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Zhang H, Xin M, Lin L, Chen C, Balestra D, Ding Q. Pleiotropic effects of different exonic nucleotide changes at the same position contribute to hemophilia B phenotypic variation. J Thromb Haemost 2024; 22:975-989. [PMID: 38184202 DOI: 10.1016/j.jtha.2023.12.031] [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: 10/20/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND The disease-causing effects of genetic variations often depend on their location within a gene. Exonic changes generally lead to alterations in protein production, secretion, activity, or clearance. However, owing to the overlap between proteins and splicing codes, missense variants can also affect messenger RNA splicing, thus adding a layer of complexity and influencing disease phenotypes. OBJECTIVES To extensively characterize a panel of 13 exonic variants in the F9 gene occurring at 6 different factor IX positions and associated with varying severities of hemophilia B (HB). METHODS Computational predictions, splicing analysis, and recombinant factor IX assays were exploited to characterize F9 variants. RESULTS We demonstrated that 5 (38%) of 13 selected F9 exonic variants have pleiotropic effects. Although bioinformatic approaches accurately classified effects, extensive experimental assays were required to elucidate and deepen the molecular mechanisms underlying the pleiotropic effects. Importantly, their characterization was instrumental in developing tailored RNA therapeutics based on engineered U7 small nuclear RNA to mask cryptic splice sites and compensatory U1 small nuclear RNA to enhance exon definition. CONCLUSION Overall, albeit a multitool bioinformatic approach suggested the molecular effects of multiple HB variants, the deep investigation of molecular mechanisms revealed insights into the HB phenotype-genotype relationship, enabling accurate classification of HB variants. Importantly, knowledge of molecular mechanisms allowed the development of tailored RNA therapeutics, which can also be translated to other genetic diseases.
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Affiliation(s)
- Huayang Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Min Xin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Liya Lin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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Gonçalves M, Santos JI, Coutinho MF, Matos L, Alves S. Development of Engineered-U1 snRNA Therapies: Current Status. Int J Mol Sci 2023; 24:14617. [PMID: 37834063 PMCID: PMC10572768 DOI: 10.3390/ijms241914617] [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: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression. The majority of human genes that encode proteins undergo alternative pre-mRNA splicing and mutations that affect splicing are more prevalent than previously thought. Targeting aberrant RNA(s) may thus provide an opportunity to correct faulty splicing and potentially treat numerous genetic disorders. To that purpose, the use of engineered U1 snRNA (either modified U1 snRNAs or exon-specific U1s-ExSpeU1s) has been applied as a potentially therapeutic strategy to correct splicing mutations, particularly those affecting the 5' splice-site (5'ss). Here we review and summarize a vast panoply of studies that used either modified U1 snRNAs or ExSpeU1s to mediate gene therapeutic correction of splicing defects underlying a considerable number of genetic diseases. We also focus on the pre-clinical validation of these therapeutic approaches both in vitro and in vivo, and summarize the main obstacles that need to be overcome to allow for their successful translation to clinic practice in the future.
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Affiliation(s)
- Mariana Gonçalves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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3
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Suda T, Yokoo T, Kanefuji T, Kamimura K, Zhang G, Liu D. Hydrodynamic Delivery: Characteristics, Applications, and Technological Advances. Pharmaceutics 2023; 15:pharmaceutics15041111. [PMID: 37111597 PMCID: PMC10141091 DOI: 10.3390/pharmaceutics15041111] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
The principle of hydrodynamic delivery was initially used to develop a method for the delivery of plasmids into mouse hepatocytes through tail vein injection and has been expanded for use in the delivery of various biologically active materials to cells in various organs in a variety of animal species through systemic or local injection, resulting in significant advances in new applications and technological development. The development of regional hydrodynamic delivery directly supports successful gene delivery in large animals, including humans. This review summarizes the fundamentals of hydrodynamic delivery and the progress that has been made in its application. Recent progress in this field offers tantalizing prospects for the development of a new generation of technologies for broader application of hydrodynamic delivery.
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4
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Hatch ST, Smargon AA, Yeo GW. Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 2022; 205:140-148. [PMID: 35764245 PMCID: PMC11185844 DOI: 10.1016/j.ymeth.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool. With the goal of providing a user-friendly protocol, we compile and demonstrate a methodological toolkit for sequence-specific targeted perturbation of alternatively spliced pre-mRNA with engineered U1 snRNAs. We observe robust modulation of endogenous pre-mRNA transcripts targeted in two contrasting splicing contexts, SMN2 exon 7 and FAS exon 6, exhibiting the utility and applicability of engineered U1 snRNA to both inclusion and exclusion of targeted exons. We anticipate that these demonstrations will contribute to the usability of U1 snRNA in investigating splicing modulation in eukaryotic cells, increasing accessibility to the broader research community.
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Affiliation(s)
- Samuel T Hatch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
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5
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Rescue of a familial dysautonomia mouse model by AAV9-Exon-specific U1 snRNA. Am J Hum Genet 2022; 109:1534-1548. [PMID: 35905737 PMCID: PMC9388384 DOI: 10.1016/j.ajhg.2022.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/30/2022] [Indexed: 02/06/2023] Open
Abstract
Familial dysautonomia (FD) is a currently untreatable, neurodegenerative disease caused by a splicing mutation (c.2204+6T>C) that causes skipping of exon 20 of the elongator complex protein 1 (ELP1) pre-mRNA. Here, we used adeno-associated virus serotype 9 (AAV9-U1-FD) to deliver an exon-specific U1 (ExSpeU1) small nuclear RNA, designed to cause inclusion of ELP1 exon 20 only in those cells expressing the target pre-mRNA, in a phenotypic mouse model of FD. Postnatal systemic and intracerebral ventricular treatment in these mice increased the inclusion of ELP1 exon 20. This also augmented the production of functional protein in several tissues including brain, dorsal root, and trigeminal ganglia. Crucially, the treatment rescued most of the FD mouse mortality before one month of age (89% vs 52%). There were notable improvements in ataxic gait as well as renal (serum creatinine) and cardiac (ejection fraction) functions. RNA-seq analyses of dorsal root ganglia from treated mice and human cells overexpressing FD-ExSpeU1 revealed only minimal global changes in gene expression and splicing. Overall then, our data prove that AAV9-U1-FD is highly specific and will likely be a safe and effective therapeutic strategy for this debilitating disease.
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6
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Sacchetto C, Peretto L, Baralle F, Maestri I, Tassi F, Bernardi F, van de Graaf SFJ, Pagani F, Pinotti M, Balestra D. OTC intron 4 variations mediate pathogenic splicing patterns caused by the c.386G>A mutation in humans and spf ash mice, and govern susceptibility to RNA-based therapies. Mol Med 2021; 27:157. [PMID: 34906067 PMCID: PMC8670272 DOI: 10.1186/s10020-021-00418-9] [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: 09/07/2021] [Accepted: 11/30/2021] [Indexed: 12/01/2022] Open
Abstract
Background Aberrant splicing is a common outcome in the presence of exonic or intronic variants that might hamper the intricate network of interactions defining an exon in a specific gene context. Therefore, the evaluation of the functional, and potentially pathological, role of nucleotide changes remains one of the major challenges in the modern genomic era. This aspect has also to be taken into account during the pre-clinical evaluation of innovative therapeutic approaches in animal models of human diseases. This is of particular relevance when developing therapeutics acting on splicing, an intriguing and expanding research area for several disorders. Here, we addressed species-specific splicing mechanisms triggered by the OTC c.386G>A mutation, relatively frequent in humans, leading to Ornithine TransCarbamylase Deficiency (OTCD) in patients and spfash mice, and its differential susceptibility to RNA therapeutics based on engineered U1snRNA. Methods Creation and co-expression of engineered U1snRNAs with human and mouse minigenes, either wild-type or harbouring different nucleotide changes, in human (HepG2) and mouse (Hepa1-6) hepatoma cells followed by analysis of splicing pattern. RNA pulldown studies to evaluate binding of specific splicing factors. Results Comparative nucleotide analysis suggested a role for the intronic +10-11 nucleotides, and pull-down assays showed that they confer preferential binding to the TIA1 splicing factor in the mouse context, where TIA1 overexpression further increases correct splicing. Consistently, the splicing profile of the human minigene with mouse +10-11 nucleotides overlapped that of mouse minigene, and restored responsiveness to TIA1 overexpression and to compensatory U1snRNA. Swapping the human +10-11 nucleotides into the mouse context had opposite effects. Moreover, the interplay between the authentic and the adjacent cryptic 5′ss in the human OTC dictates pathogenic mechanisms of several OTCD-causing 5′ss mutations, and only the c.386+5G>A change, abrogating the cryptic 5′ss, was rescuable by engineered U1snRNA. Conclusions Subtle intronic variations explain species-specific OTC splicing patterns driven by the c.386G>A mutation, and the responsiveness to engineered U1snRNAs, which suggests careful elucidation of molecular mechanisms before proposing translation of tailored therapeutics from animal models to humans. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-021-00418-9.
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Affiliation(s)
- Claudia Sacchetto
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy.,Department of Molecular Genetics, University of Maastricht, Maastricht, The Netherlands
| | - Laura Peretto
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | | | - Iva Maestri
- Department of Translational Medicine and for Romagna, Pathology Unit of Pathologic Anatomy, Histology and Cytology, University of Ferrara, Ferrara, Italy
| | - Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Academic Medical Center, Amsterdam, The Netherlands
| | - Franco Pagani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy.
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy.
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7
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Donegà S, Rogalska ME, Pianigiani G, Igreja S, Amaral MD, Pagani F. Rescue of common exon-skipping mutations in cystic fibrosis with modified U1 snRNAs. Hum Mutat 2020; 41:2143-2154. [PMID: 32935393 DOI: 10.1002/humu.24116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
In cystic fibrosis (CF), the correction of splicing defects represents an interesting therapeutic approach to restore normal CFTR function. In this study, we focused on 10 common mutations/variants 711+3A>G/C, 711+5G>A, TG13T3, TG13T5, TG12T5, 1863C>T, 1898+3A>G, 2789+5G>A, and 3120G>A that induce skipping of the corresponding CFTR exons 5, 10, 13, 16, and 18. To rescue the splicing defects we tested, in a minigene assay, a panel of modified U1 small nuclear RNAs (snRNAs), named Exon Specific U1s (ExSpeU1s), that was engineered to bind to intronic sequences downstream of each defective exon. Using this approach, we show that all 10 splicing mutations analyzed are efficiently corrected by specific ExSpeU1s. Using complementary DNA-splicing competent minigenes, we also show that the ExspeU1-mediated splicing correction at the RNA level recovered the full-length CFTR protein for 1863C>T, 1898+3A>G, 2789+5G>A variants. In addition, detailed mutagenesis experiments performed on exon 13 led us to identify a novel intronic regulatory element involved in the ExSpeU1-mediated splicing rescue. These results provide a common strategy based on modified U1 snRNAs to correct exon skipping in a group of disease-causing CFTR mutations.
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Affiliation(s)
- Stefano Donegà
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Malgorzata Ewa Rogalska
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Susana Igreja
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Margarida Duarte Amaral
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Franco Pagani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
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Erkelenz S, Poschmann G, Ptok J, Müller L, Schaal H. Profiling of cis- and trans-acting factors supporting noncanonical splice site activation. RNA Biol 2020; 18:118-130. [PMID: 32693676 DOI: 10.1080/15476286.2020.1798111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Recently, by combining transcriptomics with functional splicing reporter assays we were able to identify GT > GC > TT as the three highest ranked dinucleotides of human 5' splice sites (5'ss). Here, we have extended our investigations to the proteomic characterization of nuclear proteins that bind to canonical and noncanonical 5'ss. Surprisingly, we found that U1 snRNP binding to functional 5'ss sequences prevented components of the DNA damage response (DDR) from binding to the RNA, suggesting a close link between spliceosome arrangement and genome stability. We demonstrate that all tested noncanonical 5'ss sequences are bona-fide targets of the U2-type spliceosome and are bound by U1 snRNP, including U1-C, in the presence of splicing enhancers. The quantity of precipitated U1-C protein was similar for all noncanonical 5'ss dinucleotides, so that the highly different 5'ss usage was likely due to a later step after early U1 snRNP binding. In addition, we show that an internal GT at positions +5/+6 can be advantageous for splicing at position +1 of noncanonical splice sites. Likewise, and in agreement with previous observations, splicing inactive U1 snRNP binding sites could serve as splicing enhancers, which may also explain the higher abundance of U1 snRNPs compared to other U snRNPs. Finally, we observe that an arginine-serine (RS)-rich domain recruitment to stem loop I of the U1 snRNA is functionally sufficient to promote exon-definition and upstream 3'ss activation.
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Affiliation(s)
- Steffen Erkelenz
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany.,Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne , Cologne, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZ, Universitätsklinikum Düsseldorf , Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
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9
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Balestra D, Scalet D, Ferrarese M, Lombardi S, Ziliotto N, C. Croes C, Petersen N, Bosma P, Riccardi F, Pagani F, Pinotti M, van de Graaf SFJ. A Compensatory U1snRNA Partially Rescues FAH Splicing and Protein Expression in a Splicing-Defective Mouse Model of Tyrosinemia Type I. Int J Mol Sci 2020; 21:E2136. [PMID: 32244944 PMCID: PMC7139742 DOI: 10.3390/ijms21062136] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The elucidation of aberrant splicing mechanisms, frequently associated with disease has led to the development of RNA therapeutics based on the U1snRNA, which is involved in 5' splice site (5'ss) recognition. Studies in cellular models have demonstrated that engineered U1snRNAs can rescue different splicing mutation types. However, the assessment of their correction potential in vivo is limited by the scarcity of animal models with the targetable splicing defects. Here, we challenged the U1snRNA in the FAH5961SB mouse model of hepatic fumarylacetoacetate hydrolase (FAH) deficiency (Hereditary Tyrosinemia type I, HT1) due to the FAH c.706G>A splicing mutation. Through minigene expression studies we selected a compensatory U1snRNA (U1F) that was able to rescue this mutation. Intriguingly, adeno-associated virus-mediated delivery of U1F (AAV8-U1F), but not of U1wt, partially rescued FAH splicing in mouse hepatocytes. Consistently, FAH protein was detectable only in the liver of AAV8-U1F treated mice, which displayed a slightly prolonged survival. Moreover, RNA sequencing revealed the negligible impact of the U1F on the splicing profile and overall gene expression, thus pointing toward gene specificity. These data provide early in vivo proof-of-principle of the correction potential of compensatory U1snRNAs in HTI and encourage further optimization on a therapeutic perspective, and translation to other splicing-defective forms of metabolic diseases.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (D.S.); (M.F.); (S.L.); (N.Z.); (M.P.)
| | - Daniela Scalet
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (D.S.); (M.F.); (S.L.); (N.Z.); (M.P.)
| | - Mattia Ferrarese
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (D.S.); (M.F.); (S.L.); (N.Z.); (M.P.)
| | - Silvia Lombardi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (D.S.); (M.F.); (S.L.); (N.Z.); (M.P.)
| | - Nicole Ziliotto
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (D.S.); (M.F.); (S.L.); (N.Z.); (M.P.)
| | - Chrystal C. Croes
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (C.C.C.); (N.P.); (P.B.); (S.F.J.v.d.G.)
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology and Metabolism, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Naomi Petersen
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (C.C.C.); (N.P.); (P.B.); (S.F.J.v.d.G.)
| | - Piter Bosma
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (C.C.C.); (N.P.); (P.B.); (S.F.J.v.d.G.)
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology and Metabolism, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Federico Riccardi
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (F.R.); (F.P.)
| | - Franco Pagani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (F.R.); (F.P.)
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (D.S.); (M.F.); (S.L.); (N.Z.); (M.P.)
- LTTA, University of Ferrara, 44121 Ferrara, Italy
| | - Stan F. J. van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (C.C.C.); (N.P.); (P.B.); (S.F.J.v.d.G.)
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology and Metabolism, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Balestra D, Maestri I, Branchini A, Ferrarese M, Bernardi F, Pinotti M. An Altered Splicing Registry Explains the Differential ExSpeU1-Mediated Rescue of Splicing Mutations Causing Haemophilia A. Front Genet 2019; 10:974. [PMID: 31649737 PMCID: PMC6796300 DOI: 10.3389/fgene.2019.00974] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
The exon recognition and removal of introns (splicing) from pre-mRNA is a crucial step in the gene expression flow. The process is very complex and therefore susceptible to derangements. Not surprisingly, a significant and still underestimated proportion of disease-causing mutations affects splicing, with those occurring at the 5’ splice site (5’ss) being the most severe ones. This led to the development of a correction approach based on variants of the spliceosomal U1snRNA, which has been proven on splicing mutations in several cellular and mouse models of human disease. Since the alternative splicing mechanisms are strictly related to the sequence context of the exon, we challenged the U1snRNA-mediated strategy in the singular model of the exon 5 of coagulation factor (F)VIII gene (F8) in which the authentic 5’ss is surrounded by various cryptic 5’ss. This scenario is further complicated in the presence of nucleotide changes associated with FVIII deficiency (Haemophilia A), which weaken the authentic 5’ss and create/strengthen cryptic 5’ss. We focused on the splicing mutations (c.602-32A > G, c.602-10T > G, c.602G > A, c.655G > A, c.667G > A, c.669A > G, c.669A > T, c.670G > T, c.670+1G > T, c.670+1G > A, c.670+2T > G, c.670+5G > A, and c.670+6T > C) found in patients with severe to mild Haemophilia A. Minigenes expression studies demonstrated that all mutations occurring within the 5’ss, both intronic or exonic, lead to aberrant transcripts arising from the usage of two cryptic intronic 5’ss at positions c.670+64 and c.670+176. For most of them, the observed proportion of correct transcripts is in accordance with the coagulation phenotype of patients. In co-transfection experiments, we identified a U1snRNA variant targeting an intronic region downstream of the defective exon (Exon Specific U1snRNA, U1sh7) capable to re-direct usage of the proper 5’ss (∼80%) for several mutations. However, deep investigation of rescued transcripts from +1 and +2 variants revealed only the usage of adjacent cryptic 5’ss, leading to frameshifted transcript forms. These data demonstrate that a single ExSpeU1 can efficiently rescue different mutations in the F8 exon 5, and provide the first evidence of the applicability of the U1snRNA-based approach to Haemophilia A.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Iva Maestri
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mattia Ferrarese
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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11
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Coutinho MF, Matos L, Santos JI, Alves S. RNA Therapeutics: How Far Have We Gone? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:133-177. [PMID: 31342441 DOI: 10.1007/978-3-030-19966-1_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In recent years, the RNA molecule became one of the most promising targets for therapeutic intervention. Currently, a large number of RNA-based therapeutics are being investigated both at the basic research level and in late-stage clinical trials. Some of them are even already approved for treatment. RNA-based approaches can act at pre-mRNA level (by splicing modulation/correction using antisense oligonucleotides or U1snRNA vectors), at mRNA level (inhibiting gene expression by siRNAs and antisense oligonucleotides) or at DNA level (by editing mutated sequences through the use of CRISPR/Cas). Other RNA approaches include the delivery of in vitro transcribed (IVT) mRNA or the use of oligonucleotides aptamers. Here we review these approaches and their translation into clinics trying to give a brief overview also on the difficulties to its application as well as the research that is being done to overcome them.
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Affiliation(s)
- Maria Francisca Coutinho
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Liliana Matos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Juliana Inês Santos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Sandra Alves
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal.
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12
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Balestra D, Giorgio D, Bizzotto M, Fazzari M, Ben Zeev B, Pinotti M, Landsberger N, Frasca A. Splicing Mutations Impairing CDKL5 Expression and Activity Can be Efficiently Rescued by U1snRNA-Based Therapy. Int J Mol Sci 2019; 20:ijms20174130. [PMID: 31450582 PMCID: PMC6747535 DOI: 10.3390/ijms20174130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
Mutations in the CDKL5 gene lead to an incurable rare neurological condition characterized by the onset of seizures in the first weeks of life and severe intellectual disability. Replacement gene or protein therapies could represent intriguing options, however, their application may be inhibited by the recent demonstration that CDKL5 is dosage sensitive. Conversely, correction approaches acting on pre-mRNA splicing would preserve CDKL5 physiological regulation. Since ~15% of CDKL5 pathogenic mutations are candidates to affect splicing, we evaluated the capability of variants of the spliceosomal U1 small nuclear RNA (U1snRNA) to correct mutations affecting +1 and +5 nucleotides at the 5′ donor splice site and predicted to cause exon skipping. Our results show that CDKL5 minigene variants expressed in mammalian cells are a valid approach to assess CDKL5 splicing pattern. The expression of engineered U1snRNA effectively rescued mutations at +5 but not at the +1 nucleotides. Importantly, we proved that U1snRNA-mediated splicing correction fully restores CDKL5 protein synthesis, subcellular distribution and kinase activity. Eventually, by correcting aberrant splicing of an exogenously expressed splicing-competent CDKL5 transgene, we provided insights on the morphological rescue of CDKL5 null neurons, reporting the first proof-of-concept of the therapeutic value of U1snRNA-mediated CDKL5 splicing correction.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Domenico Giorgio
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milan, Italy
| | - Matteo Bizzotto
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milan, Italy
| | - Maria Fazzari
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milan, Italy
| | - Bruria Ben Zeev
- Pediatric Neurology Unit, Edmond and Lily Safra Pediatric Hospital, Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, 61000 Tel Aviv, Israel
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Nicoletta Landsberger
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milan, Italy.
| | - Angelisa Frasca
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milan, Italy.
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13
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Katneni UK, Liss A, Holcomb D, Katagiri NH, Hunt R, Bar H, Ismail A, Komar AA, Kimchi‐Sarfaty C. Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants. Mol Genet Genomic Med 2019; 7:e840. [PMID: 31257730 PMCID: PMC6687662 DOI: 10.1002/mgg3.840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/10/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Pre-mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease-inducing mechanism of synonymous variants, its contribution toward disease phenotype of non-synonymous variants is underappreciated. METHODS In this study, we analyzed 415 disease-causing and 120 neutral F9 exonic point variants including both synonymous and non-synonymous for their effect on splicing using a series of in silico splice site prediction tools, SRE prediction tools, and in vitro minigene assays. RESULTS The use of splice site and SRE prediction tools in tandem provided better prediction but were not always in agreement with the minigene assays. The net effect of splicing dysregulation caused by variants was context dependent. Minigene assays revealed that perturbed splicing can be found. CONCLUSION Synonymous variants primarily cause disease phenotype via splicing dysregulation while additional mechanisms such as translation rate also play an important role. Splicing dysregulation is likely to contribute to the disease phenotype of several non-synonymous variants.
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Affiliation(s)
- Upendra K. Katneni
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Aaron Liss
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - David Holcomb
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Nobuko H. Katagiri
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Ryan Hunt
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Haim Bar
- Department of StatisticsUniversity of ConnecticutStorrsConnecticut
| | - Amra Ismail
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and DiseaseCleveland State UniversityClevelandOhio
| | - Anton A. Komar
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and DiseaseCleveland State UniversityClevelandOhio
| | - Chava Kimchi‐Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
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14
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Ferraresi P, Balestra D, Guittard C, Buthiau D, Pan-Petesh B, Maestri I, Farah R, Pinotti M, Giansily-Blaizot M. Next-generation sequencing and recombinant expression characterized aberrant splicing mechanisms and provided correction strategies in factor VII deficiency. Haematologica 2019; 105:829-837. [PMID: 31273093 PMCID: PMC7049351 DOI: 10.3324/haematol.2019.217539] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023] Open
Abstract
Despite the exhaustive screening of F7 gene exons and exon-intron boundaries and promoter region, a significant proportion of mutated alleles remains unidentified in patients with coagulation factor VII deficiency. Here, we applied next-generation sequencing to 13 FVII-deficient patients displaying genotype-phenotype discrepancies upon conventional sequencing, and identified six rare intronic variants. Computational analysis predicted splicing effects for three of them, which would strengthen (c.571+78G>A; c.806-329G>A) or create (c.572-392C>G) intronic 5′ splice sites (5′ss). In F7 minigene assays, the c.806-329G>A was ineffective while the c.571+78G>A change led to usage of the +79 cryptic 5′ss with only trace levels of correct transcripts (3% of wild-type), in accordance with factor VII activity levels in homozygotes (1-3% of normal). The c.572-392C>G change led to pseudo-exonization and frame-shift, but also substantial levels of correct transcripts (approx. 70%). However, this variant was associated with the common F7 polymorphic haplotype, predicted to further decrease factor VII levels; this provided some kind of explanation for the 10% factor VII levels in the homozygous patient. Intriguingly, the effect of the c.571+78G>A and c.572-392C>G changes, and particularly of the former (the most severe and well-represented in our cohort), was counteracted by antisense U7snRNA variants targeting the intronic 5′ss, thus demonstrating their pathogenic role. In conclusion, the combination of next-generation sequencing of the entire F7 gene with the minigene expression studies elucidated the molecular bases of factor VII deficiency in 10 of 13 patients, thus improving diagnosis and genetic counseling. It also provided a potential therapeutic approach based on antisense molecules that has been successfully exploited in other disorders.
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Affiliation(s)
- Paolo Ferraresi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Caroline Guittard
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | - Delphine Buthiau
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | | | - Iva Maestri
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Roula Farah
- Department of Pediatrics, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Muriel Giansily-Blaizot
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
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15
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Ziliotto N, Marchetti G, Scapoli C, Bovolenta M, Meneghetti S, Benazzo A, Lunghi B, Balestra D, Laino LA, Bozzini N, Guidi I, Salvi F, Straudi S, Gemmati D, Menegatti E, Zamboni P, Bernardi F. C6orf10 Low-Frequency and Rare Variants in Italian Multiple Sclerosis Patients. Front Genet 2019; 10:573. [PMID: 31297130 PMCID: PMC6607989 DOI: 10.3389/fgene.2019.00573] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
In light of the complex nature of multiple sclerosis (MS) and the recently estimated contribution of low-frequency variants into disease, decoding its genetic risk components requires novel variant prioritization strategies. We selected, by reviewing MS Genome Wide Association Studies (GWAS), 107 candidate loci marked by intragenic single nucleotide polymorphisms (SNPs) with a remarkable association (p-value ≤ 5 × 10-6). A whole exome sequencing (WES)-based pilot study of SNPs with minor allele frequency (MAF) ≤ 0.04, conducted in three Italian families, revealed 15 exonic low-frequency SNPs with affected parent-child transmission. These variants were detected in 65/120 Italian unrelated MS patients, also in combination (22 patients). Compared with databases (controls gnomAD, dbSNP150, ExAC, Tuscany-1000 Genome), the allelic frequencies of C6orf10 rs16870005 and IL2RA rs12722600 were significantly higher (i.e., controls gnomAD, p = 9.89 × 10-7 and p < 1 × 10-20). TET2 rs61744960 and TRAF3 rs138943371 frequencies were also significantly higher, except in Tuscany-1000 Genome. Interestingly, the association of C6orf10 rs16870005 (Ala431Thr) with MS did not depend on its linkage disequilibrium with the HLA-DRB1 locus. Sequencing in the MS cohort of the C6orf10 3′ region revealed 14 rare mutations (10 not previously reported). Four variants were null, and significantly more frequent than in the databases. Further, the C6orf10 rare variants were observed in combinations, both intra-locus and with other low-frequency SNPs. The C6orf10 Ser389Xfr was found homozygous in a patient with early onset of the MS. Taking into account the potentially functional impact of the identified exonic variants, their expression in combination at the protein level could provide functional insights in the heterogeneous pathogenetic mechanisms contributing to MS.
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Affiliation(s)
- Nicole Ziliotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giovanna Marchetti
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Matteo Bovolenta
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Meneghetti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Barbara Lunghi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Lorenza Anna Laino
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Nicolò Bozzini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Irene Guidi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Fabrizio Salvi
- IRCCS Institute of Neurological Sciences, Hospital Bellaria, Bologna, Italy
| | - Sofia Straudi
- Department of Neurosciences and Rehabilitation, S. Anna University Hospital, Ferrara, Italy
| | - Donato Gemmati
- Department of Biomedical & Specialty Surgical Sciences and Centre Haemostasis & Thrombosis, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Erica Menegatti
- Department of Morphology, Surgery and Experimental Medicine, Vascular Diseases Center, University of Ferrara, Ferrara, Italy
| | - Paolo Zamboni
- Department of Morphology, Surgery and Experimental Medicine, Vascular Diseases Center, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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16
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Balestra D, Branchini A. Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. Int J Mol Sci 2019; 20:ijms20123036. [PMID: 31234407 PMCID: PMC6627357 DOI: 10.3390/ijms20123036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular strategies tailored to promote/correct the expression and/or processing of defective coagulation factors would represent innovative therapeutic approaches beyond standard substitutive therapy. Here, we focus on the molecular mechanisms and determinants underlying innovative approaches acting at DNA, mRNA and protein levels in inherited coagulation factor deficiencies, and in particular on: (i) gene editing approaches, which have permitted intervention at the DNA level through the specific recognition, cleavage, repair/correction or activation of target sequences, even in mutated gene contexts; (ii) the rescue of altered pre-mRNA processing through the engineering of key spliceosome components able to promote correct exon recognition and, in turn, the synthesis and secretion of functional factors, as well as the effects on the splicing of missense changes affecting exonic splicing elements; this section includes antisense oligonucleotide- or siRNA-mediated approaches to down-regulate target genes; (iii) the rescue of protein synthesis/function through the induction of ribosome readthrough targeting nonsense variants or the correction of folding defects caused by amino acid substitutions. Overall, these approaches have shown the ability to rescue the expression and/or function of potentially therapeutic levels of coagulation factors in different disease models, thus supporting further studies in the future aimed at evaluating the clinical translatability of these new strategies.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
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17
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Singh RN, Singh NN. A novel role of U1 snRNP: Splice site selection from a distance. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:634-642. [PMID: 31042550 DOI: 10.1016/j.bbagrm.2019.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/23/2022]
Abstract
Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes. However, understanding the mechanism by which exon-intron boundaries are defined remains a challenging endeavor. Published reports support that the recruitment of U1 snRNP at the 5'ss marked by GU dinucleotides defines the 5'ss as well as facilitates 3'ss recognition through cross-exon interactions. However, exceptions to this rule exist as U1 snRNP recruited away from the 5'ss retains the capability to define the splice site, where the cleavage takes place. Independent reports employing exon 7 of Survival Motor Neuron (SMN) genes suggest a long-distance effect of U1 snRNP on splice site selection upon U1 snRNP recruitment at target sequences with or without GU dinucleotides. These findings underscore that sequences distinct from the 5'ss may also impact exon definition if U1 snRNP is recruited to them through partial complementarity with the U1 snRNA. In this review we discuss the expanded role of U1 snRNP in splice-site selection due to U1 ability to be recruited at more sites than predicted solely based on GU dinucleotides.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America.
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America
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18
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DeNicola AB, Tang Y. Therapeutic approaches to treat human spliceosomal diseases. Curr Opin Biotechnol 2019; 60:72-81. [PMID: 30772756 DOI: 10.1016/j.copbio.2019.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
Mutated RNA splicing machinery drives many human diseases and is a promising therapeutic target for engineering and small molecule therapy. In the case of mutations in individual genes that cause them to be incorrectly spliced, engineered splicing factors can be introduced to correct splicing of these aberrant transcripts and reduce the effects of the disease phenotype. Mutations that occur in certain splicing factor genes themselves have been implicated in many cancers, particularly myelodysplastic syndromes. Small molecules that target splicing factors have been developed as therapies to preferentially induce apoptosis in these cancer cells. Specifically, drugs targeting the splicing factor SF3B1 have led to recent clinical trials. Here, we review the role of alternative splicing in disease, approaches to rescue incorrect splicing using engineered splicing factors, and small molecule splicing inhibitors developed to treat hematological cancers.
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Affiliation(s)
- Anthony B DeNicola
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States.
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
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19
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Montes M, Sanford BL, Comiskey DF, Chandler DS. RNA Splicing and Disease: Animal Models to Therapies. Trends Genet 2019; 35:68-87. [PMID: 30466729 PMCID: PMC6339821 DOI: 10.1016/j.tig.2018.10.002] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023]
Abstract
Alternative splicing of pre-mRNA increases genetic diversity, and recent studies estimate that most human multiexon genes are alternatively spliced. If this process is not highly regulated and accurate, it leads to mis-splicing events, which may result in proteins with altered function. A growing body of work has implicated mis-splicing events in a range of diseases, including cancer, neurodegenerative diseases, and muscular dystrophies. Understanding the mechanisms that cause aberrant splicing events and how this leads to disease is vital for designing effective therapeutic strategies. In this review, we focus on advances in therapies targeting splicing, and highlight the animal models developed to recapitulate disease phenotypes as a model for testing these therapies.
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Affiliation(s)
- Matías Montes
- 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, Columbus, OH, USA
| | - Brianne L Sanford
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel F Comiskey
- 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, 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, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
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20
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Scalet D, Maestri I, Branchini A, Bernardi F, Pinotti M, Balestra D. Disease-causing variants of the conserved +2T of 5' splice sites can be rescued by engineered U1snRNAs. Hum Mutat 2018; 40:48-52. [PMID: 30408273 DOI: 10.1002/humu.23680] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/26/2018] [Accepted: 11/05/2018] [Indexed: 12/14/2022]
Abstract
The ability of variants of the spliceosomal U1snRNA to rescue splicing has been proven in several human disease models, but not for nucleotide changes at the conserved GT nucleotide of 5' splice sites (5'ss), frequent and associated with severe phenotypes. Here, we focused on variants at the 5'ss of F9 intron 3, leading to factor IX (FIX) deficiency (hemophilia B). Through minigene expression, we demonstrated that all changes induce complete exon 3 skipping, which explains the associated hemophilia B phenotype. Interestingly, engineered U1snRNAs remarkably increased the proportion of correct transcripts in the presence of the c.277+4A>G (∼60%) and also c.277+2T>C mutation (∼20%). Expression of splicing-competent cDNA constructs indicated that the splicing rescue produces an appreciable increase of secreted FIX protein levels. These data provide the first experimental evidence that even part of variants at the conserved 5'ss +2T nucleotide can be rescued, thus expanding the applicability of this U1snRNA-based approach.
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Affiliation(s)
- Daniela Scalet
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Iva Maestri
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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21
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Donadon I, Pinotti M, Rajkowska K, Pianigiani G, Barbon E, Morini E, Motaln H, Rogelj B, Mingozzi F, Slaugenhaupt SA, Pagani F. Exon-specific U1 snRNAs improve ELP1 exon 20 definition and rescue ELP1 protein expression in a familial dysautonomia mouse model. Hum Mol Genet 2018; 27:2466-2476. [PMID: 29701768 PMCID: PMC6030917 DOI: 10.1093/hmg/ddy151] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/30/2022] Open
Abstract
Familial dysautonomia (FD) is a rare genetic disease with no treatment, caused by an intronic point mutation (c.2204+6T>C) that negatively affects the definition of exon 20 in the elongator complex protein 1 gene (ELP1 also known as IKBKAP). This substitution modifies the 5' splice site and, in combination with regulatory splicing factors, induces different levels of exon 20 skipping, in various tissues. Here, we evaluated the therapeutic potential of a novel class of U1 snRNA molecules, exon-specific U1s (ExSpeU1s), in correcting ELP1 exon 20 recognition. Lentivirus-mediated expression of ELP1-ExSpeU1 in FD fibroblasts improved ELP1 splicing and protein levels. We next focused on a transgenic mouse model that recapitulates the same tissue-specific mis-splicing seen in FD patients. Intraperitoneal delivery of ELP1-ExSpeU1s-adeno-associated virus particles successfully increased the production of full-length human ELP1 transcript and protein. This splice-switching class of molecules is the first to specifically correct the ELP1 exon 20 splicing defect. Our data provide proof of principle of ExSpeU1s-adeno-associated virus particles as a novel therapeutic strategy for FD.
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Affiliation(s)
- Irving Donadon
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Katarzyna Rajkowska
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Elisabetta Morini
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Helena Motaln
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
- Biomedical Research Institute BRIS, Ljubljana, Slovenia
| | - Federico Mingozzi
- Genethon and INSERM U951, Evry, France
- University Pierre and Marie Curie and INSERM U974, Paris, France
| | - Susan A Slaugenhaupt
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Franco Pagani
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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22
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Scalet D, Sacchetto C, Bernardi F, Pinotti M, van de Graaf SFJ, Balestra D. The somatic FAH C.1061C>A change counteracts the frequent FAH c.1062+5G>A mutation and permits U1snRNA-based splicing correction. J Hum Genet 2018; 63:683-686. [PMID: 29497141 PMCID: PMC5919117 DOI: 10.1038/s10038-018-0427-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/24/2017] [Accepted: 01/30/2018] [Indexed: 12/01/2022]
Abstract
In tyrosinaemia type 1(HT1), a mosaic pattern of fumarylacetoacetase (FAH) immunopositive or immunonegative nodules in liver tissue has been reported in many patients. This aspect is generally explained by a spontaneous reversion of the mutation into a normal genotype. In one HT1 patient carrying the frequent FAH c.1062+5G>A mutation, a second somatic change (c.1061C>A) has been reported in the same allele, and found in immunopositive nodules. Here, we demonstrated that the c.1062+5G>A prevents usage of the exon 12 5’ splice site (ss), even when forced by an engineered U1snRNA specifically designed on the FAH 5’ss to strengthen its recognition. Noticeably the new somatic c.1061C>A change, in linkage with the c.1062+5G>A mutation, partially rescues the defective 5’ss and is associated to trace level (~5%) of correct transcripts. Interestingly, this combined genetic condition strongly favored the rescue by the engineered U1snRNA, with correct transcripts reaching up to 60%. Altogether these findings elucidate the molecular basis of HT1 caused by the frequent FAH c.1062+5G>A mutation, and demonstrate the compensatory effect of the c.1061C>A change in promoting exon definition, thus unraveling a rare mechanism leading to FAH immune-reactive mosaicism.
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Affiliation(s)
- Daniela Scalet
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Claudia Sacchetto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Academic Medical Center, Amsterdam, The Netherlands
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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23
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Abstract
More than 15% of all disease-causing mutations result in mRNA splicing defects. U1 snRNA binds to the 5' splice site (5'ss) through base pairing. Mutation-adapted U1 snRNA (with compensatory U1 snRNA changes) and exon-specific U1 snRNA (complementary to intronic sequences) have been shown to suppress 5'ss mutations in cellular and animal models. Areas covered: The history, mechanism of action, and efficacy of U1 snRNA-mediated gene therapy are covered. The clinical utility of this technology and its limitations will be discussed. Expert commentary: Recently, gene therapies with mutation-adapted U1 snRNAs have been conducted on animal models, including aromatic l-amino acid decarboxylase deficiency and spinal muscular atrophy. However, although U1-mediated therapy has the advantage of maintaining the regulated expression of defective genes, its accuracy and efficacy needs to be improved before clinical application of this technique is possible.
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Affiliation(s)
- Wuh-Liang Hwu
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
| | - Yu-May Lee
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
| | - Ni-Chung Lee
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
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