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Legnini I, Di Timoteo G, Rossi F, Morlando M, Briganti F, Sthandier O, Fatica A, Santini T, Andronache A, Wade M, Laneve P, Rajewsky N, Bozzoni I. Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis. Mol Cell 2017; 66:22-37.e9. [PMID: 28344082 PMCID: PMC5387670 DOI: 10.1016/j.molcel.2017.02.017] [Citation(s) in RCA: 1454] [Impact Index Per Article: 207.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/28/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) constitute a family of transcripts with unique structures and still largely unknown functions. Their biogenesis, which proceeds via a back-splicing reaction, is fairly well characterized, whereas their role in the modulation of physiologically relevant processes is still unclear. Here we performed expression profiling of circRNAs during in vitro differentiation of murine and human myoblasts, and we identified conserved species regulated in myogenesis and altered in Duchenne muscular dystrophy. A high-content functional genomic screen allowed the study of their functional role in muscle differentiation. One of them, circ-ZNF609, resulted in specifically controlling myoblast proliferation. Circ-ZNF609 contains an open reading frame spanning from the start codon, in common with the linear transcript, and terminating at an in-frame STOP codon, created upon circularization. Circ-ZNF609 is associated with heavy polysomes, and it is translated into a protein in a splicing-dependent and cap-independent manner, providing an example of a protein-coding circRNA in eukaryotes. CircRNAs are conserved, abundant, and regulated in myogenesis High-throughput phenotypic screening reveals functional circRNAs Circ-ZNF609 regulates myoblast proliferation Circ-ZNF609 can be translated
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Affiliation(s)
- Ivano Legnini
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Mariangela Morlando
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Francesca Briganti
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Olga Sthandier
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Adrian Andronache
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Mark Wade
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Pietro Laneve
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Institut Pasteur Italy, Fondazione Cenci-Bolognetti, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I. A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA. Cell 2011. [PMCID: PMC3483535 DOI: 10.1016/j.cell.2011.10.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Cacchiarelli D, Incitti T, Martone J, Cesana M, Cazzella V, Santini T, Sthandier O, Bozzoni I. miR-31 modulates dystrophin expression: new implications for Duchenne muscular dystrophy therapy. EMBO Rep 2011; 12:136-41. [PMID: 21212803 DOI: 10.1038/embor.2010.208] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/12/2010] [Accepted: 11/22/2010] [Indexed: 11/09/2022] Open
Abstract
Duchenne muscular dystrophy (DMD)--which is caused by mutations in the dystrophin gene-is one of the most severe myopathies. Among therapeutic strategies, exon skipping allows the rescue of dystrophin synthesis through the production of a shorter but functional messenger RNA. Here, we report the identification of a microRNA--miR-31--that represses dystrophin expression by targeting its 3' untranslated region. In human DMD myoblasts treated with exon skipping, we demonstrate that miR-31 inhibition increases dystrophin rescue. These results indicate that interfering with miR-31 activity can provide an ameliorating strategy for those DMD therapies that are aimed at efficiently recovering dystrophin synthesis.
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Affiliation(s)
- Davide Cacchiarelli
- Department of Biology and Biotechnology C. Darwin, Institut Pasteur Cenci-Bolognetti and IBPM-Sapienza, University of Rome, Piazzele Aldo Moro 5, Rome 00185, Italy
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4
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Cacchiarelli D, Martone J, Girardi E, Cesana M, Incitti T, Morlando M, Nicoletti C, Santini T, Sthandier O, Barberi L, Auricchio A, Musarò A, Bozzoni I. MicroRNAs involved in molecular circuitries relevant for the Duchenne muscular dystrophy pathogenesis are controlled by the dystrophin/nNOS pathway. Cell Metab 2010; 12:341-351. [PMID: 20727829 DOI: 10.1016/j.cmet.2010.07.008] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 03/23/2010] [Accepted: 06/30/2010] [Indexed: 11/28/2022]
Abstract
In Duchenne muscular dystrophy (DMD) the absence of dystrophin at the sarcolemma delocalizes and downregulates nitric oxide synthase (nNOS); this alters S-nitrosylation of HDAC2 and its chromatin association. We show that the differential HDAC2 nitrosylation state in Duchenne versus wild-type conditions deregulates the expression of a specific subset of microRNA genes. Several circuitries controlled by the identified microRNAs, such as the one linking miR-1 to the G6PD enzyme and the redox state of cell, or miR-29 to extracellular proteins and the fibrotic process, explain some of the DMD pathogenetic traits. We also show that, at variance with other myomiRs, miR-206 escapes from the dystrophin-nNOS control being produced in activated satellite cells before dystrophin expression; in these cells, it contributes to muscle regeneration through repression of the satellite specific factor, Pax7. We conclude that the pathway activated by dystrophin/nNOS controls several important circuitries increasing the robustness of the muscle differentiation program.
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Affiliation(s)
- Davide Cacchiarelli
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Julie Martone
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Erika Girardi
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Marcella Cesana
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Tania Incitti
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Mariangela Morlando
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Carmine Nicoletti
- Department of Histology and Medical Embryology, Interuniversity Institute of Myology, "SAPIENZA" University of Rome, Via A. Scarpa, 14, 00161 Rome, Italy
| | - Tiziana Santini
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Olga Sthandier
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Laura Barberi
- Department of Histology and Medical Embryology, Interuniversity Institute of Myology, "SAPIENZA" University of Rome, Via A. Scarpa, 14, 00161 Rome, Italy
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Napoli, Italy
| | - Antonio Musarò
- Department of Histology and Medical Embryology, Interuniversity Institute of Myology, "SAPIENZA" University of Rome, Via A. Scarpa, 14, 00161 Rome, Italy
| | - Irene Bozzoni
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and IBPM, "SAPIENZA" University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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Guastafierro T, Cecchinelli B, Zampieri M, Reale A, Riggio G, Sthandier O, Zupi G, Calabrese L, Caiafa P. CCCTC-binding factor activates PARP-1 affecting DNA methylation machinery. J Biol Chem 2008; 283:21873-80. [PMID: 18539602 PMCID: PMC2494936 DOI: 10.1074/jbc.m801170200] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 05/29/2008] [Indexed: 12/31/2022] Open
Abstract
Our previous data have shown that in L929 mouse fibroblasts the control of methylation pattern depends in part on poly(ADP-ribosyl)ation and that ADP-ribose polymers (PARs), both present on poly(ADP-ribosyl)ated PARP-1 and/or protein-free, have an inhibitory effect on Dnmt1 activity. Here we show that transient ectopic overexpression of CCCTC-binding factor (CTCF) induces PAR accumulation, PARP-1, and CTCF poly(ADP-ribosyl)ation in the same mouse fibroblasts. The persistence in time of a high PAR level affects the DNA methylation machinery; the DNA methyltransferase activity is inhibited with consequences for the methylation state of genome, which becomes diffusely hypomethylated affecting centromeric minor satellite and B1 DNA repeats. In vitro data show that CTCF is able to activate PARP-1 automodification even in the absence of nicked DNA. Our new finding that CTCF is able per se to activate PARP-1 automodification in vitro is of great interest as so far a burst of poly(ADP-ribosyl)ated PARP-1 has generally been found following introduction of DNA strand breaks. CTCF is unable to inhibit DNMT1 activity, whereas poly(ADP-ribosyl)ated PARP-1 plays this inhibitory role. These data suggest that CTCF is involved in the cross-talk between poly(ADP-ribosyl)ation and DNA methylation and underscore the importance of a rapid reversal of PARP activity, as DNA methylation pattern is responsible for an important epigenetic code.
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Affiliation(s)
- Tiziana Guastafierro
- Department of Cellular Biotechnology and Haematology, University La Sapienza, Piazzale Aldo Moro 5, 00161 Rome, Italy
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Denti MA, Incitti T, Sthandier O, Nicoletti C, De Angelis FG, Rizzuto E, Auricchio A, Musarò A, Bozzoni I. Long-term benefit of adeno-associated virus/antisense-mediated exon skipping in dystrophic mice. Hum Gene Ther 2008; 19:601-8. [PMID: 18500943 DOI: 10.1089/hum.2008.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many mutations and deletions in the dystrophin gene, responsible for Duchenne muscular dystrophy (DMD), can be corrected at the posttranscriptional level by skipping specific exons. Here we show that long-term benefit can be obtained in the dystrophic mouse model through the use of adeno-associated viral vectors expressing antisense sequences: persistent exon skipping, dystrophin rescue, and functional benefit were observed 74 weeks after a single systemic administration. The therapeutic benefit was sufficient to preserve the muscle integrity of mice up to old age. These results indicate a possible long-term gene therapy treatment of the DMD pathology.
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Affiliation(s)
- Michela Alessandra Denti
- Department of Genetics and Molecular Biology, Institute Pasteur Cenci-Bolognetti, University of Rome La Sapienza, 00185 Rome, Italy
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Caruso M, Busanello A, Sthandier O, Cavaldesi M, Gentile M, Garcia MI, Amati P. Mutation in the VP1-LDV motif of the murine polyomavirus affects viral infectivity and conditions virus tissue tropism in vivo. J Mol Biol 2006; 367:54-64. [PMID: 17239397 DOI: 10.1016/j.jmb.2006.12.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Revised: 12/18/2006] [Accepted: 12/19/2006] [Indexed: 11/24/2022]
Abstract
The first contact of a virus with the host cell surface and further entry are important steps for a successful outcome of the infection process and for the virus-associated pathogenicity. We have previously shown that the entry of the murine Polyomavirus (Py) into fibroblasts is a multi-step process involving, at least, the attachment to primary sialic acids (SA)-containing cell receptors followed by post-binding interaction with secondary receptors, such as the alpha4beta1 integrin, likely through the VP1-LDV motif. Here we report on the functional role of the VP1-LDV motif in Py infectivity and in vivo virus tissue tropism. For this purpose, we have characterized a recombinant virus mutant, PyLNV, harboring a single aa substitution in this motif (D138N). Although not critical for virus viability, the D138N substitution abrogates the post-attachment Py-alpha4beta1 interaction, rendering the PyLNV mutant virus twofold less infectious than the Py wild-type (Wt) in alpha4beta1-positive fibroblasts. To study the putative role of the VP1-LDV motif in vivo, newborn C57BL/6 mice were inoculated with PyWt or PyLNV and, after six days, organs were analyzed for the presence of viral DNA. Intriguingly, PyLNV showed an altered spectrum of in vivo replication compared with PyWt, particularly in the skin and in the kidney. The implication of Py-alpha4beta1 integrin interaction in conditioning tissue-specificity of virus replication is discussed.
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Affiliation(s)
- Maddalena Caruso
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma La Sapienza, Viale Regina Elena 324, 00161 Rome, Italy.
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Denti MA, Rosa A, D'Antona G, Sthandier O, De Angelis FG, Nicoletti C, Allocca M, Pansarasa O, Parente V, Musarò A, Auricchio A, Bottinelli R, Bozzoni I. Chimeric adeno-associated virus/antisense U1 small nuclear RNA effectively rescues dystrophin synthesis and muscle function by local treatment of mdx mice. Hum Gene Ther 2006; 17:565-74. [PMID: 16716113 DOI: 10.1089/hum.2006.17.565] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a X-linked myopathy in which deletions and point mutations in the dystrophin gene abolish dystrophin expression. The defect can often be corrected at the posttranscriptional level by exon skipping. In an animal model of DMD, the mdx mouse, a point mutation in exon 23 of the dystrophin gene introduces a premature stop codon. Skipping of this exon reestablishes the open reading frame in the dystrophin mRNA. We have obtained persistent exon skipping in mdx mice by local muscle injection of AAV vectors expressing antisense sequences fused to either U1 or U7 small nuclear RNA (snRNA). In the transduced muscles, dystrophin expression, amelioration of muscle morphology, and significant force recovery were obtained. These data indicate that the expression of antisense snRNAs, combined with their efficient muscular delivery through AAV vectors, is a powerful strategy for the therapeutic treatment of DMD. Like U7 snRNA, spliceosomal U1 snRNA is also a suitable backbone for the expression of antisense molecules active in exon skipping.
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Affiliation(s)
- Michela Alessandra Denti
- Department of Genetics and Molecular Biology, Institute Pasteur Cenci-Bolognetti, and IBPM, University La Sapienza, 00185 Rome, Italy
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Carbone M, Reale A, Di Sauro A, Sthandier O, Garcia MI, Maione R, Caiafa P, Amati P. PARP-1 interaction with VP1 capsid protein regulates polyomavirus early gene expression. J Mol Biol 2006; 363:773-85. [PMID: 16979186 DOI: 10.1016/j.jmb.2006.05.077] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 05/26/2006] [Accepted: 05/30/2006] [Indexed: 11/27/2022]
Abstract
Poly(ADP-ribose)polymerases are involved in fundamental cellular events as well as they seem to be associated to some viral infection process. In this work, the poly(ADP-ribose)polymerase-1 (PARP-1) role in the polyomavirus life cycle has been investigated. Early viral transcription was reduced by competitive inhibitors of PARPs in Swiss 3T3 cells and almost abolished in PARP-1 knockout fibroblasts and in wild-type fibroblasts when PARP-1 was silenced by RNA interference. In vivo chromatin immunoprecipitation assays showed that poly(ADP-ribosyl)ation (poly(ADP-ribose)) facilitates the release of the capsid protein viral protein 1 (VP1) from the chromatin of infecting virions. In vitro experiments demonstrated that VP1 stimulates the enzymatic activity of PARP-1 and binds non-covalently both protein-free and PARP-1-bound poly(ADP-ribose). Our studies suggest that PARP-1 promotes the complete VP1 displacement from viral DNA favouring the viral early transcription.
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Affiliation(s)
- Mariarosaria Carbone
- Pasteur Institute-Fondazione Cenci Bolognetti, Department of Cellular Biotechnology and Hematology, University of Rome La Sapienza, Viale Regina Elena 324, 00161 Rome, Italy
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Denti MA, Rosa A, D'Antona G, Sthandier O, Angelis FGD, Nicoletti C, Allocca M, Pansarasa O, Parente V, Musaro A, Auricchio A, Bottinelli R, Bozzoni I. Chimeric Adeno-Associated Virus/Antisense U1 Small Nuclear RNA Effectively Rescues Dystrophin Synthesis and Muscle Function by Local Treatment of mdx Mice. Hum Gene Ther 2006. [DOI: 10.1089/hum.2006.17.ft-200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Denti MA, Rosa A, D’Antona G, Sthandier O, De Angelis FG, Nicoletti C, Allocca M, Pansarasa O, Parente V, Musarò A, Auricchio A, Bottinelli R, Bozzoni I. Body-wide gene therapy of Duchenne muscular dystrophy in the mdx mouse model. Proc Natl Acad Sci U S A 2006; 103:3758-63. [PMID: 16501048 PMCID: PMC1450150 DOI: 10.1073/pnas.0508917103] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Duchenne muscular dystrophy is an X-linked muscle disease characterized by mutations in the dystrophin gene. Many of these can be corrected at the posttranscriptional level by skipping the mutated exon. We have obtained persistent exon skipping in mdx mice by tail vein injection with an adeno-associated viral (AAV) vector expressing antisense sequences as part of the stable cellular U1 small nuclear RNA. Systemic delivery of the AAV construct resulted in effective body-wide colonization, significant recovery of the functional properties in vivo, and lower creatine kinase serum levels, suggesting an overall decrease in muscle wasting. The transduced muscles rescued dystrophin expression and displayed a significant recovery of function toward the normal values at single muscle fiber level. This approach provides solid bases for a systemic use of AAV-mediated antisense-U1 small nuclear RNA expression for the therapeutic treatment of Duchenne muscular dystrophy.
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Affiliation(s)
- Michela Alessandra Denti
- *Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and Institute of Molecular Biology and Pathology, University “La Sapienza,” P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alessandro Rosa
- *Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and Institute of Molecular Biology and Pathology, University “La Sapienza,” P. le Aldo Moro 5, 00185 Rome, Italy
| | - Giuseppe D’Antona
- Department of Experimental Medicine, Human Physiology Unit, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
| | - Olga Sthandier
- *Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and Institute of Molecular Biology and Pathology, University “La Sapienza,” P. le Aldo Moro 5, 00185 Rome, Italy
| | - Fernanda Gabriella De Angelis
- *Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and Institute of Molecular Biology and Pathology, University “La Sapienza,” P. le Aldo Moro 5, 00185 Rome, Italy
| | - Carmine Nicoletti
- Department of Histology and Medical Embryology, Centro di Eccellenza di Biologia e Medicina Molecolare and Interuniversity Institute of Myology, University of Rome “La Sapienza,” Via A. Scarpa 14, 00161 Rome, Italy
| | - Mariacarmela Allocca
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131 Naples, Italy; and
| | - Orietta Pansarasa
- Department of Experimental Medicine, Human Physiology Unit, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
| | - Valeria Parente
- Department of Experimental Medicine, Human Physiology Unit, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
| | - Antonio Musarò
- Department of Histology and Medical Embryology, Centro di Eccellenza di Biologia e Medicina Molecolare and Interuniversity Institute of Myology, University of Rome “La Sapienza,” Via A. Scarpa 14, 00161 Rome, Italy
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131 Naples, Italy; and
| | - Roberto Bottinelli
- Department of Experimental Medicine, Human Physiology Unit, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
| | - Irene Bozzoni
- *Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and Institute of Molecular Biology and Pathology, University “La Sapienza,” P. le Aldo Moro 5, 00185 Rome, Italy
- To whom correspondence should be addressed. E-mail:
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Denti MA, Rosa A, Sthandier O, De Angelis FG, Bozzoni I. A new vector, based on the PolII promoter of the U1 snRNA gene, for the expression of siRNAs in mammalian cells. Mol Ther 2005; 10:191-9. [PMID: 15272480 DOI: 10.1016/j.ymthe.2004.04.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Several vectors for the induction of RNA interference in mammalian cells have been described,based mainly on polIII-dependent promoters. They transcribe short hairpin RNAs (shRNA) that,after being processed into short interfering RNAs (siRNAs), mediate the degradation of the target mRNA. Here, we describe the construction of a new siRNA-expressing vector (psiUx) based on the strong and ubiquitous polII-dependent promoter of the human U1 small nuclear RNA (snRNA)gene. In psiUx, the only constraint for the shRNA sequence is a purine at position +1, since specific 3'-end formation is achieved by a box element located downstream of the transcribed region. Several constructs were designed against the lamin A/C target. Depending on the structure of the shRNA transcribed, a preferential or exclusive accumulation of the antisense strand is obtained, thus avoiding possible nonspecific targeting by the sense strand. In all cases tested, very effective siRNAs were produced, thus providing a proof-of-principle that a snRNA-type polII promoter can be used for the expression of siRNAs. We show that psiUx ensures high levels of expression and efficient knock down of the target gene also in stable cell lines.
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Affiliation(s)
- Michela Alessandra Denti
- Istituto Pasteur-Fondazione Centi-Bolognetti, Department of Genetics and Molecular Biology, University of Rome La Sapienza and IBPM of CNR, Rome, Italy
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Cavaldesi M, Caruso M, Sthandier O, Amati P, Garcia MI. Conformational changes of murine polyomavirus capsid proteins induced by sialic acid binding. J Biol Chem 2004; 279:41573-9. [PMID: 15292169 DOI: 10.1074/jbc.m405995200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Murine polyomavirus (Py) infection initiates by the recognition of cell membrane molecules containing terminal sialic acid (SA) residues through specific binding pockets formed at the major capsid protein VP1 surface. VP1 Pockets 1, 2, and 3 bind terminal SA, Gal, and second branched SA, respectively. The consequence of recognition on viral cell entry remains elusive. In this work, we show that preincubation of Py with soluble compounds within Pocket 1 (N-acetyl or N-glycolyl neuraminic acids) increases Py cell binding and infectivity in murine 3T6 fibroblasts. In contrast, Gal does not significantly alter Py binding nor infectivity, whereas sialyllactose, in Pockets 1 and 2, decreases cell binding and infectivity. Binding experiments with Py virus-like particles confirmed the direct involvement of VP1 in this effect. To determine whether such results could reflect VP1 conformational changes induced by SA binding, protease digestion assays were performed after pretreatment of Py or virus-like particles with soluble receptor fragments. Binding of SA with the VP1 Pocket 1, but not of compounds interacting with Pocket 2, was associated with a transition of this protein from a protease-sensitive to a protease-resistant state. This effect was transmitted to the minor capsid proteins VP2 and VP3 in virus particles. Attachment of Py to cell monolayers similarly led to a VP1 trypsin-resistant pattern. Taken together, these data present evidence that initial binding of Py to terminal SA induces conformational changes in the viral capsid, which may influence subsequent virus cell entry steps.
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Affiliation(s)
- Michaela Cavaldesi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma "La Sapienza," Viale Regina Elena 324, 00161 Rome, Italy
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Caruso M, Cavaldesi M, Gentile M, Sthandier O, Amati P, Garcia MI. Role of sialic acid-containing molecules and the α4β1 integrin receptor in the early steps of polyomavirus infection. J Gen Virol 2003; 84:2927-2936. [PMID: 14573797 DOI: 10.1099/vir.0.19369-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Murine polyomavirus (MPyV) infection occurs through recognition of sialic acid (SA) residues present on the host cell membrane, but the nature of the molecules involved and the exact role of this interaction in virus cell entry still need to be clarified. In this work, mutations at residues R(77) or H(298) of the MPyV VP1 protein were shown to lead to a complete loss of virus infectivity, which, however, could be restored by lipofection of virus particles into the cytoplasm of the host cells. Using virus-like particles (VLPs), it was demonstrated that the non-infectivity of these mutants was due to impaired cell entry caused by total abrogation of SA-dependent cell binding. This indicates that SA residues are essential primary cell receptors for MPyV. As the alpha4beta1 integrin has been identified recently as a cell receptor for MPyV, the relationship, if any, was investigated between SA-containing and alpha4beta1 integrin receptors. The ability of mutants R(77)Q and H(298)Q and wt VLPs to bind to cells overexpressing the alpha4beta1 integrin was studied in SA-positive (BALB/c 3T3 cells and Pro-5 cells) and SA-deficient (Pro5-derived Lec-2 cells) backgrounds. Overexpression of alpha4beta1 integrin did not restore binding of mutant VLPs in any of these cell lines or, indeed, that of wt VLPs in a SA-deficient background. Moreover, evidence is provided that overexpression of the sialylated alpha4beta1 integrin enhances wt VLP cell binding, suggesting that, in addition to its function at a post-attachment level, alpha4beta1 integrin acts also as one of the SA-containing receptors for initial cell binding.
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Affiliation(s)
- Maddalena Caruso
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma 'La Sapienza', Viale Regina Elena 324, 00161 Rome, Italy
| | - Michaela Cavaldesi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma 'La Sapienza', Viale Regina Elena 324, 00161 Rome, Italy
| | - Massimo Gentile
- e Dipartimento di Medicina Sperimentale e Patologia, Sezione di Virologia, Università di Roma 'La Sapienza', Viale Regina Elena 324, 00161 Rome, Italy
| | - Olga Sthandier
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma 'La Sapienza', Viale Regina Elena 324, 00161 Rome, Italy
| | - Paolo Amati
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma 'La Sapienza', Viale Regina Elena 324, 00161 Rome, Italy
| | - Marie-Isabelle Garcia
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma 'La Sapienza', Viale Regina Elena 324, 00161 Rome, Italy
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Caruso M, Belloni L, Sthandier O, Amati P, Garcia MI. Alpha4beta1 integrin acts as a cell receptor for murine polyomavirus at the postattachment level. J Virol 2003; 77:3913-21. [PMID: 12634351 PMCID: PMC150644 DOI: 10.1128/jvi.77.7.3913-3921.2003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2002] [Accepted: 12/18/2002] [Indexed: 11/20/2022] Open
Abstract
The initial interaction of murine polyomavirus (Py) with host cells occurs through direct binding of the major capsid protein VP1 with cell membrane molecules containing terminal sialic acids; however, these Py receptor molecules have not yet been identified. Analysis of the capsid protein primary sequences of all murine strains revealed the presence of integrin ligand motifs in the DE and EF loops of VP1 (LDV and DLXXL, respectively) and at the N terminus of VP2 (DGE). We show that infectivity of the Py A2 strain in mouse Swiss 3T3 fibroblasts is significantly reduced only in the presence of natural integrin ligands carrying an LDV motif or antibodies directed against the alpha4 and beta1 integrin subunits. Furthermore, we demonstrate that expression of the alpha4 subunit in the alpha4-deficient BALB/c 3T3 cells increases viral infectivity. Addition of alpha4 function-blocking antibodies, prior to or after virus adsorption, blocks this increased infectivity without affecting virus binding to cells. Taken together, these data indicate that expression of alpha4 integrin enhances permissivity to Py, probably by acting as one of the postattachment receptors.
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Affiliation(s)
- Maddalena Caruso
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Istituto Pasteur-Fondazione Cenci Bolognetti, Università di Roma La Sapienza, Rome, Italy
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De Angelis FG, Sthandier O, Berarducci B, Toso S, Galluzzi G, Ricci E, Cossu G, Bozzoni I. Chimeric snRNA molecules carrying antisense sequences against the splice junctions of exon 51 of the dystrophin pre-mRNA induce exon skipping and restoration of a dystrophin synthesis in Delta 48-50 DMD cells. Proc Natl Acad Sci U S A 2002; 99:9456-61. [PMID: 12077324 PMCID: PMC123162 DOI: 10.1073/pnas.142302299] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deletions and point mutations in the dystrophin gene cause either the severe progressive myopathy Duchenne muscular dystrophy (DMD) or the milder Becker muscular dystrophy, depending on whether the translational reading frame is lost or maintained. Because internal in-frame deletions in the protein produce only mild myopathic symptoms, it should be possible, by preventing the inclusion of specific mutated exon(s) in the mature dystrophin mRNA, to restore a partially corrected phenotype. Such control has been previously accomplished by the use of synthetic oligonucleotides; nevertheless, a significant drawback to this approach is caused by the fact that oligonucleotides would require periodic administrations. To circumvent this problem, we have produced several constructs able to express in vivo, in a stable fashion, large amounts of chimeric RNAs containing antisense sequences. In this paper we show that antisense molecules against exon 51 splice junctions are able to direct skipping of this exon in the human DMD deletion 48-50 and to rescue dystrophin synthesis. We also show that the highest skipping activity was found when antisense constructs against the 5' and 3' splice sites are coexpressed in the same cell.
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Affiliation(s)
- Fernanda Gabriella De Angelis
- Institute Pasteur Fondazione Cenci-Bolognetti, Department of Genetics and Molecular Biology, University La Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy
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Garcia MI, Perez M, Caruso M, Sthandier O, Ferreira R, Cermola M, Macchia C, Amati P. A mutation in the DE loop of the VP1 protein that prevents polyomavirus transcription and replication. Virology 2000; 272:293-301. [PMID: 10873772 DOI: 10.1006/viro.2000.0351] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natural mutants of the DE loop of the Polyomavirus (Py) major coat protein VP1 have been previously shown to display an altered host specificity (L. Ricci, R. Maione, C. Passananti, A. Felsani, and P. Amati, 1992, J. Virol. 66, 7153-7158). To better understand the role of this outfacing loop of the VP1 protein in Py infectivity, we constructed and characterized a Py mutant (Py M17) harboring a deletion of 7 AA within the tip of the DE loop. The mutant virions obtained after DNA transfection were unable to replicate and initiate early transcription in fibroblast cells. Complementation experiments performed to rescue the deficient M17 replication by means of wt functions revealed the cis-dominance of the mutation. In situ cell fractionation experiments demonstrated that the Py mutant, like the Py wt, enters the cells, reaches the nucleus and that both the viral DNA and VP1 protein are found tightly bound to the nuclear matrix. These data suggest that the VP1 protein, associated to the viral DNA, conditions early viral gene expression and that the DE loop of the protein must be involved in this process.
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Affiliation(s)
- M I Garcia
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari, Sezione di Genetica Molecolare, Università di Roma La Sapienza, Viale Regina Elena 324, Rome, 00161, Italy
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Anastasi S, Giordano S, Sthandier O, Gambarotta G, Maione R, Comoglio P, Amati P. A natural hepatocyte growth factor/scatter factor autocrine loop in myoblast cells and the effect of the constitutive Met kinase activation on myogenic differentiation. J Cell Biol 1997; 137:1057-68. [PMID: 9166406 PMCID: PMC2136220 DOI: 10.1083/jcb.137.5.1057] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
As a rule, hepatocyte growth factor/scatter factor (HGF/SF) is produced by mesenchymal cells, while its receptor, the tyrosine kinase encoded by the met proto-oncogene, is expressed by the neighboring epithelial cells in a canonical paracrine fashion. In the present work we show that both HGF/SF and met are coexpressed by undifferentiated C2 mouse myoblasts. In growing cells, the autocrine loop is active as the receptor exhibits a constitutive phosphorylation on tyrosine that can be abrogated by exogenously added anti-HGF/SF neutralizing antibodies. The transcription of HGF/SF and met genes is downregulated when myoblasts stop proliferating and differentiate. The coexpression of HGF/SF and met genes is not exclusive to C2 cells since it has been assessed also in other myogenic cell lines and in mouse primary satellite cells, suggesting that HGF/SF could play a role in muscle development through an autocrine way. To analyze the biological effects of HGF/SF receptor activation, we stably expressed the constitutively activated receptor catalytic domain (p65(tpr-met)) in C2 cells. This active kinase determined profound changes in cell shape and inhibited myogenesis at both morphological and biochemical levels. Notably, a complete absence of muscle regulatory markers such as MyoD and myogenin was observed in p65(tpr-met) highly expressing C2 clones. We also studied the effects of the ectopic expression of human isoforms of met receptor (h-met) and of HGF/SF (h-HGF/SF) in stable transfected C2 cells. Single constitutive expression of h-met or h-HGF/SF does not alter substantially the growth and differentiation properties of the myoblast cells, probably because of a species-specific ligand-receptor interaction. A C2 clone expressing simultaneously both h-met and h-HGF/SF is able to grow in soft agar and shows a decrease in myogenic potential comparable to that promoted by p65(tpr-met) kinase. These data indicate that a met kinase signal released from differentiation-dependent control provides a negative stimulus for the onset of myogenic differentiation.
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Affiliation(s)
- S Anastasi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma La Sapienza, 00161 Roma, Italy
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Abstract
Mouse fibroblasts were stably transfected with expression plasmids in which sequences of the early region of polyomavirus were inserted both in sense and antisense orientation. The cell lines that synthesize in the antisense orientation, a 1195-bp viral genome fragment covering the Ori, Cap, ATG, and all of the early mRNA splicing sites acquire resistance to viral infection. Smaller fragments covering Ori, Cap, and ATG sites or the splicing sites, as well as fragments cloned in sense orientation, failed to confer cell immunity to polyoma infection. The resistance proved to be directly dependent upon the specific antisense RNA and to be inversely proportional to the multiplicity of infecting polyoma.
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Affiliation(s)
- L Ottavio
- Dipartimento di Biopathologia Umana, Università di Roma La Sapienza, Italy
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