1
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Levchenko O, Panchuk I, Kochergin-Nikitsky K, Petrova I, Nagieva S, Pilkin M, Yakovlev I, Smirnikhina S, Deev R, Lavrov A. Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9. Biosystems 2024; 235:105072. [PMID: 37944631 DOI: 10.1016/j.biosystems.2023.105072] [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: 08/15/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The DYSF gene encoding dysferlin protein is one of the largest and has many transcripts. Pathogenic variants in the gene can lead to various types of myopathies, which makes it a good object for studying the events occurring in it during genome editing by the CRISPR/Cas method. In this study, we evaluated the possibility of permanent skipping of exons 3-4, and 26-27 which deletion does not violate the reading frame and allows to eliminate truncated variants within exons. Editing was performed with simultaneous transfection of two sgRNA- and sa/spCas9-containing plasmids on HEK293T cell cultures and healthy donor myoblasts. Skipping of exons 3-4 was performed by destroying the splicing acceptor sites, and exons 26-27 by cuts in the flanking exons with the corresponding deletion in the DNA. Some unexpected results were obtained, when exons 26-27 were skipped, exon 30 was also absent in the transcript, although it is not alternatively spliced and is normally present in all transcripts. This event indicates that DNA changes near splicing sites can affect adjacent exons and the whole gene. However, this fact requires further study.
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Affiliation(s)
- Olga Levchenko
- Research Centre for Medical Genetics, 115522, Moscow, Russia.
| | - Irina Panchuk
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | | | - Irina Petrova
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | - Sabina Nagieva
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | - Maxim Pilkin
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | | | | | - Roman Deev
- North-Western State Medical University named after I.I. Mechnikov, 191015, St. Petersburg, Russia
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2
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Shi X, Won M, Tang C, Ding Q, Sharma A, Wang F, Kim JS. RNA splicing based on reporter genes system: Detection, imaging and applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Bartas M, Volná A, Beaudoin CA, Poulsen ET, Červeň J, Brázda V, Špunda V, Blundell TL, Pečinka P. Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. Brief Bioinform 2022; 23:6539840. [PMID: 35229157 PMCID: PMC9116216 DOI: 10.1093/bib/bbac045] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/13/2022] [Accepted: 01/29/2022] [Indexed: 01/27/2023] Open
Abstract
SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein-coding loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modeling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Adriana Volná
- Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Christopher A Beaudoin
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK
| | | | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Czech Academy of Sciences, Brno, 612 65, Czech Republic
| | - Vladimír Špunda
- Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic.,Global Change Research Institute, Czech Academy of Sciences, Brno, 603 00, Czech Republic
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
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4
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Abstract
BACKGROUND RNA trans-splicing joins exons from different pre-mRNA transcripts to generate a chimeric product. Trans-splicing can also occur at the protein level, with split inteins mediating the ligation of separate gene products to generate a mature protein. SOURCES OF DATA Comprehensive literature search of published research papers and reviews using Pubmed. AREAS OF AGREEMENT Trans-splicing techniques have been used to target a wide range of diseases in both in vitro and in vivo models, resulting in RNA, protein and functional correction. AREAS OF CONTROVERSY Off-target effects can lead to therapeutically undesirable consequences. In vivo efficacy is typically low, and delivery issues remain a challenge. GROWING POINTS Trans-splicing provides a promising avenue for developing novel therapeutic approaches. However, much more research needs to be done before developing towards preclinical studies. AREAS TIMELY FOR DEVELOPING RESEARCH Increasing trans-splicing efficacy and specificity by rational design, screening and competitive inhibition of endogenous cis-splicing.
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Affiliation(s)
- Elizabeth M Hong
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Carin K Ingemarsdotter
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK
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5
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Mitsuhashi H, Homma S, Beermann ML, Ishimaru S, Takeda H, Yu BK, Liu K, Duraiswamy S, Boyce FM, Miller JB. Efficient system for upstream mRNA trans-splicing to generate covalent, head-to-tail, protein multimers. Sci Rep 2019; 9:2274. [PMID: 30783185 PMCID: PMC6381186 DOI: 10.1038/s41598-018-36684-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/20/2018] [Indexed: 01/11/2023] Open
Abstract
We present a plasmid-based system in which upstream trans-splicing efficiently generates mRNAs that encode head-to-tail protein multimers. In this system, trans-splicing occurs between one of two downstream splice donors in the sequence encoding a C-terminal V5 epitope tag and an upstream splice acceptor in the 5′ region of the pCS2(+) host plasmid. Using deletion and fusion constructs of the DUX4 protein as an example, we found that this system produced trans-spliced mRNAs in which coding regions from independent transcripts were fused in phase such that covalent head-to-tail protein multimers were translated. For a cDNA of ~450 bp, about half of the expressed proteins were multimeric, with the efficiency of trans-splicing and extent of multimer expression decreasing as cDNA length increased. This system generated covalent heterodimeric proteins upon co-transfections of plasmids encoding separate proteins and did not require a long complementary binding domain to position mRNAs for trans-splicing. This plasmid-based trans-splicing system is adaptable to multiple gene delivery systems, and it presents new opportunities for investigating molecular mechanisms of trans-splicing, generating covalent protein multimers with novel functions within cells, and producing mRNAs encoding large proteins from split precursors.
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Affiliation(s)
- Hiroaki Mitsuhashi
- Department of Applied, Biochemistry School of Engineering, Tokai University Kanagawa, Yokohama, 259-1207, Japan.
| | - Sachiko Homma
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Mary Lou Beermann
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Satoshi Ishimaru
- Department of Applied, Biochemistry School of Engineering, Tokai University Kanagawa, Yokohama, 259-1207, Japan
| | - Hayato Takeda
- Department of Applied, Biochemistry School of Engineering, Tokai University Kanagawa, Yokohama, 259-1207, Japan
| | - Bryant K Yu
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Kevin Liu
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Swetha Duraiswamy
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Frederick M Boyce
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Jeffrey Boone Miller
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA.
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6
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Tasfaout H, Cowling BS, Laporte J. Centronuclear myopathies under attack: A plethora of therapeutic targets. J Neuromuscul Dis 2019; 5:387-406. [PMID: 30103348 PMCID: PMC6218136 DOI: 10.3233/jnd-180309] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Centronuclear myopathies are a group of congenital myopathies characterized by severe muscle weakness, genetic heterogeneity, and defects in the structural organization of muscle fibers. Their names are derived from the central position of nuclei on biopsies, while they are at the fiber periphery under normal conditions. No specific therapy exists yet for these debilitating diseases. Mutations in the myotubularin phosphoinositides phosphatase, the GTPase dynamin 2, or amphiphysin 2 have been identified to cause respectively X-linked centronuclear myopathies (also called myotubular myopathy) or autosomal dominant and recessive forms. Mutations in additional genes, as RYR1, TTN, SPEG or CACNA1S, were linked to phenotypes that can overlap with centronuclear myopathies. Numerous animal models of centronuclear myopathies have been studied over the last 15 years, ranging from invertebrate to large mammalian models. Their characterization led to a partial understanding of the pathomechanisms of these diseases and allowed the recent validation of therapeutic proof-of-concepts. Here, we review the different therapeutic strategies that have been tested so far for centronuclear myopathies, some of which may be translated to patients.
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Affiliation(s)
- Hichem Tasfaout
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Belinda S. Cowling
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Correspondence to: Jocelyn Laporte, Tel.: 33 0 388653412; E-mail:
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7
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Dooley SJ, McDougald DS, Fisher KJ, Bennicelli JL, Mitchell LG, Bennett J. Spliceosome-Mediated Pre-mRNA trans-Splicing Can Repair CEP290 mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:294-308. [PMID: 30195768 PMCID: PMC6023944 DOI: 10.1016/j.omtn.2018.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/16/2018] [Accepted: 05/16/2018] [Indexed: 12/18/2022]
Abstract
Ocular gene therapy with recombinant adeno-associated virus (AAV) has shown vector-mediated gene augmentation to be safe and efficacious in the retina in one set of diseases (retinitis pigmentosa and Leber congenital amaurosis (LCA) caused by RPE65 deficiency), with excellent safety profiles to date and potential for efficacy in several additional diseases. However, size constraints imposed by the packaging capacity of the AAV genome restrict application to diseases with coding sequence lengths that are less than 5,000 nt. The most prevalent retinal diseases with monogenic inheritance are caused by mutations in genes that exceed this capacity. Here, we designed a spliceosome mediated pre-mRNA trans-splicing strategy to rescue expression of CEP290, which is associated with Leber congenital amaurosis type 10 (LCA10) and several syndromic diseases including Joubert syndrome. We used this reagent to demonstrate editing of CEP290 in cell lines in vitro and in vivo in a mini-gene mouse model. This study is the first to show broad editing of CEP290 transcripts and in vivo proof of concept for editing of CEP290 transcripts in photoreceptors and paves the way for future studies evaluating therapeutic effects.
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Affiliation(s)
- Scott J Dooley
- Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Devin S McDougald
- Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Krishna J Fisher
- Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeanette L Bennicelli
- Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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De Rosa L, Koller U, Bauer JW, De Luca M, Reichelt J. Advances on potential therapeutic options for epidermolysis bullosa. Expert Opin Orphan Drugs 2018. [DOI: 10.1080/21678707.2018.1463216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Laura De Rosa
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Ulrich Koller
- EB House Austria, University Hospital of Dermatology, Paracelsus Medical University, Salzburg, Austria
| | - Johann W. Bauer
- EB House Austria, University Hospital of Dermatology, Paracelsus Medical University, Salzburg, Austria
| | - Michele De Luca
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Julia Reichelt
- EB House Austria, University Hospital of Dermatology, Paracelsus Medical University, Salzburg, Austria
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9
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Liemberger B, Piñón Hofbauer J, Wally V, Arzt C, Hainzl S, Kocher T, Murauer EM, Bauer JW, Reichelt J, Koller U. RNA Trans-Splicing Modulation via Antisense Molecule Interference. Int J Mol Sci 2018. [PMID: 29518954 PMCID: PMC5877623 DOI: 10.3390/ijms19030762] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In recent years, RNA trans-splicing has emerged as a suitable RNA editing tool for the specific replacement of mutated gene regions at the pre-mRNA level. Although the technology has been successfully applied for the restoration of protein function in various genetic diseases, a higher trans-splicing efficiency is still desired to facilitate its clinical application. Here, we describe a modified, easily applicable, fluorescence-based screening system for the generation and analysis of antisense molecules specifically capable of improving the RNA reprogramming efficiency of a selected KRT14-specific RNA trans-splicing molecule. Using this screening procedure, we identified several antisense RNAs and short rationally designed oligonucleotides, which are able to increase the trans-splicing efficiency. Thus, we assume that besides the RNA trans-splicing molecule, short antisense molecules can act as splicing modulators, thereby increasing the trans-splicing efficiency to a level that may be sufficient to overcome the effects of certain genetic predispositions, particularly those associated with dominantly inherited diseases.
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Affiliation(s)
- Bernadette Liemberger
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Josefina Piñón Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Claudia Arzt
- Laboratory for Immunological and Molecular Cancer Research, Department of Internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Stefan Hainzl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Thomas Kocher
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Eva M Murauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Johann W Bauer
- Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Julia Reichelt
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
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10
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Charton K, Suel L, Henriques SF, Moussu JP, Bovolenta M, Taillepierre M, Becker C, Lipson K, Richard I. Exploiting the CRISPR/Cas9 system to study alternative splicing in vivo: application to titin. Hum Mol Genet 2018; 25:4518-4532. [PMID: 28173117 DOI: 10.1093/hmg/ddw280] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/29/2016] [Accepted: 08/18/2016] [Indexed: 11/12/2022] Open
Abstract
The giant protein titin is the third most abundant protein in striated muscle. Mutations in its gene are responsible for diseases affecting the cardiac and/or the skeletal muscle. Titin has been reported to be expressed in multiple isoforms with considerable variability in the I-band, ensuring the modulation of the passive mechanical properties of the sarcomere. In the M-line, only the penultimate Mex5 exon coding for the specific is7 domain has been reported to be subjected to alternative splicing. Using the CRISPR-Cas9 editing technology, we generated a mouse model where we stably prevent the expression of alternative spliced variant(s) carrying the corresponding domain. Interestingly, the suppression of the domain induces a phenotype mostly in tissues usually expressing the isoform that has been suppressed, indicating that it fulfills (a) specific function(s) in these tissues allowing a perfect adaptation of the M-line to physiological demands of different muscles.
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Affiliation(s)
- Karine Charton
- INSERM, U951, INTEGRARE research unit Evry, France,Généthon, Evry, France
| | - Laurence Suel
- INSERM, U951, INTEGRARE research unit Evry, France,Généthon, Evry, France
| | - Sara F Henriques
- INSERM, U951, INTEGRARE research unit Evry, France,Généthon, Evry, France,University of Evry-Val-D’Essone, Evry, France
| | - Jean-Paul Moussu
- SEAT - SErvice des Animaux Transgéniques CNRS -TAAM -phenomin UPS44 Bâtiment G 7, rue Guy Môquet 94800 Villejuif, France
| | - Matteo Bovolenta
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Miguel Taillepierre
- SEAT - SErvice des Animaux Transgéniques CNRS -TAAM -phenomin UPS44 Bâtiment G 7, rue Guy Môquet 94800 Villejuif, France
| | - Céline Becker
- SEAT - SErvice des Animaux Transgéniques CNRS -TAAM -phenomin UPS44 Bâtiment G 7, rue Guy Môquet 94800 Villejuif, France
| | - Karelia Lipson
- SEAT - SErvice des Animaux Transgéniques CNRS -TAAM -phenomin UPS44 Bâtiment G 7, rue Guy Môquet 94800 Villejuif, France
| | - Isabelle Richard
- INSERM, U951, INTEGRARE research unit Evry, France,Généthon, Evry, France
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11
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Poddar S, Loh PS, Ooi ZH, Osman F, Eul J, Patzel V. RNA Structure Design Improves Activity and Specificity of trans-Splicing-Triggered Cell Death in a Suicide Gene Therapy Approach. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 11:41-56. [PMID: 29858076 PMCID: PMC5849863 DOI: 10.1016/j.omtn.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/17/2018] [Accepted: 01/17/2018] [Indexed: 01/20/2023]
Abstract
Spliceosome-mediated RNA trans-splicing enables correction or labeling of pre-mRNA, but therapeutic applications are hampered by issues related to the activity and target specificity of trans-splicing RNA (tsRNA). We employed computational RNA structure design to improve both on-target activity and specificity of tsRNA in a herpes simplex virus thymidine kinase/ganciclovir suicide gene therapy approach targeting alpha fetoprotein (AFP), a marker of hepatocellular carcinoma (HCC) or human papillomavirus type 16 (HPV-16) pre-mRNA. While unstructured, mismatched target binding domains significantly improved 3′ exon replacement (3’ER), 5′ exon replacement (5’ER) correlated with the thermodynamic stability of the tsRNA 3′ end. Alternative on-target trans-splicing was found to be a prevalent event. The specificity of trans-splicing with the intended target splice site was improved 10-fold by designing tsRNA that harbors secondary target binding domains shielding alternative on-target and blinding off-target splicing events. Such rationally designed suicide RNAs efficiently triggered death of HPV-16-transduced or hepatoblastoma-derived human tissue culture cells without evidence for off-target cell killing. Highest cell death activities were observed with novel dual-targeting tsRNAs programmed for trans-splicing toward AFP and a second HCC pre-mRNA biomarker. Our observations suggest trans-splicing represents a promising approach to suicide gene therapy.
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Affiliation(s)
- Sushmita Poddar
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore
| | - Pei She Loh
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore
| | - Zi Hao Ooi
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore
| | - Farhana Osman
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore
| | - Joachim Eul
- INEIDFO GmbH, Weserstrasse 23, 12045 Berlin, Germany
| | - Volker Patzel
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore; Department of Medicine, Division of Infectious Diseases, University of Cambridge, Addenbrooke's Hospital, Level 5, Hills Road, Cambridge CB2 0QQ, UK.
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12
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Azibani F, Brull A, Arandel L, Beuvin M, Nelson I, Jollet A, Ziat E, Prudhon B, Benkhelifa-Ziyyat S, Bitoun M, Lorain S, Bonne G, Bertrand AT. Gene Therapy via Trans-Splicing for LMNA-Related Congenital Muscular Dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:376-386. [PMID: 29499949 PMCID: PMC5862133 DOI: 10.1016/j.omtn.2017.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 11/28/2022]
Abstract
We assessed the potential of Lmna-mRNA repair by spliceosome-mediated RNA trans-splicing as a therapeutic approach for LMNA-related congenital muscular dystrophy. This gene therapy strategy leads to reduction of mutated transcript expression for the benefit of corresponding wild-type (WT) transcripts. We developed 5′-RNA pre-trans-splicing molecules containing the first five exons of Lmna and targeting intron 5 of Lmna pre-mRNA. Among nine pre-trans-splicing molecules, differing in the targeted sequence in intron 5 and tested in C2C12 myoblasts, three induced trans-splicing events on endogenous Lmna mRNA and confirmed at protein level. Further analyses performed in primary myotubes derived from an LMNA-related congenital muscular dystrophy (L-CMD) mouse model led to a partial rescue of the mutant phenotype. Finally, we tested this approach in vivo using adeno-associated virus (AAV) delivery in newborn mice and showed that trans-splicing events occurred in WT mice 50 days after AAV delivery, although at a low rate. Altogether, while these results provide the first evidence for reprogramming LMNA mRNA in vitro, strategies to improve the rate of trans-splicing events still need to be developed for efficient application of this therapeutic approach in vivo.
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Affiliation(s)
- Feriel Azibani
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Astrid Brull
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Ludovic Arandel
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Maud Beuvin
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Isabelle Nelson
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Arnaud Jollet
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Esma Ziat
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Bernard Prudhon
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | | | - Marc Bitoun
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Stéphanie Lorain
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Gisèle Bonne
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Anne T Bertrand
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France.
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13
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Rindt H, Tom CM, Lorson CL, Mattis VB. Optimization of trans-Splicing for Huntington's Disease RNA Therapy. Front Neurosci 2017; 11:544. [PMID: 29066943 PMCID: PMC5641306 DOI: 10.3389/fnins.2017.00544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/19/2017] [Indexed: 11/16/2022] Open
Abstract
Huntington's disease (HD) is a devastating neurodegenerative disorder caused by a polyglutamine (polyQ) expansion in exon 1 of the Huntingtin (HTT) gene. We have previously demonstrated that spliceosome-mediated trans-splicing is a viable molecular strategy to specifically reduce and repair mutant HTT (mtHTT). Here, the targeted tethering efficacy of the pre-mRNA trans-splicing modules (PTM) in HTT was optimized. Various PTMs that targeted the 3′ end of HTT intron 1 or the intron 1 branch point were shown trans-splice into an HTT mini-gene, as well as the endogenous HTT pre-mRNA. PTMs that specifically target the endogenous intron 1 branch point increased the trans-splicing efficacy from 1–5 to 10–15%. Furthermore, lentiviral expression of PTMs in a human HD patient iPSC-derived neural culture significantly reversed two previously established polyQ-length dependent phenotypes. These results suggest that pre-mRNA repair of mtHTT could hold therapeutic benefit and it demonstrates an alternative platform to correct the mRNA product produced by the mtHTT allele in the context of HD.
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Affiliation(s)
- Hansjörg Rindt
- Department of Veterinary Pathobiology, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Colton M Tom
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA, United States
| | - Christian L Lorson
- Department of Veterinary Pathobiology, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Virginia B Mattis
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA, United States
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14
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Huang D, Fletcher S, Wilton SD, Palmer N, McLenachan S, Mackey DA, Chen FK. Inherited Retinal Disease Therapies Targeting Precursor Messenger Ribonucleic Acid. Vision (Basel) 2017; 1:vision1030022. [PMID: 31740647 PMCID: PMC6836112 DOI: 10.3390/vision1030022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 02/07/2023] Open
Abstract
Inherited retinal diseases are an extremely diverse group of genetically and phenotypically heterogeneous conditions characterized by variable maturation of retinal development, impairment of photoreceptor cell function and gradual loss of photoreceptor cells and vision. Significant progress has been made over the last two decades in identifying the many genes implicated in inherited retinal diseases and developing novel therapies to address the underlying genetic defects. Approximately one-quarter of exonic mutations related to human inherited diseases are likely to induce aberrant splicing products, providing opportunities for the development of novel therapeutics that target splicing processes. The feasibility of antisense oligomer mediated splice intervention to treat inherited diseases has been demonstrated in vitro, in vivo and in clinical trials. In this review, we will discuss therapeutic approaches to treat inherited retinal disease, including strategies to correct splicing and modify exon selection at the level of pre-mRNA. The challenges of clinical translation of this class of emerging therapeutics will also be discussed.
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Affiliation(s)
- Di Huang
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Sue Fletcher
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Steve D. Wilton
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Norman Palmer
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth 6000, Australia
- Correspondence: ; Tel.: +61-8-9381-0817
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15
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Ingemarsdotter CK, Poddar S, Mercier S, Patzel V, Lever AML. Expression of Herpes Simplex Virus Thymidine Kinase/Ganciclovir by RNA Trans-Splicing Induces Selective Killing of HIV-Producing Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 7:140-154. [PMID: 28624190 PMCID: PMC5415956 DOI: 10.1016/j.omtn.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/20/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Antiviral strategies targeting hijacked cellular processes are less easily evaded by the virus than viral targets. If selective for viral functions, they can have a high therapeutic index. We used RNA trans-splicing to deliver the herpes simplex virus thymidine kinase-ganciclovir (HSV-tk/GCV) cell suicide system into HIV-producing cells. Using an extensive in silico bioinformatics and RNA structural analysis approach, ten HIV RNA trans-splicing constructs were designed targeting eight different HIV splice donor or acceptor sites and were tested in cells expressing HIV. Trans-spliced mRNAs were identified in HIV-expressing cells using qRT-PCR with successful detection of fusion RNA transcripts between HIV RNA and the HSV-tk RNA transcripts from six of ten candidate RNA trans-splicing constructs. Conventional PCR and Sanger sequencing confirmed RNA trans-splicing junctions. Measuring cell viability in the presence or absence of GCV expression of HSV-tk by RNA trans-splicing led to selective killing of HIV-producing cells using either 3' exon replacement or 5' exon replacement in the presence of GCV. Five constructs targeting four HIV splice donor and acceptor sites, D4, A5, A7, and A8, involved in regulating the generation of multiple HIV RNA transcripts proved to be effective for trans-splicing mediated selective killing of HIV-infected cells, within which individual constructs targeting D4 and A8 were the most efficient.
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Affiliation(s)
- Carin K Ingemarsdotter
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sushmita Poddar
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Sarah Mercier
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Volker Patzel
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Andrew M L Lever
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK.
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16
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Bornert O, Peking P, Bremer J, Koller U, van den Akker PC, Aartsma-Rus A, Pasmooij AMG, Murauer EM, Nyström A. RNA-based therapies for genodermatoses. Exp Dermatol 2017; 26:3-10. [PMID: 27376675 PMCID: PMC5593095 DOI: 10.1111/exd.13141] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2016] [Indexed: 12/14/2022]
Abstract
Genetic disorders affecting the skin, genodermatoses, constitute a large and heterogeneous group of diseases, for which treatment is generally limited to management of symptoms. RNA-based therapies are emerging as a powerful tool to treat genodermatoses. In this review, we discuss in detail RNA splicing modulation by antisense oligonucleotides and RNA trans-splicing, transcript replacement and genome editing by in vitro-transcribed mRNAs, and gene knockdown by small interfering RNA and antisense oligonucleotides. We present the current state of these therapeutic approaches and critically discuss their opportunities, limitations and the challenges that remain to be solved. The aim of this review was to set the stage for the development of new and better therapies to improve the lives of patients and families affected by a genodermatosis.
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Affiliation(s)
- Olivier Bornert
- Department of Dermatology, Medical Center – University of
Freiburg, Freiburg, Germany
| | - Patricia Peking
- EB House Austria, Research Program for Molecular Therapy of
Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus
Medical University, Salzburg, Austria
| | - Jeroen Bremer
- Department of Dermatology, University Medical Center Groningen,
University of Groningen, Groningen, The Netherlands
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of
Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus
Medical University, Salzburg, Austria
| | - Peter C. van den Akker
- Department of Dermatology, University Medical Center Groningen,
University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen,
University of Groningen, Groningen, The Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center,
Leiden, The Netherlands
| | - Anna M. G. Pasmooij
- Department of Dermatology, University Medical Center Groningen,
University of Groningen, Groningen, The Netherlands
| | - Eva M. Murauer
- EB House Austria, Research Program for Molecular Therapy of
Genodermatoses, Department of Dermatology, University Hospital of the Paracelsus
Medical University, Salzburg, Austria
| | - Alexander Nyström
- Department of Dermatology, Medical Center – University of
Freiburg, Freiburg, Germany
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17
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18
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Designing Efficient Double RNA trans-Splicing Molecules for Targeted RNA Repair. Int J Mol Sci 2016; 17:ijms17101609. [PMID: 27669223 PMCID: PMC5085642 DOI: 10.3390/ijms17101609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/24/2016] [Accepted: 09/14/2016] [Indexed: 11/17/2022] Open
Abstract
RNA trans-splicing is a promising tool for mRNA modification in a diversity of genetic disorders. In particular, the substitution of internal exons of a gene by combining 3' and 5' RNA trans-splicing seems to be an elegant way to modify especially large pre-mRNAs. Here we discuss a robust method for designing double RNA trans-splicing molecules (dRTM). We demonstrate how the technique can be implemented in an endogenous setting, using COL7A1, the gene encoding type VII collagen, as a target. An RTM screening system was developed with the aim of testing the replacement of two internal COL7A1 exons, harbouring a homozygous mutation, with the wild-type version. The most efficient RTMs from a pool of randomly generated variants were selected via our fluorescence-based screening system and adapted for use in an in vitro disease model system. Transduction of type VII collagen-deficient keratinocytes with the selected dRTM led to accurate replacement of two internal COL7A1 exons resulting in a restored wild-type RNA sequence. This is the first study demonstrating specific exon replacement by double RNA trans-splicing within an endogenous transcript in cultured cells, corroborating the utility of this technology for mRNA repair in a variety of genetic disorders.
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19
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Reprogramming the Dynamin 2 mRNA by Spliceosome-mediated RNA Trans-splicing. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e362. [PMID: 27623444 PMCID: PMC5056991 DOI: 10.1038/mtna.2016.67] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/20/2016] [Indexed: 02/04/2023]
Abstract
Dynamin 2 (DNM2) is a large GTPase, ubiquitously expressed, involved in membrane trafficking and regulation of actin and microtubule cytoskeletons. DNM2 mutations cause autosomal dominant centronuclear myopathy which is a rare congenital myopathy characterized by skeletal muscle weakness and histopathological features including nuclear centralization in absence of regeneration. No curative treatment is currently available for the DNM2-related autosomal dominant centronuclear myopathy. In order to develop therapeutic strategy, we evaluated here the potential of Spliceosome-Mediated RNA Trans-splicing technology to reprogram the Dnm2-mRNA in vitro and in vivo in mice. We show that classical 3′-trans-splicing strategy cannot be considered as accurate therapeutic strategy regarding toxicity of the pre-trans-splicing molecules leading to low rate of trans-splicing in vivo. Thus, we tested alternative strategies devoted to prevent this toxicity and enhance frequency of trans-splicing events. We succeeded to overcome the toxicity through a 5′-trans-splicing strategy which also allows detection of trans-splicing events at mRNA and protein levels in vitro and in vivo. These results suggest that the Spliceosome-Mediated RNA Trans-splicing strategy may be used to reprogram mutated Dnm2-mRNA but highlight the potential toxicity linked to the molecular tools which have to be carefully investigated during preclinical development.
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20
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Construction and validation of an RNA trans-splicing molecule suitable to repair a large number of COL7A1 mutations. Gene Ther 2016; 23:775-784. [PMID: 27434145 PMCID: PMC5097067 DOI: 10.1038/gt.2016.57] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/22/2016] [Accepted: 07/11/2016] [Indexed: 12/17/2022]
Abstract
RNA trans-splicing has become a versatile tool in the gene therapy of monogenetic diseases. This technique is especially valuable for the correction of mutations in large genes such as COL7A1, which underlie the dystrophic subtype of the skin blistering disease epidermolysis bullosa. Over 800 mutations spanning the entire length of the COL7A1 gene have been associated with defects in type VII collagen, leading to excessive fragility of epithelial tissues, the hallmark of dystrophic epidermolysis bullosa (DEB). In the present study, we designed an RNA trans-splicing molecule (RTM) that is capable of repairing any given mutation within a 4200 nucleotide region spanning the 3′ half of COL7A1. The selected RTM, RTM28, was able to induce accurate trans-splicing into endogenous COL7A1 pre-mRNA transcripts in a type VII collagen-deficient DEB patient-derived cell line. Correct trans-splicing was detected at the RNA level by semiquantitative RT-PCR and correction of full-length type VII collagen was confirmed at the protein level by immunofluorescence and western blot analyses. Our results demonstrate that RTM28, which covers >60% of all mutations reported in DEB and is thus the longest RTM described so far for the repair of COL7A1, represents a promising candidate for therapeutic applications.
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21
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Berger A, Maire S, Gaillard MC, Sahel JA, Hantraye P, Bemelmans AP. mRNA trans-splicing in gene therapy for genetic diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:487-98. [PMID: 27018401 PMCID: PMC5071737 DOI: 10.1002/wrna.1347] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/27/2016] [Accepted: 02/22/2016] [Indexed: 11/12/2022]
Abstract
Spliceosome-mediated RNA trans-splicing, or SMaRT, is a promising strategy to design innovative gene therapy solutions for currently intractable genetic diseases. SMaRT relies on the correction of mutations at the post-transcriptional level by modifying the mRNA sequence. To achieve this, an exogenous RNA is introduced into the target cell, usually by means of gene transfer, to induce a splice event in trans between the exogenous RNA and the target endogenous pre-mRNA. This produces a chimeric mRNA composed partly of exons of the latter, and partly of exons of the former, encoding a sequence free of mutations. The principal challenge of SMaRT technology is to achieve a reaction as complete as possible, i.e., resulting in 100% repairing of the endogenous mRNA target. The proof of concept of SMaRT feasibility has already been established in several models of genetic diseases caused by recessive mutations. In such cases, in fact, the repair of only a portion of the mutant mRNA pool may be sufficient to obtain a significant therapeutic effect. However in the case of dominant mutations, the target cell must be freed from the majority of mutant mRNA copies, requiring a highly efficient trans-splicing reaction. This likely explains why only a few examples of SMaRT approaches targeting dominant mutations are reported in the literature. In this review, we explain in details the mechanism of trans-splicing, review the different strategies that are under evaluation to lead to efficient trans-splicing, and discuss the advantages and limitations of SMaRT. WIREs RNA 2016, 7:487-498. doi: 10.1002/wrna.1347 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Adeline Berger
- Centre de recherche Institut de la Vision, Sorbonne Universités, Université Pierre et Marie Curie UM80, Paris, France
| | - Séverine Maire
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, Fontenay-aux-Roses, France
| | - Marie-Claude Gaillard
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, Fontenay-aux-Roses, France
| | - José-Alain Sahel
- Centre de recherche Institut de la Vision, Sorbonne Universités, Université Pierre et Marie Curie UM80, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Institute of Ophthalmology, University College of London, London, UK
| | - Philippe Hantraye
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, Fontenay-aux-Roses, France
| | - Alexis-Pierre Bemelmans
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, Fontenay-aux-Roses, France
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22
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Can we be SMaRT-er in our approach to cancer therapy? EBioMedicine 2015; 2:621-2. [PMID: 26288827 PMCID: PMC4534698 DOI: 10.1016/j.ebiom.2015.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/02/2015] [Indexed: 11/22/2022] Open
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23
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Philippi S, Lorain S, Beley C, Peccate C, Précigout G, Spuler S, Garcia L. Dysferlin rescue by spliceosome-mediated pre-mRNA trans-splicing targeting introns harbouring weakly defined 3' splice sites. Hum Mol Genet 2015; 24:4049-60. [PMID: 25904108 DOI: 10.1093/hmg/ddv141] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 12/12/2022] Open
Abstract
The modification of the pre-mRNA cis-splicing process employing a pre-mRNA trans-splicing molecule (PTM) is an attractive strategy for the in situ correction of genes whose careful transcription regulation and full-length expression is determinative for protein function, as it is the case for the dysferlin (DYSF, Dysf) gene. Loss-of-function mutations of DYSF result in different types of muscular dystrophy mainly manifesting as limb girdle muscular dystrophy 2B (LGMD2B) and Miyoshi muscular dystrophy 1 (MMD1). We established a 3' replacement strategy for mutated DYSF pre-mRNAs induced by spliceosome-mediated pre-mRNA trans-splicing (SmaRT) by the use of a PTM. In contrast to previously established SmaRT strategies, we particularly focused on the identification of a suitable pre-mRNA target intron other than the optimization of the PTM design. By targeting DYSF pre-mRNA introns harbouring differentially defined 3' splice sites (3' SS), we found that target introns encoding weakly defined 3' SSs were trans-spliced successfully in vitro in human LGMD2B myoblasts as well as in vivo in skeletal muscle of wild-type and Dysf(-/-) mice. For the first time, we demonstrate rescue of Dysf protein by SmaRT in vivo. Moreover, we identified concordant qualities among the successfully targeted Dysf introns and targeted endogenous introns in previously reported SmaRT approaches that might facilitate a selective choice of target introns in future SmaRT strategies.
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Affiliation(s)
- Susanne Philippi
- Université de Versailles St-Quentin, INSERM U1179, LIA BAHN Centre Scientifique de Monaco, 2 Avenue de la Source de la Bievre, Montigny-le-Bretonneux 78180, France, Muscle Research Unit, Experimental and Clinical Research Center, a Joint Cooperation Between Max-Delbrück-Center for Molecular Medicine and Charité Medical Faculty, Berlin, Germany and Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Myology Research Center, Paris, France
| | - Stéphanie Lorain
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Myology Research Center, Paris, France
| | - Cyriaque Beley
- Université de Versailles St-Quentin, INSERM U1179, LIA BAHN Centre Scientifique de Monaco, 2 Avenue de la Source de la Bievre, Montigny-le-Bretonneux 78180, France
| | - Cécile Peccate
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Myology Research Center, Paris, France
| | - Guillaume Précigout
- Université de Versailles St-Quentin, INSERM U1179, LIA BAHN Centre Scientifique de Monaco, 2 Avenue de la Source de la Bievre, Montigny-le-Bretonneux 78180, France
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, a Joint Cooperation Between Max-Delbrück-Center for Molecular Medicine and Charité Medical Faculty, Berlin, Germany and
| | - Luis Garcia
- Université de Versailles St-Quentin, INSERM U1179, LIA BAHN Centre Scientifique de Monaco, 2 Avenue de la Source de la Bievre, Montigny-le-Bretonneux 78180, France,
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24
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Shang Y, Tesar D, Hötzel I. Modular protein expression by RNA trans-splicing enables flexible expression of antibody formats in mammalian cells from a dual-host phage display vector. Protein Eng Des Sel 2015; 28:437-44. [PMID: 25855659 DOI: 10.1093/protein/gzv018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 03/03/2015] [Indexed: 01/09/2023] Open
Abstract
A recently described dual-host phage display vector that allows expression of immunoglobulin G (IgG) in mammalian cells bypasses the need for subcloning of phage display clone inserts to mammalian vectors for IgG expression in large antibody discovery and optimization campaigns. However, antibody discovery and optimization campaigns usually need different antibody formats for screening, requiring reformatting of the clones in the dual-host phage display vector to an alternative vector. We developed a modular protein expression system mediated by RNA trans-splicing to enable the expression of different antibody formats from the same phage display vector. The heavy-chain region encoded by the phage display vector is directly and precisely fused to different downstream heavy-chain sequences encoded by complementing plasmids simply by joining exons in different pre-mRNAs by trans-splicing. The modular expression system can be used to efficiently express structurally correct IgG and Fab fragments or other antibody formats from the same phage display clone in mammalian cells without clone reformatting.
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Affiliation(s)
- Yonglei Shang
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Devin Tesar
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Isidro Hötzel
- Department of Antibody Engineering, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
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25
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Berger A, Lorain S, Joséphine C, Desrosiers M, Peccate C, Voit T, Garcia L, Sahel JA, Bemelmans AP. Repair of rhodopsin mRNA by spliceosome-mediated RNA trans-splicing: a new approach for autosomal dominant retinitis pigmentosa. Mol Ther 2015; 23:918-930. [PMID: 25619725 PMCID: PMC4427870 DOI: 10.1038/mt.2015.11] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 01/12/2015] [Indexed: 12/26/2022] Open
Abstract
The promising clinical results obtained for ocular gene therapy in recent years have paved the way for gene supplementation to treat recessively inherited forms of retinal degeneration. The situation is more complex for dominant mutations, as the toxic mutant gene product must be removed. We used spliceosome-mediated RNA trans-splicing as a strategy for repairing the transcript of the rhodopsin gene, the gene most frequently mutated in autosomal dominant retinitis pigmentosa. We tested 17 different molecules targeting the pre-mRNA intron 1, by transient transfection of HEK-293T cells, with subsequent trans-splicing quantification at the transcript level. We found that the targeting of some parts of the intron promoted trans-splicing more efficiently than the targeting of other areas, and that trans-splicing rate could be increased by modifying the replacement sequence. We then developed cell lines stably expressing the rhodopsin gene, for the assessment of phenotypic criteria relevant to the pathogenesis of retinitis pigmentosa. Using this model, we showed that trans-splicing restored the correct localization of the protein to the plasma membrane. Finally, we tested our best candidate by AAV gene transfer in a mouse model of retinitis pigmentosa that expresses a mutant allele of the human rhodopsin gene, and demonstrated the feasibility of trans-splicing in vivo. This work paves the way for trans-splicing gene therapy to treat retinitis pigmentosa due to rhodopsin gene mutation and, more generally, for the treatment of genetic diseases with dominant transmission.
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Affiliation(s)
- Adeline Berger
- Centre de recherche Institut de la Vision, Sorbonne Universités, Université Pierre et Marie Curie UM80, INSERM U968, and CNRS UMR 7210, Paris, France
| | - Stéphanie Lorain
- Centre de recherche en Myologie, Sorbonne Universités, Université Pierre et Marie Curie, UM76, INSERM U974 and CNRS FRE 3617, Paris, France
| | - Charlène Joséphine
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), MIRCen, Fontenay-aux-Roses, France; Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR9199, Neurodegenerative Diseases Laboratory, Fontenay-aux-Roses, France
| | - Melissa Desrosiers
- Centre de recherche Institut de la Vision, Sorbonne Universités, Université Pierre et Marie Curie UM80, INSERM U968, and CNRS UMR 7210, Paris, France
| | - Cécile Peccate
- Centre de recherche en Myologie, Sorbonne Universités, Université Pierre et Marie Curie, UM76, INSERM U974 and CNRS FRE 3617, Paris, France
| | - Thomas Voit
- Centre de recherche en Myologie, Sorbonne Universités, Université Pierre et Marie Curie, UM76, INSERM U974 and CNRS FRE 3617, Paris, France
| | - Luis Garcia
- UFR des sciences de la santé Simone Veil, Université Versailles Saint-Quentin, Montigny-le-Bretonneux, France
| | - José-Alain Sahel
- Centre de recherche Institut de la Vision, Sorbonne Universités, Université Pierre et Marie Curie UM80, INSERM U968, and CNRS UMR 7210, Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 503, Paris, France; Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Institute of Ophthalmology, University College of London, London, UK
| | - Alexis-Pierre Bemelmans
- Centre de recherche Institut de la Vision, Sorbonne Universités, Université Pierre et Marie Curie UM80, INSERM U968, and CNRS UMR 7210, Paris, France; Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), MIRCen, Fontenay-aux-Roses, France; Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR9199, Neurodegenerative Diseases Laboratory, Fontenay-aux-Roses, France.
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