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Bartolomé-Nafría A, García-Pardo J, Ventura S. Mutations in human prion-like domains: pathogenic but not always amyloidogenic. Prion 2024; 18:28-39. [PMID: 38512820 PMCID: PMC10962614 DOI: 10.1080/19336896.2024.2329186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are multifunctional proteins with integral roles in RNA metabolism and the regulation of alternative splicing. These proteins typically contain prion-like domains of low complexity (PrLDs or LCDs) that govern their assembly into either functional or pathological amyloid fibrils. To date, over 60 mutations targeting the LCDs of hnRNPs have been identified and associated with a spectrum of neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD). The cryo-EM structures of pathological and functional fibrils formed by different hnRNPs have been recently elucidated, including those of hnRNPA1, hnRNPA2, hnRNPDL-2, TDP-43, and FUS. In this review, we discuss the structural features of these amyloid assemblies, placing particular emphasis on scrutinizing the impact of prevalent disease-associated mutations mapping within their LCDs. By performing systematic energy calculations, we reveal a prevailing trend of destabilizing effects induced by these mutations in the amyloid structure, challenging the traditionally assumed correlation between pathogenicity and amyloidogenic propensity. Understanding the molecular basis of this discrepancy might provide insights for developing targeted therapeutic strategies to combat hnRNP-associated diseases.
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Affiliation(s)
- Andrea Bartolomé-Nafría
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier García-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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2
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Giudice J, Jiang H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00739-7. [PMID: 38773325 DOI: 10.1038/s41580-024-00739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Biomolecular condensates, sometimes also known as membraneless organelles (MLOs), can form through weak multivalent intermolecular interactions of proteins and nucleic acids, a process often associated with liquid-liquid phase separation. Biomolecular condensates are emerging as sites and regulatory platforms of vital cellular functions, including transcription and RNA processing. In the first part of this Review, we comprehensively discuss how alternative splicing regulates the formation and properties of condensates, and conversely the roles of biomolecular condensates in splicing regulation. In the second part, we focus on the spatial connection between splicing regulation and nuclear MLOs such as transcriptional condensates, splicing condensates and nuclear speckles. We then discuss key studies showing how splicing regulation through biomolecular condensates is implicated in human pathologies such as neurodegenerative diseases, different types of cancer, developmental disorders and cardiomyopathies, and conclude with a discussion of outstanding questions pertaining to the roles of condensates and MLOs in splicing regulation and how to experimentally study them.
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Affiliation(s)
- Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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3
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Fischer S, Lichtenthaeler C, Stepanenko A, Heyl F, Maticzka D, Kemmerer K, Klostermann M, Backofen R, Zarnack K, Weigand JE. Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions. Biol Chem 2024; 405:229-239. [PMID: 37942876 DOI: 10.1515/hsz-2023-0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023]
Abstract
HnRNPs are ubiquitously expressed RNA-binding proteins, tightly controlling posttranscriptional gene regulation. Consequently, hnRNP networks are essential for cellular homeostasis and their dysregulation is associated with cancer and other diseases. However, the physiological function of hnRNPs in non-cancerous cell systems are poorly understood. We analyzed the importance of HNRNPDL in endothelial cell functions. Knockdown of HNRNPDL led to impaired proliferation, migration and sprouting of spheroids. Transcriptome analysis identified cyclin D1 (CCND1) and tropomyosin 4 (TPM4) as targets of HNRNPDL, reflecting the phenotypic changes after knockdown. Our findings underline the importance of HNRNPDL for the homeostasis of physiological processes in endothelial cells.
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Affiliation(s)
- Sandra Fischer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
| | - Chiara Lichtenthaeler
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
| | - Anastasiya Stepanenko
- Buchmann Institute for Molecular Life Sciences and Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Florian Heyl
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany
| | - Daniel Maticzka
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany
| | - Katrin Kemmerer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences and Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Rolf Backofen
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences and Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Julia E Weigand
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
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4
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Nashabat M, Nabavizadeh N, Saraçoğlu HP, Sarıbaş B, Avcı Ş, Börklü E, Beillard E, Yılmaz E, Uygur SE, Kayhan CK, Bosco L, Eren ZB, Steindl K, Richter MF, Bademci G, Rauch A, Fattahi Z, Valentino ML, Connolly AM, Bahr A, Viola L, Bergmann AK, Rocha ME, Peart L, Castro-Rojas DL, Bültmann E, Khan S, Giarrana ML, Teleanu RI, Gonzalez JM, Pini A, Schädlich IS, Vill K, Brugger M, Zuchner S, Pinto A, Donkervoort S, Bivona SA, Riza A, Streata I, Gläser D, Baquero-Montoya C, Garcia-Restrepo N, Kotzaeridou U, Brunet T, Epure DA, Bertoli-Avella A, Kariminejad A, Tekin M, von Hardenberg S, Bönnemann CG, Stettner GM, Zanni G, Kayserili H, Oflazer ZP, Escande-Beillard N. SNUPN deficiency causes a recessive muscular dystrophy due to RNA mis-splicing and ECM dysregulation. Nat Commun 2024; 15:1758. [PMID: 38413582 PMCID: PMC10899626 DOI: 10.1038/s41467-024-45933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
SNURPORTIN-1, encoded by SNUPN, plays a central role in the nuclear import of spliceosomal small nuclear ribonucleoproteins. However, its physiological function remains unexplored. In this study, we investigate 18 children from 15 unrelated families who present with atypical muscular dystrophy and neurological defects. Nine hypomorphic SNUPN biallelic variants, predominantly clustered in the last coding exon, are ascertained to segregate with the disease. We demonstrate that mutant SPN1 failed to oligomerize leading to cytoplasmic aggregation in patients' primary fibroblasts and CRISPR/Cas9-mediated mutant cell lines. Additionally, mutant nuclei exhibit defective spliceosomal maturation and breakdown of Cajal bodies. Transcriptome analyses reveal splicing and mRNA expression dysregulation, particularly in sarcolemmal components, causing disruption of cytoskeletal organization in mutant cells and patient muscle tissues. Our findings establish SNUPN deficiency as the genetic etiology of a previously unrecognized subtype of muscular dystrophy and provide robust evidence of the role of SPN1 for muscle homeostasis.
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Affiliation(s)
- Marwan Nashabat
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Nasrinsadat Nabavizadeh
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Hilal Pırıl Saraçoğlu
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Burak Sarıbaş
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Şahin Avcı
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
| | - Esra Börklü
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
| | | | - Elanur Yılmaz
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Seyide Ecesu Uygur
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Cavit Kerem Kayhan
- Pathology Laboratory, Acıbadem Maslak Hospital, Istanbul, Turkey
- Department of Biotechnology, Nişantaşı University, Istanbul, Turkey
| | - Luca Bosco
- Unit of Muscular and Neurodegenerative Disorders and Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Science, University "Roma Tre", Rome, Italy
| | - Zeynep Bengi Eren
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | | | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
- Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Centre, Tehran, Iran
| | - Maria Lucia Valentino
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Anne M Connolly
- Division of Neurology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Laura Viola
- Unit of Clinical Pediatrics, State Hospital, San Marino Republic, Italy
| | | | | | - LeShon Peart
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derly Liseth Castro-Rojas
- Genomics Laboratory, Center of Immunology and Genetics (CIGE), SURA Ayudas Diagnosticas, Medellín, Colombia
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | | | | | - Raluca Ioana Teleanu
- Dr Victor Gomoiu Children's Hospital, Bucharest, Romania
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Joanna Michelle Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Antonella Pini
- Neuromuscular Pediatric Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Ines Sophie Schädlich
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-University, Munich, Germany
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | - Melanie Brugger
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Ann Bivona
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anca Riza
- Human Genomics Laboratory, University of Medicine and Pharmacy, Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital, Craiova, Romania
| | - Ioana Streata
- Human Genomics Laboratory, University of Medicine and Pharmacy, Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital, Craiova, Romania
| | | | | | | | - Urania Kotzaeridou
- Division of Child Neurology and Inherited Metabolic Diseases, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Theresa Brunet
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-University, Munich, Germany
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | | | | | | | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Georg M Stettner
- Neuromuscular Center Zurich and Department of Pediatric Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Hülya Kayserili
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
- Department of Medical Genetics, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Zehra Piraye Oflazer
- Department of Neurology, Koç University Hospital Muscle Center, Istanbul, Turkey
| | - Nathalie Escande-Beillard
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey.
- Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine (KUSoM), Istanbul, Turkey.
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5
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Garcia-Pardo J, Ventura S. Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies. Trends Biochem Sci 2024; 49:119-133. [PMID: 37926650 DOI: 10.1016/j.tibs.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Amyloids are implicated in neurodegenerative and systemic diseases, yet they serve important functional roles in numerous organisms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that control central events of RNA biogenesis in normal and diseased cellular conditions. Many of these proteins contain prion-like sequences of low complexity, which not only assemble into functional fibrils in response to cellular cues but can also lead to disease when missense mutations arise in their sequences. Recent advances in cryo-electron microscopy (cryo-EM) have provided unprecedented high-resolution structural insights into diverse amyloid assemblies formed by hnRNPs and structurally related RBPs, including TAR DNA-binding protein 43 (TDP-43), Fused in Sarcoma (FUS), Orb2, hnRNPA1, hnRNPA2, and hnRNPDL-2. This review provides a comprehensive overview of these structures and explores their functional and pathological implications.
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Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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6
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Wang F, Zhang Y. Physiology and pharmacological targeting of phase separation. J Biomed Sci 2024; 31:11. [PMID: 38245749 PMCID: PMC10800077 DOI: 10.1186/s12929-024-00993-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) in biology describes a process by which proteins form membraneless condensates within a cellular compartment when conditions are met, including the concentration and posttranslational modifications of the protein components, the condition of the aqueous solution (pH, ionic strength, pressure, and temperature), and the existence of assisting factors (such as RNAs or other proteins). In these supramolecular liquid droplet-like inclusion bodies, molecules are held together through weak intermolecular and/or intramolecular interactions. With the aid of LLPS, cells can assemble functional sub-units within a given cellular compartment by enriching or excluding specific factors, modulating cellular function, and rapidly responding to environmental or physiological cues. Hence, LLPS is emerging as an important means to regulate biology and physiology. Yet, excessive inclusion body formation by, for instance, higher-than-normal concentrations or mutant forms of the protein components could result in the conversion from dynamic liquid condensates into more rigid gel- or solid-like aggregates, leading to the disruption of the organelle's function followed by the development of human disorders like neurodegenerative diseases. In summary, well-controlled formation and de-formation of LLPS is critical for normal biology and physiology from single cells to individual organisms, whereas abnormal LLPS is involved in the pathophysiology of human diseases. In turn, targeting these aggregates or their formation represents a promising approach in treating diseases driven by abnormal LLPS including those neurodegenerative diseases that lack effective therapies.
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Affiliation(s)
- Fangfang Wang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA.
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7
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Li Z, Wei H, Hu D, Li X, Guo Y, Ding X, Guo H, Zhang L. Research Progress on the Structural and Functional Roles of hnRNPs in Muscle Development. Biomolecules 2023; 13:1434. [PMID: 37892116 PMCID: PMC10604023 DOI: 10.3390/biom13101434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a superfamily of RNA-binding proteins consisting of more than 20 members. These proteins play a crucial role in various biological processes by regulating RNA splicing, transcription, and translation through their binding to RNA. In the context of muscle development and regeneration, hnRNPs are involved in a wide range of regulatory mechanisms, including alternative splicing, transcription regulation, miRNA regulation, and mRNA stability regulation. Recent studies have also suggested a potential association between hnRNPs and muscle-related diseases. In this report, we provide an overview of our current understanding of how hnRNPs regulate RNA metabolism and emphasize the significance of the key members of the hnRNP family in muscle development. Furthermore, we explore the relationship between the hnRNP family and muscle-related diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Linlin Zhang
- Key Laboratory of Animal Breeding and Healthy Livestock Farming, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China; (Z.L.); (H.W.); (D.H.); (X.L.); (Y.G.); (X.D.); (H.G.)
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8
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Bouchard C, Tremblay JP. Limb-Girdle Muscular Dystrophies Classification and Therapies. J Clin Med 2023; 12:4769. [PMID: 37510884 PMCID: PMC10381329 DOI: 10.3390/jcm12144769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Limb-girdle muscular dystrophies (LGMDs) are caused by mutations in multiple genes. This review article presents 39 genes associated with LGMDs. Some forms are inherited in a dominant fashion, while for others this occurs recessively. The classification of LGMDs has evolved through time. Lately, to be considered an LGMD, the mutation has to cause a predominant proximal muscle weakness and must be found in two or more unrelated families. This article also presents therapies for LGMDs, examining both available treatments and those in development. For now, only symptomatic treatments are available for patients. The goal is now to solve the problem at the root of LGMDs instead of treating each symptom individually. In the last decade, multiple other potential treatments were developed and studied, such as stem-cell transplantation, exon skipping, gene delivery, RNAi, and gene editing.
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Affiliation(s)
- Camille Bouchard
- Departement de Médecine Moléculaire, Université Laval, Quebec, QC G1V 0A6, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Quebec, Quebec, QC G1E 6W2, Canada
| | - Jacques P Tremblay
- Departement de Médecine Moléculaire, Université Laval, Quebec, QC G1V 0A6, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Quebec, Quebec, QC G1E 6W2, Canada
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9
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Tesoriero C, Greco F, Cannone E, Ghirotto F, Facchinello N, Schiavone M, Vettori A. Modeling Human Muscular Dystrophies in Zebrafish: Mutant Lines, Transgenic Fluorescent Biosensors, and Phenotyping Assays. Int J Mol Sci 2023; 24:8314. [PMID: 37176020 PMCID: PMC10179009 DOI: 10.3390/ijms24098314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Muscular dystrophies (MDs) are a heterogeneous group of myopathies characterized by progressive muscle weakness leading to death from heart or respiratory failure. MDs are caused by mutations in genes involved in both the development and organization of muscle fibers. Several animal models harboring mutations in MD-associated genes have been developed so far. Together with rodents, the zebrafish is one of the most popular animal models used to reproduce MDs because of the high level of sequence homology with the human genome and its genetic manipulability. This review describes the most important zebrafish mutant models of MD and the most advanced tools used to generate and characterize all these valuable transgenic lines. Zebrafish models of MDs have been generated by introducing mutations to muscle-specific genes with different genetic techniques, such as (i) N-ethyl-N-nitrosourea (ENU) treatment, (ii) the injection of specific morpholino, (iii) tol2-based transgenesis, (iv) TALEN, (v) and CRISPR/Cas9 technology. All these models are extensively used either to study muscle development and function or understand the pathogenetic mechanisms of MDs. Several tools have also been developed to characterize these zebrafish models by checking (i) motor behavior, (ii) muscle fiber structure, (iii) oxidative stress, and (iv) mitochondrial function and dynamics. Further, living biosensor models, based on the expression of fluorescent reporter proteins under the control of muscle-specific promoters or responsive elements, have been revealed to be powerful tools to follow molecular dynamics at the level of a single muscle fiber. Thus, zebrafish models of MDs can also be a powerful tool to search for new drugs or gene therapies able to block or slow down disease progression.
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Affiliation(s)
- Chiara Tesoriero
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
| | - Francesca Greco
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
| | - Elena Cannone
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy;
| | - Francesco Ghirotto
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
| | - Nicola Facchinello
- Neuroscience Institute, Italian National Research Council (CNR), 35131 Padua, Italy
| | - Marco Schiavone
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy;
| | - Andrea Vettori
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
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10
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Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3. Nat Commun 2023; 14:239. [PMID: 36646699 PMCID: PMC9842712 DOI: 10.1038/s41467-023-35854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
hnRNPDL is a ribonucleoprotein (RNP) involved in transcription and RNA-processing that hosts missense mutations causing limb-girdle muscular dystrophy D3 (LGMD D3). Mammalian-specific alternative splicing (AS) renders three natural isoforms, hnRNPDL-2 being predominant in humans. We present the cryo-electron microscopy structure of full-length hnRNPDL-2 amyloid fibrils, which are stable, non-toxic, and bind nucleic acids. The high-resolution amyloid core consists of a single Gly/Tyr-rich and highly hydrophilic filament containing internal water channels. The RNA binding domains are located as a solenoidal coat around the core. The architecture and activity of hnRNPDL-2 fibrils are reminiscent of functional amyloids, our results suggesting that LGMD D3 might be a loss-of-function disease associated with impaired fibrillation. Strikingly, the fibril core matches exon 6, absent in the soluble hnRNPDL-3 isoform. This provides structural evidence for AS controlling hnRNPDL assembly by precisely including/skipping an amyloid exon, a mechanism that holds the potential to generate functional diversity in RNPs.
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11
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Amodeo ME, Mitchell SPC, Pavan V, Kuehner JN. RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif. G3 (BETHESDA, MD.) 2022; 13:6782960. [PMID: 36315099 PMCID: PMC9836349 DOI: 10.1093/g3journal/jkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10-15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1-Nab3-Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3'-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
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Affiliation(s)
- Maria E Amodeo
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Shane P C Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Vincent Pavan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Jason N Kuehner
- Corresponding author: Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA.
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12
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Lee J, Cho H, Kwon I. Phase separation of low-complexity domains in cellular function and disease. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1412-1422. [PMID: 36175485 PMCID: PMC9534829 DOI: 10.1038/s12276-022-00857-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
In this review, we discuss the ways in which recent studies of low-complexity (LC) domains have challenged our understanding of the mechanisms underlying cellular organization. LC sequences, long believed to function in the absence of a molecular structure, are abundant in the proteomes of all eukaryotic organisms. Over the past decade, the phase separation of LC domains has emerged as a fundamental mechanism driving dynamic multivalent interactions of many cellular processes. We review the key evidence showing the role of phase separation of individual proteins in organizing cellular assemblies and facilitating biological function while implicating the dynamics of phase separation as a key to biological validity and functional utility. We also highlight the evidence showing that pathogenic LC proteins alter various phase separation-dependent interactions to elicit debilitating human diseases, including cancer and neurodegenerative diseases. Progress in understanding the biology of phase separation may offer useful hints toward possible therapeutic interventions to combat the toxicity of pathogenic proteins.
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Affiliation(s)
- Jiwon Lee
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Hana Cho
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
| | - Ilmin Kwon
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
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13
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Narendiran S, Debnath M, Shivaram S, Kannan R, Sharma S, Christopher R, Seshagiri DV, Jain S, Purushottam M, Mangalore S, Bharath RD, Bindu PS, Sinha S, Taly AB, Nagappa M. Novel insights into the genetic profile of hereditary spastic paraplegia in India. J Neurogenet 2022; 36:21-31. [DOI: 10.1080/01677063.2022.2064463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sundarapandian Narendiran
- Departments of Neurology and Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Monojit Debnath
- Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sumanth Shivaram
- Departments of Neurology and Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Ramakrishnan Kannan
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Shivani Sharma
- Departments of Neurology and Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Rita Christopher
- Department of Neuroimaging and Interventional Radiology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Doniparthi V. Seshagiri
- Departments of Neurology and Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sanjeev Jain
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Meera Purushottam
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sandhya Mangalore
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Rose Dawn Bharath
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | | | - Sanjib Sinha
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Arun B. Taly
- Departments of Neurology and Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Madhu Nagappa
- Departments of Neurology and Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
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14
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Kim HJ, Mohassel P, Donkervoort S, Guo L, O'Donovan K, Coughlin M, Lornage X, Foulds N, Hammans SR, Foley AR, Fare CM, Ford AF, Ogasawara M, Sato A, Iida A, Munot P, Ambegaonkar G, Phadke R, O'Donovan DG, Buchert R, Grimmel M, Töpf A, Zaharieva IT, Brady L, Hu Y, Lloyd TE, Klein A, Steinlin M, Kuster A, Mercier S, Marcorelles P, Péréon Y, Fleurence E, Manzur A, Ennis S, Upstill-Goddard R, Bello L, Bertolin C, Pegoraro E, Salviati L, French CE, Shatillo A, Raymond FL, Haack TB, Quijano-Roy S, Böhm J, Nelson I, Stojkovic T, Evangelista T, Straub V, Romero NB, Laporte J, Muntoni F, Nishino I, Tarnopolsky MA, Shorter J, Bönnemann CG, Taylor JP. Heterozygous frameshift variants in HNRNPA2B1 cause early-onset oculopharyngeal muscular dystrophy. Nat Commun 2022; 13:2306. [PMID: 35484142 PMCID: PMC9050844 DOI: 10.1038/s41467-022-30015-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 03/25/2022] [Indexed: 01/05/2023] Open
Abstract
Missense variants in RNA-binding proteins (RBPs) underlie a spectrum of disease phenotypes, including amyotrophic lateral sclerosis, frontotemporal dementia, and inclusion body myopathy. Here, we present ten independent families with a severe, progressive muscular dystrophy, reminiscent of oculopharyngeal muscular dystrophy (OPMD) but of much earlier onset, caused by heterozygous frameshift variants in the RBP hnRNPA2/B1. All disease-causing frameshift mutations abolish the native stop codon and extend the reading frame, creating novel transcripts that escape nonsense-mediated decay and are translated to produce hnRNPA2/B1 protein with the same neomorphic C-terminal sequence. In contrast to previously reported disease-causing missense variants in HNRNPA2B1, these frameshift variants do not increase the propensity of hnRNPA2 protein to fibrillize. Rather, the frameshift variants have reduced affinity for the nuclear import receptor karyopherin β2, resulting in cytoplasmic accumulation of hnRNPA2 protein in cells and in animal models that recapitulate the human pathology. Thus, we expand the phenotypes associated with HNRNPA2B1 to include an early-onset form of OPMD caused by frameshift variants that alter its nucleocytoplasmic transport dynamics. Missense variants in RNA-binding proteins underlie many diseases. Here the authors report an oculopharyngeal muscular dystrophy caused by heterozygous frameshift mutations in HNRNPA2B1 that alter its nucleocytoplasmic transport dynamics and result in cytoplasmic accumulation of hnRNPA2 protein.
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Affiliation(s)
- Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Payam Mohassel
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sandra Donkervoort
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Lin Guo
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Kevin O'Donovan
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Maura Coughlin
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Xaviere Lornage
- Département Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U1258, Centre National de la Recherche Scientifique UMR7104, Université de Strasbourg, Illkirch, France
| | - Nicola Foulds
- Wessex Clinical Genetics Services, Princess Anne Hospital, Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, England
| | - Simon R Hammans
- Wessex Neurological Centre, University Hospital Southampton, Southampton, UK
| | - A Reghan Foley
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Charlotte M Fare
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Alice F Ford
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Medical Genome Center, NCNP, Kodaira, Tokyo, Japan
| | - Aki Sato
- Department of Neurology, Niigata City General Hospital, Niigata, Japan
| | | | - Pinki Munot
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Gautam Ambegaonkar
- Department of Paediatric Neurology, Cambridge University Hospital NHS Trust, Addenbrookes Hospital, Cambridge, CB2 0QQ, UK
| | - Rahul Phadke
- Division of Neuropathology, University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, UK and Division of Neuropathology, UCL Institute of Neurology, Dubowitz Neuromuscular Centre, London, UK
| | - Dominic G O'Donovan
- Department of Histopathology Box 235, Level 5 John Bonnett Clinical Laboratories Addenbrooke's Hospital, Cambridge, UK
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Irina T Zaharieva
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Lauren Brady
- Division of Neuromuscular & Neurometabolic Disorders, Department of Pediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Ying Hu
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrea Klein
- Division of Neuropaediatrics, Development and Rehabilitation, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Pediatric Neurology, University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | - Maja Steinlin
- Division of Neuropaediatrics, Development and Rehabilitation, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alice Kuster
- Department of Neurometabolism, University Hospital of Nantes, Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de génétique médicale, Centre de Référence des Maladies Neuromusculaires AOC, 44000, Nantes, France.,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Pascale Marcorelles
- Service d'anatomopathologie, CHU Brest and EA 4685 LIEN, Université de Bretagne Occidentale, Brest, France
| | - Yann Péréon
- CHU de Nantes, Centre de Référence des Maladies Neuromusculaires, Filnemus, Euro-NMD, Hôtel-Dieu, Nantes, France
| | - Emmanuelle Fleurence
- Etablissement de Santé pour Enfants et Adolescents de la région Nantaise, Nantes, France
| | - Adnan Manzur
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rosanna Upstill-Goddard
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Luca Bello
- Department of Neurosciences, DNS, University of Padova, Padova, Italy
| | - Cinzia Bertolin
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, IRP Città della Speranza, Padova, Italy
| | - Elena Pegoraro
- Department of Neurosciences, DNS, University of Padova, Padova, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women and Children's Health, CIR-Myo Myology Center, University of Padova, IRP Città della Speranza, Padova, Italy
| | | | - Andriy Shatillo
- Institute of Neurology, Psychiatry and Narcology of NAMS of Ukraine, Kharkiv, Ukraine
| | - F Lucy Raymond
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susana Quijano-Roy
- Neuromuscular Unit, Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches, France
| | - Johann Böhm
- Département Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U1258, Centre National de la Recherche Scientifique UMR7104, Université de Strasbourg, Illkirch, France
| | - Isabelle Nelson
- Sorbonne Université, INSERM, Centre of Research in Myology, UMRS974, Paris, France
| | - Tanya Stojkovic
- APHP, Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Teresinha Evangelista
- Unité de Morphologie Neuromusculaire, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Norma B Romero
- APHP, Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France.,Unité de Morphologie Neuromusculaire, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jocelyn Laporte
- Département Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U1258, Centre National de la Recherche Scientifique UMR7104, Université de Strasbourg, Illkirch, France
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Medical Genome Center, NCNP, Kodaira, Tokyo, Japan
| | - Mark A Tarnopolsky
- Division of Neuromuscular & Neurometabolic Disorders, Department of Pediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - James Shorter
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States.
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States. .,Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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15
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Dasgupta S, Leong C, Simonich MT, Truong L, Liu H, Tanguay RL. Transcriptomic and Long-Term Behavioral Deficits Associated with Developmental 3.5 GHz Radiofrequency Radiation Exposures in Zebrafish. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2022; 9:327-332. [PMID: 35434172 PMCID: PMC9009179 DOI: 10.1021/acs.estlett.2c00037] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 05/31/2023]
Abstract
The rapid deployment of the fifth-generation (5G) spectrum by the telecommunication industry is intended to promote better connectivity and data integration among various industries. However, concerns among the public about the safety and health effects of radiofrequency radiations (RFRs) emitted from the newer-generation cell phone frequencies remain, partly due to the lack of robust scientific data. Previously, we used developmental zebrafish to model the bioactivity of 3.5 GHz RFR, a frequency used by 5G-enabled cell phones, in a novel RFR exposure chamber. With RFR exposures from 6 h post-fertilization (hpf) to 48 hpf, we observed that, despite no teratogenic effects, embryos showed subtle hypoactivity in a startle response behavior assay, suggesting abnormal sensorimotor behavior. This study builds upon the previous one by investigating the transcriptomic basis of RFR-associated behavior effects and their persistence into adulthood. Using mRNA sequencing, we found a modest transcriptomic disruption at 48 hpf, with 28 differentially expressed genes. KEGG pathway analysis showed that biochemical pathways related to metabolism were significantly perturbed. Embryos were grown to adulthood, and then a battery of behavioral assays suggested subtle but significant abnormal responses in RFR-exposed fish across the different assays evaluated that suggest potential long-term behavioral effects. Overall, our study suggests the impacts of RFRs on the developing brain, behavior, and the metabolome should be further explored.
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Affiliation(s)
- Subham Dasgupta
- Sinnhuber
Aquatic Research Laboratory, Department of Environmental and Molecular
Toxicology, Oregon State University, Corvallis, Oregon 97333, United States
| | - Connor Leong
- Sinnhuber
Aquatic Research Laboratory, Department of Environmental and Molecular
Toxicology, Oregon State University, Corvallis, Oregon 97333, United States
| | - Michael T. Simonich
- Sinnhuber
Aquatic Research Laboratory, Department of Environmental and Molecular
Toxicology, Oregon State University, Corvallis, Oregon 97333, United States
| | - Lisa Truong
- Sinnhuber
Aquatic Research Laboratory, Department of Environmental and Molecular
Toxicology, Oregon State University, Corvallis, Oregon 97333, United States
| | - Huaping Liu
- School
of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, United States
| | - Robyn L. Tanguay
- Sinnhuber
Aquatic Research Laboratory, Department of Environmental and Molecular
Toxicology, Oregon State University, Corvallis, Oregon 97333, United States
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16
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Nedelsky NB, Taylor JP. Pathological phase transitions in ALS-FTD impair dynamic RNA-protein granules. RNA (NEW YORK, N.Y.) 2022; 28:97-113. [PMID: 34706979 PMCID: PMC8675280 DOI: 10.1261/rna.079001.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The genetics of human disease serves as a robust and unbiased source of insight into human biology, both revealing fundamental cellular processes and exposing the vulnerabilities associated with their dysfunction. Over the last decade, the genetics of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have epitomized this concept, as studies of ALS-FTD-causing mutations have yielded fundamental discoveries regarding the role of biomolecular condensation in organizing cellular contents while implicating disturbances in condensate dynamics as central drivers of neurodegeneration. Here we review this genetic evidence, highlight its intersection with patient pathology, and discuss how studies in model systems have revealed a role for aberrant condensation in neuronal dysfunction and death. We detail how multiple, distinct types of disease-causing mutations promote pathological phase transitions that disturb the dynamics and function of ribonucleoprotein (RNP) granules. Dysfunction of RNP granules causes pleiotropic defects in RNA metabolism and can drive the evolution of these structures to end-stage pathological inclusions characteristic of ALS-FTD. We propose that aberrant phase transitions of these complex condensates in cells provide a parsimonious explanation for the widespread cellular abnormalities observed in ALS as well as certain histopathological features that characterize late-stage disease.
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Affiliation(s)
- Natalia B Nedelsky
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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17
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Abstract
This review covers research findings reported over the past decade concerning the ability of low complexity (LC) domains to self-associate in a manner leading to their phase separation from aqueous solution. We focus our message upon the reductionist use of two forms of phase separation as biochemical assays to study how LC domains might function in living cells. Cells and their varied compartments represent extreme examples of material condensates. Over the past half century, biochemists, structural biologists, and molecular biologists have resolved the mechanisms driving innumerable forms of macromolecular condensation. In contrast, we remain largely ignorant as to how 10%-20% of our proteins actually work to assist in cell organization. This enigmatic 10%-20% of the proteome corresponds to gibberish-like LC sequences. We contend that many of these LC sequences move in and out of a structurally ordered, self-associated state as a means of offering a combination of organizational specificity and dynamic pliability to living cells. Finally, we speculate that ancient proteins may have behaved similarly, helping to condense, organize, and protect RNA early during evolution.
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Affiliation(s)
- Masato Kato
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Xiaoming Zhou
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Steven L McKnight
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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18
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The low-complexity domain of the FUS RNA binding protein self-assembles via the mutually exclusive use of two distinct cross-β cores. Proc Natl Acad Sci U S A 2021; 118:2114412118. [PMID: 34654750 PMCID: PMC8545455 DOI: 10.1073/pnas.2114412118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 11/24/2022] Open
Abstract
Single amino acid changes causative of neurologic disease often map to the cross-β forming regions of low-complexity (LC) domains. All such mutations studied to date lead to enhanced avidity of cross-β interactions. The LC domain of the fused in sarcoma (FUS) RNA binding protein contains three different regions that are capable of forming labile cross-β interactions. Here we describe the perplexing effect of amyotrophic lateral sclerosis (ALS)-causing mutations localized to the LC domain of FUS to substantially weaken its ability to form one of its three cross-β interactions. An understanding of how these mutations abet uncontrolled polymerization of the FUS LC domain may represent an important clue as to how LC domains achieve their proper biological function. The low-complexity (LC) domain of the fused in sarcoma (FUS) RNA binding protein self-associates in a manner causing phase separation from an aqueous environment. Incubation of the FUS LC domain under physiologically normal conditions of salt and pH leads to rapid formation of liquid-like droplets that mature into a gel-like state. Both examples of phase separation have enabled reductionist biochemical assays allowing discovery of an N-terminal region of 57 residues that assembles into a labile, cross-β structure. Here we provide evidence of a nonoverlapping, C-terminal region of the FUS LC domain that also forms specific cross-β interactions. We propose that biologic function of the FUS LC domain may operate via the mutually exclusive use of these N- and C-terminal cross-β cores. Neurodegenerative disease–causing mutations in the FUS LC domain are shown to imbalance the two cross-β cores, offering an unanticipated concept of LC domain function and dysfunction.
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19
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Abstract
Assembly of intermediate filaments (IFs) is reliant upon amino-terminal head domains. These head domains are of low sequence complexity and are assumed to function in the absence of structural order. Herein, we provide evidence that the head domains of the desmin and neurofilament light (NFL) IF proteins self-associate via the formation of labile but structurally specific cross-β interaction. Disease-causing mutations in the head domains of both proteins cause enhanced cross-β interactions. By assembling desmin and NFL IFs bearing isotopically labeled head domains, we provide evidence of structural order in properly assembled biological filaments. We propose that these observations on IF head domains may be instructive to the function of low complexity domains operative in other aspects of cell biology. Low complexity (LC) head domains 92 and 108 residues in length are, respectively, required for assembly of neurofilament light (NFL) and desmin intermediate filaments (IFs). As studied in isolation, these IF head domains interconvert between states of conformational disorder and labile, β-strand–enriched polymers. Solid-state NMR (ss-NMR) spectroscopic studies of NFL and desmin head domain polymers reveal spectral patterns consistent with structural order. A combination of intein chemistry and segmental isotope labeling allowed preparation of fully assembled NFL and desmin IFs that could also be studied by ss-NMR. Assembled IFs revealed spectra overlapping with those observed for β-strand–enriched polymers formed from the isolated NFL and desmin head domains. Phosphorylation and disease-causing mutations reciprocally alter NFL and desmin head domain self-association yet commonly impede IF assembly. These observations show how facultative structural assembly of LC domains via labile, β-strand–enriched self-interactions may broadly influence cell morphology.
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20
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de Castro Fonseca M, de Oliveira JF, Araujo BHS, Canateli C, do Prado PFV, Amorim Neto DP, Bosque BP, Rodrigues PV, de Godoy JVP, Tostes K, Filho HVR, Nascimento AFZ, Saito A, Tonoli CCC, Batista FAH, de Oliveira PSL, Figueira AC, Souza da Costa S, Krepischi ACV, Rosenberg C, Westfahl H, da Silva AJR, Franchini KG. Molecular and cellular basis of hyperassembly and protein aggregation driven by a rare pathogenic mutation in DDX3X. iScience 2021; 24:102841. [PMID: 34381968 PMCID: PMC8335631 DOI: 10.1016/j.isci.2021.102841] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 12/30/2022] Open
Abstract
Current studies estimate that 1–3% of females with unexplained intellectual disability (ID) present de novo splice site, nonsense, frameshift, or missense mutations in the DDX3X protein (DEAD-Box Helicase 3 X-Linked). However, the cellular and molecular mechanisms by which DDX3X mutations impair brain development are not fully comprehended. Here, we show that the ID-linked missense mutation L556S renders DDX3X prone to aggregation. By using a combination of biophysical assays and imaging approaches, we demonstrate that this mutant assembles solid-like condensates and amyloid-like fibrils. Although we observed greatly reduced expression of the mutant allele in a patient who exhibits skewed X inactivation, this appears to be enough to sequestrate healthy proteins into solid-like ectopic granules, compromising cell function. Therefore, our data suggest ID-linked DDX3X L556S mutation as a disorder arising from protein misfolding and aggregation. DDX3X mutations skew X-inactivation and are found in 1-3% of unexplained ID in females DDX3X mutant proteins assemble solid-like condensates and amyloid-like fibrils Aberrant granules formed by DDX3X mutants sequestrate healthy DDX3X protein ID-linked DDX3X L556S mutation decreases cell viability and induces apoptosis
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Affiliation(s)
- Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Juliana Ferreira de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Bruno Henrique Silva Araujo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Camila Canateli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paula Favoretti Vital do Prado
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Dionísio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Andrey Fabricio Ziem Nascimento
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Angela Saito
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Fernanda Aparecida Heleno Batista
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Ana Carolina Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Harry Westfahl
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antônio José Roque da Silva
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil
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Abstract
The limb-girdle muscular dystrophies (LGMD) are a collection of genetic diseases united in their phenotypical expression of pelvic and shoulder area weakness and wasting. More than 30 subtypes have been identified, five dominant and 26 recessive. The increase in the characterization of new genotypes in the family of LGMDs further adds to the heterogeneity of the disease. Meanwhile, better understanding of the phenotype led to the reconsideration of the disease definition, which resulted in eight old subtypes to be no longer recognized officially as LGMD and five new diseases to be added to the LGMD family. The unique variabilities of LGMD stem from genetic mutations, which then lead to protein and ultimately muscle dysfunction. Herein, we review the LGMD pathway, starting with the genetic mutations that encode proteins involved in muscle maintenance and repair, and including the genotype–phenotype relationship of the disease, the epidemiology, disease progression, burden of illness, and emerging treatments.
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22
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El Marabti E, Abdel-Wahab O. Therapeutic Modulation of RNA Splicing in Malignant and Non-Malignant Disease. Trends Mol Med 2021; 27:643-659. [PMID: 33994320 DOI: 10.1016/j.molmed.2021.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/24/2023]
Abstract
RNA splicing is the enzymatic process by which non-protein coding sequences are removed from RNA to produce mature protein-coding mRNA. Splicing is thereby a major mediator of proteome diversity as well as a dynamic regulator of gene expression. Genetic alterations disrupting splicing of individual genes or altering the function of splicing factors contribute to a wide range of human genetic diseases as well as cancer. These observations have resulted in the development of therapies based on oligonucleotides that bind to RNA sequences and modulate splicing for therapeutic benefit. In parallel, small molecules that bind to splicing factors to alter their function or modify RNA processing of individual transcripts are being pursued for monogenic disorders as well as for cancer.
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Affiliation(s)
- Ettaib El Marabti
- Clinical Transplant Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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23
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Batlle C, Ventura S. Prion-like domain disease-causing mutations and misregulation of alternative splicing relevance in limb-girdle muscular dystrophy (LGMD) 1G. Neural Regen Res 2020; 15:2239-2240. [PMID: 32594036 PMCID: PMC7749493 DOI: 10.4103/1673-5374.284988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Cristina Batlle
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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24
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Splicing Factor SRSF1 Is Essential for Satellite Cell Proliferation and Postnatal Maturation of Neuromuscular Junctions in Mice. Stem Cell Reports 2020; 15:941-954. [PMID: 32888503 PMCID: PMC7561493 DOI: 10.1016/j.stemcr.2020.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/08/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023] Open
Abstract
Satellite cells are main muscle stem cells that could provide myonuclei for myofiber growth and synaptic-specific gene expression during the early postnatal development. Here, we observed that splicing factor SRSF1 is highly expressed in myoblasts and its expression is closely related with satellite cell activation and proliferation. By genetic deletion of SRSF1 in myogenic progenitors, we found that SRSF1 is critical for satellite cell proliferation in vitro and in vivo. Most notably we also observed that SRSF1 is required for the functional neuromuscular junction (NMJ) formation, as SRSF1-deficient mice fail to form mature pretzel-like NMJs, which leads to muscle weakness and premature death in mice. Finally, we demonstrated that SRSF1 contributes to muscle innervation and muscle development likely by regulating a restricted set of tissue-specific alternative splicing events. Thus, our data define a unique role for SRSF1 in postnatal skeletal muscle growth and function in mice. SRSF1 is highly expressed in activated satellite cells Loss of SRSF1 dramatically impairs satellite cell proliferation in vitro and in vivo SRSF1 is also required for the functional neuromuscular junction formation in mice SRSF1-deficient mice display muscle weakness and die prematurely
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25
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The ties that bind: functional clusters in limb-girdle muscular dystrophy. Skelet Muscle 2020; 10:22. [PMID: 32727611 PMCID: PMC7389686 DOI: 10.1186/s13395-020-00240-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
The limb-girdle muscular dystrophies (LGMDs) are a genetically pleiomorphic class of inherited muscle diseases that are known to share phenotypic features. Selected LGMD genetic subtypes have been studied extensively in affected humans and various animal models. In some cases, these investigations have led to human clinical trials of potential disease-modifying therapies, including gene replacement strategies for individual subtypes using adeno-associated virus (AAV) vectors. The cellular localizations of most proteins associated with LGMD have been determined. However, the functions of these proteins are less uniformly characterized, thus limiting our knowledge of potential common disease mechanisms across subtype boundaries. Correspondingly, broad therapeutic strategies that could each target multiple LGMD subtypes remain less developed. We believe that three major "functional clusters" of subcellular activities relevant to LGMD merit further investigation. The best known of these is the glycosylation modifications associated with the dystroglycan complex. The other two, mechanical signaling and mitochondrial dysfunction, have been studied less systematically but are just as promising with respect to the identification of significant mechanistic subgroups of LGMD. A deeper understanding of these disease pathways could yield a new generation of precision therapies that would each be expected to treat a broader range of LGMD patients than a single subtype, thus expanding the scope of the molecular medicines that may be developed for this complex array of muscular dystrophies.
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26
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Vicente LM, Martí P, Azorín I, Olivé M, Muelas N, Vilchez JJ. HNRNPDL-related limb girdle muscular dystrophy in a Spanish family with scapulo-peroneal phenotype, the first family in Europe. J Neurol Sci 2020; 414:116875. [PMID: 32407983 DOI: 10.1016/j.jns.2020.116875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Affiliation(s)
- L M Vicente
- Neuromuscular Reference Centre ERN EURO-NMD and Research Group on NMD and Ataxias, IIS La Fe and CIBERER, Hospital Universitari i Politècnic La Fe, Avenida Fernando Abril Martorell 106, floor 5, tower C, 46026, Valencia, Spain.
| | - P Martí
- Neuromuscular Reference Centre ERN EURO-NMD and Research Group on NMD and Ataxias, IIS La Fe and CIBERER, Hospital Universitari i Politècnic La Fe, Avenida Fernando Abril Martorell 106, floor 5, tower C, 46026, Valencia, Spain
| | - I Azorín
- Neuromuscular Reference Centre ERN EURO-NMD and Research Group on NMD and Ataxias, IIS La Fe and CIBERER, Hospital Universitari i Politècnic La Fe, Avenida Fernando Abril Martorell 106, floor 5, tower C, 46026, Valencia, Spain
| | - M Olivé
- IDIBELL, Hospital Universitari de Bellvitge, Carrer de la Feixa Llarga, s/n, 08907 L'Hospitalet de Llobregat. Barcelona, Spain.
| | - N Muelas
- Neuromuscular Reference Centre ERN EURO-NMD and Research Group on NMD and Ataxias, IIS La Fe and CIBERER, Hospital Universitari i Politècnic La Fe, Avenida Fernando Abril Martorell 106, floor 5, tower C, 46026, Valencia, Spain
| | - J J Vilchez
- Neuromuscular Reference Centre ERN EURO-NMD and Research Group on NMD and Ataxias, IIS La Fe and CIBERER, Hospital Universitari i Politècnic La Fe, Avenida Fernando Abril Martorell 106, floor 5, tower C, 46026, Valencia, Spain.
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27
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Nicolau S, Liewluck T, Milone M. Myopathies with finger flexor weakness: Not only inclusion-body myositis. Muscle Nerve 2020; 62:445-454. [PMID: 32478919 DOI: 10.1002/mus.26914] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/29/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022]
Abstract
Muscle disorders are characterized by differential involvement of various muscle groups. Among these, weakness predominantly affecting finger flexors is an uncommon pattern, most frequently found in sporadic inclusion-body myositis. This finding is particularly significant when the full range of histopathological findings of inclusion-body myositis is not found on muscle biopsy. Prominent finger flexor weakness, however, is also observed in other myopathies. It occurs commonly in myotonic dystrophy types 1 and 2. In addition, individual reports and small case series have documented finger flexor weakness in sarcoid and amyloid myopathy, and in inherited myopathies caused by ACTA1, CRYAB, DMD, DYSF, FLNC, GAA, GNE, HNRNPDL, LAMA2, MYH7, and VCP mutations. Therefore, the finding of finger flexor weakness requires consideration of clinical, myopathological, genetic, electrodiagnostic, and sometimes muscle imaging findings to establish a diagnosis.
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Affiliation(s)
- Stefan Nicolau
- Department of Neurology, Mayo Clinic, 200 1st Street SW, Rochester, Minnesota, 55905, USA
| | - Teerin Liewluck
- Department of Neurology, Mayo Clinic, 200 1st Street SW, Rochester, Minnesota, 55905, USA
| | - Margherita Milone
- Department of Neurology, Mayo Clinic, 200 1st Street SW, Rochester, Minnesota, 55905, USA
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28
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Malfatti E, Cassandrini D, Rubegni A, Sartorelli FM, Villanova M. Respiratory muscle involvement in HNRNPDL LGMD D3 muscular dystrophy: an extensive clinical description of the first Italian patient. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2020; 39:98-100. [PMID: 32904822 PMCID: PMC7460734 DOI: 10.36185/2532-1900-013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/27/2020] [Indexed: 11/25/2022]
Abstract
Limb girdle muscular dystrophy is a genetically inherited condition that primarily affects skeletal muscle leading to progressive, predominantly proximal muscle weakness at presentation. Autosomal dominant LGMD represent 10% of all LGMDs. HNRNPDL-related muscular dystrophy, LGMD1G/LGMD D3 (MIM#609115), is an extremely rare autosomal dominant adult onset myopathy described in a handful of families. Here we fully characterized the muscular and respiratory involvement of a 58 years old Italian woman presenting the previously reported pathogenic variant c.1132G > C p.(Asp378Asn) in the HNRNPDL gene.
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Affiliation(s)
- Edoardo Malfatti
- Neurology Department, Centre de Référence Maladies Neuromusculaires Nord-Est-Ile-de-France, CHU Raymond-Poincaré, Garches, France; U1179 UVSQ-INSERM Handicap Neuromusculaire: Physiologie, Biothérapie et Pharmacologie appliquées, UFR des sciences de la santé Simone Veil, Université Versailles-Saint-Quentin-en-Yvelines, France,Correspondence Edoardo Malfatti Service de Neurologie, Centre de Référence de Maladies Neuromusculaires Nord/Est/Ile-de-France, U1179 UVSQ-INSERM Handicap Neuromusculaire: Physiologie, Biothérapie et Pharmacologie appliquées, UFR Simone Veil-Santé, Université Versailles-Saint-Quentin-en-Yvelines, Pôle neuro-locomoteur, Hôpital Raymond Poincaré, 104 boulevard Raymond Poincaré, 92380 Garches. Tel.: +33 147107900. Fax: +33 171144993. E-mail:
| | - Denise Cassandrini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Calambrone, Pisa, Italy
| | - Anna Rubegni
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Calambrone, Pisa, Italy
| | - Filippo M. Sartorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Calambrone, Pisa, Italy
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29
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Cao X, Jin X, Liu B. The involvement of stress granules in aging and aging-associated diseases. Aging Cell 2020; 19:e13136. [PMID: 32170904 PMCID: PMC7189987 DOI: 10.1111/acel.13136] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are nonmembrane assemblies formed in cells in response to stress conditions. SGs mainly contain untranslated mRNA and a variety of proteins. RNAs and scaffold proteins with intrinsically disordered regions or RNA-binding domains are essential for the assembly of SGs, and multivalent macromolecular interactions among these components are thought to be the driving forces for SG assembly. The SG assembly process includes regulation through post-translational modification and involvement of the cytoskeletal system. During aging, many intracellular bioprocesses become disrupted by factors such as cellular environmental changes, mitochondrial dysfunction, and decline in the protein quality control system. Such changes could lead to the formation of aberrant SGs, as well as alterations in their maintenance, disassembly, and clearance. These aberrant SGs might in turn promote aging and aging-associated diseases. In this paper, we first review the latest progress on the molecular mechanisms underlying SG assembly and SG functioning under stress conditions. Then, we provide a detailed discussion of the relevance of SGs to aging and aging-associated diseases.
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Affiliation(s)
- Xiuling Cao
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
- Department of Chemistry and Molecular Biology University of Gothenburg Goteborg Sweden
- Center for Large‐scale Cell‐based Screening Faculty of Science University of Gothenburg Goteborg Sweden
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30
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Picchiarelli G, Dupuis L. Role of RNA Binding Proteins with prion-like domains in muscle and neuromuscular diseases. Cell Stress 2020; 4:76-91. [PMID: 32292882 PMCID: PMC7146060 DOI: 10.15698/cst2020.04.217] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A number of neuromuscular and muscular diseases, including amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and several myopathies, are associated to mutations in related RNA-binding proteins (RBPs), including TDP-43, FUS, MATR3 or hnRNPA1/B2. These proteins harbor similar modular primary sequence with RNA binding motifs and low complexity domains, that enables them to phase separate and create liquid microdomains. These RBPs have been shown to critically regulate multiple events of RNA lifecycle, including transcriptional events, splicing and RNA trafficking and sequestration. Here, we review the roles of these disease-related RBPs in muscle and motor neurons, and how their dysfunction in these cell types might contribute to disease.
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Affiliation(s)
- Gina Picchiarelli
- Université de Strasbourg, INSERM, Mécanismes Centraux et Périphériques de la Neurodégénérescence, UMR_S 1118, Strasbourg, France
| | - Luc Dupuis
- Université de Strasbourg, INSERM, Mécanismes Centraux et Périphériques de la Neurodégénérescence, UMR_S 1118, Strasbourg, France
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31
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Batlle C, Yang P, Coughlin M, Messing J, Pesarrodona M, Szulc E, Salvatella X, Kim HJ, Taylor JP, Ventura S. hnRNPDL Phase Separation Is Regulated by Alternative Splicing and Disease-Causing Mutations Accelerate Its Aggregation. Cell Rep 2020; 30:1117-1128.e5. [PMID: 31995753 PMCID: PMC6996132 DOI: 10.1016/j.celrep.2019.12.080] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/12/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
Prion-like proteins form multivalent assemblies and phase separate into membraneless organelles. Heterogeneous ribonucleoprotein D-like (hnRNPDL) is a RNA-processing prion-like protein with three alternative splicing (AS) isoforms, which lack none, one, or both of its two disordered domains. It has been suggested that AS might regulate the assembly properties of RNA-processing proteins by controlling the incorporation of multivalent disordered regions in the isoforms. This, in turn, would modulate their activity in the downstream splicing program. Here, we demonstrate that AS controls the phase separation of hnRNPDL, as well as the size and dynamics of its nuclear complexes, its nucleus-cytoplasm shuttling, and amyloidogenicity. Mutation of the highly conserved D378 in the disordered C-terminal prion-like domain of hnRNPDL causes limb-girdle muscular dystrophy 1G. We show that D378H/N disease mutations impact hnRNPDL assembly properties, accelerating aggregation and dramatically reducing the protein solubility in the muscle of Drosophila, suggesting a genetic loss-of-function mechanism for this muscular disorder.
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Affiliation(s)
- Cristina Batlle
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
| | - Peiguo Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maura Coughlin
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA.
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain.
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32
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Bridging biophysics and neurology: aberrant phase transitions in neurodegenerative disease. Nat Rev Neurol 2020; 15:272-286. [PMID: 30890779 DOI: 10.1038/s41582-019-0157-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biomolecular condensation arising through phase transitions has emerged as an essential organizational strategy that governs many aspects of cell biology. In particular, the role of phase transitions in the assembly of large, complex ribonucleoprotein (RNP) granules has become appreciated as an important regulator of RNA metabolism. In parallel, genetic, histopathological and cell and molecular studies have provided evidence that disturbance of phase transitions is an important driver of neurological diseases, notably amyotrophic lateral sclerosis (ALS), but most likely also other diseases. Indeed, our growing knowledge of the biophysics underlying biological phase transitions suggests that this process offers a unifying mechanism to explain the numerous and diverse disturbances in RNA metabolism that have been observed in ALS and some related diseases - specifically, that these diseases are driven by disturbances in the material properties of RNP granules. Here, we review the evidence for this hypothesis, emphasizing the reciprocal roles in which disease-related protein and disease-related RNA can lead to disturbances in the material properties of RNP granules and consequent pathogenesis. Additionally, we review evidence that implicates aberrant phase transitions as a contributing factor to a larger set of neurodegenerative diseases, including frontotemporal dementia, certain repeat expansion diseases and Alzheimer disease.
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Cascarina SM, Ross ED. Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes. BMC Genomics 2020; 21:23. [PMID: 31914925 PMCID: PMC6947906 DOI: 10.1186/s12864-019-6425-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Impaired proteostatic regulation of proteins with prion-like domains (PrLDs) is associated with a variety of human diseases including neurodegenerative disorders, myopathies, and certain forms of cancer. For many of these disorders, current models suggest a prion-like molecular mechanism of disease, whereby proteins aggregate and spread to neighboring cells in an infectious manner. The development of prion prediction algorithms has facilitated the large-scale identification of PrLDs among "reference" proteomes for various organisms. However, the degree to which intraspecies protein sequence diversity influences predicted prion propensity has not been systematically examined. RESULTS Here, we explore protein sequence variation introduced at genetic, post-transcriptional, and post-translational levels, and its influence on predicted aggregation propensity for human PrLDs. We find that sequence variation is relatively common among PrLDs and in some cases can result in relatively large differences in predicted prion propensity. Sequence variation introduced at the post-transcriptional level (via alternative splicing) also commonly affects predicted aggregation propensity, often by direct inclusion or exclusion of a PrLD. Finally, analysis of a database of sequence variants associated with human disease reveals a number of mutations within PrLDs that are predicted to increase prion propensity. CONCLUSIONS Our analyses expand the list of candidate human PrLDs, quantitatively estimate the effects of sequence variation on the aggregation propensity of PrLDs, and suggest the involvement of prion-like mechanisms in additional human diseases.
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Affiliation(s)
- Sean M Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Eric D Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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Oncogenic heterogeneous nuclear ribonucleoprotein D-like modulates the growth and imatinib response of human chronic myeloid leukemia CD34 + cells via pre-B-cell leukemia homeobox 1. Oncogene 2019; 39:443-453. [PMID: 31488872 DOI: 10.1038/s41388-019-0998-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Chronic myeloid leukemia (CML) originates from normal hematopoietic stem cells acquiring BCR-ABL fusion gene, specific BCR-ABL inhibitors (e.g., imatinib mesylate, IM) have greatly improved patient management. However, some patients are still suffering from relapse and drug resistance, which urges better understanding of the growth/survival mechanisms of CML stem/progenitor cells. In the present study, the role and its underlying mechanism of heterogeneous nuclear ribonucleoprotein D-like (HNRPDL) in CML cells were investigated. Firstly, overexpression of HNRPDL promoted the growth of murine BaF3 cells in vitro and induced leukemia in vivo, which was enhanced by co-expression of BCR-ABL. Conversely, HNRPDL silencing inhibited colony-forming cell (CFC) production of CML CD34+ cells and attenuated BCR-ABL induced leukemia. In addition, HNRPDL modulated imatinib response of K562 cells and HNRPDL silencing sensitized CML CD34+ cells to imatinib treatment. Mechanistically, we found the stability of pre-B-cell leukemia homeobox 1 (PBX1) mRNA was sustained by HNRPDL through its binding to a specific motif (ACUAGC) in 3'-untranslated region (3'-UTR) of PBX1. The expression of PBX1 was significantly higher in CML CD34+ cells than that in control cells and PBX silencing inhibited the growth of CML cells and sensitized them to imatinib treatment. In contrast, overexpression of PBX1 elevated the CFC production of normal hematopoietic CD34+ cells and "rescued" HNRPDL silencing induced growth inhibition and imatinib sensitization. Taken together, our data have demonstrated that HNRPDL transforms hematopoietic cells and a novel HNRPDL/PBX1 axis plays an important role in human CML CD34+ cells.
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35
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Berardo A, Lornage X, Johari M, Evangelista T, Cejas C, Barroso F, Dubrovsky A, Bui MT, Brochier G, Saccoliti M, Bohm J, Udd B, Laporte J, Romero NB, Taratuto AL. HNRNPDL-related muscular dystrophy: expanding the clinical, morphological and MRI phenotypes. J Neurol 2019; 266:2524-2534. [PMID: 31267206 DOI: 10.1007/s00415-019-09437-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 11/25/2022]
Abstract
Autosomal dominant limb girdle muscular dystrophy D3 HNRNPDL-related is a rare dominant myopathy caused by mutations in HNRNPDL. Only three unrelated families have been described worldwide, a Brazilian and a Chinese carrying the mutation c.1132G>A p.(Asp378Asn), and one Uruguayan with the mutation c.1132G>C p. (Asp378His), both mutations occurring in the same codon. The present study enlarges the clinical, morphological and muscle MRI spectrum of AD-HNRNPDL-related myopathies demonstrating the significant particularities of the disease. We describe two new unrelated Argentinean families, carrying the previously reported c.1132G>C p.(Asp378His) HNRNPDL mutation. There was a wide phenotypic spectrum including oligo-symptomatic cases, pure limb girdle muscle involvement or distal lower limb muscle weakness. Scapular winging was the most common finding, observed in all patients. Muscle MRIs of the thigh, at different stages of the disease, showed particular involvement of adductor magnus and vastus besides a constant preservation of the rectus femoris and the adductor longus muscles, defining a novel MRI pattern. Muscle biopsy findings were characterized by the presence of numerous rimmed vacuoles, cytoplasmic bodies, and abundant autophagic material at the histochemistry and ultrastructural levels. HNRNPDL-related LGMD D3 results in a wide range of clinical phenotypes from the classic proximal form of LGMD to a more distal phenotype. Thigh MRI suggests a specific pattern. Codon 378 of HNRNPDL gene can be considered a mutation hotspot for HNRNPDL-related myopathy. Pathologically, the disease can be classified among the autophagic rimmed vacuolar myopathies as with the other multisystem proteinopathies.
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Affiliation(s)
- Andrés Berardo
- Neuropsychiatry Center Valencia Positiva, Córdoba, Argentina
| | - Xavière Lornage
- Department of Translational Medicine, Institut de Génétique Et de Biologie Moléculaire Et Cellulaire (IGBMC)INSERM U1258, UMR7104, Strasbourg University, Illkirch, France
| | - Mridul Johari
- Department of Medical Genetics, University of Helsinki, Medicum, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Teresinha Evangelista
- Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, NeuromuscularParis, France.,Sorbonne Université, AP-HP, INSERM, Centre de référence Des Maladies Neuromusculaires Nord/Est, Ile de France, Paris, France
| | - Claudia Cejas
- Instituto de Investigaciones Neurológicas FLENI, Buenos Aires, Argentina
| | - Fabio Barroso
- Instituto de Investigaciones Neurológicas FLENI, Buenos Aires, Argentina
| | | | - Mai Thao Bui
- Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, NeuromuscularParis, France
| | - Guy Brochier
- Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, NeuromuscularParis, France.,Sorbonne Université, AP-HP, INSERM, Centre de référence Des Maladies Neuromusculaires Nord/Est, Ile de France, Paris, France
| | - Maria Saccoliti
- Neuropathology and Neuromuscular Diseases Laboratory, Buenos Aires, Argentina
| | - Johann Bohm
- Department of Translational Medicine, Institut de Génétique Et de Biologie Moléculaire Et Cellulaire (IGBMC)INSERM U1258, UMR7104, Strasbourg University, Illkirch, France
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland.,Neuromuscular Research Center, Tampere University and University Hospital, Tampere, Finland
| | - Jocelyn Laporte
- Department of Translational Medicine, Institut de Génétique Et de Biologie Moléculaire Et Cellulaire (IGBMC)INSERM U1258, UMR7104, Strasbourg University, Illkirch, France
| | - Norma Beatriz Romero
- Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, NeuromuscularParis, France. .,Sorbonne Université, AP-HP, INSERM, Centre de référence Des Maladies Neuromusculaires Nord/Est, Ile de France, Paris, France.
| | - Ana Lia Taratuto
- Neuropathology and Neuromuscular Diseases Laboratory, Buenos Aires, Argentina
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36
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Angelini C, Pegoraro V, Cenacchi G. The clinical and molecular spectrum of autosomal dominant limb-girdle muscular dystrophies focusing on transportinopathy. Expert Opin Orphan Drugs 2019. [DOI: 10.1080/21678707.2019.1622412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | | | - Giovanna Cenacchi
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum–University of Bologna, Bologna, Italy
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37
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Muscle development and regeneration controlled by AUF1-mediated stage-specific degradation of fate-determining checkpoint mRNAs. Proc Natl Acad Sci U S A 2019; 116:11285-11290. [PMID: 31113881 DOI: 10.1073/pnas.1901165116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AUF1 promotes rapid decay of mRNAs containing 3' untranslated region (3'UTR) AU-rich elements (AREs). AUF1 depletion in mice accelerates muscle loss and causes limb girdle muscular dystrophy. Here, we demonstrate that the selective, targeted degradation by AUF1 of key muscle stem cell fate-determining checkpoint mRNAs regulates each stage of muscle development and regeneration by reprogramming each myogenic stage. Skeletal muscle stem (satellite) cell explants show that Auf1 transcription is activated with satellite cell activation by stem cell regulatory factor CTCF. AUF1 then targets checkpoint ARE-mRNAs for degradation, progressively reprogramming the transcriptome through each stage of myogenesis. Transition steps in myogenesis, from stem cell proliferation to differentiation to muscle fiber development, are each controlled by fate-determining checkpoint mRNAs, which, surprisingly, were found to be controlled in their expression by AUF1-targeted mRNA decay. Checkpoint mRNAs targeted by AUF1 include Twist1, decay of which promotes myoblast development; CyclinD1, decay of which blocks myoblast proliferation and initiates differentiation; and RGS5, decay of which activates Sonic Hedgehog (SHH) pathway-mediated differentiation of mature myotubes. AUF1 therefore orchestrates muscle stem cell proliferation, self-renewal, myoblast differentiation, and ultimately formation of muscle fibers through targeted, staged mRNA decay.
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38
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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39
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Iglesias V, Conchillo-Sole O, Batlle C, Ventura S. AMYCO: evaluation of mutational impact on prion-like proteins aggregation propensity. BMC Bioinformatics 2019; 20:24. [PMID: 30642249 PMCID: PMC6332698 DOI: 10.1186/s12859-019-2601-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/03/2019] [Indexed: 02/06/2023] Open
Abstract
Background Around 1% of human proteins are predicted to contain a disordered and low complexity prion-like domain (PrLD). Mutations in PrLDs have been shown promote a transition towards an aggregation-prone state in several diseases. Results Recently, we have shown that an algorithm that considers the effects of mutations on PrLDs composition, as well as on localized amyloid propensity can predict the impact of these amino acid changes on protein intracellular aggregation. In this application note, we implement this concept into the AMYCO web server, a refined algorithm that forecasts the influence of amino acid changes in prion-like proteins aggregation propensity better than state-of-the-art predictors. Conclusions The AMYCO web server allows for a fast and automated evaluation of the effect of mutations on the aggregation properties of prion-like proteins. This might uncover novel disease-linked amino acid changes in the sequences of human prion-like proteins. Additionally, it can find application in the in silico design of synthetic prion-like proteins with tuned aggregation propensities for different purposes. AMYCO does not require previous registration and is freely available to all users at: http://bioinf.uab.cat/amyco/. Electronic supplementary material The online version of this article (10.1186/s12859-019-2601-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valentin Iglesias
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Oscar Conchillo-Sole
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Cristina Batlle
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain. .,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
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40
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Limb girdle muscular dystrophy D3 HNRNPDL related in a Chinese family with distal muscle weakness caused by a mutation in the prion-like domain. J Neurol 2019; 266:498-506. [PMID: 30604053 DOI: 10.1007/s00415-018-9165-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/21/2022]
Abstract
Limb-girdle muscular dystrophies (LGMD) are a group of clinically and genetically heterogeneous diseases characterized by weakness and wasting of the pelvic and shoulder girdle muscles. Twenty-four recessive LGMD (types R1-R24) and five dominant LGMD (types D1-D5) have been identified with characterization of mutations in various genes. To date, LGMD D3 (previously known as LGMD1G) has been characterized in only two families with Brazilian or Uruguayan origin. Each was caused by a distinct mutation at codon 378 in the prion-like domain of HNRNPDL encoding heterogeneous nuclear ribonucleoprotein D like (HNRNPDL), an RNA processing protein. Our study characterized eight patients suffering from LGMD D3 in a Chinese family spanning three generations. Muscle biopsy specimens from two patients showed a myopathy with rimmed vacuoles. Sequencing analysis revealed a heterozygous c.1132G > A (p.D378N) mutation in HNRNPDL that co-segregated with disease phenotype in the family. The same mutation has been identified previously in the Brazilian family with LGMD D3. However, most patients in the current family showed distal as well as proximal limb weakness rather than weakness of toe and finger flexor muscles that were typical features in the other two LGMD D3 families reported previously. The present study indicates that the same mutation in HNRNPDL results in various phenotypes of LGMD D3. That all mutations in three unrelated families with different ethnic background occur at the same position in codon 378 of HNRNPDL gene suggests a mutation hotspot. Acceleration of intrinsic self-aggregation of HNRNPDL caused by mutation of the prior-like domain may contribute to the pathogenesis of the disease.
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41
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Taghizadeh E, Rezaee M, Barreto GE, Sahebkar A. Prevalence, pathological mechanisms, and genetic basis of limb-girdle muscular dystrophies: A review. J Cell Physiol 2018; 234:7874-7884. [PMID: 30536378 DOI: 10.1002/jcp.27907] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/23/2018] [Indexed: 12/17/2022]
Abstract
Limb-girdle muscular dystrophies (LGMDs) are a highly heterogeneous group of neuromuscular disorders that are associated with weakness and wasting of muscles in legs and arms. Signs and symptoms may begin at any age and usually worsen by time. LGMDs are autosomal disorders with different types and their prevalence is not the same in different areas. New technologies such as next-generation sequencing can accelerate their diagnosis. Several important pathological mechanisms that are involved in the pathology of the LGMD include abnormalities in dystrophin-glycoprotein complex, the sarcomere, glycosylation of dystroglycan, vesicle and molecular trafficking, signal transduction pathways, and nuclear functions. Here, we provide a comprehensive review that integrates LGMD clinical manifestations, prevalence, and some pathological mechanisms involved in LGMDs.
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Affiliation(s)
- Eskandar Taghizadeh
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Department of Medical Genetics, Faculity of Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Mehdi Rezaee
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C, Colombia.,Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Science, Mashhad, Iran.,Neurogenic Inflammation Research Center, Mashhad University of Medical Science, Mashhad, Iran.,School of Pharmacy, Mashhad University of Medical Science, Mashhad, Iran
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42
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hnRNPDL extensively regulates transcription and alternative splicing. Gene 2018; 687:125-134. [PMID: 30447347 DOI: 10.1016/j.gene.2018.11.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/30/2018] [Accepted: 11/08/2018] [Indexed: 01/31/2023]
Abstract
RNA binding proteins (RBPs) are key players of genome regulation. Here we report the transcriptome study of HnRNP D-Like protein, which belongs to the hnRNP family. We used RNA-seq to analyze the global transcript level and alternative splicing on hnRNPDL shRNA-treated cells and control. Sh-hnRNPDL extensively increased in the expression of genes involved in female pregnancy, cell apoptosis, cell proliferation and cell migration. HnRNPDL regulated alternative splicing of hundreds of genes enriched in transcription regulation and signaling pathways including NOD-like receptor signaling, Notch signaling, and TNF signaling. This study provides the first transcriptome-wide analysis of hnRNPDL regulation of gene expression, which adds to the understanding of critical hnRNPDL functions.
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43
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Murray DT, Zhou X, Kato M, Xiang S, Tycko R, McKnight SL. Structural characterization of the D290V mutation site in hnRNPA2 low-complexity-domain polymers. Proc Natl Acad Sci U S A 2018; 115:E9782-E9791. [PMID: 30279180 PMCID: PMC6196502 DOI: 10.1073/pnas.1806174115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Human genetic studies have given evidence of familial, disease-causing mutations in the analogous amino acid residue shared by three related RNA binding proteins causative of three neurological diseases. Alteration of aspartic acid residue 290 of hnRNPA2 to valine is believed to predispose patients to multisystem proteinopathy. Mutation of aspartic acid 262 of hnRNPA1 to either valine or asparagine has been linked to either amyotrophic lateral sclerosis or multisystem proteinopathy. Mutation of aspartic acid 378 of hnRNPDL to either asparagine or histidine has been associated with limb girdle muscular dystrophy. All three of these aspartic acid residues map to evolutionarily conserved regions of low-complexity (LC) sequence that may function in states of either intrinsic disorder or labile self-association. Here, we present a combination of solid-state NMR spectroscopy with segmental isotope labeling and electron microscopy on the LC domain of the hnRNPA2 protein. We show that, for both the wild-type protein and the aspartic acid 290-to-valine mutant, labile polymers are formed in which the LC domain associates into an in-register cross-β conformation. Aspartic acid 290 is shown to be charged at physiological pH and immobilized within the polymer core. Polymers of the aspartic acid 290-to-valine mutant are thermodynamically more stable than wild-type polymers. These observations give evidence that removal of destabilizing electrostatic interactions may be responsible for the increased propensity of the mutated LC domains to self-associate in disease-causing conformations.
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Affiliation(s)
- Dylan T Murray
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, MD 20892
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, Bethesda, MD 20892
| | - Xiaoming Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Siheng Xiang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, MD 20892;
| | - Steven L McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
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44
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Zhang P, Ji D, Hu X, Ni H, Ma W, Zhang X, Liao S, Zeng Z, Zhao Y, Zhou H. Oncogenic heterogeneous nuclear ribonucleoprotein D-like promotes the growth of human colon cancer SW620 cells via its regulation of cell-cycle. Acta Biochim Biophys Sin (Shanghai) 2018; 50:880-887. [PMID: 30052712 DOI: 10.1093/abbs/gmy085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Indexed: 01/01/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins. Heterogeneous nuclear ribonucleoprotein D-like (HNRPDL) is a member of this family. Though aberrant expression of HNRPDL has been reported in a few cancers, whether HNRPDL is deregulated in colon cancer patients and what role this protein plays in these cells are not known yet. In this study, we found that HNRPDL was significantly up-regulated in colon cancer specimens than control. We also demonstrated that HNRPDL silencing inhibited the growth of SW620 cells both in vitro and in vivo. Conversely, we constructed a retroviral vector to deliver HNRPDL into non-malignant NIH-3T3 cells and injected these cells into nude mice. HNRPDL-overexpressing NIH-3T3 cells generated tumors in nude mice but not the control cells. Mechanistically, HNRPDL promoted cell-cycle progression associated with enhanced expressions of cyclin D3 and Ki-67 but decreased expressions of p53 and p21. Taken together, our data demonstrate that HNRPDL is aberrantly expressed in colon cancer cells, which promotes the growth of these cells by activating cell-cycle progression.
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Affiliation(s)
- Pengshan Zhang
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Dehuan Ji
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Xiaohui Hu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hengli Ni
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Wenjuan Ma
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Xiuyan Zhang
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Shibing Liao
- Department of Oncology, The Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Zheng Zeng
- Department of Oncology, The Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Yun Zhao
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
- The Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Haixia Zhou
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
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45
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Kato M, McKnight SL. A Solid-State Conceptualization of Information Transfer from Gene to Message to Protein. Annu Rev Biochem 2018; 87:351-390. [DOI: 10.1146/annurev-biochem-061516-044700] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this review, we describe speculative ideas and early stage research concerning the flow of genetic information from the nuclear residence of genes to the disparate, cytoplasmic sites of protein synthesis. We propose that this process of information transfer is meticulously guided by transient structures formed from protein segments of low sequence complexity/intrinsic disorder. These low complexity domains are ubiquitously associated with regulatory proteins that control gene expression and RNA biogenesis, but they are also found in the central channel of nuclear pores, the nexus points of intermediate filament assembly, and the locations of action of other well-studied cellular proteins and pathways. Upon being organized into localized cellular positions via mechanisms utilizing properly folded protein domains, thereby facilitating elevated local concentration, certain low complexity domains adopt cross-β interactions that are both structurally specific and labile to disassembly. These weakly tethered assemblies, we propose, are built to relay the passage of genetic information from one site to another within a cell, ensuring that the process is of extreme fidelity.
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Affiliation(s)
- Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9152, USA
| | - Steven L. McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9152, USA
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Alberti S, Carra S. Quality Control of Membraneless Organelles. J Mol Biol 2018; 430:4711-4729. [PMID: 29758260 DOI: 10.1016/j.jmb.2018.05.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023]
Abstract
The formation of membraneless organelles (MLOs) by phase separation has emerged as a new way of organizing the cytoplasm and nucleoplasm of cells. Examples of MLOs forming via phase separation are nucleoli in the nucleus and stress granules in the cytoplasm. The main components of these MLOs are macromolecules such as RNAs and proteins. In order to assemble by phase separation, these proteins and RNAs have to undergo many cooperative interactions. These cooperative interactions are supported by specific molecular features within phase-separating proteins, such as multivalency and the presence of disordered domains that promote weak and transient interactions. However, these features also predispose phase-separating proteins to aberrant behavior. Indeed, evidence is emerging for a strong link between phase-separating proteins, MLOs, and age-related diseases. In this review, we discuss recent progress in understanding the formation, properties, and functions of MLOs. We pay special attention to the emerging link between MLOs and age-related diseases, and we explain how changes in the composition and physical properties of MLOs promote their conversion into an aberrant state. Furthermore, we discuss the key role of the protein quality control machinery in regulating the properties and functions of MLOs and thus in preventing age-related diseases.
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Science, University of Modena and Reggio Emilia, Center for Neuroscience and Neurotechnology, 41125 Modena, Italy.
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Chuartzman SG, Schuldiner M. Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast. Yeast 2018; 35:477-483. [PMID: 29574976 PMCID: PMC6055851 DOI: 10.1002/yea.3312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/04/2018] [Accepted: 03/07/2018] [Indexed: 12/21/2022] Open
Abstract
In the last decade several collections of Saccharomyces cerevisiae yeast strains have been created. In these collections every gene is modified in a similar manner such as by a deletion or the addition of a protein tag. Such libraries have enabled a diversity of systematic screens, giving rise to large amounts of information regarding gene functions. However, often papers describing such screens focus on a single gene or a small set of genes and all other loci affecting the phenotype of choice (‘hits’) are only mentioned in tables that are provided as supplementary material and are often hard to retrieve or search. To help unify and make such data accessible, we have created a Database of High Throughput Screening Hits (dHITS). The dHITS database enables information to be obtained about screens in which genes of interest were found as well as the other genes that came up in that screen – all in a readily accessible and downloadable format. The ability to query large lists of genes at the same time provides a platform to easily analyse hits obtained from transcriptional analyses or other screens. We hope that this platform will serve as a tool to facilitate investigation of protein functions to the yeast community.
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Affiliation(s)
- Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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48
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Witherick J, Brady S. Update on muscle disease. J Neurol 2018; 265:1717-1725. [DOI: 10.1007/s00415-018-8856-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/30/2018] [Indexed: 12/24/2022]
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49
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Kemmerer K, Fischer S, Weigand JE. Auto- and cross-regulation of the hnRNPs D and DL. RNA (NEW YORK, N.Y.) 2018; 24:324-331. [PMID: 29263134 PMCID: PMC5824352 DOI: 10.1261/rna.063420.117] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/18/2017] [Indexed: 05/17/2023]
Abstract
HnRNP D, better known as AUF1, is an extensively studied protein that controls a variety of cellular pathways. Consequently, its expression has to be tightly regulated to prevent the onset of pathologies. In contrast, the cellular functions and regulation of its ubiquitously expressed paralog hnRNP DL are barely explored. Here, we present an intricate crosstalk between these two proteins. Both hnRNP D and DL are able to control their own expression by alternative splicing of cassette exons in their 3'UTRs. Exon inclusion produces mRNAs degraded by nonsense-mediated decay. Moreover, hnRNP D and DL control the expression of one another by the same mechanism. Thus, we identified two novel ways of how hnRNP D expression is controlled. The tight interconnection of expression control directly links hnRNP DL to hnRNP D-related diseases and emphasizes the importance of a systematic analysis of its cellular functions.
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Affiliation(s)
- Katrin Kemmerer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Sandra Fischer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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50
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Lee Y, Jonson PH, Sarparanta J, Palmio J, Sarkar M, Vihola A, Evilä A, Suominen T, Penttilä S, Savarese M, Johari M, Minot MC, Hilton-Jones D, Maddison P, Chinnery P, Reimann J, Kornblum C, Kraya T, Zierz S, Sue C, Goebel H, Azfer A, Ralston SH, Hackman P, Bucelli RC, Taylor JP, Weihl CC, Udd B. TIA1 variant drives myodegeneration in multisystem proteinopathy with SQSTM1 mutations. J Clin Invest 2018; 128:1164-1177. [PMID: 29457785 DOI: 10.1172/jci97103] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/09/2018] [Indexed: 12/14/2022] Open
Abstract
Multisystem proteinopathy (MSP) involves disturbances of stress granule (SG) dynamics and autophagic protein degradation that underlie the pathogenesis of a spectrum of degenerative diseases that affect muscle, brain, and bone. Specifically, identical mutations in the autophagic adaptor SQSTM1 can cause varied penetrance of 4 distinct phenotypes: amyotrophic lateral sclerosis (ALS), frontotemporal dementia, Paget's disease of the bone, and distal myopathy. It has been hypothesized that clinical pleiotropy relates to additional genetic determinants, but thus far, evidence has been lacking. Here, we provide evidence that a TIA1 (p.N357S) variant dictates a myodegenerative phenotype when inherited, along with a pathogenic SQSTM1 mutation. Experimentally, the TIA1-N357S variant significantly enhances liquid-liquid-phase separation in vitro and impairs SG dynamics in living cells. Depletion of SQSTM1 or the introduction of a mutant version of SQSTM1 similarly impairs SG dynamics. TIA1-N357S-persistent SGs have increased association with SQSTM1, accumulation of ubiquitin conjugates, and additional aggregated proteins. Synergistic expression of the TIA1-N357S variant and a SQSTM1-A390X mutation in myoblasts leads to impaired SG clearance and myotoxicity relative to control myoblasts. These findings demonstrate a pathogenic connection between SG homeostasis and ubiquitin-mediated autophagic degradation that drives the penetrance of an MSP phenotype.
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Affiliation(s)
- YouJin Lee
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Per Harald Jonson
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Jaakko Sarparanta
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Johanna Palmio
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Mohona Sarkar
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anna Vihola
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Anni Evilä
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Tiina Suominen
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Sini Penttilä
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Marco Savarese
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Mridul Johari
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Marie-Christine Minot
- Neuromuscular Competence Center, Centre Hospitalier Universitaire (CHU) de Rennes, Rennes, France
| | - David Hilton-Jones
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Paul Maddison
- Department of Neurology, University of Nottingham, Nottingham, United Kingdom
| | - Patrick Chinnery
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom.,Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - Jens Reimann
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
| | - Cornelia Kornblum
- Department of Neurology, University Hospital of Bonn, Bonn, Germany.,Centre for Rare Diseases Bonn (ZSEB), Department of Neurology, University Hospital of Bonn, Bonn, Germany
| | - Torsten Kraya
- Department of Neurology, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale, Germany
| | - Stephan Zierz
- Department of Neurology, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale, Germany
| | - Carolyn Sue
- Department of Neurogenetics, Kolling Institute of Medical Research, Royal North Shore Hospital and University of Sydney, St Leonard's, New South Wales, Australia
| | - Hans Goebel
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Asim Azfer
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, United Kingdom
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, United Kingdom
| | - Peter Hackman
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Robert C Bucelli
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Conrad C Weihl
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bjarne Udd
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland.,Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland.,Department of Neurology, Vaasa Central Hospital, Vaasa, Finland
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