. Developing therapeutic ASOs for as few as even a single patient has been shown feasible with the development of Milasen for an individual with Batten disease. Efforts to develop individualized ASOs for patients with different genetic diseases are ongoing globally. The N = 1 Collaborative (N1C) is an umbrella organization dedicated to supporting the nascent field of individualized medicine. N1C recently organized a workshop to discuss and advance standards for the rigorous design and testing of splice-switching ASOs. In this study, we present guidelines resulting from that meeting and the key recommendations: (1) dissemination of standardized experimental designs, (2) use of standardized reference ASOs, and (3) a commitment to data sharing and exchange.
Collapse
Affiliation(s)
- Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,N = 1 Collaborative
| | - Alejandro Garanto
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Pediatrics and Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willeke van Roon-Mom
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Victoria Suslovitch
- N = 1 Collaborative.,Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Jonathan K Watts
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Timothy W Yu
- N = 1 Collaborative.,Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Division of Genetics and Genomics, Boston, Massachusetts, USA
| | | |
Collapse
|
39
|
Scheijmans FEV, Cuppen I, Zwartkruis MM, Signoria I, van Ekris C, Asselman F, Wadman RI, Knol EF, van der Pol WL, Groen EJN. Inflammatory markers in cerebrospinal fluid of paediatric spinal muscular atrophy patients receiving nusinersen treatment. Eur J Paediatr Neurol 2023; 42:34-41. [PMID: 36525882 DOI: 10.1016/j.ejpn.2022.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Spinal muscular atrophy (SMA) is a progressive motor neuron disease with onset during infancy or early childhood. Recent therapeutic advances targeting the genetic defect that underlies SMA improved survival in patients with infantile onset SMA (type 1) and improved motor function in SMA type 1-3. The most commonly used therapy for SMA, the antisense oligonucleotide nusinersen, is delivered by repeated intrathecal injections. The long-term safety effects of this procedure, however, have not yet been investigated in detail. We here present case reports of three children with SMA in which routine laboratory investigation revealed increased leukocyte counts in cerebrospinal fluid (CSF) collected during the course of nusinersen treatment. To further characterize this observation, we used a multiplex method to analyse a broad spectrum of inflammatory markers in the CSF of these patients. We found that interleukin-10 (IL10) was consistently elevated in CSF with increased leukocyte counts, but other inflammatory markers were not. Based on this analysis we selected 7 markers for further analysis in a cohort of 38 children with SMA and determined their expression during the course of nusinersen therapy. No consistent association was found between levels of inflammatory markers and the duration of nusinersen therapy in individual patients. However, monocyte chemoactive protein 1 (MCP1/CCL2) -a neuroprotective protein secreted by astrocytes and previously associated with SMA- levels increased over the course of nusinersen treatment, indicating a possible neuroprotective mechanism associated with nusinersen therapy. In summary, our findings confirm that repeated intrathecal injections are safe and do not trigger unwanted immune responses.
Collapse
Affiliation(s)
- F E V Scheijmans
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - I Cuppen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - M M Zwartkruis
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - I Signoria
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - C van Ekris
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - F Asselman
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - R I Wadman
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - E F Knol
- Department of Dermatology and Allergology, Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - W L van der Pol
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - E J N Groen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands.
| |
Collapse
|
40
|
Kotulska K, Jozwiak S, Jedrzejowska M, Gos M, Ogrodnik M, Wysocki J, Czajka H, Kuchar E. Newborn screening and gene therapy in SMA: Challenges related to vaccinations. Front Neurol 2022; 13:890860. [PMID: 36504644 PMCID: PMC9727226 DOI: 10.3389/fneur.2022.890860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
Spinal muscular atrophy (SMA) affects one in 7,500-10,000 newborns. Before the era of disease-modifying therapies, it used to be the major genetic cause of mortality in infants. Currently, there are three therapies approved for SMA, including two molecules modifying the splicing of the SMN2 gene and one gene therapy providing a healthy copy of the SMN gene with a viral vector. The best effects of any of these therapies are achieved when the treatment is administered in the presymptomatic stage of the disease, therefore newborn screening programs are being introduced in many countries. Patients identified in newborn screening might be eligible for gene therapy. However, gene therapy and the associated administration of steroids in newborns might interfere with the vaccination schedule, which includes live immunization against tuberculosis in some countries. The timing of gene therapy in patients who received live vaccinations has not yet been addressed neither in the clinical trials nor in the existing international guidelines. The Polish Vaccinology Association has developed the first recommendations for gene therapy administration in newborns who received live vaccination against tuberculosis. Their statement was implemented in the current guidelines for Polish SMA patients identified in the newborn screening program and might be helpful for medical professionals in other countries where live vaccine against tuberculosis is still in routine use in newborns.
Collapse
Affiliation(s)
- Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Sergiusz Jozwiak
- Research Department, The Children's Memorial Health Institute, Warsaw, Poland,*Correspondence: Sergiusz Jozwiak
| | | | - Monika Gos
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Magdalena Ogrodnik
- Department of Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Jacek Wysocki
- Department of Preventive Medicine, Poznań University of Medical Sciences, Poznań, Poland
| | - Hanna Czajka
- Pediatric Department, Rzeszów University, Rzeszów, Poland
| | - Ernest Kuchar
- Department of Pediatrics with Clinical Assessment Unit, Medical University of Warsaw, Warsaw, Poland
| |
Collapse
|
41
|
Sarli SL, Watts JK. Harnessing nucleic acid technologies for human health on earth and in space. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:113-126. [PMID: 36336357 DOI: 10.1016/j.lssr.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid therapeutics are a versatile class of sequence-programmable drugs that offer a robust and clinically viable strategy to modulate expression or correct genetic defects contributing to disease. The majority of drugs currently on the market target proteins; however, proteins only represent a subset of possible disease targets. Nucleic acid therapeutics allow intuitive engagement with genome sequences providing a more direct way to target many diseases at their genetic root cause. Their clinical success depends on platform technologies which can support durable and well tolerated pharmacological activity in a given tissue. Nucleic acid drugs possess a potent combination of target specificity and adaptability required to advance drug development for many diseases. As these therapeutic technologies mature, their clinical applications can also expand access to personalized therapies for patients with rare or solo genetic diseases. Spaceflight crew members exposed to the unique hazards of spaceflight, especially those related to galactic cosmic radiation (GCR) exposure, represent another patient subset who may also benefit from nucleic acid drugs as countermeasures. In this review, we will discuss the various classes of RNA- and DNA-targeted nucleic acid drugs, provide an overview of their present-day clinical applications, and describe major strategies to improve their delivery, safety, and overall efficacy.
Collapse
Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| |
Collapse
|
42
|
Swinney DC. Why medicines work. Pharmacol Ther 2022; 238:108175. [DOI: 10.1016/j.pharmthera.2022.108175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022]
|
43
|
Rozza R, Janoš P, Spinello A, Magistrato A. Role of computational and structural biology in the development of small-molecule modulators of the spliceosome. Expert Opin Drug Discov 2022; 17:1095-1109. [PMID: 35983696 DOI: 10.1080/17460441.2022.2114452] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION RNA splicing is a pivotal step of eukaryotic gene expression during which the introns are excised from the precursor (pre-)RNA and the exons are joined together to form mature RNA products (i.e a protein-coding mRNA or long non-coding (lnc)RNAs). The spliceosome, a complex ribonucleoprotein machine, performs pre-RNA splicing with extreme precision. Deregulated splicing is linked to cancer, genetic, and neurodegenerative diseases. Hence, the discovery of small-molecules targeting core spliceosome components represents an appealing therapeutic opportunity. AREA COVERED Several atomic-level structures of the spliceosome and distinct splicing-modulators bound to its protein/RNA components have been solved. Here, we review recent advances in the discovery of small-molecule splicing-modulators, discuss opportunities and challenges for their therapeutic applicability, and showcase how structural data and/or all-atom simulations can illuminate key facets of their mechanism, thus contributing to future drug-discovery campaigns. EXPERT OPINION This review highlights the potential of modulating pre-RNA splicing with small-molecules, and anticipates how the synergy of computer and wet-lab experiments will enrich our understanding of splicing regulation/deregulation mechanisms. This information will aid future structure-based drug-discovery efforts aimed to expand the currently limited portfolio of selective splicing-modulators.
Collapse
Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, Palermo, Italy
| | - Alessandra Magistrato
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| |
Collapse
|
44
|
Singh NN, O'Leary CA, Eich T, Moss WN, Singh RN. Structural Context of a Critical Exon of Spinal Muscular Atrophy Gene. Front Mol Biosci 2022; 9:928581. [PMID: 35847983 PMCID: PMC9283826 DOI: 10.3389/fmolb.2022.928581] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Humans contain two nearly identical copies of Survival Motor Neuron genes, SMN1 and SMN2. Deletion or mutation of SMN1 causes spinal muscular atrophy (SMA), one of the leading genetic diseases associated with infant mortality. SMN2 is unable to compensate for the loss of SMN1 due to predominant exon 7 skipping, leading to the production of a truncated protein. Antisense oligonucleotide and small molecule-based strategies aimed at the restoration of SMN2 exon 7 inclusion are approved therapies of SMA. Many cis-elements and transacting factors have been implicated in regulation of SMN exon 7 splicing. Also, several structural elements, including those formed by a long-distance interaction, have been implicated in the modulation of SMN exon 7 splicing. Several of these structures have been confirmed by enzymatic and chemical structure-probing methods. Additional structures formed by inter-intronic interactions have been predicted by computational algorithms. SMN genes generate a vast repertoire of circular RNAs through inter-intronic secondary structures formed by inverted Alu repeats present in large number in SMN genes. Here, we review the structural context of the exonic and intronic cis-elements that promote or prevent exon 7 recognition. We discuss how structural rearrangements triggered by single nucleotide substitutions could bring drastic changes in SMN2 exon 7 splicing. We also propose potential mechanisms by which inter-intronic structures might impact the splicing outcomes.
Collapse
Affiliation(s)
- Natalia N. Singh
- Department of Biomedical Science, Iowa State University, Ames, IA, United States
| | - Collin A. O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Taylor Eich
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | | |
Collapse
|
45
|
Rossoll W, Singh RN. Commentary: Current Status of Gene Therapy for Spinal Muscular Atrophy. Front Cell Neurosci 2022; 16:916065. [PMID: 35656408 PMCID: PMC9152110 DOI: 10.3389/fncel.2022.916065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- *Correspondence: Wilfried Rossoll
| | - Ravindra N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
- Ravindra N. Singh
| |
Collapse
|
46
|
High Concentration or Combined Treatment of Antisense Oligonucleotides for Spinal Muscular Atrophy Perturbed SMN2 Splicing in Patient Fibroblasts. Genes (Basel) 2022; 13:genes13040685. [PMID: 35456491 PMCID: PMC9027857 DOI: 10.3390/genes13040685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
Spinal muscular atrophy (SMA) is caused by survival motor neuron 1 SMN1 deletion. The survival motor neuron 2 (SMN2) encodes the same protein as SMN1 does, but it has a splicing defect of exon 7. Some antisense oligonucleotides (ASOs) have been proven to correct this defect. One of these, nusinersen, is effective in SMA-affected infants, but not as much so in advanced-stage patients. Furthermore, the current regimen may exhibit a ceiling effect. To overcome these problems, high-dose ASOs or combined ASOs have been explored. Here, using SMA fibroblasts, we examined the effects of high-concentration ASOs and of combining two ASOs. Three ASOs were examined: one targeting intronic splicing suppressor site N1 (ISS-N1) in intron 7, and two others targeting the 3′ splice site and 5′ region of exon 8. In our experiments on all ASO types, a low or intermediate concentration (50 or 100 nM) showed better splicing efficiency than a high concentration (200 nM). In addition, a high concentration of each ASO created a cryptic exon in exon 6. When a mixture of two different ASOs (100 nM each) was added to the cells, the cryptic exon was included in the mRNA. In conclusion, ASOs at a high concentration or used in combination may show less splicing correction and cryptic exon creation.
Collapse
|
47
|
D'Silva AM, Holland S, Kariyawasam D, Herbert K, Barclay P, Cairns A, MacLennan SC, Ryan MM, Sampaio H, Smith N, Woodcock IR, You EM, Alexander IE, Farrar MA. Onasemnogene abeparvovec in spinal muscular atrophy: an Australian experience of safety and efficacy. Ann Clin Transl Neurol 2022; 9:339-350. [PMID: 35170254 PMCID: PMC8935277 DOI: 10.1002/acn3.51519] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 01/07/2023] Open
Abstract
Objective To provide a greater understanding of the tolerability, safety and clinical outcomes of onasemnogene abeparvovec in real‐world practice, in a broad population of infants with spinal muscular atrophy (SMA). Methods A prospective cohort study of children with SMA treated with onasemnogene abeparvovec at Sydney Children's Hospital Network, Australia was conducted from August 2019 to November 2021. Safety outcomes included clinical and laboratory evaluations. Efficacy assessments included World Health Organisation (WHO) motor milestones, oral and swallowing abilities, and requirements for respiratory support. The implementation of a model of care for onasemnogene abeparvovec administration in health practice is described. Results 21 children were treated (age range, 0.65–24 months; body weight range, 2.5–12.5 kg) and 19/21 (90.4%) had previous nusinersen. Transient treatment‐related side effects occurred in all children; vomiting (100%), transaminitis (57%) and thrombocytopaenia (33%). Incidence of moderate/severe transaminitis was significantly greater in infants weighing ≥8 kg compared with <8 kg (p < 0.05). Duration of prednisolone following treatment was prolonged (mean 87.5 days, range 57–274 days). 16/21 (76%) children gained at least one WHO motor milestone. Stabilisation or improvement in bulbar or respiratory function was observed in 20/21 (95.2%) patients. Implementation challenges were mitigated by developing standard operating procedures and facilitating exchange of knowledge. Interpretation This study provides real‐world evidence to inform treatment decisions and guide therapeutic expectations for onasemnogene abeparvovec and combination therapy for SMA in health practice, especially for children weighing ≥8 kg receiving higher vector loads. Proactive clinical and laboratory surveillance is essential to facilitate individualised management of risks.
Collapse
Affiliation(s)
- Arlene M D'Silva
- Department of Neurology, Sydney Children's Hospital Network, Sydney, New South Wales, Australia.,School of Clinical Medicine, UNSW Medicine & Health, Randwick Clinical Campus, Discipline of Paediatrics, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandra Holland
- Department of Neurology, Sydney Children's Hospital Network, Sydney, New South Wales, Australia
| | - Didu Kariyawasam
- Department of Neurology, Sydney Children's Hospital Network, Sydney, New South Wales, Australia.,School of Clinical Medicine, UNSW Medicine & Health, Randwick Clinical Campus, Discipline of Paediatrics, University of New South Wales, Sydney, New South Wales, Australia
| | - Karen Herbert
- Physiotherapy, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Peter Barclay
- Department of Pharmacy, Prince of Wales Hospital, Sydney Children's Hospital Randwick and The Royal Hospital for Women, Randwick, New South Wales, Australia
| | - Anita Cairns
- Neurosciences Department, Queensland's Children Hospital, South Brisbane, Queensland, Australia
| | - Suzanna C MacLennan
- Neurology Department, Women's & Children's Hospital, North Adelaide, South Australia, Australia.,School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Monique M Ryan
- Department of Neurology, Royal Children's Hospital, Melbourne, Australia.,Neuroscience Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Hugo Sampaio
- Department of Neurology, Sydney Children's Hospital Network, Sydney, New South Wales, Australia
| | - Nicholas Smith
- Gene Therapy Research Unit, Sydney Children's Hospitals Network and Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Ian R Woodcock
- Department of Neurology, Royal Children's Hospital, Melbourne, Australia.,Neuroscience Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Eppie M You
- Department of Neurology, Royal Children's Hospital, Melbourne, Australia.,Neuroscience Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Sydney Children's Hospitals Network and Children's Medical Research Institute, The University of Sydney, Westmead, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Michelle A Farrar
- Department of Neurology, Sydney Children's Hospital Network, Sydney, New South Wales, Australia.,School of Clinical Medicine, UNSW Medicine & Health, Randwick Clinical Campus, Discipline of Paediatrics, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
48
|
Dominguez CE, Cunningham D, Venkataramany AS, Chandler DS. Heat increases full-length SMN splicing: promise for splice-augmenting therapies for SMA. Hum Genet 2022; 141:239-256. [PMID: 35088120 DOI: 10.1007/s00439-021-02408-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/30/2021] [Indexed: 11/28/2022]
Abstract
Spinal muscular atrophy (SMA) is a debilitating neurodegenerative pediatric disease characterized by low levels of the survival motor protein (SMN). Humans have two SMN genes that produce identical SMN proteins, but they differ at a key nucleotide in exon 7 that induces differential mRNA splicing. SMN1 primarily produces full-length SMN protein, but due to the spliceosome's inability to efficiently recognize exon 7, SMN2 transcripts are often truncated. SMA occurs primarily through mutations or deletions in the SMN1 gene; therefore, current therapies use antisense oligonucleotides (ASOs) to target exon 7 inclusion in SMN2 mRNA and promote full-length SMN protein production. Here, we explore additional methods that can target SMN splicing and therapeutically increase full-length SMN protein. We demonstrate that in vitro heat treatment of cells increases exon 7 inclusion and relative abundance of full-length SMN2 mRNA and protein, a response that is modulated through the upregulation of the positive splicing factor TRA2 beta. We also observe that HSP90, but not HSP40 or HSP70, in the heat shock response is essential for SMN2 exon 7 splicing under hyperthermic conditions. Finally, we show that pulsatile heat treatments for one hour in vitro and in vivo are effective in increasing full-length SMN2 levels. These findings suggest that timed interval treatments could be a therapeutic alternative for SMA patients who do not respond to current ASO-based therapies or require a unique combination regimen.
Collapse
Affiliation(s)
- Catherine E Dominguez
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - David Cunningham
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - Akila S Venkataramany
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA.,Medical Scientist Training Program, The Ohio State University, Columbus, OH, USA
| | - Dawn S Chandler
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA. .,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA. .,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
| |
Collapse
|
49
|
Abstract
RNA-based therapeutics have entered the mainstream with seemingly limitless possibilities to treat all categories of neurological disease. Here, common RNA-based drug modalities such as antisense oligonucleotides, small interfering RNAs, RNA aptamers, RNA-based vaccines and mRNA drugs are reviewed highlighting their current and potential applications. Rapid progress has been made across rare genetic diseases and neurodegenerative disorders, but safe and effective delivery to the brain remains a significant challenge for many applications. The advent of individualized RNA-based therapies for ultra-rare diseases is discussed against the backdrop of the emergence of this field into more common conditions such as Alzheimer's disease and ischaemic stroke. There remains significant untapped potential in the use of RNA-based therapeutics for behavioural disorders and tumours of the central nervous system; coupled with the accelerated development expected over the next decade, the true potential of RNA-based therapeutics to transform the therapeutic landscape in neurology remains to be uncovered.
Collapse
Affiliation(s)
- Karen Anthony
- Centre for Physical Activity and Life Sciences, University of Northampton, Northampton, UK
| |
Collapse
|
50
|
Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
Collapse
Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| |
Collapse
|