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Jeng CJ, Fu SJ, You CY, Peng YJ, Hsiao CT, Chen TY, Tang CY. Defective Gating and Proteostasis of Human ClC-1 Chloride Channel: Molecular Pathophysiology of Myotonia Congenita. Front Neurol 2020; 11:76. [PMID: 32117034 PMCID: PMC7026490 DOI: 10.3389/fneur.2020.00076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/22/2020] [Indexed: 01/17/2023] Open
Abstract
The voltage-dependent ClC-1 chloride channel, whose open probability increases with membrane potential depolarization, belongs to the superfamily of CLC channels/transporters. ClC-1 is almost exclusively expressed in skeletal muscles and is essential for stabilizing the excitability of muscle membranes. Elucidation of the molecular structures of human ClC-1 and several CLC homologs provides important insight to the gating and ion permeation mechanisms of this chloride channel. Mutations in the human CLCN1 gene, which encodes the ClC-1 channel, are associated with a hereditary skeletal muscle disease, myotonia congenita. Most disease-causing CLCN1 mutations lead to loss-of-function phenotypes in the ClC-1 channel and thus increase membrane excitability in skeletal muscles, consequently manifesting as delayed relaxations following voluntary muscle contractions in myotonic subjects. The inheritance pattern of myotonia congenita can be autosomal dominant (Thomsen type) or recessive (Becker type). To date over 200 myotonia-associated ClC-1 mutations have been identified, which are scattered throughout the entire protein sequence. The dominant inheritance pattern of some myotonia mutations may be explained by a dominant-negative effect on ClC-1 channel gating. For many other myotonia mutations, however, no clear relationship can be established between the inheritance pattern and the location of the mutation in the ClC-1 protein. Emerging evidence indicates that the effects of some mutations may entail impaired ClC-1 protein homeostasis (proteostasis). Proteostasis of membrane proteins comprises of biogenesis at the endoplasmic reticulum (ER), trafficking to the surface membrane, and protein turn-over at the plasma membrane. Maintenance of proteostasis requires the coordination of a wide variety of different molecular chaperones and protein quality control factors. A number of regulatory molecules have recently been shown to contribute to post-translational modifications of ClC-1 and play critical roles in the ER quality control, membrane trafficking, and peripheral quality control of this chloride channel. Further illumination of the mechanisms of ClC-1 proteostasis network will enhance our understanding of the molecular pathophysiology of myotonia congenita, and may also bring to light novel therapeutic targets for skeletal muscle dysfunction caused by myotonia and other pathological conditions.
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Affiliation(s)
- Chung-Jiuan Jeng
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Ssu-Ju Fu
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Ying You
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Jheng Peng
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng-Tsung Hsiao
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tsung-Yu Chen
- Center for Neuroscience, University of California, Davis, Davis, CA, United States
| | - Chih-Yung Tang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan.,College of Medicine, Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan
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de Winter JM, Molenaar JP, Yuen M, van der Pijl R, Shen S, Conijn S, van de Locht M, Willigenburg M, Bogaards SJ, van Kleef ES, Lassche S, Persson M, Rassier DE, Sztal TE, Ruparelia AA, Oorschot V, Ramm G, Hall TE, Xiong Z, Johnson CN, Li F, Kiss B, Lozano-Vidal N, Boon RA, Marabita M, Nogara L, Blaauw B, Rodenburg RJ, Küsters B, Doorduin J, Beggs AH, Granzier H, Campbell K, Ma W, Irving T, Malfatti E, Romero NB, Bryson-Richardson RJ, van Engelen BG, Voermans NC, Ottenheijm CA. KBTBD13 is an actin-binding protein that modulates muscle kinetics. J Clin Invest 2020; 130:754-767. [PMID: 31671076 PMCID: PMC6994151 DOI: 10.1172/jci124000] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/24/2019] [Indexed: 11/17/2022] Open
Abstract
The mechanisms that modulate the kinetics of muscle relaxation are critically important for muscle function. A prime example of the impact of impaired relaxation kinetics is nemaline myopathy caused by mutations in KBTBD13 (NEM6). In addition to weakness, NEM6 patients have slow muscle relaxation, compromising contractility and daily life activities. The role of KBTBD13 in muscle is unknown, and the pathomechanism underlying NEM6 is undetermined. A combination of transcranial magnetic stimulation-induced muscle relaxation, muscle fiber- and sarcomere-contractility assays, low-angle x-ray diffraction, and superresolution microscopy revealed that the impaired muscle-relaxation kinetics in NEM6 patients are caused by structural changes in the thin filament, a sarcomeric microstructure. Using homology modeling and binding and contractility assays with recombinant KBTBD13, Kbtbd13-knockout and Kbtbd13R408C-knockin mouse models, and a GFP-labeled Kbtbd13-transgenic zebrafish model, we discovered that KBTBD13 binds to actin - a major constituent of the thin filament - and that mutations in KBTBD13 cause structural changes impairing muscle-relaxation kinetics. We propose that this actin-based impaired relaxation is central to NEM6 pathology.
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Affiliation(s)
| | - Joery P. Molenaar
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Neurology, Rijnstate Hospital, Arnhem, Netherlands
| | - Michaela Yuen
- Department of Physiology, Amsterdam University Medical Center, Netherlands
- Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Australia
| | - Robbert van der Pijl
- Department of Physiology, Amsterdam University Medical Center, Netherlands
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Shengyi Shen
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Stefan Conijn
- Department of Physiology, Amsterdam University Medical Center, Netherlands
| | | | - Menne Willigenburg
- Department of Physiology, Amsterdam University Medical Center, Netherlands
| | | | - Esmee S.B. van Kleef
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Saskia Lassche
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Malin Persson
- Department of Kinesiology and Physical Education, McGill University, Montreal, Canada
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Dilson E. Rassier
- Department of Kinesiology and Physical Education, McGill University, Montreal, Canada
| | - Tamar E. Sztal
- School of Biological Sciences, Monash University, Melbourne, Australia
| | | | - Viola Oorschot
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Melbourne, Australia
| | - Georg Ramm
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Melbourne, Australia
- Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Thomas E. Hall
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Zherui Xiong
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Christopher N. Johnson
- Division of Clinical Pharmacology, Center for Arrhythmia Research and Therapeutics and Center for Structural Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Frank Li
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Balazs Kiss
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | | | - Reinier A. Boon
- Department of Physiology, Amsterdam University Medical Center, Netherlands
| | - Manuela Marabita
- Venetian Institute of Molecular Medicine, Department of Biomedical Sciences, University of Padova, Italy
| | - Leonardo Nogara
- Venetian Institute of Molecular Medicine, Department of Biomedical Sciences, University of Padova, Italy
| | - Bert Blaauw
- Venetian Institute of Molecular Medicine, Department of Biomedical Sciences, University of Padova, Italy
| | - Richard J. Rodenburg
- Department of Pediatrics, Radboud University Medical Centre, Translational Metabolic Laboratory, Nijmegen, Netherlands
| | - Benno Küsters
- Department of Pathology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jonne Doorduin
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Ken Campbell
- Department of Physiology and Division of Cardiovascular Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Weikang Ma
- BioCAT, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Thomas Irving
- BioCAT, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Edoardo Malfatti
- Service Neurologie Médicale, Centre de Référence Maladies Neuromusculaire Paris-Nord CHU Raymond-Poincaré, U1179 UVSQ-INSERM Handicap Neuromusculaire: Physiologie, Biothérapie et Pharmacologie Appliquées, UFR des Sciences de la Santé Simone Veil, Université Versailles-Saint-Quentin-en-Yvelines, Garches, France
| | - Norma B. Romero
- Sorbonne Université, Myology Institute, Neuromuscular Morphology Unit, Center for Research in Myology, GH Pitié-Salpêtrière Paris, France
- Centre de Référence de Pathologie Neuromusculaire Paris-Est, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Baziel G.M. van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicol C. Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Coen A.C. Ottenheijm
- Department of Physiology, Amsterdam University Medical Center, Netherlands
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
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Barbato M, Hailer F, Upadhyay M, Del Corvo M, Colli L, Negrini R, Kim ES, Crooijmans RPMA, Sonstegard T, Ajmone-Marsan P. Adaptive introgression from indicine cattle into white cattle breeds from Central Italy. Sci Rep 2020; 10:1279. [PMID: 31992729 PMCID: PMC6987186 DOI: 10.1038/s41598-020-57880-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/26/2019] [Indexed: 11/19/2022] Open
Abstract
Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.
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Affiliation(s)
- Mario Barbato
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcello Del Corvo
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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54
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Regulation of Stem Cells by Cullin-RING Ligase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:79-98. [PMID: 31898223 DOI: 10.1007/978-981-15-1025-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stem cells can remain quiescent, self-renewal, and differentiate into many types of cells and even cancer stem cells. The coordination of these complex processes maintains the homeostasis of the organism. Ubiquitination is an important posttranslational modification process that regulates protein stability and activity. The ubiquitination levels of stem cell-associated proteins are closely related with stem cell characteristics. Cullin-RING Ligases (CRLs) are the largest family of E3 ubiquitin ligases, accounting for approximately 20% of proteins degraded by proteasome. In this review, we discuss the role of CRLs in stem cell homeostasis, self-renewal, and differentiation and expound their ubiquitination substrates. In addition, we also discuss the effect of CRLs on the formation of cancer stem cells that may provide promising therapy strategies for cancer.
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55
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Bolling MC, Jonkman MF. KLHL24: Beyond Skin Fragility. J Invest Dermatol 2019; 139:22-24. [PMID: 30579426 DOI: 10.1016/j.jid.2018.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 02/05/2023]
Abstract
KLHL24 mutations have recently been associated with epidermolysis bullosa simplex. Initial studies focused on skin fragility. However, the picture of KLHL24 mutations causing extracutaneous human disease is emerging, with dilated cardiomyopathy as a strong association. In addition, neurological disease is suspected as well. Careful clinical follow-up and functional studies of (mutated) KLHL24 in these tissues are needed.
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Affiliation(s)
- Maria C Bolling
- University of Groningen, University Medical Center Groningen, Department of Dermatology, Center for Blistering Diseases, Groningen, The Netherlands
| | - Marcel F Jonkman
- University of Groningen, University Medical Center Groningen, Department of Dermatology, Center for Blistering Diseases, Groningen, The Netherlands.
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56
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Previtali SC, Zhao E, Lazarevic D, Pipitone GB, Fabrizi GM, Manganelli F, Mazzeo A, Pareyson D, Schenone A, Taroni F, Vita G, Bellone E, Ferrarini M, Garibaldi M, Magri S, Padua L, Pennisi E, Pisciotta C, Riva N, Scaioli V, Scarlato M, Tozza S, Geroldi A, Jordanova A, Ferrari M, Molineris I, Reilly MM, Comi G, Carrera P, Devoto M, Bolino A. Expanding the spectrum of genes responsible for hereditary motor neuropathies. J Neurol Neurosurg Psychiatry 2019; 90:1171-1179. [PMID: 31167812 DOI: 10.1136/jnnp-2019-320717] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/24/2019] [Accepted: 05/17/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inherited peripheral neuropathies (IPNs) represent a broad group of genetically and clinically heterogeneous disorders, including axonal Charcot-Marie-Tooth type 2 (CMT2) and hereditary motor neuropathy (HMN). Approximately 60%-70% of cases with HMN/CMT2 still remain without a genetic diagnosis. Interestingly, mutations in HMN/CMT2 genes may also be responsible for motor neuron disorders or other neuromuscular diseases, suggesting a broad phenotypic spectrum of clinically and genetically related conditions. Thus, it is of paramount importance to identify novel causative variants in HMN/CMT2 patients to better predict clinical outcome and progression. METHODS We designed a collaborative study for the identification of variants responsible for HMN/CMT2. We collected 15 HMN/CMT2 families with evidence for autosomal recessive inheritance, who had tested negative for mutations in 94 known IPN genes, who underwent whole-exome sequencing (WES) analyses. Candidate genes identified by WES were sequenced in an additional cohort of 167 familial or sporadic HMN/CMT2 patients using next-generation sequencing (NGS) panel analysis. RESULTS Bioinformatic analyses led to the identification of novel or very rare variants in genes, which have not been previously associated with HMN/CMT2 (ARHGEF28, KBTBD13, AGRN and GNE); in genes previously associated with HMN/CMT2 but in combination with different clinical phenotypes (VRK1 and PNKP), and in the SIGMAR1 gene, which has been linked to HMN/CMT2 in only a few cases. These findings were further validated by Sanger sequencing, segregation analyses and functional studies. CONCLUSIONS These results demonstrate the broad spectrum of clinical phenotypes that can be associated with a specific disease gene, as well as the complexity of the pathogenesis of neuromuscular disorders.
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Affiliation(s)
- Stefano C Previtali
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Edward Zhao
- Division of Genetics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dejan Lazarevic
- Center for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Giovanni Battista Pipitone
- Laboratory of Clinical and Molecular Biology and Unit of Genomics for Diagnosis of Genetic Diseases, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Gian Maria Fabrizi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Fiore Manganelli
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Napoli, Italy
| | - Anna Mazzeo
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Davide Pareyson
- Unit of Rare Neurodegenerative and Neurometabolic Diseases, Department of Clinical Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Angelo Schenone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal Infantile Sciences, University of Genoa, and IRCCS Policlinico San Martino, Genova, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Giuseppe Vita
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Emilia Bellone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal Infantile Sciences, University of Genoa, and IRCCS Policlinico San Martino, Genova, Italy
| | - Moreno Ferrarini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Matteo Garibaldi
- Unit of Neuromuscular Disorders, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sapienza University of Rome, Sant'Andrea Hospital, Roma, Italy
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Luca Padua
- Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica, Roma, Italy
| | | | - Chiara Pisciotta
- Unit of Rare Neurodegenerative and Neurometabolic Diseases, Department of Clinical Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Nilo Riva
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Vidmer Scaioli
- Neurophysiopathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Marina Scarlato
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Stefano Tozza
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Napoli, Italy
| | - Alessandro Geroldi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal Infantile Sciences, University of Genoa, and IRCCS Policlinico San Martino, Genova, Italy
| | - Albena Jordanova
- VIB-UAntwerp Center for Molecular Neurology, Antwerp, Belgium
- Department of Medical Chemistry and Biochemistry, Medical University-Sofia, Sofia, Bulgaria
| | - Maurizio Ferrari
- Laboratory of Clinical and Molecular Biology and Unit of Genomics for Diagnosis of Genetic Diseases, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ivan Molineris
- Center for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Giancarlo Comi
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Paola Carrera
- Laboratory of Clinical and Molecular Biology and Unit of Genomics for Diagnosis of Genetic Diseases, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Marcella Devoto
- Division of Genetics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Translational and Precision Medicine, University La Sapienza, Roma, Italy
| | - Alessandra Bolino
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
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57
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Kelch-like proteins: Physiological functions and relationships with diseases. Pharmacol Res 2019; 148:104404. [DOI: 10.1016/j.phrs.2019.104404] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023]
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58
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Martín-Pardillos A, Cajal SRY. Characterization of Kelch domain-containing protein 7B in breast tumours and breast cancer cell lines. Oncol Lett 2019; 18:2853-2860. [PMID: 31452764 PMCID: PMC6704290 DOI: 10.3892/ol.2019.10672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/29/2019] [Indexed: 12/24/2022] Open
Abstract
Adenocarcinomas exhibit great heterogeneity, with many genetic and epigenetic alterations. The Kelch domain-containing protein 7B (KLHDC7B) has recently been identified as epigenetically modified and upregulated in breast cancer. The potential reversibility of epigenetic states offers exciting possibilities for novel cancer diagnostics and drugs. However, to properly evaluate specific inhibitors, the role of KLHDC7B in the development and progression of breast cancer should be established. With that objective in mind, the present study investigated a series of human breast tumours and correlated their clinicopathology, according to the Elston-Ellis modification of the Scarff-Bloom-Richardson (SBR) grading system, with KLHDC7B mRNA expression, analysed using quantitative PCR (qPCR). The results revealed that KLHDC7B was significantly upregulated in grade 3 tumours, and that KLHDC7B expression varied according to the tumour grade and the individual, being downregulated in well-differentiated and moderately-differentiated tumours (grade 1–2) and upregulated in poorly-differentiated tumours (grade 3). Immunohistochemical staining revealed that ductal tumours and tumours with a higher percentage of Ki67 positive cells showed the highest levels of KLHDC7B. Receptor expression, HER, p53 status, presence of metastasis, and vascular invasion showed no association with KLHDC7B expression. Previous studies have proposed KLHDC7B as an epigenetic marker of breast cancer. We propose that KLHDC7B should be used as a marker for poorly-differentiated tumours only; use of KLHDC7B without considering tumour grade could lead to an inaccurate diagnosis. Finally, we suggest the appropriate breast cancer cell lines to use to determine the functions of KLHDC7B. KLHDC7B expression was tested in the non-tumour cell line MCF-10A and in the breast cancer cell lines MCF-7, MDA-MB-231 and MDA-MB-468, using qPCR and western blotting. The results revealed that all tested cancer cell lines overexpressed KLHDC7B mRNA, but MDA-MB-468 exhibited a much lower level of protein expression relative to mRNA. Although the breast cancer cell lines used may be appropriate for studying KLHDC7B epigenetic status, MDA-MB-468 should be excluded from functional experiments.
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Affiliation(s)
- Ana Martín-Pardillos
- Translational Molecular Pathology Group, Oncology Department, Vall d'Hebron Institut de Recerca, Edificio Collserola, Hospital Vall d'Hebron, 08035 Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, 28029 Madrid, Spain
| | - Santiago Ramón Y Cajal
- Translational Molecular Pathology Group, Oncology Department, Vall d'Hebron Institut de Recerca, Edificio Collserola, Hospital Vall d'Hebron, 08035 Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, 28029 Madrid, Spain.,Hospital Vall d'Hebron, Anatomical Pathology Department, 08035 Barcelona, Spain
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Coppée R, Jeffares DC, Miteva MA, Sabbagh A, Clain J. Comparative structural and evolutionary analyses predict functional sites in the artemisinin resistance malaria protein K13. Sci Rep 2019; 9:10675. [PMID: 31337835 PMCID: PMC6650413 DOI: 10.1038/s41598-019-47034-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/03/2019] [Indexed: 01/31/2023] Open
Abstract
Numerous mutations in the Plasmodium falciparum Kelch13 (K13) protein confer resistance to artemisinin derivatives, the current front-line antimalarial drugs. K13 is an essential protein that contains BTB and Kelch-repeat propeller (KREP) domains usually found in E3 ubiquitin ligase complexes that target substrate protein(s) for ubiquitin-dependent degradation. K13 is thought to bind substrate proteins, but its functional/interaction sites and the structural alterations associated with artemisinin resistance mutations remain unknown. Here, we screened for the most evolutionarily conserved sites in the protein structure of K13 as indicators of structural and/or functional constraints. We inferred structure-dependent substitution rates at each amino acid site of the highly conserved K13 protein during the evolution of Apicomplexa parasites. We found two solvent-exposed patches of extraordinarily conserved sites likely involved in protein-protein interactions, one in BTB and the other one in KREP. The conserved patch in K13 KREP overlaps with a shallow pocket that displays a differential electrostatic surface potential, relative to neighboring sites, and that is rich in serine and arginine residues. Comparative structural and evolutionary analyses revealed that these properties were also found in the functionally-validated shallow pocket of other KREPs including that of the cancer-related KEAP1 protein. Finally, molecular dynamics simulations carried out on PfK13 R539T and C580Y artemisinin resistance mutant structures revealed some local structural destabilization of KREP but not in its shallow pocket. These findings open new avenues of research on one of the most enigmatic malaria proteins with the utmost clinical importance.
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Affiliation(s)
- Romain Coppée
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | - Daniel C Jeffares
- Department of Biology and York Biomedical Research Institute, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Maria A Miteva
- Université de Paris, Inserm U1268 MCTR, CiTCom UMR 8038 CNRS, Paris, France
| | - Audrey Sabbagh
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France.
| | - Jérôme Clain
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France. .,Centre National de Référence du Paludisme, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, F-75018 Paris, France.
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60
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Abstract
Nemaline myopathy (NM) is among the most common non-dystrophic congenital myopathies (incidence 1:50.000). Hallmark features of NM are skeletal muscle weakness and the presence of nemaline bodies in the muscle fiber. The clinical phenotype of NM patients is quite diverse, ranging from neonatal death to normal lifespan with almost normal motor function. As the respiratory muscles are involved as well, severely affected patients are ventilator-dependent. The mechanisms underlying muscle weakness in NM are currently poorly understood. Therefore, no therapeutic treatment is available yet. Eleven implicated genes have been identified: ten genes encode proteins that are either components of thin filament, or are thought to contribute to stability or turnover of thin filament proteins. The thin filament is a major constituent of the sarcomere, the smallest contractile unit in muscle. It is at this level of contraction – thin-thick filament interaction – where muscle weakness originates in NM patients. This review focusses on how sarcomeric gene mutations directly compromise sarcomere function in NM. Insight into the contribution of sarcomeric dysfunction to muscle weakness in NM, across the genes involved, will direct towards the development of targeted therapeutic strategies.
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Affiliation(s)
| | - Coen A.C. Ottenheijm
- Correspondence to: Coen Ottenheijm, PhD, Department of Physiology, VU University Medical Center, O|2 building, 12W-51, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands. Tel.: +31 20 4448123; Fax: +31 20 4448124; E-mail:
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61
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dos Santos Silva DB, Fonseca LFS, Pinheiro DG, Muniz MMM, Magalhães AFB, Baldi F, Ferro JA, Chardulo LAL, de Albuquerque LG. Prediction of hub genes associated with intramuscular fat content in Nelore cattle. BMC Genomics 2019; 20:520. [PMID: 31238883 PMCID: PMC6591902 DOI: 10.1186/s12864-019-5904-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 06/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed genes (DEGs) associated with intramuscular fat content. RESULTS A total of 30 transcriptomics datasets (RNA-Seq) obtained from longissimus thoracis muscle were selected based on the phenotypic value of divergent intramuscular fat content: 15 with the highest intramuscular fat content (HIF) and 15 with the lowest intramuscular fat content (LIF). The transcriptomics datasets were aligned with a reference genome and 65 differentially expressed genes (DEGs) were identified, including 21 upregulated and 44 downregulated genes in HIF animals. The normalized count data from DEGs was then used for co-expression network construction. From the co-expression network, four modules were identified. The topological properties of the network were analyzed; those genes engaging in the most interactions (maximal clique centrality method) with other DEGs were predicted to be hub genes (PDE4D, KLHL30 and IL1RAP), which consequently may play a role in cellular and/or systemic lipid biology in Nelore cattle. Top modules screened from the gene co-expression network were identify. The two candidate modules had clear associated biological pathways related to fat development, cell adhesion, and muscle differentiation, immune system, among others. The hub genes belonged in top modules and were downregulated in HIF animals. PDE4D and IL1RAP have known effects on lipid metabolism and the immune system through the regulation of cAMP signaling. Given that cAMP is known to play a role in lipid systems, PDE4D and IL1RAP downregulation may contribute to increased levels of intracellular cAMP and thus may have effects on IF content differences in Nelore cattle. KLHL30 may have effects on muscle metabolism. Klhl protein families play a role in protein degradation. However, the downregulation of this gene and its role in lipid metabolism has not yet been clarified. CONCLUSIONS The results reported in this study indicate candidate genes and molecular mechanisms involved in IF content difference in Nelore cattle.
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Affiliation(s)
- Danielly Beraldo dos Santos Silva
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
- National Council for Scientific and Technological Development (CNPq), Brasilia, DF Brazil
| | - Larissa Fernanda Simielli Fonseca
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
- National Council for Scientific and Technological Development (CNPq), Brasilia, DF Brazil
| | - Daniel Guariz Pinheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | | | | | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
- National Council for Scientific and Technological Development (CNPq), Brasilia, DF Brazil
| | - Jesus Aparecido Ferro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
- National Council for Scientific and Technological Development (CNPq), Brasilia, DF Brazil
| | | | - Lucia Galvão de Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
- National Council for Scientific and Technological Development (CNPq), Brasilia, DF Brazil
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62
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Sewry CA, Laitila JM, Wallgren-Pettersson C. Nemaline myopathies: a current view. J Muscle Res Cell Motil 2019; 40:111-126. [PMID: 31228046 PMCID: PMC6726674 DOI: 10.1007/s10974-019-09519-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
Abstract
Nemaline myopathies are a heterogenous group of congenital myopathies caused by de novo, dominantly or recessively inherited mutations in at least twelve genes. The genes encoding skeletal α-actin (ACTA1) and nebulin (NEB) are the commonest genetic cause. Most patients have congenital onset characterized by muscle weakness and hypotonia, but the spectrum of clinical phenotypes is broad, ranging from severe neonatal presentations to onset of a milder disorder in childhood. Most patients with adult onset have an autoimmune-related myopathy with a progressive course. The wide application of massively parallel sequencing methods is increasing the number of known causative genes and broadening the range of clinical phenotypes. Nemaline myopathies are identified by the presence of structures that are rod-like or ovoid in shape with electron microscopy, and with light microscopy stain red with the modified Gömöri trichrome technique. These rods or nemaline bodies are derived from Z lines (also known as Z discs or Z disks) and have a similar lattice structure and protein content. Their shape in patients with mutations in KLHL40 and LMOD3 is distinctive and can be useful for diagnosis. The number and distribution of nemaline bodies varies between fibres and different muscles but does not correlate with severity or prognosis. Additional pathological features such as caps, cores and fibre type disproportion are associated with the same genes as those known to cause the presence of rods. Animal models are advancing the understanding of the effects of various mutations in different genes and paving the way for the development of therapies, which at present only manage symptoms and are aimed at maintaining muscle strength, joint mobility, ambulation, respiration and independence in the activities of daily living.
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Affiliation(s)
- Caroline A Sewry
- Dubowitz Neuromuscular Centre, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London, WC1N 1EH, UK. .,Wolfson Centre of Inherited Neuromuscular Disorders, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK.
| | - Jenni M Laitila
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
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63
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Shaping Striated Muscles with Ubiquitin Proteasome System in Health and Disease. Trends Mol Med 2019; 25:760-774. [PMID: 31235369 DOI: 10.1016/j.molmed.2019.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 02/06/2023]
Abstract
For long-lived contractile cells, such as striated muscle cells, maintaining proteome integrity is a challenging task. These cells require hundreds of components that must be properly synthesized, folded, and incorporated into the basic contractile unit, the sarcomere. Muscle protein quality control in cells is mainly guaranteed by the ubiquitin-proteasome system (UPS), the lysosome-autophagy system, and various molecular chaperones. Recent studies establish the concept of dedicated UPS in the regulation of sarcomere assembly during development and in adult life to maintain the intricate and interwoven organization of protein complexes in muscle. Failure of sarcomere protein quality control often represents the basis of severe myopathies and cardiomyopathies in human, further highlighting its importance in producing and maintaining the contractile machinery of muscle cells in shape.
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64
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Arora R, S. NK, S. S, Fairoze MN, Kaur M, Sharma A, Girdhar Y, M. SR, Devatkal SK, Ahlawat S, Vijh RK, S. MS. Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India. PLoS One 2019; 14:e0217461. [PMID: 31170190 PMCID: PMC6553717 DOI: 10.1371/journal.pone.0217461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 05/13/2019] [Indexed: 12/16/2022] Open
Abstract
This study describes the muscle transcriptome profile of Bandur breed, a consumer favoured, meat type sheep of India. The transcriptome was compared to the less desirable, unregistered local sheep population, in order to understand the molecular factors related to muscle traits in Indian sheep breeds. Bandur sheep have tender muscles and higher backfat thickness than local sheep. The longissimus thoracis transcriptome profiles of Bandur and local sheep were obtained using RNA sequencing (RNA Seq). The animals were male, non-castrated, with uniform age and reared under similar environment, as well as management conditions. We could identify 568 significantly up-regulated and 538 significantly down-regulated genes in Bandur sheep (p≤0.05). Among these, 181 up-regulated and 142 down-regulated genes in Bandur sheep, with a fold change ≥1.5, were considered for further analysis. Significant Gene Ontology terms for the up-regulated dataset in Bandur sheep included transporter activity, substrate specific transmembrane, lipid and fatty acid binding. The down-regulated activities in Bandur sheep were mainly related to RNA degradation, regulation of ERK1 and ERK2 cascades and innate immune response. The MAPK signaling pathway, Adipocytokine signaling pathway and PPAR signaling pathway were enriched for Bandur sheep. The highly connected genes identified by network analysis were CNOT2, CNOT6, HSPB1, HSPA6, MAP3K14 and PPARD, which may be important regulators of energy metabolism, cellular stress and fatty acid metabolism in the skeletal muscles. These key genes affect the CCR4-NOT complex, PPAR and MAPK signaling pathways. The highly connected genes identified in this study, form interesting candidates for further research on muscle traits in Bandur sheep.
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Affiliation(s)
- Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- * E-mail:
| | - Naveen Kumar S.
- Karnataka Veterinary Animal and Fisheries Sciences University, Bangalore, Karnataka, India
| | - Sudarshan S.
- Karnataka Veterinary Animal and Fisheries Sciences University, Bangalore, Karnataka, India
| | - Mohamed Nadeem Fairoze
- Karnataka Veterinary Animal and Fisheries Sciences University, Bangalore, Karnataka, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Anju Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Yashila Girdhar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Sreesujatha R. M.
- Karnataka Veterinary Animal and Fisheries Sciences University, Bangalore, Karnataka, India
| | | | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manjunatha S. S.
- Karnataka Veterinary Animal and Fisheries Sciences University, Bangalore, Karnataka, India
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65
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Blondelle J, Tallapaka K, Seto JT, Ghassemian M, Clark M, Laitila JM, Bournazos A, Singer JD, Lange S. Cullin-3 dependent deregulation of ACTN1 represents a new pathogenic mechanism in nemaline myopathy. JCI Insight 2019; 5:125665. [PMID: 30990797 PMCID: PMC6542616 DOI: 10.1172/jci.insight.125665] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/11/2019] [Indexed: 12/11/2022] Open
Abstract
Nemaline myopathy is a congenital neuromuscular disorder characterized by muscle weakness, fiber atrophy and presence of nemaline bodies within myofibers. However, the understanding of underlying pathomechanisms is lacking. Recently, mutations in KBTBD13, KLHL40 and KLHL41, three substrate adaptors for the E3-ubiquitin ligase Cullin-3, have been associated with early-onset nemaline myopathies. We hypothesized that deregulation of Cullin-3 and its muscle protein substrates may be responsible for the disease development. Using Cullin-3 knockout mice, we identified accumulation of non-muscle alpha-Actinins (ACTN1 and ACTN4) in muscles of these mice, which we also observed in KBTBD13 patients. Our data reveal that proper regulation of Cullin-3 activity and ACTN1 levels is essential for normal muscle and neuromuscular junction development. While ACTN1 is naturally downregulated during myogenesis, its overexpression in C2C12 myoblasts triggered defects in fusion, myogenesis and acetylcholine receptor clustering; features that we characterized in Cullin-3 deficient mice. Taken together, our data highlight the importance for Cullin-3 mediated degradation of ACTN1 for muscle development, and indicate a new pathomechanism for the etiology of myopathies seen in Cullin-3 knockout mice and nemaline myopathy patients.
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Affiliation(s)
- Jordan Blondelle
- Division of Cardiology, School of Medicine, UCSD, La Jolla, California, USA
| | - Kavya Tallapaka
- Division of Cardiology, School of Medicine, UCSD, La Jolla, California, USA
| | - Jane T. Seto
- Neuromuscular Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Majid Ghassemian
- Department of Chemistry and Biochemistry. UCSD, La Jolla, California, USA
| | - Madison Clark
- Division of Cardiology, School of Medicine, UCSD, La Jolla, California, USA
| | - Jenni M. Laitila
- Folkhälsan Research Center and Medicum, University of Helsinki, Helsinki, Finland
| | - Adam Bournazos
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Jeffrey D. Singer
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Stephan Lange
- Division of Cardiology, School of Medicine, UCSD, La Jolla, California, USA
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
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66
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Norman GL, Reig A, Viñas O, Mahler M, Wunsch E, Milkiewicz P, Swain MG, Mason A, Stinton LM, Aparicio MB, Aldegunde MJ, Fritzler MJ, Parés A. The Prevalence of Anti-Hexokinase-1 and Anti-Kelch-Like 12 Peptide Antibodies in Patients With Primary Biliary Cholangitis Is Similar in Europe and North America: A Large International, Multi-Center Study. Front Immunol 2019; 10:662. [PMID: 31001269 PMCID: PMC6456688 DOI: 10.3389/fimmu.2019.00662] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
Primary biliary cholangitis (PBC), formerly known as primary biliary cirrhosis, is present worldwide. Autoantibodies, in particular anti-mitochondrial antibodies (AMA) detected by indirect immunofluorescence assays or newer solid phase immunoassays can detect most, but not all individuals with PBC. Detection of antibodies to the anti-nuclear antigens sp100 and gp210 can identify additional PBC patients, but some seronegative patients remain, often resulting in delayed diagnosis and treatment. Antibodies to kelch-like 12 (KLHL12) and hexokinase 1 (HK-1) were recently identified as new biomarkers for PBC and notably identify patients who are negative for conventional autoantibodies. To become globally adopted, it is important to validate these new biomarkers in different geographic areas. In the present study we evaluated the prevalence of anti-KLHL12 (measured by a KLHL12-derived peptide referred to as KL-p) and anti-HK-1 antibodies by ELISA at five sites within Europe and North America and demonstrated the presence of these antibodies in patients with PBC in all geographies.
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Affiliation(s)
- Gary L Norman
- Department of Research and Development, Inova Diagnostics, San Diego, CA, United States
| | - Anna Reig
- Liver Unit, Hospital Clínic, Institut D'Investigacions Biomèdiques August Pi i Sunyer, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Odette Viñas
- Immunology Department, Hospital Clínic, Centre Diagnòstic Biomèdic, Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Michael Mahler
- Department of Research and Development, Inova Diagnostics, San Diego, CA, United States
| | - Ewa Wunsch
- Translational Medicine Group, Pomeranian Medicine University, Szczecin, Poland
| | - Piotr Milkiewicz
- Translational Medicine Group, Pomeranian Medicine University, Szczecin, Poland.,Liver and Internal Medicine Unit, Department General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Mark G Swain
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Andrew Mason
- Division of Gastroenterology (Liver Unit), University of Alberta, Edmonton, AB, Canada
| | - Laura M Stinton
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Maria Belen Aparicio
- Laboratorio Autoimmunidad, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Maria Jose Aldegunde
- Laboratorio Autoimmunidad, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Marvin J Fritzler
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Albert Parés
- Liver Unit, Hospital Clínic, Institut D'Investigacions Biomèdiques August Pi i Sunyer, CIBERehd, University of Barcelona, Barcelona, Spain
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67
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Abstract
The congenital myopathies form a large clinically and genetically heterogeneous group of disorders. Currently mutations in at least 27 different genes have been reported to cause a congenital myopathy, but the number is expected to increase due to the accelerated use of next-generation sequencing methods. There is substantial overlap between the causative genes and the clinical and histopathologic features of the congenital myopathies. The mode of inheritance can be autosomal recessive, autosomal dominant or X-linked. Both dominant and recessive mutations in the same gene can cause a similar disease phenotype, and the same clinical phenotype can also be caused by mutations in different genes. Clear genotype-phenotype correlations are few and far between.
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Affiliation(s)
- Katarina Pelin
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; The Folkhälsan Institute of Genetics, Folkhälsan Research Center, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
| | - Carina Wallgren-Pettersson
- The Folkhälsan Institute of Genetics, Folkhälsan Research Center, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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68
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Narahara S, Sakai E, Kadowaki T, Yamaguchi Y, Narahara H, Okamoto K, Asahina I, Tsukuba T. KBTBD11, a novel BTB-Kelch protein, is a negative regulator of osteoclastogenesis through controlling Cullin3-mediated ubiquitination of NFATc1. Sci Rep 2019; 9:3523. [PMID: 30837587 PMCID: PMC6401029 DOI: 10.1038/s41598-019-40240-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/12/2019] [Indexed: 01/10/2023] Open
Abstract
Kelch repeat and BTB domain-containing protein 11 (KBTBD11) is a member of the KBTBD subfamily of proteins that possess a BTB domain and Kelch repeats. Despite the presence of the Kbtbd11 gene in mammalian genomes, there are few reports about KBTBD11 at present. In this study, we identified the novel protein KBTBD11 as a negative regulator of osteoclast differentiation. We found that expression of KBTBD11 increased during osteoclastogenesis. Small-interfering-RNA-mediated knockdown of KBTBD11 enhanced osteoclast formation, and markedly increased the expression of several osteoclast marker genes compared with control cells. Conversely, KBTBD11 overexpression impaired osteoclast differentiation, and decreased the expression of osteoclast marker genes. Among six major signaling pathways regulating osteoclast differentiation, KBTBD11 predominantly influenced the nuclear factor of activated T cell cytoplasmic-1 (NFATc1) pathway. Mechanistically, KBTBD11 was found to interact with an E3 ubiquitin ligase, Cullin3. Further experiments involving immunoprecipitation and treatment with MG132, a proteasome inhibitor, showed that the KBTBD11–Cullin3 promotes ubiquitination and degradation of NFATc1 by the proteasome. Considering that NFATc1 is an essential factor for osteoclast differentiation, the KBTBD11 and Cullin3 probably regulate the levels of NFATc1 through the ubiquitin-proteasome degradation system. Thus, KBTBD11 negatively modulates osteoclast differentiation by controlling Cullin3-mediated ubiquitination of NFATc1.
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Affiliation(s)
- Shun Narahara
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan.,Department of Regenerative Oral Surgery, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan
| | - Eiko Sakai
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan
| | - Tomoko Kadowaki
- Department of Frontier Life Science, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan
| | - Yu Yamaguchi
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan
| | - Haruna Narahara
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan
| | - Kuniaki Okamoto
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan.,Department of Dental Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8525, Japan
| | - Izumi Asahina
- Department of Regenerative Oral Surgery, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan
| | - Takayuki Tsukuba
- Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8588, Japan.
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69
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Beltrán-Anaya FO, Romero-Córdoba S, Rebollar-Vega R, Arrieta O, Bautista-Piña V, Dominguez-Reyes C, Villegas-Carlos F, Tenorio-Torres A, Alfaro-Riuz L, Jiménez-Morales S, Cedro-Tanda A, Ríos-Romero M, Reyes-Grajeda JP, Tagliabue E, Iorio MV, Hidalgo-Miranda A. Expression of long non-coding RNA ENSG00000226738 (LncKLHDC7B) is enriched in the immunomodulatory triple-negative breast cancer subtype and its alteration promotes cell migration, invasion, and resistance to cell death. Mol Oncol 2019; 13:909-927. [PMID: 30648789 PMCID: PMC6441920 DOI: 10.1002/1878-0261.12446] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/29/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022] Open
Abstract
Triple negative breast cancer (TNBC) represents an aggressive phenotype with poor prognosis compared with ER, PR, and HER2‐positive tumors. TNBC is a heterogeneous disease, and gene expression analysis has identified seven molecular subtypes. Accumulating evidence demonstrates that long non‐coding RNA (lncRNA) are involved in regulation of gene expression and cancer biology, contributing to essential cancer cell functions. In this study, we analyzed the expression profile of lncRNA in TNBC subtypes from 156 TNBC samples, and then characterized the functional role of LncKLHDC7B (ENSG00000226738). A total of 710 lncRNA were found to be differentially expressed between TNBC subtypes, and a subset of these altered lncRNA were independently validated. We discovered that LncKLHDC7B (ENSG00000226738) acts as a transcriptional modulator of its neighboring coding gene KLHDC7B in the immunomodulatory subtype. Furthermore, LncKLHDC7B knockdown enhanced migration and invasion, and promoted resistance to cellular death. Our findings confirmed the contribution of LncKLHDC7B to induction of apoptosis and inhibition of cell migration and invasion, suggesting that TNBC tumors with enrichment of LncKLHDC7B may exhibit distinct regulatory activity, or that this may be a generalized process in breast cancer. Additionally, in silico analysis confirmed for the first time that the low expression of KLHDC7B and LncKLHDC7B is associated with poor prognosis in patients with breast cancer.
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Affiliation(s)
- Fredy Omar Beltrán-Anaya
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Sandra Romero-Córdoba
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Department of Experimental Oncology and Molecular Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Rosa Rebollar-Vega
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | | | | | | | - Luis Alfaro-Riuz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Alberto Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Magdalena Ríos-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Elda Tagliabue
- Department of Experimental Oncology and Molecular Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Marilena V Iorio
- Department of Experimental Oncology and Molecular Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Hudson AM, Mannix KM, Gerdes JA, Kottemann MC, Cooley L. Targeted substrate degradation by Kelch controls the actin cytoskeleton during ring canal expansion. Development 2019; 146:dev.169219. [PMID: 30559276 DOI: 10.1242/dev.169219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/27/2018] [Indexed: 11/20/2022]
Abstract
During Drosophila oogenesis, specialized actin-based structures called ring canals form and expand to accommodate growth of the oocyte. Previous work demonstrated that Kelch and Cullin 3 function together in a Cullin 3-RING ubiquitin ligase complex (CRL3Kelch) to organize the ring canal cytoskeleton, presumably by targeting a substrate for proteolysis. Here, we use tandem affinity purification followed by mass spectrometry to identify HtsRC as the CRL3Kelch ring canal substrate. CRISPR-mediated mutagenesis of HtsRC revealed its requirement in the recruitment of the ring canal F-actin cytoskeleton. We present genetic evidence consistent with HtsRC being the CRL3Kelch substrate, as well as biochemical evidence indicating that HtsRC is ubiquitylated and degraded by the proteasome. Finally, we identify a short sequence motif in HtsRC that is necessary for Kelch binding. These findings uncover an unusual mechanism during development wherein a specialized cytoskeletal structure is regulated and remodeled by the ubiquitin-proteasome system.
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Affiliation(s)
- Andrew M Hudson
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Katelynn M Mannix
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Julianne A Gerdes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Molly C Kottemann
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lynn Cooley
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA
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71
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A novel long non-coding RNA, lncKBTBD10, involved in bovine skeletal muscle myogenesis. In Vitro Cell Dev Biol Anim 2018; 55:25-35. [PMID: 30465303 DOI: 10.1007/s11626-018-0306-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/25/2018] [Indexed: 12/27/2022]
Abstract
Accumulating evidence suggests that long non-coding RNAs (lncRNAs) play a crucial role in regulating skeletal muscle myogenesis, a highly coordinated multistep biological process. However, most studies of lncRNAs have focused on humans, mouse, and other model animals. In this study, we identified a novel lncRNA, named lncKBTBD10, located in the nucleus and involved in the proliferation and differentiation of bovine skeletal muscle satellite cells. Prediction of coding potential and in vitro translation system illustrated that lncKBTBD10 has no encoding capability. With the process of myogenic differentiation, the expression of lncKBTBD10 gradually increased. To elucidate the functions of lncKBTBD10 during myogenesis, the gain/loss-of-function experiments were performed. Results showed that the proliferation and differentiation of bovine skeletal muscle satellite cells were all suppressed whether lncKBTBD10 was knocked down or over-expressed. Furthermore, we found that lncKBTBD10 may affect its proximity gene KBTBD10 to involve in myogenesis. Results indicated that the protein level of KBTBD10 was all diminished after induced differentiation for 2 d in differentiation medium (DM2) whether lncKBTBD10 was knocked down or over-expressed. It may support why the altering of lncKBTBD10 can suppress the proliferation and differentiation of bovine skeletal muscle satellite cells. In short, our study elucidated that lncKBTBD10 could induce a decrease of KBTBD10 protein and further to affect bovine skeletal muscle myogenesis. The novel identified lncKBTBD10 may provide a reference for lncRNAs involved in myogenesis of bovine skeletal muscle.
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72
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Lam LT, Holt I, Laitila J, Hanif M, Pelin K, Wallgren-Pettersson C, Sewry CA, Morris GE. Two alternatively-spliced human nebulin isoforms with either exon 143 or exon 144 and their developmental regulation. Sci Rep 2018; 8:15728. [PMID: 30356055 PMCID: PMC6200726 DOI: 10.1038/s41598-018-33281-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/07/2018] [Indexed: 11/09/2022] Open
Abstract
Nebulin is a very large protein required for assembly of the contractile machinery in muscle. Mutations in the nebulin gene NEB are a common cause of nemaline myopathy. Nebulin mRNA is alternatively-spliced so that each mRNA contains either exon 143 or exon 144. We have produced monoclonal antibodies specific for the regions of nebulin encoded by these two exons, enabling analysis of expression of isoforms at the protein level for the first time. All antibodies recognized a protein of the expected size (600–900 kD) and stained cross-striations of sarcomeres in muscle sections. Expression of exon 143 is developmentally-regulated since newly-formed myotubes in cell culture expressed nebulin with exon 144 only; this was confirmed at the mRNA level by qPCR. In fetal muscle, nebulin with exon 143 was expressed in some myotubes by 12-weeks of gestation and strongly-expressed in most myotubes by 17-weeks. In mature human muscle, the exon 144 antibody stained all fibres, but the exon 143 antibody staining varied from very strong in some fibres to almost-undetectable in other fibres. The results show that nebulin containing exon 144 is the default isoform early in myogenesis, while regulated expression of nebulin containing exon 143 occurs at later stages of muscle development.
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Affiliation(s)
- Le Thanh Lam
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
| | - Ian Holt
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK.,Institute for Science and Technology in Medicine, Keele University, Keele, UK
| | - Jenni Laitila
- The Folkhälsan Institute of Genetics, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Mubashir Hanif
- The Folkhälsan Institute of Genetics, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Katarina Pelin
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- The Folkhälsan Institute of Genetics, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Caroline A Sewry
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK.,Dubowitz Neuromuscular Centre, Institute for Child Health and Great Ormond Street Hospital, London, UK
| | - Glenn E Morris
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK. .,Institute for Science and Technology in Medicine, Keele University, Keele, UK.
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73
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Salem M, Al-Tobasei R, Ali A, Lourenco D, Gao G, Palti Y, Kenney B, Leeds TD. Genome-Wide Association Analysis With a 50K Transcribed Gene SNP-Chip Identifies QTL Affecting Muscle Yield in Rainbow Trout. Front Genet 2018; 9:387. [PMID: 30283492 PMCID: PMC6157414 DOI: 10.3389/fgene.2018.00387] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. This study has two-fold objectives, first to develop, and validate a 50K transcribed gene SNP-chip using RNA-Seq data. To achieve this objective, two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs ere identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was ≥ 98.5%. The second objective of this study was to test the feasibility of using the new SNP-chip in GWA (Genome-wide association) analysis to identify QTL explaining muscle yield variance. GWA study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71 and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.
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Affiliation(s)
- Mohamed Salem
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, United States.,Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, United States.,Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ali Ali
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV, United States
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV, United States
| | - Brett Kenney
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV, United States
| | - Timothy D Leeds
- National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV, United States
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74
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Shafiee G, Asgari Y, Soltani A, Larijani B, Heshmat R. Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis. PeerJ 2018; 6:e5239. [PMID: 30202641 PMCID: PMC6129146 DOI: 10.7717/peerj.5239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/24/2018] [Indexed: 12/25/2022] Open
Abstract
Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein-protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin-proteasome system-it regulates the proteolysis. P53 is recognized as a central regulator of the cell cycle and apoptosis. These proteins, which have been identified as the most significant hubs, may be involved in aging muscle and sarcopenia.
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Affiliation(s)
- Gita Shafiee
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Yazdan Asgari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Akbar Soltani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Heshmat
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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75
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Gonorazky HD, Bönnemann CG, Dowling JJ. The genetics of congenital myopathies. HANDBOOK OF CLINICAL NEUROLOGY 2018; 148:549-564. [PMID: 29478600 DOI: 10.1016/b978-0-444-64076-5.00036-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Congenital myopathies are a clinically and genetically heterogeneous group of conditions that most commonly present at or around the time of birth with hypotonia, muscle weakness, and (often) respiratory distress. Historically, this group of disorders has been subclassified based on muscle histopathologic characteristics. There has been an explosion of gene discovery, and there are now at least 32 different genetic causes of disease. With this increased understanding of the genetic basis of disease has come the knowledge that the mutations in congenital myopathy genes can present with a wide variety of clinical phenotypes and can result in a broad spectrum of histopathologic findings on muscle biopsy. In addition, mutations in several genes can share the same histopathologic features. The identification of new genes and interpretation of different pathomechanisms at a molecular level have helped us to understand the clinical and histopathologic similarities that this group of disorders share. In this review, we highlight the genetic understanding for each subtype, its pathogenesis, and the future key issues in congenital myopathies.
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Affiliation(s)
- Hernan D Gonorazky
- Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, United States
| | - James J Dowling
- Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.
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76
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Suresh N, Haldar K. Mechanisms of artemisinin resistance in Plasmodium falciparum malaria. Curr Opin Pharmacol 2018; 42:46-54. [PMID: 30077118 PMCID: PMC6314025 DOI: 10.1016/j.coph.2018.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/31/2018] [Accepted: 06/04/2018] [Indexed: 11/28/2022]
Abstract
Artemisinin-based combination therapies (ACTs) have substantially reduced worldwide malaria burden and deaths. But malaria parasites have become resistant to artemisinins. Prior studies suggested two different molecular pathways of artemisinin-resistance. Here we unify recent findings into a single model, where elevation of a lipid, phosphatidylinositol-3- phosphate (PI3P) results in vesicle expansion that increases the engagement with the unfolded protein response (UPR). Vesicle expansion (rather than increasing individual genetic determinants of the UPR) efficiently induces artemisinin resistance likely by promoting ‘proteostasis’ (protein translation coupled to proper protein folding and vesicular remodeling) to mitigate artemisinin-induced proteopathy (death from global abnormal protein-toxicity). Vesicular amplification engages the host red cell, suggesting that artemisinin resistant malaria may also persist by taking advantage of host niches and escaping the immune response.
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Affiliation(s)
- Niraja Suresh
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, 103 Galvin Life Sciences, Notre Dame, IN 46556, USA; Department of Biological Sciences, University of Notre Dame, 103 Galvin Life Sciences, Notre Dame, IN 46556, USA
| | - Kasturi Haldar
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, 103 Galvin Life Sciences, Notre Dame, IN 46556, USA; Department of Biological Sciences, University of Notre Dame, 103 Galvin Life Sciences, Notre Dame, IN 46556, USA.
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77
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Karttunen M, Choy WY, Cino EA. Prediction of Binding Energy of Keap1 Interaction Motifs in the Nrf2 Antioxidant Pathway and Design of Potential High-Affinity Peptides. J Phys Chem B 2018; 122:5851-5859. [PMID: 29745220 DOI: 10.1021/acs.jpcb.8b03295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor and principal regulator of the antioxidant pathway. The Kelch domain of Kelch-like ECH-associated protein 1 (Keap1) binds to motifs in the N-terminal region of Nrf2, promoting its degradation. There is interest in developing ligands that can compete with Nrf2 for binding to Kelch, thereby activating its transcriptional activities and increasing antioxidant levels. Using experimental Δ Gbind values of Kelch-binding motifs determined previously, a revised hydrophobicity-based model was developed for estimating Δ Gbind from amino acid sequence and applied to rank potential uncharacterized Kelch-binding motifs identified from interaction databases and BLAST searches. Model predictions and molecular dynamics (MD) simulations suggested that full-length MAD2A binds Kelch more favorably than a high-affinity 20-mer Nrf2 E78P peptide, but that the motif in isolation is not a particularly strong binder. Endeavoring to develop shorter peptides for activating Nrf2, new designs were created based on the E78P peptide, some of which showed considerable propensity to form binding-competent structures in MD, and were predicted to interact with Kelch more favorably than the E78P peptide. The peptides could be promising new ligands for enhancing the oxidative stress response.
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Affiliation(s)
- Mikko Karttunen
- Department of Chemistry and Department of Applied Mathematics , The University of Western Ontario , London , Ontario , Canada N6A 5B7
| | - Wing-Yiu Choy
- Department of Biochemistry , The University of Western Ontario , London , Ontario , Canada N6A 5C1
| | - Elio A Cino
- Department of Biochemistry and Immunology , Federal University of Minas Gerais , Belo Horizonte 31270-901 , Brazil
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78
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Papizan JB, Vidal AH, Bezprozvannaya S, Bassel-Duby R, Olson EN. Cullin-3-RING ubiquitin ligase activity is required for striated muscle function in mice. J Biol Chem 2018; 293:8802-8811. [PMID: 29653945 DOI: 10.1074/jbc.ra118.002104] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/12/2018] [Indexed: 12/25/2022] Open
Abstract
Control of protein homeostasis is an essential cellular process that, when perturbed, can result in the deregulation or toxic accumulation of proteins. Owing to constant mechanical stress, striated muscle proteins are particularly prone to wear and tear and require several protein quality-control mechanisms to coordinate protein turnover and removal of damaged proteins. Kelch-like proteins, substrate adapters for the Cullin-3 (Cul3)-RING ligase (CRL3) complex, are emerging as critical regulators of striated muscle development and function, highlighting the importance of Cul3-mediated proteostasis in muscle function. To explore the role of Cul3-mediated proteostasis in striated muscle, here we deleted Cul3 specifically in either skeletal muscle (SkM-Cul3 KO) or cardiomyocytes (CM-Cul3 KO) of mice. The loss of Cul3 caused neonatal lethality and dramatic alterations in the proteome, which were unique to each striated muscle type. Many of the proteins whose expression was significantly changed in the SkM-Cul3 KO were components of the extracellular matrix and sarcomere, whereas proteins altered in the CM-Cul3 KO were involved in metabolism. These findings highlight the requirement for striated muscle-specific CRL3 activity and indicate how the CRL3 complex can control different nodes of protein interaction networks in different types of striated muscle. Further identification of Cul3 substrates, and how these substrates are targeted, may reveal therapeutic targets and treatment regimens for striated muscle diseases.
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Affiliation(s)
- James B Papizan
- From the Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Alexander H Vidal
- From the Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Svetlana Bezprozvannaya
- From the Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Rhonda Bassel-Duby
- From the Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Eric N Olson
- From the Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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79
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Congenital myopathies: disorders of excitation-contraction coupling and muscle contraction. Nat Rev Neurol 2018; 14:151-167. [PMID: 29391587 DOI: 10.1038/nrneurol.2017.191] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The congenital myopathies are a group of early-onset, non-dystrophic neuromuscular conditions with characteristic muscle biopsy findings, variable severity and a stable or slowly progressive course. Pronounced weakness in axial and proximal muscle groups is a common feature, and involvement of extraocular, cardiorespiratory and/or distal muscles can implicate specific genetic defects. Central core disease (CCD), multi-minicore disease (MmD), centronuclear myopathy (CNM) and nemaline myopathy were among the first congenital myopathies to be reported, and they still represent the main diagnostic categories. However, these entities seem to belong to a much wider phenotypic spectrum. To date, congenital myopathies have been attributed to mutations in over 20 genes, which encode proteins implicated in skeletal muscle Ca2+ homeostasis, excitation-contraction coupling, thin-thick filament assembly and interactions, and other mechanisms. RYR1 mutations are the most frequent genetic cause, and CCD and MmD are the most common subgroups. Next-generation sequencing has vastly improved mutation detection and has enabled the identification of novel genetic backgrounds. At present, management of congenital myopathies is largely supportive, although new therapeutic approaches are reaching the clinical trial stage.
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80
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Abstract
A marked decrease in malaria-related deaths worldwide has been attributed to the administration of effective antimalarials against Plasmodium falciparum, in particular, artemisinin-based combination therapies (ACTs). Increasingly, ACTs are also used to treat Plasmodium vivax, the second major human malaria parasite. However, resistance to frontline artemisinins and partner drugs is now causing the failure of P. falciparum ACTs in southeast Asia. In this Review, we discuss our current knowledge of markers and mechanisms of resistance to artemisinins and ACTs. In particular, we describe the identification of mutations in the propeller domains of Kelch 13 as the primary marker for artemisinin resistance in P. falciparum and explore two major mechanisms of resistance that have been independently proposed: the activation of the unfolded protein response and proteostatic dysregulation of parasite phosphatidylinositol 3- kinase. We emphasize the continuing challenges and the imminent need to understand mechanisms of resistance to improve parasite detection strategies, develop new combinations to eliminate resistant parasites and prevent their global spread.
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81
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Cullin 3-Based Ubiquitin Ligases as Master Regulators of Mammalian Cell Differentiation. Trends Biochem Sci 2017; 43:95-107. [PMID: 29249570 DOI: 10.1016/j.tibs.2017.11.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 01/09/2023]
Abstract
Specificity of the ubiquitin proteasome system is controlled by ubiquitin E3 ligases, including their major representatives, the multisubunit cullin-RING ubiquitin (Ub) ligases (CRLs). More than 200 different CRLs are divided into seven families according to their cullin scaffolding proteins (CUL1-7) around which they are assembled. Research over two decades has revealed that different CRL families are specialized to fulfill specific cellular functions. Whereas many CUL1-based CRLs (CRL1s) ubiquitylate cell cycle regulators, CRL4 complexes often associate with chromatin to control DNA metabolism. Based on studies about differentiation programs of mesenchymal stem cells (MSCs), including myogenesis, neurogenesis, chondrogenesis, osteogenesis and adipogenesis, we propose here that CRL3 complexes evolved to fulfill a pivotal role in mammalian cell differentiation.
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82
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Papizan JB, Garry GA, Brezprozvannaya S, McAnally JR, Bassel-Duby R, Liu N, Olson EN. Deficiency in Kelch protein Klhl31 causes congenital myopathy in mice. J Clin Invest 2017; 127:3730-3740. [PMID: 28872460 DOI: 10.1172/jci93445] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/19/2017] [Indexed: 01/19/2023] Open
Abstract
Maintenance of muscle structure and function depends on the precise organization of contractile proteins into sarcomeres and coupling of the contractile apparatus to the sarcoplasmic reticulum (SR), which serves as the reservoir for calcium required for contraction. Several members of the Kelch superfamily of proteins, which modulate protein stability as substrate-specific adaptors for ubiquitination, have been implicated in sarcomere formation. The Kelch protein Klhl31 is expressed in a muscle-specific manner under control of the transcription factor MEF2. To explore its functions in vivo, we created a mouse model of Klhl31 loss of function using the CRISPR-Cas9 system. Mice lacking Klhl31 exhibited stunted postnatal skeletal muscle growth, centronuclear myopathy, central cores, Z-disc streaming, and SR dilation. We used proteomics to identify several candidate Klhl31 substrates, including Filamin-C (FlnC). In the Klhl31-knockout mice, FlnC protein levels were highly upregulated with no change in transcription, and we further demonstrated that Klhl31 targets FlnC for ubiquitination and degradation. These findings highlight a role for Klhl31 in the maintenance of skeletal muscle structure and provide insight into the mechanisms underlying congenital myopathies.
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83
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Bertocci B, Lecoeuche D, Sterlin D, Kühn J, Gaillard B, De Smet A, Lembo F, Bole-Feysot C, Cagnard N, Fadeev T, Dahan A, Weill JC, Reynaud CA. Klhl6 Deficiency Impairs Transitional B Cell Survival and Differentiation. THE JOURNAL OF IMMUNOLOGY 2017; 199:2408-2420. [PMID: 28807996 DOI: 10.4049/jimmunol.1700708] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022]
Abstract
Klhl6 belongs to the KLHL gene family, which is composed of an N-terminal BTB-POZ domain and four to six Kelch motifs in tandem. Several of these proteins function as adaptors of the Cullin3 E3 ubiquitin ligase complex. In this article, we report that Klhl6 deficiency induces, as previously described, a 2-fold reduction in mature B cells. However, we find that this deficit is centered on the inability of transitional type 1 B cells to survive and to progress toward the transitional type 2 B cell stage, whereas cells that have passed this step generate normal germinal centers (GCs) upon a T-dependent immune challenge. Klhl6-deficient type 1 B cells showed a 2-fold overexpression of genes linked with cell proliferation, including most targets of the anaphase-promoting complex/cyclosome complex, a set of genes whose expression is precisely downmodulated upon culture of splenic transitional B cells in the presence of BAFF. These results thus suggest a delay in the differentiation process of Klhl6-deficient B cells between the immature and transitional stage. We further show, in the BL2 Burkitt's lymphoma cell line, that KLHL6 interacts with Cullin3, but also that it binds to HBXIP/Lamtor5, a protein involved in cell-cycle regulation and cytokinesis. Finally, we report that KLHL6, which is recurrently mutated in B cell lymphomas, is an off-target of the normal somatic hypermutation process taking place in GC B cells in both mice and humans, thus leaving open whether, despite the lack of impact of Klhl6 deficiency on GC B cell expansion, mutants could contribute to the oncogenic process.
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Affiliation(s)
- Barbara Bertocci
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France;
| | - Damiana Lecoeuche
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France
| | - Delphine Sterlin
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France
| | - Julius Kühn
- Institute of Cellular and Molecular Immunology, Georg-August-University Medicine Göttingen, 37073 Göttingen, Germany
| | - Baptiste Gaillard
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France
| | - Annie De Smet
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France
| | - Frederique Lembo
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068-CNRS UMR7258, 13273 Marseille Cedex 09, France
| | - Christine Bole-Feysot
- Plateforme de Génomique, Imagine Institut des Maladies Génétiques-Structure Fédérative de Recherche Necker, INSERM 1163 and INSERM US24/CNRS UMS3633, 75015 Paris, France; and
| | - Nicolas Cagnard
- Plateforme de Bioinformatique, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, 75993 Paris Cedex 14, France
| | - Tatiana Fadeev
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France
| | - Auriel Dahan
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France
| | - Jean-Claude Weill
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France
| | - Claude-Agnès Reynaud
- Équipe Développement du Systéme Immunitaire, Institut Necker-Enfant Malades, INSERM U1151-CNRS UMR8253, Faculté de Médecine Paris Decartes, Université Paris Descartes, Sorbone Paris Cité, 75993 Paris Cedex 14, France;
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84
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Ramirez-Martinez A, Cenik BK, Bezprozvannaya S, Chen B, Bassel-Duby R, Liu N, Olson EN. KLHL41 stabilizes skeletal muscle sarcomeres by nonproteolytic ubiquitination. eLife 2017; 6:26439. [PMID: 28826497 PMCID: PMC5589419 DOI: 10.7554/elife.26439] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022] Open
Abstract
Maintenance of muscle function requires assembly of contractile proteins into highly organized sarcomeres. Mutations in Kelch-like protein 41 (KLHL41) cause nemaline myopathy, a fatal muscle disorder associated with sarcomere disarray. We generated KLHL41 mutant mice, which display lethal disruption of sarcomeres and aberrant expression of muscle structural and contractile proteins, mimicking the hallmarks of the human disease. We show that KLHL41 is poly-ubiquitinated and acts, at least in part, by preventing aggregation and degradation of Nebulin, an essential component of the sarcomere. Furthermore, inhibition of KLHL41 poly-ubiquitination prevents its stabilization of nebulin, suggesting a unique role for ubiquitination in protein stabilization. These findings provide new insights into the molecular etiology of nemaline myopathy and reveal a mechanism whereby KLHL41 stabilizes sarcomeres and maintains muscle function by acting as a molecular chaperone. Similar mechanisms for protein stabilization likely contribute to the actions of other Kelch proteins.
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Affiliation(s)
- Andres Ramirez-Martinez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Bercin Kutluk Cenik
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Beibei Chen
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Eric N Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, United States
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85
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Werner A, Manford AG, Rape M. Ubiquitin-Dependent Regulation of Stem Cell Biology. Trends Cell Biol 2017; 27:568-579. [PMID: 28528988 PMCID: PMC5643009 DOI: 10.1016/j.tcb.2017.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Abstract
The growth of a metazoan body relies on a series of highly coordinated cell-fate decisions by stem cells which can undergo self-renewal, reversibly enter a quiescent state, or terminally commit to a cell specification program. To guide their decisions, stem cells make frequent use of ubiquitylation, a post-translational modification that can affect the activity, interaction landscape, or stability of stem cell proteins. In this review we discuss novel findings that have provided insight into ubiquitin-dependent mechanisms of stem cell control and revealed how an essential and highly conserved protein modification can shape metazoan development.
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Affiliation(s)
- Achim Werner
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Andrew G Manford
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA.
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86
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Chen Q, Li C, Gong Z, Chan ECY, Snyder SA, Lam SH. Common deregulated gene expression profiles and morphological changes in developing zebrafish larvae exposed to environmental-relevant high to low concentrations of glucocorticoids. CHEMOSPHERE 2017; 172:429-439. [PMID: 28092764 DOI: 10.1016/j.chemosphere.2017.01.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
Synthetic glucocorticoids have been detected in environmental waters and their biological potency have raised concerns of their impact on aquatic vertebrates especially fish. In this study, developing zebrafish larvae exposed to representative glucocorticoids (dexamethasone, prednisolone and triamcinolone) at 50 pM to 50 nM from 3 h post-fertilisation to 5 days post-fertilisation were investigated. Microarray analysis identified 1255, 1531, and 2380 gene probes, which correspondingly mapped to 660, 882 and 1238 human/rodent homologs, as deregulated by dexamethasone, prednisolone and triamcinolone, respectively. A total of 248 gene probes which mapped to 159 human/rodent homologs were commonly deregulated by the three glucocorticoids. These homologs were associated with over 20 molecular functions from cell cycle to cellular metabolisms, and were involved in the development and function of connective tissue, nervous, haematological, and digestive systems. Glucocorticoid receptor signalling, NRF2-mediated oxidative stress response and RAR signalling were among the top perturbed canonical pathways. Morphological analyses using four transgenic zebrafish lines revealed that the hepatic and endothelial-vascular systems were affected by all three glucocorticoids while nervous, pancreatic and myeloid cell systems were affected by one of them. Quantitative real-time PCR detected significant change in the expression of seven genes at 50 pM of all three glucocorticoids, a concentration comparable to total glucocorticoids reported in environmental waters. Three genes (cry2b, fbxo32, and klhl38b) responded robustly to all glucocorticoid concentrations tested. The common deregulated genes with the associated biological processes and morphological changes can be used for biological inference of glucocorticoid exposure in fish for future studies.
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Affiliation(s)
- Qiyu Chen
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Caixia Li
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore; Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Zhiyuan Gong
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Eric Chun Yong Chan
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Shane A Snyder
- University of Arizona, 1133 E. James E. Rogers Way, Harshbarger 108, Tucson, AZ 85721-0011, USA
| | - Siew Hong Lam
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore; Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
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87
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Blondelle J, Shapiro P, Domenighetti AA, Lange S. Cullin E3 Ligase Activity Is Required for Myoblast Differentiation. J Mol Biol 2017; 429:1045-1066. [PMID: 28238764 DOI: 10.1016/j.jmb.2017.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 01/06/2023]
Abstract
The role of cullin E3-ubiquitin ligases for muscle homeostasis is best known during muscle atrophy, as the cullin-1 substrate adaptor atrogin-1 is among the most well-characterized muscle atrogins. We investigated whether cullin activity was also crucial during terminal myoblast differentiation and aggregation of acetylcholine receptors for the establishment of neuromuscular junctions in vitro. The activity of cullin E3-ligases is modulated through post-translational modification with the small ubiquitin-like modifier nedd8. Using either the Nae1 inhibitor MLN4924 (Pevonedistat) or siRNA against nedd8 in early or late stages of differentiation on C2C12 myoblasts, and primary satellite cells from mouse and human, we show that cullin E3-ligase activity is necessary for each step of the muscle cell differentiation program in vitro. We further investigate known transcriptional repressors for terminal muscle differentiation, namely ZBTB38, Bhlhe41, and Id1. Due to their identified roles for terminal muscle differentiation, we hypothesize that the accumulation of these potential cullin E3-ligase substrates may be partially responsible for the observed phenotype. MLN4924 is currently undergoing clinical trials in cancer patients, and our experiments highlight concerns on the homeostasis and regenerative capacity of muscles in these patients who often experience cachexia.
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Affiliation(s)
- Jordan Blondelle
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA
| | - Paige Shapiro
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA
| | - Andrea A Domenighetti
- Rehabilitation Institute of Chicago, Chicago, IL-60611 USA; Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL-60611, USA
| | - Stephan Lange
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA.
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88
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Muscle weakness in respiratory and peripheral skeletal muscles in a mouse model for nebulin-based nemaline myopathy. Neuromuscul Disord 2016; 27:83-89. [PMID: 27890461 DOI: 10.1016/j.nmd.2016.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 09/21/2016] [Accepted: 10/11/2016] [Indexed: 12/28/2022]
Abstract
Nemaline myopathy is among the most common non-dystrophic congenital myopathies, and is characterized by the presence of nemaline rods in skeletal muscles fibers, general muscle weakness, and hypotonia. Although respiratory failure is the main cause of death in nemaline myopathy, only little is known regarding the contractile strength of the diaphragm, the main muscle of inspiration. To investigate diaphragm contractility, in the present study we took advantage of a mouse model for nebulin-based nemaline myopathy that we recently developed. In this mouse model, exon 55 of Neb is deleted (NebΔExon55), a mutation frequently found in patients. Diaphragm contractility was determined in permeabilized muscle fibers and was compared to the contractility of permeabilized fibers from three peripheral skeletal muscles: soleus, extensor digitorum longus, and gastrocnemius. The force generating capacity of diaphragm muscle fibers of NebΔExon55 mice was reduced to 25% of wildtype levels, indicating severe contractile weakness. The contractile weakness of diaphragm fibers was more pronounced than that observed in soleus muscle, but not more pronounced than that observed in extensor digitorum longus and gastrocnemius muscles. The reduced muscle contractility was at least partly caused by changes in cross-bridge cycling kinetics which reduced the number of bound cross-bridges. The severe diaphragm weakness likely contributes to the development of respiratory failure in NebΔExon55 mice and might explain their early, postnatal death.
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89
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Characterisation of equine satellite cell transcriptomic profile response to β-hydroxy-β-methylbutyrate (HMB). Br J Nutr 2016; 116:1315-1325. [PMID: 27691998 PMCID: PMC5082287 DOI: 10.1017/s000711451600324x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
β-Hydroxy-β-methylbutyrate (HMB) is a popular ergogenic
aid used by human athletes and as a supplement to sport horses, because of its ability to
aid muscle recovery, improve performance and body composition. Recent findings suggest
that HMB may stimulate satellite cells and affect expressions of genes regulating skeletal
muscle cell growth. Despite the scientific data showing benefits of HMB supplementation in
horses, no previous study has explained the mechanism of action of HMB in this species.
The aim of this study was to reveal the molecular background of HMB action on equine
skeletal muscle by investigating the transcriptomic profile changes induced by HMB in
equine satellite cells in vitro. Upon isolation from the
semitendinosus muscle, equine satellite cells were cultured until the
2nd day of differentiation. Differentiating cells were incubated with HMB for 24 h. Total
cellular RNA was isolated, amplified, labelled and hybridised to microarray slides.
Microarray data validation was performed with real-time quantitative PCR. HMB induced
differential expressions of 361 genes. Functional analysis revealed that the main
biological processes influenced by HMB in equine satellite cells were related to muscle
organ development, protein metabolism, energy homoeostasis and lipid metabolism. In
conclusion, this study demonstrated for the first time that HMB has the potential to
influence equine satellite cells by controlling global gene expression. Genes and
biological processes targeted by HMB in equine satellite cells may support HMB utility in
improving growth and regeneration of equine skeletal muscle; however, the overall role of
HMB in horses remains equivocal and requires further proteomic, biochemical and
pharmacokinetic studies.
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90
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Chaharbakhshi E, Jemc JC. Broad-complex, tramtrack, and bric-à-brac (BTB) proteins: Critical regulators of development. Genesis 2016; 54:505-518. [DOI: 10.1002/dvg.22964] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Edwin Chaharbakhshi
- Department of Biology; Loyola University Chicago; Chicago IL
- Stritch School of Medicine; Loyola University Chicago; Maywood IL
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91
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Ravenscroft G, Davis MR, Lamont P, Forrest A, Laing NG. New era in genetics of early-onset muscle disease: Breakthroughs and challenges. Semin Cell Dev Biol 2016; 64:160-170. [PMID: 27519468 DOI: 10.1016/j.semcdb.2016.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 08/07/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022]
Abstract
Early-onset muscle disease includes three major entities that present generally at or before birth: congenital myopathies, congenital muscular dystrophies and congenital myasthenic syndromes. Almost exclusively there is weakness and hypotonia, although cases manifesting hypertonia are increasingly being recognised. These diseases display a wide phenotypic and genetic heterogeneity, with the uptake of next generation sequencing resulting in an unparalleled extension of the phenotype-genotype correlations and "diagnosis by sequencing" due to unbiased sequencing. Perhaps now more than ever, detailed clinical evaluations are necessary to guide the genetic diagnosis; with arrival at a molecular diagnosis frequently occurring following dialogue between the molecular geneticist, the referring clinician and the pathologist. There is an ever-increasing blurring of the boundaries between the congenital myopathies, dystrophies and myasthenic syndromes. In addition, many novel disease genes have been described and new insights have been gained into skeletal muscle development and function. Despite the advances made, a significant percentage of patients remain without a molecular diagnosis, suggesting that there are many more human disease genes and mechanisms to identify. It is now technically- and clinically-feasible to perform next generation sequencing for severe diseases on a population-wide scale, such that preconception-carrier screening can occur. Newborn screening for selected early-onset muscle diseases is also technically and ethically-achievable, with benefits to the patient and family from early management of these diseases and should also be implemented. The need for world-wide Reference Centres to meticulously curate polymorphisms and mutations within a particular gene is becoming increasingly apparent, particularly for interpretation of variants in the large genes which cause early-onset myopathies: NEB, RYR1 and TTN. Functional validation of candidate disease variants is crucial for accurate interpretation of next generation sequencing and appropriate genetic counseling. Many published "pathogenic" variants are too frequent in control populations and are thus likely rare polymorphisms. Mechanisms need to be put in place to systematically update the classification of variants such that accurate interpretation of variants occurs. In this review, we highlight the recent advances made and the challenges ahead for the molecular diagnosis of early-onset muscle diseases.
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Affiliation(s)
- Gianina Ravenscroft
- Harry Perkins Institute of Medical Research and the Centre for Medical Research, University of Western Australia, Nedlands, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, Pathwest, QEII Medical Centre, Nedlands, Australia
| | - Phillipa Lamont
- Harry Perkins Institute of Medical Research and the Centre for Medical Research, University of Western Australia, Nedlands, Australia; Neurogenetic unit, Dept of Neurology, Royal Perth Hospital and The Perth Children's Hospital, Western Australia, Australia
| | - Alistair Forrest
- Harry Perkins Institute of Medical Research and the Centre for Medical Research, University of Western Australia, Nedlands, Australia
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research and the Centre for Medical Research, University of Western Australia, Nedlands, Australia; Department of Diagnostic Genomics, Pathwest, QEII Medical Centre, Nedlands, Australia.
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92
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Winter JMD, Joureau B, Lee EJ, Kiss B, Yuen M, Gupta VA, Pappas CT, Gregorio CC, Stienen GJM, Edvardson S, Wallgren-Pettersson C, Lehtokari VL, Pelin K, Malfatti E, Romero NB, Engelen BGV, Voermans NC, Donkervoort S, Bönnemann CG, Clarke NF, Beggs AH, Granzier H, Ottenheijm CAC. Mutation-specific effects on thin filament length in thin filament myopathy. Ann Neurol 2016; 79:959-69. [PMID: 27074222 DOI: 10.1002/ana.24654] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Thin filament myopathies are among the most common nondystrophic congenital muscular disorders, and are caused by mutations in genes encoding proteins that are associated with the skeletal muscle thin filament. Mechanisms underlying muscle weakness are poorly understood, but might involve the length of the thin filament, an important determinant of force generation. METHODS We investigated the sarcomere length-dependence of force, a functional assay that provides insights into the contractile strength of muscle fibers as well as the length of the thin filaments, in muscle fibers from 51 patients with thin filament myopathy caused by mutations in NEB, ACTA1, TPM2, TPM3, TNNT1, KBTBD13, KLHL40, and KLHL41. RESULTS Lower force generation was observed in muscle fibers from patients of all genotypes. In a subset of patients who harbor mutations in NEB and ACTA1, the lower force was associated with downward shifted force-sarcomere length relations, indicative of shorter thin filaments. Confocal microscopy confirmed shorter thin filaments in muscle fibers of these patients. A conditional Neb knockout mouse model, which recapitulates thin filament myopathy, revealed a compensatory mechanism; the lower force generation that was associated with shorter thin filaments was compensated for by increasing the number of sarcomeres in series. This allowed muscle fibers to operate at a shorter sarcomere length and maintain optimal thin-thick filament overlap. INTERPRETATION These findings might provide a novel direction for the development of therapeutic strategies for thin filament myopathy patients with shortened thin filament lengths. Ann Neurol 2016;79:959-969.
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Affiliation(s)
- Josine M de Winter
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands
| | - Barbara Joureau
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands
| | - Eun-Jeong Lee
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Balázs Kiss
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Michaela Yuen
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
| | - Vandana A Gupta
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Christopher T Pappas
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Ger J M Stienen
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands.,Department of Physics and Astronomy, VU University, Amsterdam, the Netherlands
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Jerusalem, Israel
| | - Carina Wallgren-Pettersson
- Department of Medical and Clinical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland.,Folkhaelsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
| | - Vilma-Lotta Lehtokari
- Department of Medical and Clinical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland.,Folkhaelsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
| | - Katarina Pelin
- Folkhaelsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland.,Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Edoardo Malfatti
- Center for Research in Myology, Pitié-Salpêtrière Hospital Group, Paris, France
| | - Norma B Romero
- Center for Research in Myology, Pitié-Salpêtrière Hospital Group, Paris, France
| | - Baziel G van Engelen
- Department of Neurology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicol C Voermans
- Department of Neurology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD
| | - C G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD
| | - Nigel F Clarke
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
| | - Alan H Beggs
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Coen A C Ottenheijm
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands.,Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
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93
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Lian YF, Yuan J, Cui Q, Feng QS, Xu M, Bei JX, Zeng YX, Feng L. Upregulation of KLHDC4 Predicts a Poor Prognosis in Human Nasopharyngeal Carcinoma. PLoS One 2016; 11:e0152820. [PMID: 27030985 PMCID: PMC4816273 DOI: 10.1371/journal.pone.0152820] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/18/2016] [Indexed: 11/18/2022] Open
Abstract
Kelch proteins are implicated in the pathogenesis of many human diseases, including cancer. Nasopharyngeal carcinoma (NPC) is a rare malignancy in most countries, but prevalent in southern China and certain areas of Southeast Asia. In this study, we identified Kelch Domain Containing 4 (KLHDC4), an orphan member of the kelch repeat superfamily, as a prognosis marker for NPC. We examined the expression of KLHDC4 in 168 NPC cases by immunohistochemical staining and found a substantially higher level of KLHDC4 in NPC biopsies compared to adjacent normal nasopharyngeal mucosa. KLHDC4 expression was significantly related to the T classification (P <0.05), N classification (P <0.05) and total staging (P <0.01) in NPC, and patients with higher KLHDC4 expression had poorer overall (P <0.01) and metastasis-free survival (P <0.05) rates. Knockout (KO) of KLHDC4 via CRISPR/Cas9-mediated gene editing in NPC cell line dramatically inhibited cell proliferation, colony formation in soft agar and tumor formation in nude mice. In addition, cell migration and invasion were also impaired by KLHDC4 depletion as revealed by wound healing and Transwell assay. Mechanically, loss of KLHDC4 markedly induced spontaneous apoptosis in NPC cells, as evidenced by increased levels of cleaved caspase-3 and cleaved PARP. Consistently, KLHDC4 knockout cell-derived xenografts also showed elevated cleaved caspase-3 and PARP but reduced Ki-67 staining. In conclusion, our results suggest that KLHDC4 promotes NPC oncogenesis by suppressing cellular apoptosis. Thus, KLHDC4 may serve as a prognosis biomarker and a potential therapeutic target for NPC.
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Affiliation(s)
- Yi-Fan Lian
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Jing Yuan
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Qian Cui
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Qi-Sheng Feng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Miao Xu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Jin-Xin Bei
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yi-Xin Zeng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
- Beijing Hospital, Beijing, China
- * E-mail: (LF); (YXZ)
| | - Lin Feng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
- * E-mail: (LF); (YXZ)
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94
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Topa A, Tulinius M, Oldfors A, Hedberg-Oldfors C. Novel myopathy in a newborn with Shwachman-Diamond syndrome and review of neonatal presentation. Am J Med Genet A 2016; 170A:1155-64. [DOI: 10.1002/ajmg.a.37593] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/27/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Alexandra Topa
- Department of Clinical Pathology and Genetics; Sahlgrenska University Hospital; Gothenburg Sweden
| | - Mar Tulinius
- Department of Pediatrics; University of Gothenburg; The Queen Silvia Children's Hospital; Gothenburg Sweden
| | - Anders Oldfors
- Department of Pathology; University of Gothenburg; Gothenburg Sweden
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95
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Lambrughi M, Lucchini M, Pignataro M, Sola M, Bortolotti CA. The dynamics of the β-propeller domain in Kelch protein KLHL40 changes upon nemaline myopathy-associated mutation. RSC Adv 2016. [DOI: 10.1039/c6ra06312h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The nemaline myopathy-associated E528K mutation in the KLHL40 alters the communication between the Kelch propeller blades.
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Affiliation(s)
- Matteo Lambrughi
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Matteo Lucchini
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Marcello Pignataro
- Department of Chemical and Geological Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Marco Sola
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Carlo Augusto Bortolotti
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
- CNR-Nano Institute of Nanoscience
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96
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Pilling LC, Joehanes R, Kacprowski T, Peters M, Jansen R, Karasik D, Kiel DP, Harries LW, Teumer A, Powell J, Levy D, Lin H, Lunetta K, Munson P, Bandinelli S, Henley W, Hernandez D, Singleton A, Tanaka T, van Grootheest G, Hofman A, Uitterlinden AG, Biffar R, Gläser S, Homuth G, Malsch C, Völker U, Penninx B, van Meurs JBJ, Ferrucci L, Kocher T, Murabito J, Melzer D. Gene transcripts associated with muscle strength: a CHARGE meta-analysis of 7,781 persons. Physiol Genomics 2016; 48:1-11. [PMID: 26487704 PMCID: PMC4757025 DOI: 10.1152/physiolgenomics.00054.2015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/08/2015] [Indexed: 12/22/2022] Open
Abstract
Lower muscle strength in midlife predicts disability and mortality in later life. Blood-borne factors, including growth differentiation factor 11 (GDF11), have been linked to muscle regeneration in animal models. We aimed to identify gene transcripts associated with muscle strength in adults. Meta-analysis of whole blood gene expression (overall 17,534 unique genes measured by microarray) and hand-grip strength in four independent cohorts (n = 7,781, ages: 20-104 yr, weighted mean = 56), adjusted for age, sex, height, weight, and leukocyte subtypes. Separate analyses were performed in subsets (older/younger than 60, men/women). Expression levels of 221 genes were associated with strength after adjustment for cofactors and for multiple statistical testing, including ALAS2 (rate-limiting enzyme in heme synthesis), PRF1 (perforin, a cytotoxic protein associated with inflammation), IGF1R, and IGF2BP2 (both insulin like growth factor related). We identified statistical enrichment for hemoglobin biosynthesis, innate immune activation, and the stress response. Ten genes were associated only in younger individuals, four in men only and one in women only. For example, PIK3R2 (a negative regulator of PI3K/AKT growth pathway) was negatively associated with muscle strength in younger (<60 yr) individuals but not older (≥ 60 yr). We also show that 115 genes (52%) have not previously been linked to muscle in NCBI PubMed abstracts. This first large-scale transcriptome study of muscle strength in human adults confirmed associations with known pathways and provides new evidence for over half of the genes identified. There may be age- and sex-specific gene expression signatures in blood for muscle strength.
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Affiliation(s)
- L C Pilling
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - R Joehanes
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; Population Studies Branch, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - T Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - M Peters
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands
| | - R Jansen
- Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - D Karasik
- Hebrew SeniorLife Institute for Aging Research, Boston, Massachusetts
| | - D P Kiel
- Hebrew SeniorLife Institute for Aging Research, Boston, Massachusetts
| | - L W Harries
- RNA mechanisms of complex diseases group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - A Teumer
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - J Powell
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - D Levy
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; Population Studies Branch, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - H Lin
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - K Lunetta
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - P Munson
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; The Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland
| | - S Bandinelli
- Geriatric Unit, Azienda Sanitaria di Firenze, Florence, Italy
| | - W Henley
- Institute for Health Services Research, University of Exeter Medical School, Exeter, United Kingdom
| | - D Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - A Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - T Tanaka
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland
| | - G van Grootheest
- Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - A Hofman
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, the Netherlands
| | - A G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, the Netherlands
| | - R Biffar
- Department of Prosthetic Dentistry, Gerostomatology and Dental Materials, University Medicine Greifswald, Greifswald, Germany
| | - S Gläser
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University of Greifswald, Greifswald, Germany
| | - G Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - C Malsch
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - U Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - B Penninx
- Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - J B J van Meurs
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands
| | - L Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland
| | - T Kocher
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology and Endodontology, University Medicine Greifswald, Greifswald, Germany; and
| | - J Murabito
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; General Internal Medicine Section, Boston University, Boston, Massachusetts
| | - D Melzer
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom;
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97
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Wenzel MA, James MC, Douglas A, Piertney SB. Genome-wide association and genome partitioning reveal novel genomic regions underlying variation in gastrointestinal nematode burden in a wild bird. Mol Ecol 2015; 24:4175-92. [PMID: 26179597 DOI: 10.1111/mec.13313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 06/23/2015] [Accepted: 07/03/2015] [Indexed: 02/06/2023]
Abstract
Identifying the genetic architecture underlying complex phenotypes is a notoriously difficult problem that often impedes progress in understanding adaptive eco-evolutionary processes in natural populations. Host-parasite interactions are fundamentally important drivers of evolutionary processes, but a lack of understanding of the genes involved in the host's response to chronic parasite insult makes it particularly difficult to understand the mechanisms of host life history trade-offs and the adaptive dynamics involved. Here, we examine the genetic basis of gastrointestinal nematode (Trichostrongylus tenuis) burden in 695 red grouse (Lagopus lagopus scotica) individuals genotyped at 384 genome-wide SNPs. We first use genome-wide association to identify individual SNPs associated with nematode burden. We then partition genome-wide heritability to identify chromosomes with greater heritability than expected from gene content, due to harbouring a multitude of additive SNPs with individually undetectable effects. We identified five SNPs on five chromosomes that accounted for differences of up to 556 worms per bird, but together explained at best 4.9% of the phenotypic variance. These SNPs were closely linked to genes representing a range of physiological processes including the immune system, protein degradation and energy metabolism. Genome partitioning indicated genome-wide heritability of up to 29% and three chromosomes with excess heritability of up to 4.3% (total 8.9%). These results implicate SNPs and novel genomic regions underlying nematode burden in this system and suggest that this phenotype is somewhere between being based on few large-effect genes (oligogenic) and based on a large number of genes with small individual but large combined effects (polygenic).
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Affiliation(s)
- Marius A Wenzel
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Marianne C James
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Stuart B Piertney
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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98
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de Rezende Pinto WBV, de Souza PVS, Oliveira ASB. Normal muscle structure, growth, development, and regeneration. Curr Rev Musculoskelet Med 2015; 8:176-81. [PMID: 25860794 PMCID: PMC4596171 DOI: 10.1007/s12178-015-9267-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Knowledge about biochemical, structural and physiological aspects, and properties regarding the skeletal muscle has been widely obtained in the last decades. Muscle disorders, mainly represented in neuromuscular clinical practice by acquired and hereditary myopathies, are well-recognized and frequently diagnosed in practice. Most clinical complaints and biochemical characterizations of each myopathy depends on the appropriate knowledge and interpretation of pathological findings and their comparison with normal muscle findings. Great improvement has been obtained in the last decades mainly involving the mechanisms of normal muscle architecture and physiological function in the healthy individuals. Genetic mechanisms have also been widely studied. We provide an extensive literature review involving current knowledge regarding muscle cell structure and function and embryological and regenerative processes linked to muscle lesion. An updated comprehensive description involving the main nuclear genomic regulatory mechanisms of muscle regeneration and embryogenesis is provided in this review.
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Affiliation(s)
- Wladimir Bocca Vieira de Rezende Pinto
- Division of Neuromuscular Diseases, Department of Neurology and Neurosurgery, Federal University of São Paulo (UNIFESP), Estado de Israel Street, 899. Vila Clementino, São Paulo, SP 04022-002 Brazil
| | - Paulo Victor Sgobbi de Souza
- Division of Neuromuscular Diseases, Department of Neurology and Neurosurgery, Federal University of São Paulo (UNIFESP), Estado de Israel Street, 899. Vila Clementino, São Paulo, SP 04022-002 Brazil
| | - Acary Souza Bulle Oliveira
- Division of Neuromuscular Diseases, Department of Neurology and Neurosurgery, Federal University of São Paulo (UNIFESP), Estado de Israel Street, 899. Vila Clementino, São Paulo, SP 04022-002 Brazil
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99
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Klhl31 attenuates β-catenin dependent Wnt signaling and regulates embryo myogenesis. Dev Biol 2015; 402:61-71. [DOI: 10.1016/j.ydbio.2015.02.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 11/19/2022]
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100
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Gong W, Gohla RM, Bowlin KM, Koyano-Nakagawa N, Garry DJ, Shi X. Kelch Repeat and BTB Domain Containing Protein 5 (Kbtbd5) Regulates Skeletal Muscle Myogenesis through the E2F1-DP1 Complex. J Biol Chem 2015; 290:15350-61. [PMID: 25940086 DOI: 10.1074/jbc.m114.629956] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 01/14/2023] Open
Abstract
We have previously isolated a muscle-specific Kelch gene, Kelch repeat and BTB domain containing protein 5 (Kbtbd5)/Kelch-like protein 40 (Klhl40). In this report, we identified DP1 as a direct interacting factor for Kbtbd5 using a yeast two-hybrid screen and in vitro binding assays. Our studies demonstrate that Kbtbd5 interacts and regulates the cytoplasmic localization of DP1. GST pulldown assays demonstrate that the dimerization domain of DP1 interacts with all three of the Kbtbd5 domains. We further show that Kbtbd5 promotes the ubiquitination and degradation of DP1, thereby inhibiting E2F1-DP1 activity. To investigate the in vivo function of Kbtbd5, we used gene disruption technology and engineered Kbtbd5 null mice. Targeted deletion of Kbtbd5 resulted in postnatal lethality. Histological studies reveal that the Kbtbd5 null mice have smaller muscle fibers, a disorganized sarcomeric structure, increased extracellular matrix, and decreased numbers of mitochondria compared with wild-type controls. RNA sequencing and quantitative PCR analyses demonstrate the up-regulation of E2F1 target apoptotic genes (Bnip3 and p53inp1) in Kbtbd5 null skeletal muscle. Consistent with these observations, the cellular apoptosis in Kbtbd5 null mice was increased. Breeding of Kbtbd5 null mouse into the E2F1 null background rescues the lethal phenotype of the Kbtbd5 null mice but not the growth defect. The expression of Bnip3 and p53inp1 in Kbtbd5 mutant skeletal muscle are also restored to control levels in the E2F1 null background. In summary, our studies demonstrate that Kbtbd5 regulates skeletal muscle myogenesis through the regulation of E2F1-DP1 activity.
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Affiliation(s)
- Wuming Gong
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Rachel M Gohla
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Kathy M Bowlin
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Naoko Koyano-Nakagawa
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Daniel J Garry
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Xiaozhong Shi
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
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