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Pharmacological inhibition of HDAC6 improves muscle phenotypes in dystrophin-deficient mice by downregulating TGF-β via Smad3 acetylation. Nat Commun 2022; 13:7108. [PMID: 36402791 PMCID: PMC9675748 DOI: 10.1038/s41467-022-34831-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 11/01/2022] [Indexed: 11/21/2022] Open
Abstract
The absence of dystrophin in Duchenne muscular dystrophy disrupts the dystrophin-associated glycoprotein complex resulting in skeletal muscle fiber fragility and atrophy, associated with fibrosis as well as microtubule and neuromuscular junction disorganization. The specific, non-conventional cytoplasmic histone deacetylase 6 (HDAC6) was recently shown to regulate acetylcholine receptor distribution and muscle atrophy. Here, we report that administration of the HDAC6 selective inhibitor tubastatin A to the Duchenne muscular dystrophy, mdx mouse model increases muscle strength, improves microtubule, neuromuscular junction, and dystrophin-associated glycoprotein complex organization, and reduces muscle atrophy and fibrosis. Interestingly, we found that the beneficial effects of HDAC6 inhibition involve the downregulation of transforming growth factor beta signaling. By increasing Smad3 acetylation in the cytoplasm, HDAC6 inhibition reduces Smad2/3 phosphorylation, nuclear translocation, and transcriptional activity. These findings provide in vivo evidence that Smad3 is a new target of HDAC6 and implicate HDAC6 as a potential therapeutic target in Duchenne muscular dystrophy.
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Wein N, Vetter TA, Vulin A, Simmons TR, Frair EC, Bradley AJ, Gushchina LV, Almeida CF, Huang N, Lesman D, Rajakumar D, Weiss RB, Flanigan KM. Systemic delivery of an AAV9 exon-skipping vector significantly improves or prevents features of Duchenne muscular dystrophy in the Dup2 mouse. Mol Ther Methods Clin Dev 2022; 26:279-293. [PMID: 35949298 PMCID: PMC9356240 DOI: 10.1016/j.omtm.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022]
Abstract
Duchenne muscular dystrophy (DMD) is typically caused by mutations that disrupt the DMD reading frame, but nonsense mutations in the 5′ part of the gene induce utilization of an internal ribosomal entry site (IRES) in exon 5, driving expression of a highly functional N-truncated dystrophin. We have developed an AAV9 vector expressing U7 small nuclear RNAs targeting DMD exon 2 and have tested it in a mouse containing a duplication of exon 2, in which skipping of both exon 2 copies induces IRES-driven expression, and skipping of one copy leads to wild-type dystrophin expression. One-time intravascular injection either at postnatal days 0–1 or at 2 months results in efficient exon skipping and dystrophin expression, and significant protection from functional and pathologic deficits. Immunofluorescence quantification showed 33%–53% average dystrophin intensity and 55%–79% average dystrophin-positive fibers in mice treated in adulthood, with partial amelioration of DMD pathology and correction of DMD-associated alterations in gene expression. In mice treated neonatally, dystrophin immunofluorescence reached 49%–85% of normal intensity and 76%–99% dystrophin-positive fibers, with near-complete correction of dystrophic pathology, and these beneficial effects persisted for at least 6 months. Our results demonstrate the robustness, durability, and safety of exon 2 skipping using scAAV9.U7snRNA.ACCA, supporting its clinical use.
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Affiliation(s)
- Nicolas Wein
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Tatyana A Vetter
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Adeline Vulin
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Tabatha R Simmons
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Emma C Frair
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Adrienne J Bradley
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Liubov V Gushchina
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Camila F Almeida
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Nianyuan Huang
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Daniel Lesman
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Dhanarajan Rajakumar
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Robert B Weiss
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kevin M Flanigan
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Neurology, The Ohio State University, Columbus, OH, USA
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3
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Sergeeva OV, Shcherbinina EY, Shomron N, Zatsepin TS. Modulation of RNA Splicing by Oligonucleotides: Mechanisms of Action and Therapeutic Implications. Nucleic Acid Ther 2022; 32:123-138. [PMID: 35166605 DOI: 10.1089/nat.2021.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation via AS-NMD and NGD pathways. We briefly discuss the current progress and future perspectives of SSO therapy for rare and ultrarare diseases.
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Affiliation(s)
- Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry, Moscow State University, Moscow, Russia
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Falzarano MS, Grilli A, Zia S, Fang M, Rossi R, Gualandi F, Rimessi P, El Dani R, Fabris M, Lu Z, Li W, Mongini T, Ricci F, Pegoraro E, Bello L, Barp A, Sansone VA, Hegde M, Roda B, Reschiglian P, Bicciato S, Selvatici R, Ferlini A. RNA-seq in DMD urinary stem cells recognized muscle-related transcription signatures and addressed the identification of atypical mutations by whole-genome sequencing. HGG ADVANCES 2022; 3:100054. [PMID: 35047845 PMCID: PMC8756543 DOI: 10.1016/j.xhgg.2021.100054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Urinary stem cells (USCs) are a non-invasive, simple, and affordable cell source to study human diseases. Here we show that USCs are a versatile tool for studying Duchenne muscular dystrophy (DMD), since they are able to address RNA signatures and atypical mutation identification. Gene expression profiling of DMD individuals' USCs revealed a profound deregulation of inflammation, muscle development, and metabolic pathways that mirrors the known transcriptional landscape of DMD muscle and worsens following USCs' myogenic transformation. This pathogenic transcription signature was reverted by an exon-skipping corrective approach, suggesting the utility of USCs in monitoring DMD antisense therapy. The full DMD transcript profile performed in USCs from three undiagnosed DMD individuals addressed three splicing abnormalities, which were decrypted and confirmed as pathogenic variations by whole-genome sequencing (WGS). This combined genomic approach allowed the identification of three atypical and complex DMD mutations due to a deep intronic variation and two large inversions, respectively. All three mutations affect DMD gene splicing and cause a lack of dystrophin protein production, and one of these also generates unique fusion genes and transcripts. Further characterization of USCs using a novel cell-sorting technology (Celector) highlighted cell-type variability and the representation of cell-specific DMD isoforms. Our comprehensive approach to USCs unraveled RNA, DNA, and cell-specific features and demonstrated that USCs are a robust tool for studying and diagnosing DMD.
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Affiliation(s)
- Maria S Falzarano
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Andrea Grilli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | | | | | - Rachele Rossi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Francesca Gualandi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Paola Rimessi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Reem El Dani
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Marina Fabris
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | | | - Wenyan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Elena Pegoraro
- ERN Neuromuscular Center, Department of Neurosciences, Unit of Neurology, University of Padua, Padua 35122, Italy
| | - Luca Bello
- ERN Neuromuscular Center, Department of Neurosciences, Unit of Neurology, University of Padua, Padua 35122, Italy
| | - Andrea Barp
- The NEMO Clinical Center, Neurorehabilitation Unit, University of Milan, Milan 20162, Italy
| | - Valeria A Sansone
- The NEMO Clinical Center, Neurorehabilitation Unit, University of Milan, Milan 20162, Italy
| | - Madhuri Hegde
- PerkinElmer Genomics, 3950 Shackleford Rd., Ste. 195, Duluth, GA 30096, USA
| | - Barbara Roda
- Stem Sel s.r.l., Bologna 40127, Italy
- Department of Chemistry "G. Ciamician," University of Bologna, Bologna 40126, Italy
| | - Pierluigi Reschiglian
- Stem Sel s.r.l., Bologna 40127, Italy
- Department of Chemistry "G. Ciamician," University of Bologna, Bologna 40126, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | - Rita Selvatici
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Alessandra Ferlini
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
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Lesman D, Rodriguez Y, Rajakumar D, Wein N. U7 snRNA, a Small RNA with a Big Impact in Gene Therapy. Hum Gene Ther 2021; 32:1317-1329. [PMID: 34139889 DOI: 10.1089/hum.2021.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The uridine-rich 7 (U7) small nuclear RNA (snRNA) is a component of a small nuclear ribonucleoprotein (snRNP) complex. U7 snRNA naturally contains an antisense sequence that identifies histone premessenger RNAs (pre-mRNAs) and is involved in their 3' end processing. By altering this antisense sequence, researchers have turned U7 snRNA into a versatile tool for targeting pre-mRNAs and modifying splicing. Encapsulating a modified U7 snRNA into a viral vector such as adeno-associated virus (also referred as vectorized exon skipping/inclusion, or VES/VEI) enables the delivery of this highly efficacious splicing modulator into a range of cell lines, primary cells, and tissues. In addition, and in contrast to antisense oligonucleotides, viral delivery of U7 snRNA enables long-term expression of antisense sequences in the nucleus as part of a stable snRNP complex. As a result, VES/VEI has emerged as a promising therapeutic platform for treating a large variety of human diseases caused by errors in pre-mRNA splicing or its regulation. Here we provide an overview of U7 snRNA's natural function and its applications in gene therapy.
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Affiliation(s)
- Daniel Lesman
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Yacidzohara Rodriguez
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Dhanarajan Rajakumar
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Nicolas Wein
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatric, The Ohio State University, Columbus, Ohio, USA
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Wein N, Dunn DM, Waldrop MA, Gushchina LV, Frair EC, Weiss RB, Flanigan KM. Absence of Significant Off-Target Splicing Variation with a U7snRNA Vector Targeting DMD Exon 2 Duplications. Hum Gene Ther 2021; 32:1346-1359. [PMID: 34060935 DOI: 10.1089/hum.2020.315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Exon skipping therapies for Duchenne muscular dystrophy that restore an open reading frame can be induced by the use of noncoding U7 small nuclear RNA (U7snRNA) modified by an antisense exon-targeting sequence delivered by an adeno-associated virus (AAV) vector. We have developed an AAV vector (AAV9.U7-ACCA) containing four U7snRNAs targeting the splice donor and acceptor sites of dystrophin exon 2, resulting in highly efficient exclusion of DMD exon 2. We assessed the specificity of splice variation induced by AAV9.U7-ACCA delivery in the Dmd exon 2 duplication (Dup2) mouse model through an unbiased RNA-seq approach. Treatment-related effects on pre-mRNA splicing were quantified using local splicing variation (LSV) analysis. Filtering the transcriptome for differences in treatment-related splicing resulted in only 16 candidate off-target LSVs. Only a single candidate off-target LSV was found in both skeletal and cardiac muscle tissue and occurred at a known variable cassette exon. In contrast, four LSVs represented significant on-target correction of Dmd exon 2 splicing and transcriptome analysis showed correction of known dystrophin-deficient gene dysregulation. We conclude that the absence of off-target splicing induced by treatment with the U7-ACCA vector supports the continued clinical development of this approach.
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Affiliation(s)
- Nicolas Wein
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Megan A Waldrop
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Liubov V Gushchina
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Emma C Frair
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Kevin M Flanigan
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Neurology, The Ohio State University, Columbus, Ohio, USA
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7
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Beckers P, Caberg JH, Dideberg V, Dangouloff T, den Dunnen JT, Bours V, Servais L, Boemer F. Newborn screening of duchenne muscular dystrophy specifically targeting deletions amenable to exon-skipping therapy. Sci Rep 2021; 11:3011. [PMID: 33542429 PMCID: PMC7862591 DOI: 10.1038/s41598-021-82725-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/25/2021] [Indexed: 11/08/2022] Open
Abstract
Duchenne Muscular Dystrophy (DMD) is a lethal progressive muscle-wasting disease. New treatment strategies relying on DMD gene exon-skipping therapy have recently been approved and about 30% of patients could be amenable to exon 51, 53 or 45 skipping. We evaluated the spectrum of deletions reported in DMD registries, and designed a method to screen newborns and identify DMD deletions amenable to exon 51, 53 and 45 skipping. We developed a multiplex qPCR assay identifying hemi(homo)-zygotic deletions of the flanking exons of these therapeutic targets in DMD exons (i.e. exons 44, 46, 50, 52 and 54). We conducted an evaluation of our new method in 51 male patients with a DMD phenotype, 50 female carriers of a DMD deletion and 19 controls. Studies were performed on dried blood spots with patient's consent. We analyzed qPCR amplification curves of controls, carriers, and DMD patients to discern the presence or the absence of the target exons. Analysis of the exons flanking the exon-skipping targets permitted the identification of patients that could benefit from exon-skipping. All samples were correctly genotyped, with either presence or absence of amplification of the target exon. This proof-of-concept study demonstrates that this new assay is a highly sensitive method to identify DMD patients carrying deletions that are rescuable by exon-skipping treatment. The method is easily scalable to population-based screening. This targeted screening approach could address the new management paradigm in DMD, and could help to optimize the beneficial therapeutic effect of DMD therapies by permitting pre-symptomatic care.
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Affiliation(s)
- Pablo Beckers
- Biochemical Genetics Laboratory, Human Genetic Department, CHU de Liège, Université de Liège, CHU Sart-Tilman, Domaine Universitaire du Sart-Tilman, Avenue de l'Hôpital, 1, 4000, Liège, Belgium
| | - Jean-Hubert Caberg
- Molecular Genetics Laboratory, Human Genetic Department, CHU Sart-Tilman, University of Liege, Liège, Belgium
| | - Vinciane Dideberg
- Molecular Genetics Laboratory, Human Genetic Department, CHU Sart-Tilman, University of Liege, Liège, Belgium
| | - Tamara Dangouloff
- Division of Child Neurology, Neuromuscular Reference Center Disease, Department of Pediatrics, University Hospital Liège & University of Liège, Liège, Belgium
| | - Johan T den Dunnen
- Department of Human Genetics and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Vincent Bours
- Head of Human Genetics Department, CHU Sart-Tilman, University of Liege, Liège, Belgium
| | - Laurent Servais
- Division of Child Neurology, Neuromuscular Reference Center Disease, Department of Pediatrics, University Hospital Liège & University of Liège, Liège, Belgium
- Department of Paediatrics, MDUK Neuromuscular Center, University of Oxford, Oxford, UK
| | - François Boemer
- Biochemical Genetics Laboratory, Human Genetic Department, CHU de Liège, Université de Liège, CHU Sart-Tilman, Domaine Universitaire du Sart-Tilman, Avenue de l'Hôpital, 1, 4000, Liège, Belgium.
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