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Lebek S, Caravia XM, Chemello F, Tan W, McAnally JR, Chen K, Xu L, Liu N, Bassel-Duby R, Olson EN. Elimination of CaMKIIδ Autophosphorylation by CRISPR-Cas9 Base Editing Improves Survival and Cardiac Function in Heart Failure in Mice. Circulation 2023; 148:1490-1504. [PMID: 37712250 PMCID: PMC10842988 DOI: 10.1161/circulationaha.123.065117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Cardiovascular diseases are the main cause of worldwide morbidity and mortality, highlighting the need for new therapeutic strategies. Autophosphorylation and subsequent overactivation of the cardiac stress-responsive enzyme CaMKIIδ (Ca2+/calmodulin-dependent protein kinase IIδ) serves as a central driver of multiple cardiac disorders. METHODS To develop a comprehensive therapy for heart failure, we used CRISPR-Cas9 adenine base editing to ablate the autophosphorylation site of CaMKIIδ. We generated mice harboring a phospho-resistant CaMKIIδ mutation in the germline and subjected these mice to severe transverse aortic constriction, a model for heart failure. Cardiac function, transcriptional changes, apoptosis, and fibrosis were assessed by echocardiography, RNA sequencing, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and standard histology, respectively. Specificity toward CaMKIIδ gene editing was assessed using deep amplicon sequencing. Cellular Ca2+ homeostasis was analyzed using epifluorescence microscopy in Fura-2-loaded cardiomyocytes. RESULTS Within 2 weeks after severe transverse aortic constriction surgery, 65% of all wild-type mice died, and the surviving mice showed dramatically impaired cardiac function. In contrast to wild-type mice, CaMKIIδ phospho-resistant gene-edited mice showed a mortality rate of only 11% and exhibited substantially improved cardiac function after severe transverse aortic constriction. Moreover, CaMKIIδ phospho-resistant mice were protected from heart failure-related aberrant changes in cardiac gene expression, myocardial apoptosis, and subsequent fibrosis, which were observed in wild-type mice after severe transverse aortic constriction. On the basis of identical mouse and human genome sequences encoding the autophosphorylation site of CaMKIIδ, we deployed the same editing strategy to modify this pathogenic site in human induced pluripotent stem cells. It is notable that we detected a >2000-fold increased specificity for editing of CaMKIIδ compared with other CaMKII isoforms, which is an important safety feature. While wild-type cardiomyocytes showed impaired Ca2+ transients and an increased frequency of arrhythmias after chronic β-adrenergic stress, CaMKIIδ-edited cardiomyocytes were protected from these adverse responses. CONCLUSIONS Ablation of CaMKIIδ autophosphorylation by adenine base editing may offer a potential broad-based therapeutic concept for human cardiac disease.
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Affiliation(s)
- Simon Lebek
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
- Department of Internal Medicine II, University Hospital Regensburg; Regensburg, Germany
| | - Xurde M. Caravia
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Wei Tan
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - John R. McAnally
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
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2
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Zhang Y, Ramirez-Martinez A, Chen K, McAnally JR, Cai C, Durbacz MZ, Chemello F, Wang Z, Xu L, Bassel-Duby R, Liu N, Olson EN. Net39 protects muscle nuclei from mechanical stress during the pathogenesis of Emery-Dreifuss muscular dystrophy. J Clin Invest 2023; 133:e163333. [PMID: 37395273 DOI: 10.1172/jci163333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 05/16/2023] [Indexed: 07/04/2023] Open
Abstract
Mutations in genes encoding nuclear envelope proteins lead to diseases known as nuclear envelopathies, characterized by skeletal muscle and heart abnormalities, such as Emery-Dreifuss muscular dystrophy (EDMD). The tissue-specific role of the nuclear envelope in the etiology of these diseases has not been extensively explored. We previously showed that global deletion of the muscle-specific nuclear envelope protein NET39 in mice leads to neonatal lethality due to skeletal muscle dysfunction. To study the potential role of the Net39 gene in adulthood, we generated a muscle-specific conditional knockout (cKO) of Net39 in mice. cKO mice recapitulated key skeletal muscle features of EDMD, including muscle wasting, impaired muscle contractility, abnormal myonuclear morphology, and DNA damage. The loss of Net39 rendered myoblasts hypersensitive to mechanical stretch, resulting in stretch-induced DNA damage. Net39 was downregulated in a mouse model of congenital myopathy, and restoration of Net39 expression through AAV gene delivery extended life span and ameliorated muscle abnormalities. These findings establish NET39 as a direct contributor to the pathogenesis of EDMD that acts by protecting against mechanical stress and DNA damage.
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Affiliation(s)
- Yichi Zhang
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Andres Ramirez-Martinez
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, and
| | - John R McAnally
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Chunyu Cai
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Mateusz Z Durbacz
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Francesco Chemello
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Zhaoning Wang
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, and
| | - Rhonda Bassel-Duby
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Ning Liu
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Eric N Olson
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
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3
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Chai AC, Chemello F, Li H, Nishiyama T, Chen K, Zhang Y, Sánchez-Ortiz E, Alomar A, Xu L, Liu N, Bassel-Duby R, Olson EN. Single-swap editing for the correction of common Duchenne muscular dystrophy mutations. Mol Ther Nucleic Acids 2023; 32:522-535. [PMID: 37215149 PMCID: PMC10192335 DOI: 10.1016/j.omtn.2023.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disease of progressive muscle weakness and wasting caused by the absence of dystrophin protein. Current gene therapy approaches using antisense oligonucleotides require lifelong dosing and have limited efficacy in restoring dystrophin production. A gene editing approach could permanently correct the genome and restore dystrophin protein expression. Here, we describe single-swap editing, in which an adenine base editor edits a single base pair at a splice donor site or splice acceptor site to enable exon skipping or reframing. In human induced pluripotent stem cell-derived cardiomyocytes, we demonstrate that single-swap editing can enable beneficial exon skipping or reframing for the three most therapeutically relevant exons-DMD exons 45, 51, and 53-which could be beneficial for 30% of all DMD patients. Furthermore, an adeno-associated virus delivery method for base editing components can efficiently restore dystrophin production locally and systemically in skeletal and cardiac muscles of a DMD mouse model containing a deletion of Dmd exon 44. Our studies demonstrate single-swap editing as a potential gene editing therapy for common DMD mutations.
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Affiliation(s)
- Andreas C. Chai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Takahiko Nishiyama
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Efraín Sánchez-Ortiz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adeeb Alomar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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Abstract
Duchenne muscular dystrophy (DMD) is a debilitating genetic disorder that results in progressive muscle degeneration and premature death. DMD is caused by mutations in the gene encoding dystrophin protein, a membrane-associated protein required for maintenance of muscle structure and function. Although the genetic mutations causing the disease are well known, no curative therapies have been developed to date. The advent of genome-editing technologies provides new opportunities to correct the underlying mutations responsible for DMD. These mutations have been successfully corrected in human cells, mice, and large animal models through different strategies based on CRISPR-Cas9 gene editing. Ideally, CRISPR-editing could offer a one-time treatment for DMD by correcting the genetic mutations and enabling normal expression of the repaired gene. However, numerous challenges remain to be addressed, including optimization of gene editing, delivery of gene-editing components to all the muscles of the body, and the suppression of possible immune responses to the CRISPR-editing therapy. This review provides an overview of the recent advances toward CRISPR-editing therapy for DMD and discusses the opportunities and the remaining challenges in the path to clinical translation.
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Affiliation(s)
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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5
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Lebek S, Chemello F, Caravia XM, Tan W, Li H, Chen K, Xu L, Liu N, Bassel-Duby R, Olson EN. Ablation of CaMKIIδ oxidation by CRISPR-Cas9 base editing as a therapy for cardiac disease. Science 2023; 379:179-185. [PMID: 36634166 PMCID: PMC10150399 DOI: 10.1126/science.ade1105] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CRISPR-Cas9 gene editing is emerging as a prospective therapy for genomic mutations. However, current editing approaches are directed primarily toward relatively small cohorts of patients with specific mutations. Here, we describe a cardioprotective strategy potentially applicable to a broad range of patients with heart disease. We used base editing to ablate the oxidative activation sites of CaMKIIδ, a primary driver of cardiac disease. We show in cardiomyocytes derived from human induced pluripotent stem cells that editing the CaMKIIδ gene to eliminate oxidation-sensitive methionine residues confers protection from ischemia/reperfusion (IR) injury. Moreover, CaMKIIδ editing in mice at the time of IR enables the heart to recover function from otherwise severe damage. CaMKIIδ gene editing may thus represent a permanent and advanced strategy for heart disease therapy.
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Affiliation(s)
- Simon Lebek
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Internal Medicine II, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xurde M Caravia
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Tan
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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6
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Ramirez-Martinez A, Zhang Y, van den Boogaard MJ, McAnally JR, Rodriguez-Caycedo C, Chai AC, Chemello F, Massink MP, Cuppen I, Elferink MG, van Es RJ, Janssen NG, Walraven-van Oijen LP, Liu N, Bassel-Duby R, van Jaarsveld RH, Olson EN. Impaired activity of the fusogenic micropeptide Myomixer causes myopathy resembling Carey-Fineman-Ziter syndrome. J Clin Invest 2022; 132:159002. [PMID: 35642635 PMCID: PMC9151691 DOI: 10.1172/jci159002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 01/19/2023] Open
Abstract
Skeletal muscle fibers contain hundreds of nuclei, which increase the overall transcriptional activity of the tissue and perform specialized functions. Multinucleation occurs through myoblast fusion, mediated by the muscle fusogens Myomaker (MYMK) and Myomixer (MYMX). We describe a human pedigree harboring a recessive truncating variant of the MYMX gene that eliminates an evolutionarily conserved extracellular hydrophobic domain of MYMX, thereby impairing fusogenic activity. Homozygosity of this human variant resulted in a spectrum of abnormalities that mimicked the clinical presentation of Carey-Fineman-Ziter syndrome (CFZS), caused by hypomorphic MYMK variants. Myoblasts generated from patient-derived induced pluripotent stem cells displayed defective fusion, and mice bearing the human MYMX variant died perinatally due to muscle abnormalities. In vitro assays showed that the human MYMX variant conferred minimal cell-cell fusogenicity, which could be restored with CRISPR/Cas9-mediated base editing, thus providing therapeutic potential for this disorder. Our findings identify MYMX as a recessive, monogenic human disease gene involved in CFZS, and provide new insights into the contribution of myoblast fusion to neuromuscular diseases.
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Affiliation(s)
- Andres Ramirez-Martinez
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yichi Zhang
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - John R McAnally
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Cristina Rodriguez-Caycedo
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Andreas C Chai
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Francesco Chemello
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | | | | | - Robert Jj van Es
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, Netherlands
| | - Nard G Janssen
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Ning Liu
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Eric N Olson
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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7
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Karri DR, Zhang Y, Chemello F, Min YL, Huang J, Kim J, Mammen PP, Xu L, Liu N, Bassel-Duby R, Olson EN. Long-term maintenance of dystrophin expression and resistance to injury of skeletal muscle in gene edited DMD mice. Molecular Therapy - Nucleic Acids 2022; 28:154-167. [PMID: 35402069 PMCID: PMC8956962 DOI: 10.1016/j.omtn.2022.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
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8
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Peterson JM, Chemello F, Calore F. Editorial: MicroRNAs and Muscle Cell Death in Cancer. Front Genet 2022; 13:892136. [PMID: 35646081 PMCID: PMC9136531 DOI: 10.3389/fgene.2022.892136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Jennifer M. Peterson
- School of Exercise and rehabilitation Sciences, University of Toledo, Toledo, OH, United States
| | - Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Federica Calore
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- *Correspondence: Federica Calore,
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9
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Corso D, Chemello F, Alessio E, Urso I, Ferrarese G, Bazzega M, Romualdi C, Lanfranchi G, Sales G, Cagnin S. MyoData: An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle. Comput Struct Biotechnol J 2021; 19:4142-4155. [PMID: 34527188 PMCID: PMC8342900 DOI: 10.1016/j.csbj.2021.07.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of gene expression through non-coding RNAs at single myofiber and nucleus resolution. Reinterpretation of KEGG pathways with microRNA and long non-coding RNA activities. miR-149, -214, and let-7e alter mitochondrial shape. The long non-coding RNA Pvt1 is a sponge for miR-27a. miR-208b regulates Sox6; miR-214 regulates both Sox6 and Slc16a3.
Non-coding RNAs represent the largest part of transcribed mammalian genomes and prevalently exert regulatory functions. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) can modulate the activity of each other. Skeletal muscle is the most abundant tissue in mammals. It is composed of different cell types with myofibers that represent the smallest complete contractile system. Considering that lncRNAs and miRNAs are more cell type-specific than coding RNAs, to understand their function it is imperative to evaluate their expression and action within single myofibers. In this database, we collected gene expression data for coding and non-coding genes in single myofibers and used them to produce interaction networks based on expression correlations. Since biological pathways are more informative than networks based on gene expression correlation, to understand how altered genes participate in the studied phenotype, we integrated KEGG pathways with miRNAs and lncRNAs. The database also integrates single nucleus gene expression data on skeletal muscle in different patho-physiological conditions. We demonstrated that these networks can serve as a framework from which to dissect new miRNA and lncRNA functions to experimentally validate. Some interactions included in the database have been previously experimentally validated using high throughput methods. These can be the basis for further functional studies. Using database information, we demonstrate the involvement of miR-149, -214 and let-7e in mitochondria shaping; the ability of the lncRNA Pvt1 to mitigate the action of miR-27a via sponging; and the regulatory activity of miR-214 on Sox6 and Slc16a3. The MyoData is available at https://myodata.bio.unipd.it.
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Affiliation(s)
- Davide Corso
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Francesco Chemello
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Enrico Alessio
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Ilenia Urso
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Giulia Ferrarese
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Martina Bazzega
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
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10
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Chemello F, Chai AC, Li H, Rodriguez-Caycedo C, Sanchez-Ortiz E, Atmanli A, Mireault AA, Liu N, Bassel-Duby R, Olson EN. Precise correction of Duchenne muscular dystrophy exon deletion mutations by base and prime editing. Sci Adv 2021; 7:7/18/eabg4910. [PMID: 33931459 PMCID: PMC8087404 DOI: 10.1126/sciadv.abg4910] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 05/06/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle disease caused by the lack of dystrophin, which maintains muscle membrane integrity. We used an adenine base editor (ABE) to modify splice donor sites of the dystrophin gene, causing skipping of a common DMD deletion mutation of exon 51 (∆Ex51) in cardiomyocytes derived from human induced pluripotent stem cells, restoring dystrophin expression. Prime editing was also capable of reframing the dystrophin open reading frame in these cardiomyocytes. Intramuscular injection of ∆Ex51 mice with adeno-associated virus serotype-9 encoding ABE components as a split-intein trans-splicing system allowed gene editing and disease correction in vivo. Our findings demonstrate the effectiveness of nucleotide editing for the correction of diverse DMD mutations with minimal modification of the genome, although improved delivery methods will be required before these strategies can be used to sufficiently edit the genome in patients with DMD.
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Affiliation(s)
- F Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - A C Chai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - H Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - C Rodriguez-Caycedo
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - E Sanchez-Ortiz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - A Atmanli
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - A A Mireault
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - N Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - R Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - E N Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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11
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Chemello F, Wang Z, Li H, McAnally JR, Liu N, Bassel-Duby R, Olson EN. Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing. Proc Natl Acad Sci U S A 2020; 117:29691-29701. [PMID: 33148801 PMCID: PMC7703557 DOI: 10.1073/pnas.2018391117] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle disorder characterized by cycles of degeneration and regeneration of multinucleated myofibers and pathological activation of a variety of other muscle-associated cell types. The extent to which different nuclei within the shared cytoplasm of a myofiber may display transcriptional diversity and whether individual nuclei within a multinucleated myofiber might respond differentially to DMD pathogenesis is unknown. Similarly, the potential transcriptional diversity among nonmuscle cell types within dystrophic muscle has not been explored. Here, we describe the creation of a mouse model of DMD caused by deletion of exon 51 of the dystrophin gene, which represents a prevalent disease-causing mutation in humans. To understand the transcriptional abnormalities and heterogeneity associated with myofiber nuclei, as well as other mononucleated cell types that contribute to the muscle pathology associated with DMD, we performed single-nucleus transcriptomics of skeletal muscle of mice with dystrophin exon 51 deletion. Our results reveal distinctive and previously unrecognized myonuclear subtypes within dystrophic myofibers and uncover degenerative and regenerative transcriptional pathways underlying DMD pathogenesis. Our findings provide insights into the molecular underpinnings of DMD, controlled by the transcriptional activity of different types of muscle and nonmuscle nuclei.
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Affiliation(s)
- Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zhaoning Wang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hui Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - John R McAnally
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Eric N Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
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12
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Min YL, Chemello F, Li H, Rodriguez-Caycedo C, Sanchez-Ortiz E, Mireault AA, McAnally JR, Shelton JM, Zhang Y, Bassel-Duby R, Olson EN. Correction of Three Prominent Mutations in Mouse and Human Models of Duchenne Muscular Dystrophy by Single-Cut Genome Editing. Mol Ther 2020; 28:2044-2055. [PMID: 32892813 PMCID: PMC7474267 DOI: 10.1016/j.ymthe.2020.05.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/09/2020] [Accepted: 05/26/2020] [Indexed: 01/18/2023] Open
Abstract
Duchenne muscular dystrophy (DMD), one of the most common neuromuscular disorders of children, is caused by the absence of dystrophin protein in striated muscle. Deletions of exons 43, 45, and 52 represent mutational "hotspot" regions in the dystrophin gene. We created three new DMD mouse models harboring deletions of exons 43, 45, and 52 to represent common DMD mutations. To optimize CRISPR-Cas9 genome editing using the single-cut strategy, we identified single guide RNAs (sgRNAs) capable of restoring dystrophin expression by inducing exon skipping and reframing. Intramuscular delivery of AAV9 encoding SpCas9 and selected sgRNAs efficiently restored dystrophin expression in these new mouse models, offering a platform for future studies of dystrophin gene correction therapies. To validate the therapeutic potential of this approach, we identified sgRNAs capable of restoring dystrophin expression by the single-cut strategy in cardiomyocytes derived from human induced pluripotent stem cells (iPSCs) with each of these hotspot deletion mutations. We found that the potential effectiveness of individual sgRNAs in correction of DMD mutations cannot be predicted a priori, highlighting the importance of sgRNA design and testing as a prelude for applying gene editing as a therapeutic strategy for DMD.
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MESH Headings
- Animals
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- Dependovirus/genetics
- Disease Models, Animal
- Dystrophin/metabolism
- Exons
- Gene Deletion
- Gene Editing/methods
- Genetic Therapy/methods
- Humans
- Induced Pluripotent Stem Cells/metabolism
- Mice
- Mice, Inbred C57BL
- Muscle, Skeletal/metabolism
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Myocytes, Cardiac/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
- Yi-Li Min
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Francesco Chemello
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Cristina Rodriguez-Caycedo
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Efrain Sanchez-Ortiz
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Alex A Mireault
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - John R McAnally
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - John M Shelton
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Zhang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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13
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Abstract
Muscular dystrophies are debilitating disorders that result in progressive weakness and degeneration of skeletal muscle. Although the genetic mutations and clinical abnormalities of a variety of neuromuscular diseases are well known, no curative therapies have been developed to date. The advent of genome editing technology provides new opportunities to correct the underlying mutations responsible for many monogenic neuromuscular diseases. For example, Duchenne muscular dystrophy, which is caused by mutations in the dystrophin gene, has been successfully corrected in mice, dogs, and human cells through CRISPR/Cas9 editing. In this Review, we focus on the potential for, and challenges of, correcting muscular dystrophies by editing disease-causing mutations at the genomic level. Ideally, because muscle tissues are extremely long-lived, CRISPR technology could offer a one-time treatment for muscular dystrophies by correcting the culprit genomic mutations and enabling normal expression of the repaired gene.
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14
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Chemello F, Grespi F, Zulian A, Cancellara P, Hebert-Chatelain E, Martini P, Bean C, Alessio E, Buson L, Bazzega M, Armani A, Sandri M, Ferrazza R, Laveder P, Guella G, Reggiani C, Romualdi C, Bernardi P, Scorrano L, Cagnin S, Lanfranchi G. Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle. Cell Rep 2020; 26:3784-3797.e8. [PMID: 30917329 DOI: 10.1016/j.celrep.2019.02.105] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/29/2018] [Accepted: 02/26/2019] [Indexed: 12/27/2022] Open
Abstract
Skeletal muscle is composed of different myofiber types that preferentially use glucose or lipids for ATP production. How fuel preference is regulated in these post-mitotic cells is largely unknown, making this issue a key question in the fields of muscle and whole-body metabolism. Here, we show that microRNAs (miRNAs) play a role in defining myofiber metabolic profiles. mRNA and miRNA signatures of all myofiber types obtained at the single-cell level unveiled fiber-specific regulatory networks and identified two master miRNAs that coordinately control myofiber fuel preference and mitochondrial morphology. Our work provides a complete and integrated mouse myofiber type-specific catalog of gene and miRNA expression and establishes miR-27a-3p and miR-142-3p as regulators of lipid use in skeletal muscle.
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Affiliation(s)
- Francesco Chemello
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Alessandra Zulian
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Pasqua Cancellara
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Etienne Hebert-Chatelain
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Camilla Bean
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Enrico Alessio
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Martina Bazzega
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Marco Sandri
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Ruggero Ferrazza
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Paolo Laveder
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
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15
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Codolo G, Toffoletto M, Chemello F, Coletta S, Soler Teixidor G, Battaggia G, Munari G, Fassan M, Cagnin S, de Bernard M. Helicobacter pylori Dampens HLA-II Expression on Macrophages via the Up-Regulation of miRNAs Targeting CIITA. Front Immunol 2020; 10:2923. [PMID: 31969878 PMCID: PMC6960189 DOI: 10.3389/fimmu.2019.02923] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/28/2019] [Indexed: 12/17/2022] Open
Abstract
Macrophages have a major role in infectious and inflammatory diseases, and the available data suggest that Helicobacter pylori persistence can be explained in part by the failure of the bacterium to be killed by professional phagocytes. Macrophages are cells ready to kill the engulfed pathogen, through oxygen-dependent and -independent mechanisms; however, their killing potential can be further augmented by the intervention of T helper (Th) cells upon the specific recognition of human leukocyte antigen (HLA)-II–peptide complexes on the surface of the phagocytic cells. As it pertains to H. pylori, the bacterium is engulfed by macrophages, but it interferes with the phagosome maturation process leading to phagosomes with an altered degradative capacity, and to megasomes, wherein H. pylori resists killing. We recently showed that macrophages infected with H. pylori strongly reduce the expression of HLA-II molecules on the plasma membrane and this compromises the bacterial antigen presentation to Th lymphocytes. In this work, we demonstrate that H. pylori hampers HLA-II expression in macrophages, activated or non-activated by IFN-γ, by down-regulating the expression of the class II major histocompatibility complex transactivator (CIITA), the “master control factor” for the expression of HLA class II genes. We provided evidence that this effect relies on the up-regulation of let-7f-5p, let-7i-5p, miR-146b-5p, and -185-5p targeting CIITA. MiRNA expression analysis performed on biopsies from H. pylori-infected patients confirmed the up-regulation of let-7i-5p, miR-146b-5p, and -185-5p in gastritis, in pre-invasive lesions, and in gastric cancer. Taken together, our results suggest that specific miRNAs may be directly involved in the H. pylori infection persistence and may contribute to confer the risk of developing gastric neoplasia in infected patients.
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Affiliation(s)
- Gaia Codolo
- Department of Biology, University of Padua, Padua, Italy
| | | | - Francesco Chemello
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - Sara Coletta
- Department of Biology, University of Padua, Padua, Italy
| | | | | | - Giada Munari
- Istituto Oncologico Veneto (IRCCS), Padua, Italy
| | - Matteo Fassan
- Department of Medicine, University of Padua, Padua, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy.,CIR-Myo Myology Center, University of Padua, Padua, Italy
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16
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Chemello F, Alessio E, Buson L, Pacchioni B, Millino C, Lanfranchi G, Cagnin S. Isolation and Transcriptomic Profiling of Single Myofibers from Mice. Bio Protoc 2019; 9:e3378. [PMID: 33654874 DOI: 10.21769/bioprotoc.3378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/02/2022] Open
Abstract
Skeletal muscle is composed of different cells and myofiber types, with distinct metabolic and structural features. Generally, transcriptomic analysis of skeletal muscle is performed using whole muscle, resulting in average information as all cells composing the organ contribute to the expression value detected for each gene with the loss of information about the distinctive features of each specific myofiber type. Since myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism, it would be beneficial to have fiber-specific information about gene expression. Here, we describe a protocol for the isolation and the transcriptomic analysis of single individual myofibers. The protocol was set up using single myofibers isolated from soleus and Extensor Digitorum Longus (EDL) muscles, but it can be applied to all skeletal muscles. Briefly, muscles are enzymatically dissociated and individually collected. Long RNAs (> 200 nt) and short RNAs (< 200 nt) are separately purified from each myofiber and used to produce libraries for microarray or sequencing analysis. Through this approach, myofiber-specific transcriptional profiles can be produced, free from transcripts from other non-contractile cell types, in order to identify mRNA-miRNA-lncRNA regulatory networks specific for each myofiber type.
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Affiliation(s)
| | - Enrico Alessio
- Department of Biology, University of Padova, Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, Padova, Italy
| | - Beniamina Pacchioni
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy.,CIR-Myo Myology Center, University of Padova, Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy.,CIR-Myo Myology Center, University of Padova, Padova, Italy
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17
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Alessio E, Buson L, Chemello F, Peggion C, Grespi F, Martini P, Massimino ML, Pacchioni B, Millino C, Romualdi C, Bertoli A, Scorrano L, Lanfranchi G, Cagnin S. Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network. Nucleic Acids Res 2019; 47:1653-1670. [PMID: 30649422 PMCID: PMC6393313 DOI: 10.1093/nar/gkz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 10/31/2018] [Revised: 12/05/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function, it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell and tissue specificity and subcellular compartmentalization. Myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism. How lncRNAs are expressed in different myofibers, participate in metabolism regulation and muscle atrophy or how they are compartmentalized within a single myofiber is still unknown. We compiled a comprehensive catalog of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, and demonstrating that many lncRNAs can be involved in the biological processes de-regulated during muscle atrophy. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy, apoptosis and myofiber size in vivo. This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.
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Affiliation(s)
- Enrico Alessio
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Beniamina Pacchioni
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, 35131 Padova, Italy
- Venetian Institute of Molecular Medicine, 35131 Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
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18
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Pereira MG, Dyar KA, Nogara L, Solagna F, Marabita M, Baraldo M, Chemello F, Germinario E, Romanello V, Nolte H, Blaauw B. Comparative Analysis of Muscle Hypertrophy Models Reveals Divergent Gene Transcription Profiles and Points to Translational Regulation of Muscle Growth through Increased mTOR Signaling. Front Physiol 2017; 8:968. [PMID: 29255421 PMCID: PMC5723052 DOI: 10.3389/fphys.2017.00968] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/14/2017] [Indexed: 01/07/2023] Open
Abstract
Skeletal muscle mass is a result of the balance between protein breakdown and protein synthesis. It has been shown that multiple conditions of muscle atrophy are characterized by the common regulation of a specific set of genes, termed atrogenes. It is not known whether various models of muscle hypertrophy are similarly regulated by a common transcriptional program. Here, we characterized gene expression changes in three different conditions of muscle growth, examining each condition during acute and chronic phases. Specifically, we compared the transcriptome of Extensor Digitorum Longus (EDL) muscles collected (1) during the rapid phase of postnatal growth at 2 and 4 weeks of age, (2) 24 h or 3 weeks after constitutive activation of AKT, and (3) 24 h or 3 weeks after overload hypertrophy caused by tenotomy of the Tibialis Anterior muscle. We observed an important overlap between significantly regulated genes when comparing each single condition at the two different timepoints. Furthermore, examining the transcriptional changes occurring 24 h after a hypertrophic stimulus, we identify an important role for genes linked to a stress response, despite the absence of muscle damage in the AKT model. However, when we compared all different growth conditions, we did not find a common transcriptional fingerprint. On the other hand, all conditions showed a marked increase in mTORC1 signaling and increased ribosome biogenesis, suggesting that muscle growth is characterized more by translational, than transcriptional regulation.
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Affiliation(s)
- Marcelo G Pereira
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Kenneth A Dyar
- Venetian Institute of Molecular Medicine, Padova, Italy.,Molecular Endocrinology, Institute for Diabetes and Obesity, Helmholtz Diabetes Center and German Center for Diabetes Research, Neuherberg, Germany
| | - Leonardo Nogara
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | | | - Martina Baraldo
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Elena Germinario
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Vanina Romanello
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Hendrik Nolte
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Bert Blaauw
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
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Pagliari M, Munari F, Toffoletto M, Lonardi S, Chemello F, Codolo G, Millino C, Della Bella C, Pacchioni B, Vermi W, Fassan M, de Bernard M, Cagnin S. Helicobacter pylori Affects the Antigen Presentation Activity of Macrophages Modulating the Expression of the Immune Receptor CD300E through miR-4270. Front Immunol 2017; 8:1288. [PMID: 29085364 PMCID: PMC5649134 DOI: 10.3389/fimmu.2017.01288] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/25/2017] [Indexed: 12/12/2022] Open
Abstract
Helicobacter pylori (Hp) is a Gram-negative bacterium that infects the human gastric mucosa, leading to chronic inflammation. If not eradicated with antibiotic treatment, the bacterium persists in the human stomach for decades increasing the risk to develop chronic gastritis, gastroduodenal ulcer, and gastric adenocarcinoma. The lifelong persistence of Hp in the human stomach suggests that the host response fails to clear the infection. It has been recently shown that during Hp infection phagocytic cells promote high Hp loads rather than contributing to bacterial clearance. Within these cells Hp survives in "megasomes," large structures arising from homotypic fusion of phagosomes, but the mechanism that Hp employs to avoid phagocytic killing is not completely understood. Here, we show that Hp infection induces the downregulation of specific microRNAs involved in the regulation of transcripts codifying for inflammatory proteins. miR-4270 targets the most upregulated gene: the immune receptor CD300E, whose expression is strictly dependent on Hp infection. CD300E engagement enhances the pro-inflammatory potential of macrophages, but in parallel it affects their ability to express and expose MHC class II molecules on the plasma membrane, without altering phagocytosis. This effect compromises the possibility for effector T cells to recognize and activate the killing potential of macrophages, which, in turn would become a survival niche for the bacterium. Taken together, our data add another piece to the complicate puzzle represented by the long-life coexistence between Hp and the human host and contribute with new insights toward understanding the regulation and function of the immune receptor CD300E.
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Affiliation(s)
| | - Fabio Munari
- Department of Biomedical Sciences, University of Padua, Venetian Institute of Molecular Medicine (VIMM), Padua, Italy
| | | | - Silvia Lonardi
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, Brescia, Italy
| | - Francesco Chemello
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - Gaia Codolo
- Department of Biology, University of Padua, Padua, Italy
| | - Caterina Millino
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | | | - Beniamina Pacchioni
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - William Vermi
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, Brescia, Italy
| | - Matteo Fassan
- Department of Medicine, University of Padua, Padua, Italy
| | | | - Stefano Cagnin
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
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20
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Mammucari C, Gherardi G, Zamparo I, Raffaello A, Boncompagni S, Chemello F, Cagnin S, Braga A, Zanin S, Pallafacchina G, Zentilin L, Sandri M, De Stefani D, Protasi F, Lanfranchi G, Rizzuto R. The mitochondrial calcium uniporter controls skeletal muscle trophism in vivo. Cell Rep 2015; 10:1269-79. [PMID: 25732818 DOI: 10.1016/j.celrep.2015.01.056] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/23/2014] [Accepted: 01/24/2015] [Indexed: 12/18/2022] Open
Abstract
Muscle atrophy contributes to the poor prognosis of many pathophysiological conditions, but pharmacological therapies are still limited. Muscle activity leads to major swings in mitochondrial [Ca(2+)], which control aerobic metabolism, cell death, and survival pathways. We investigated in vivo the effects of mitochondrial Ca(2+) homeostasis in skeletal muscle function and trophism by overexpressing or silencing the mitochondrial calcium uniporter (MCU). The results demonstrate that in both developing and adult muscles, MCU-dependent mitochondrial Ca(2+) uptake has a marked trophic effect that does not depend on aerobic control but impinges on two major hypertrophic pathways of skeletal muscle, PGC-1α4 and IGF1-Akt/PKB. In addition, MCU overexpression protects from denervation-induced atrophy. These data reveal a novel Ca(2+)-dependent organelle-to-nucleus signaling route that links mitochondrial function to the control of muscle mass and may represent a possible pharmacological target in conditions of muscle loss.
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Affiliation(s)
- Cristina Mammucari
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy.
| | - Gaia Gherardi
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy
| | - Ilaria Zamparo
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy
| | - Anna Raffaello
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy
| | - Simona Boncompagni
- Ce.S.I. (Center for Research on Ageing) and D.N.I.C.S. (Department of Neuroscience, Imaging and Clinical Sciences), University "G. D'Annunzio" of Chieti, Chieti 66100, Italy
| | - Francesco Chemello
- Department of Biology and CRIBI Biotechnology Center, University of Padua, Padua 35131, Italy
| | - Stefano Cagnin
- Department of Biology and CRIBI Biotechnology Center, University of Padua, Padua 35131, Italy
| | - Alessandra Braga
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy
| | - Sofia Zanin
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy
| | - Giorgia Pallafacchina
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy; Neuroscience Institute, National Research Council, Padua 35131, Italy
| | - Lorena Zentilin
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste 34159, Italy
| | - Marco Sandri
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy; Neuroscience Institute, National Research Council, Padua 35131, Italy; Dulbecco Telethon Institute at Venetian Institute of Molecular Medicine, Padua 35129, Italy; Telethon Institute of Genetics and Medicine (TIGEM), Naples 80131, Italy
| | - Diego De Stefani
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy
| | - Feliciano Protasi
- Ce.S.I. (Center for Research on Ageing) and D.N.I.C.S. (Department of Neuroscience, Imaging and Clinical Sciences), University "G. D'Annunzio" of Chieti, Chieti 66100, Italy
| | - Gerolamo Lanfranchi
- Department of Biology and CRIBI Biotechnology Center, University of Padua, Padua 35131, Italy
| | - Rosario Rizzuto
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy; Neuroscience Institute, National Research Council, Padua 35131, Italy.
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21
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Soares RJ, Cagnin S, Chemello F, Silvestrin M, Musaro A, De Pitta C, Lanfranchi G, Sandri M. Involvement of microRNAs in the regulation of muscle wasting during catabolic conditions. J Biol Chem 2014; 289:21909-25. [PMID: 24891504 PMCID: PMC4139209 DOI: 10.1074/jbc.m114.561845] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Loss of muscle proteins and the consequent weakness has important clinical consequences in diseases such as cancer, diabetes, chronic heart failure, and in aging. In fact, excessive proteolysis causes cachexia, accelerates disease progression, and worsens life expectancy. Muscle atrophy involves a common pattern of transcriptional changes in a small subset of genes named atrophy-related genes or atrogenes. Whether microRNAs play a role in the atrophy program and muscle loss is debated. To understand the involvement of miRNAs in atrophy we performed miRNA expression profiling of mouse muscles under wasting conditions such as fasting, denervation, diabetes, and cancer cachexia. We found that the miRNA signature is peculiar of each catabolic condition. We then focused on denervation and we revealed that changes in transcripts and microRNAs expression did not occur simultaneously but were shifted. Indeed, whereas transcriptional control of the atrophy-related genes peaks at 3 days, changes of miRNA expression maximized at 7 days after denervation. Among the different miRNAs, microRNA-206 and -21 were the most induced in denervated muscles. We characterized their pattern of expression and defined their role in muscle homeostasis. Indeed, in vivo gain and loss of function experiments revealed that miRNA-206 and miRNA-21 were sufficient and required for atrophy program. In silico and in vivo approaches identified transcription factor YY1 and the translational initiator factor eIF4E3 as downstream targets of these miRNAs. Thus miRNAs are important for fine-tuning the atrophy program and their modulation can be a novel potential therapeutic approach to counteract muscle loss and weakness in catabolic conditions.
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Affiliation(s)
- Ricardo José Soares
- From the Dulbecco Telethon Institute, Venetian Institute of Molecular Medicine, 35129 Padova, Italy, the Ph.D. Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Stefano Cagnin
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy
| | - Francesco Chemello
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy
| | - Matteo Silvestrin
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy
| | - Antonio Musaro
- the DAHFMO-Unit of Histology and Medical Embryology, Sapienza University, 00161 Roma, Italy, and
| | - Cristiano De Pitta
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy,
| | - Gerolamo Lanfranchi
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy,
| | - Marco Sandri
- From the Dulbecco Telethon Institute, Venetian Institute of Molecular Medicine, 35129 Padova, Italy, the Department of Biomedical Sciences and the Institute of Neuroscience, Consiglio Nazionale delle Ricerche, 35121 Padova, Italy, the Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
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22
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Martini P, Sales G, Brugiolo M, Gandaglia A, Naso F, De Pittà C, Spina M, Gerosa G, Chemello F, Romualdi C, Cagnin S, Lanfranchi G. Tissue-specific expression and regulatory networks of pig microRNAome. PLoS One 2014; 9:e89755. [PMID: 24699212 PMCID: PMC3974652 DOI: 10.1371/journal.pone.0089755] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/23/2014] [Indexed: 12/19/2022] Open
Abstract
Background Despite the economic and medical importance of the pig, knowledge about its genome organization, gene expression regulation, and molecular mechanisms involved in physiological processes is far from that achieved for mouse and rat, the two most used model organisms in biomedical research. MicroRNAs (miRNAs) are a wide class of molecules that exert a recognized role in gene expression modulation, but only 280 miRNAs in pig have been characterized to date. Results We applied a novel computational approach to predict species-specific and conserved miRNAs in the pig genome, which were then subjected to experimental validation. We experimentally identified candidate miRNAs sequences grouped in high-confidence (424) and medium-confidence (353) miRNAs according to RNA-seq results. A group of miRNAs was also validated by PCR experiments. We established the subtle variability in expression of isomiRs and miRNA-miRNA star couples supporting a biological function for these molecules. Finally, miRNA and mRNA expression profiles produced from the same sample of 20 different tissue of the animal were combined, using a correlation threshold to filter miRNA-target predictions, to identify tissue-specific regulatory networks. Conclusions Our data represent a significant progress in the current understanding of miRNAome in pig. The identification of miRNAs, their target mRNAs, and the construction of regulatory circuits will provide new insights into the complex biological networks in several tissues of this important animal model.
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Affiliation(s)
- Paolo Martini
- Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, Padova, Italy
| | - Mattia Brugiolo
- Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Alessandro Gandaglia
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | - Filippo Naso
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | | | - Michele Spina
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Gino Gerosa
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | | | | | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy
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23
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Bean C, Verma NK, Yamamoto DL, Chemello F, Cenni V, Filomena MC, Chen J, Bang ML, Lanfranchi G. Ankrd2 is a modulator of NF-κB-mediated inflammatory responses during muscle differentiation. Cell Death Dis 2014; 5:e1002. [PMID: 24434510 PMCID: PMC4040671 DOI: 10.1038/cddis.2013.525] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/23/2013] [Accepted: 11/25/2013] [Indexed: 12/29/2022]
Abstract
Adaptive responses of skeletal muscle regulate the nuclear shuttling of the sarcomeric protein Ankrd2 that can transduce different stimuli into specific adaptations by interacting with both structural and regulatory proteins. In a genome-wide expression study on Ankrd2-knockout or -overexpressing primary proliferating or differentiating myoblasts, we found an inverse correlation between Ankrd2 levels and the expression of proinflammatory genes and identified Ankrd2 as a potent repressor of inflammatory responses through direct interaction with the NF-κB repressor subunit p50. In particular, we identified Gsk3β as a novel direct target of the p50/Ankrd2 repressosome dimer and found that the recruitment of p50 by Ankrd2 is dependent on Akt2-mediated phosphorylation of Ankrd2 upon oxidative stress during myogenic differentiation. Surprisingly, the absence of Ankrd2 in slow muscle negatively affected the expression of cytokines and key calcineurin-dependent genes associated with the slow-twitch muscle program. Thus, our findings support a model in which alterations in Ankrd2 protein and phosphorylation levels modulate the balance between physiological and pathological inflammatory responses in muscle.
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Affiliation(s)
- C Bean
- Department of Biology, Innovative Biotechnologies Interdepartmental Research Center, University of Padova, Padova, Italy
| | - N K Verma
- Department of Biology, Innovative Biotechnologies Interdepartmental Research Center, University of Padova, Padova, Italy
| | - D L Yamamoto
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - F Chemello
- Department of Biology, Innovative Biotechnologies Interdepartmental Research Center, University of Padova, Padova, Italy
| | - V Cenni
- Institute of Molecular Genetics, National Research Council, Bologna Unit/IOR, Bologna, Italy
| | - M C Filomena
- 1] Department of Translational Medicine, University of Milan, Milan, Italy [2] Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - J Chen
- University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - M L Bang
- 1] Humanitas Clinical and Research Center, Rozzano, Milan, Italy [2] Milan Unit, Institute of Genetic and Biomedical Research, National Research Council, Milan, Italy
| | - G Lanfranchi
- Department of Biology, Innovative Biotechnologies Interdepartmental Research Center, University of Padova, Padova, Italy
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Frangini M, Franzolin E, Chemello F, Laveder P, Romualdi C, Bianchi V, Rampazzo C. Synthesis of mitochondrial DNA precursors during myogenesis, an analysis in purified C2C12 myotubes. J Biol Chem 2013; 288:5624-35. [PMID: 23297407 PMCID: PMC3581417 DOI: 10.1074/jbc.m112.441147] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
During myogenesis, myoblasts fuse into multinucleated myotubes that acquire the contractile fibrils and accessory structures typical of striated skeletal muscle fibers. To support the high energy requirements of muscle contraction, myogenesis entails an increase in mitochondrial (mt) mass with stimulation of mtDNA synthesis and consumption of DNA precursors (dNTPs). Myotubes are quiescent cells and as such down-regulate dNTP production despite a high demand for dNTPs. Although myogenesis has been studied extensively, changes in dNTP metabolism have not been examined specifically. In differentiating cultures of C2C12 myoblasts and purified myotubes, we analyzed expression and activities of enzymes of dNTP biosynthesis, dNTP pools, and the expansion of mtDNA. Myotubes exibited pronounced post-mitotic modifications of dNTP synthesis with a particularly marked down-regulation of de novo thymidylate synthesis. Expression profiling revealed the same pattern of enzyme down-regulation in adult murine muscles. The mtDNA increased steadily after myoblast fusion, turning over rapidly, as revealed after treatment with ethidium bromide. We individually down-regulated p53R2 ribonucleotide reductase, thymidine kinase 2, and deoxyguanosine kinase by siRNA transfection to examine how a further reduction of these synthetic enzymes impacted myotube development. Silencing of p53R2 had little effect, but silencing of either mt kinase caused 50% mtDNA depletion and an unexpected decrease of all four dNTP pools independently of the kinase specificity. We suggest that during development of myotubes the shortage of even a single dNTP may affect all four pools through dysregulation of ribonucleotide reduction and/or dissipation of the non-limiting dNTPs during unproductive elongation of new DNA chains.
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Affiliation(s)
- Miriam Frangini
- Department of Biology, University of Padova, 35131 Padova, Italy
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25
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Chemello F, Bean C, Cancellara P, Laveder P, Reggiani C, Lanfranchi G. Microgenomic analysis in skeletal muscle: expression signatures of individual fast and slow myofibers. PLoS One 2011; 6:e16807. [PMID: 21364935 PMCID: PMC3043066 DOI: 10.1371/journal.pone.0016807] [Citation(s) in RCA: 70] [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] [Received: 10/14/2010] [Accepted: 12/30/2010] [Indexed: 11/18/2022] Open
Abstract
Background Skeletal muscle is a complex, versatile tissue composed of a variety of functionally diverse fiber types. Although the biochemical, structural and functional properties of myofibers have been the subject of intense investigation for the last decades, understanding molecular processes regulating fiber type diversity is still complicated by the heterogeneity of cell types present in the whole muscle organ. Methodology/Principal Findings We have produced a first catalogue of genes expressed in mouse slow-oxidative (type 1) and fast-glycolytic (type 2B) fibers through transcriptome analysis at the single fiber level (microgenomics). Individual fibers were obtained from murine soleus and EDL muscles and initially classified by myosin heavy chain isoform content. Gene expression profiling on high density DNA oligonucleotide microarrays showed that both qualitative and quantitative improvements were achieved, compared to results with standard muscle homogenate. First, myofiber profiles were virtually free from non-muscle transcriptional activity. Second, thousands of muscle-specific genes were identified, leading to a better definition of gene signatures in the two fiber types as well as the detection of metabolic and signaling pathways that are differentially activated in specific fiber types. Several regulatory proteins showed preferential expression in slow myofibers. Discriminant analysis revealed novel genes that could be useful for fiber type functional classification. Conclusions/Significance As gene expression analyses at the single fiber level significantly increased the resolution power, this innovative approach would allow a better understanding of the adaptive transcriptomic transitions occurring in myofibers under physiological and pathological conditions.
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Affiliation(s)
- Francesco Chemello
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Camilla Bean
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Pasqua Cancellara
- Department of Anatomy and Physiology, University of Padova, Padova, Italy
| | - Paolo Laveder
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Carlo Reggiani
- Department of Anatomy and Physiology, University of Padova, Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
- * E-mail:
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26
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Sutil de Naranjo R, Marquez M, Barrios M, Chemello F, Torres M, Yepez C, Hernandez N. W01.126 Risk factors for atherosclerosis in children with family history of premature coronary artery disease. ATHEROSCLEROSIS SUPP 2004. [DOI: 10.1016/s1567-5688(04)90125-6] [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: 11/25/2022]
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27
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Abstract
The authors report their experience of 30 patients with colorectal anastomotic stenosis treated by 62 dilatation sessions in order to evaluate which anastomotic characteristics could influence the success of dilatation therapy. Patients were subdivided into group A (dilatation successful) and group B (dilatation unsuccessful). Overall, dilatation was successful in 73.3% of cases, with only one important complication. The prognostic factors considered were anastomotic dehiscence, adjuvant radiotherapy, presence of colostomy at dilatation, site, morphology and length of the stenosis, presence of neoplastic recurrence, type of anastomosis and type of dilatation. Radiotherapy, local neoplastic recurrence and large anastomotic dehiscence were the more important independent prognostic factors. If present together, they were associated with an almost 100% probability of failure and, vice versa, if they were absent this probability was 5%.
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28
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Lise M, Nitti D, Chemello F, Zane D, Taboga L, De Carli GL, Bachi V, Civalleri D, Bonalumi U. [Adjuvant treatment in rectal cancer]. Ann Ital Chir 1992; 63:321-32. [PMID: 1443998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M Lise
- Istituto di Patologia Chirurgia I, Università di Padova
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