1
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Liu S, Hu Y, Liu F, Jiang Y, Wang H, Wu X, Hu D. Identifying Key Genes as Progression Indicators of Prostate Cancer with Castration Resistance Based on Dynamic Network Biomarker Algorithm and Weighted Gene Correlation Network Analysis. Biomedicines 2024; 12:2157. [PMID: 39335669 PMCID: PMC11429123 DOI: 10.3390/biomedicines12092157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/11/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Background: Androgen deprivation therapy (ADT) is the mainstay of treatment for prostate cancer, yet dynamic molecular changes from hormone-sensitive to castration-resistant states in patients treated with ADT remain unclear. Methods: In this study, we combined the dynamic network biomarker (DNB) method and the weighted gene co-expression network analysis (WGCNA) to identify key genes associated with the progression to a castration-resistant state in prostate cancer via the integration of single-cell and bulk RNA sequencing data. Based on the gene expression profiles of CRPC in the GEO dataset, the DNB method was used to clarify the condition of epithelial cells and find out the most significant transition signal DNB modules and genes included. Then, we calculated gene modules associated with the clinical phenotype stage based on the WGCNA. IHC was conducted to validate the expression of the key genes in CRPC and primary PCa patients Results:Nomograms, calibration plots, and ROC curves were applied to evaluate the good prognostic accuracy of the risk prediction model. Results: By combining single-cell RNA sequence data and bulk RNA sequence data, we identified a set of DNBs, whose roles involved in androgen-associated activities indicated the signals of a prostate cancer cell transition from an androgen-dependent state to a castration-resistant state. In addition, a risk prediction model including the risk score of four key genes (SCD, NARS2, ALDH1A1, and NFXL1) and other clinical-pathological characteristics was constructed and verified to be able to reasonably predict the prognosis of patients receiving ADT. Conclusions: In summary, four key genes from DNBs were identified as potential diagnostic markers for patients treated with ADT and a risk score-based nomogram will facilitate precise prognosis prediction and individualized therapeutic interventions of CRPC.
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Affiliation(s)
- Siyuan Liu
- School of Life Sciences, Central South University, Changsha 410013, China; (S.L.); (Y.H.); (Y.J.); (H.W.)
| | - Yi Hu
- School of Life Sciences, Central South University, Changsha 410013, China; (S.L.); (Y.H.); (Y.J.); (H.W.)
| | - Fei Liu
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China;
| | - Yizheng Jiang
- School of Life Sciences, Central South University, Changsha 410013, China; (S.L.); (Y.H.); (Y.J.); (H.W.)
| | - Hongrui Wang
- School of Life Sciences, Central South University, Changsha 410013, China; (S.L.); (Y.H.); (Y.J.); (H.W.)
| | - Xusheng Wu
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China;
| | - Dehua Hu
- School of Life Sciences, Central South University, Changsha 410013, China; (S.L.); (Y.H.); (Y.J.); (H.W.)
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2
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Douglas J, Cui H, Perona JJ, Vargas-Rodriguez O, Tyynismaa H, Carreño CA, Ling J, Ribas de Pouplana L, Yang XL, Ibba M, Becker H, Fischer F, Sissler M, Carter CW, Wills PR. AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases. IUBMB Life 2024. [PMID: 39247978 DOI: 10.1002/iub.2911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/07/2024] [Indexed: 09/10/2024]
Abstract
The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like tool curated by an international consortium of field experts. This platform systematizes existing knowledge about the aaRS by showcasing a taxonomically diverse selection of aaRS sequences and structures. Through its graphical user interface, AARS Online facilitates a seamless exploration between protein sequence and structure, providing a friendly introduction to the material for non-experts and a useful resource for experts. Curated multiple sequence alignments can be extracted for downstream analyses. Accessible at www.aars.online, AARS Online is a free resource to delve into the world of the aaRS.
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Affiliation(s)
- Jordan Douglas
- Department of Physics, University of Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, New Zealand
| | - Haissi Cui
- Department of Chemistry, University of Toronto, Canada
| | - John J Perona
- Department of Chemistry, Portland State University, Portland, Oregon, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut, Storrs, Connecticut, USA
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Michael Ibba
- Biological Sciences, Chapman University, Orange, California, USA
| | - Hubert Becker
- Génétique Moléculaire, Génomique Microbiologique, University of Strasbourg, France
| | - Frédéric Fischer
- Génétique Moléculaire, Génomique Microbiologique, University of Strasbourg, France
| | - Marie Sissler
- Génétique Moléculaire, Génomique Microbiologique, University of Strasbourg, France
| | - Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Peter R Wills
- Department of Physics, University of Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, New Zealand
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3
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Domínguez-Ruiz M, Olarte M, Onecha E, García-Vaquero I, Gelvez N, López G, Villamar M, Morín M, Moreno-Pelayo MA, Morales-Angulo C, Polo R, Tamayo ML, del Castillo I. Novel Cases of Non-Syndromic Hearing Impairment Caused by Pathogenic Variants in Genes Encoding Mitochondrial Aminoacyl-tRNA Synthetases. Genes (Basel) 2024; 15:951. [PMID: 39062730 PMCID: PMC11276111 DOI: 10.3390/genes15070951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Dysfunction of some mitochondrial aminoacyl-tRNA synthetases (encoded by the KARS1, HARS2, LARS2 and NARS2 genes) results in a great variety of phenotypes ranging from non-syndromic hearing impairment (NSHI) to very complex syndromes, with a predominance of neurological signs. The diversity of roles that are played by these moonlighting enzymes and the fact that most pathogenic variants are missense and affect different domains of these proteins in diverse compound heterozygous combinations make it difficult to establish genotype-phenotype correlations. We used a targeted gene-sequencing panel to investigate the presence of pathogenic variants in those four genes in cohorts of 175 Spanish and 18 Colombian familial cases with non-DFNB1 autosomal recessive NSHI. Disease-associated variants were found in five cases. Five mutations were novel as follows: c.766C>T in KARS1, c.475C>T, c.728A>C and c.1012G>A in HARS2, and c.795A>G in LARS2. We provide audiograms from patients at different ages to document the evolution of the hearing loss, which is mostly prelingual and progresses from moderate/severe to profound, the middle frequencies being more severely affected. No additional clinical sign was observed in any affected subject. Our results confirm the involvement of KARS1 in DFNB89 NSHI, for which until now there was limited evidence.
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Affiliation(s)
- María Domínguez-Ruiz
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Margarita Olarte
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Esther Onecha
- Servicio de Genética, Hospital Universitario Marqués de Valdecilla, IDIVAL, 39008 Santander, Spain
| | - Irene García-Vaquero
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Programa de Doctorado en Biología, Escuela de Doctorado de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Nancy Gelvez
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Greizy López
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Manuela Villamar
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Miguel A. Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Carmelo Morales-Angulo
- Servicio de Otorrinolaringología, Hospital Universitario Marqués de Valdecilla, IDIVAL, 39008 Santander, Spain
- Facultad de Medicina, Universidad de Cantabria, 39005 Santander, Spain
| | - Rubén Polo
- Servicio de Otorrinolaringología, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Martha L. Tamayo
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
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4
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Aneli S, Ceccatelli Berti C, Gilea AI, Birolo G, Mutti G, Pavesi A, Baruffini E, Goffrini P, Capelli C. Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae. Hum Mol Genet 2024; 33:1152-1163. [PMID: 38558123 DOI: 10.1093/hmg/ddae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, Turin 10126, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Via Santena 5, Turin 10126, Italy
| | - Giacomo Mutti
- Barcelona Supercomputing Centre (BSC-CNS), Department of Life Sciences, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Department of Mechanisms of Disease, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, United Kingdom
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5
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Antolínez-Fernández Á, Esteban-Ramos P, Fernández-Moreno MÁ, Clemente P. Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis. Front Cell Dev Biol 2024; 12:1410245. [PMID: 38855161 PMCID: PMC11157125 DOI: 10.3389/fcell.2024.1410245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Mitochondria play a central role in cellular metabolism producing the necessary ATP through oxidative phosphorylation. As a remnant of their prokaryotic past, mitochondria contain their own genome, which encodes 13 subunits of the oxidative phosphorylation system, as well as the tRNAs and rRNAs necessary for their translation in the organelle. Mitochondrial protein synthesis depends on the import of a vast array of nuclear-encoded proteins including the mitochondrial ribosome protein components, translation factors, aminoacyl-tRNA synthetases or assembly factors among others. Cryo-EM studies have improved our understanding of the composition of the mitochondrial ribosome and the factors required for mitochondrial protein synthesis and the advances in next-generation sequencing techniques have allowed for the identification of a growing number of genes involved in mitochondrial pathologies with a defective translation. These disorders are often multisystemic, affecting those tissues with a higher energy demand, and often present with neurodegenerative phenotypes. In this article, we review the known proteins required for mitochondrial translation, the disorders that derive from a defective mitochondrial protein synthesis and the animal models that have been established for their study.
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Affiliation(s)
- Álvaro Antolínez-Fernández
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Esteban-Ramos
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Clemente
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
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6
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Zhang JH, Eriani G, Zhou XL. Pathophysiology of human mitochondrial tRNA metabolism. Trends Endocrinol Metab 2024; 35:285-289. [PMID: 38307811 DOI: 10.1016/j.tem.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Mitochondria play multiple critical roles in cellular activity. In particular, mitochondrial translation is pivotal in the regulation of mitochondrial and cellular homeostasis. In this forum article, we discuss human mitochondrial tRNA metabolism and highlight its tight connection with various mitochondrial diseases caused by mutations in aminoacyl-tRNA synthetases, tRNAs, and tRNA-modifying enzymes.
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Affiliation(s)
- Jian-Hui Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, 67084 Strasbourg, France.
| | - Xiao-Long Zhou
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.
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7
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Gerard A, Mizerik E, Mohila CA, AlAwami S, Hunter JV, Kearney DL, Lalani SR, Scaglia F. Intracranial calcifications simulating Aicardi-Goutières syndrome in PARS2-related mitochondrial disease. Am J Med Genet A 2024:e63589. [PMID: 38469956 DOI: 10.1002/ajmg.a.63589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/05/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
PARS2 encodes an aminoacyl-tRNA synthetase that catalyzes the ligation of proline to mitochondrial prolyl-tRNA molecules. Diseases associated with PARS2 primarily affect the central nervous system, causing early infantile developmental epileptic encephalopathies (EIDEE; DEE75; MIM #618437) with infantile-onset neurodegeneration. Dilated cardiomyopathy has also been reported in the affected individuals. About 10 individuals to date have been described with pathogenic biallelic variants in PARS2. While many of the reported individuals succumbed to the disease in the first two decades of life, autopsy findings have not yet been reported. Here, we describe neuropathological findings in a deceased male with evidence of intracranial calcifications in the basal ganglia, thalamus, cerebellum, and white matter, similar to Aicardi-Goutières syndrome. This report describes detailed autopsy findings in a child with PARS2-related mitochondrial disease and provides plausible evidence that intracranial calcifications may be a previously unrecognized feature of this disorder.
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Affiliation(s)
- Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Elizabeth Mizerik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Carrie A Mohila
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Sarah AlAwami
- King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas, USA
| | - Debra L Kearney
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Joint BCM-CUHK Center of Medical Genetics, Chinese University of Hong Kong, Hong Kong SAR, China
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8
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Pizzamiglio C, Hanna MG, Pitceathly RDS. Primary mitochondrial diseases. HANDBOOK OF CLINICAL NEUROLOGY 2024; 204:53-76. [PMID: 39322395 DOI: 10.1016/b978-0-323-99209-1.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Primary mitochondrial diseases (PMDs) are a heterogeneous group of hereditary disorders characterized by an impairment of the mitochondrial respiratory chain. They are the most common group of genetic metabolic disorders, with a prevalence of 1 in 4,300 people. The presence of leukoencephalopathy is recognized as an important feature in many PMDs and can be a manifestation of mutations in both mitochondrial DNA (classic syndromes such as mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes; myoclonic epilepsy with ragged-red fibers [RRFs]; Leigh syndrome; and Kearns-Sayre syndrome) and nuclear DNA (mutations in maintenance genes such as POLG, MPV17, and TYMP; Leigh syndrome; and mitochondrial aminoacyl-tRNA synthetase disorders). In this chapter, PMDs associated with white matter involvement are outlined, including details of clinical presentations, brain MRI features, and elements of differential diagnoses. The current approach to the diagnosis of PMDs and management strategies are also discussed. A PMD diagnosis in a subject with leukoencephalopathy should be considered in the presence of specific brain MRI features (for example, cyst-like lesions, bilateral basal ganglia lesions, and involvement of both cerebral hemispheres and cerebellum), in addition to a complex neurologic or multisystem disorder. Establishing a genetic diagnosis is crucial to ensure appropriate genetic counseling, multidisciplinary team input, and eligibility for clinical trials.
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Affiliation(s)
- Chiara Pizzamiglio
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, London, United Kingdom.
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9
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Accogli A, Lin SJ, Severino M, Kim SH, Huang K, Rocca C, Landsverk M, Zaki MS, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D, Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Sawyer LB, Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingappa L, McDunnah P, Horvath R, Cognè B, Isidor B, Hahn A, Gripp KW, Jafarnejad SM, Østergaard E, Prada CE, Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK, Maroofian R. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genet Med 2023; 25:100938. [PMID: 37454282 PMCID: PMC11157694 DOI: 10.1016/j.gim.2023.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
PURPOSE Biallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase, have been reported in a small group of individuals displaying a neurodevelopmental phenotype but with limited neuroradiological data and insufficient evidence for causality of the variants. METHODS Exome or genome sequencing was carried out in 15 families. Clinical and neuroradiological evaluation was performed for all affected individuals, including review of 10 previously reported individuals. The pathogenicity of TARS2 variants was evaluated using in vitro assays and a zebrafish model. RESULTS We report 18 new individuals harboring biallelic TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual disability, regression, cerebellar and cerebral atrophy, basal ganglia signal alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro studies showed that variants within the TARS2301-381 region had decreased binding to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated key features of the human phenotype and unraveled dysregulation of downstream targets of mTORC1 signaling. Functional testing of the variants confirmed the pathogenicity in a zebrafish model. CONCLUSION We define the clinico-radiological spectrum of TARS2-related mitochondrial disease, unveil the likely involvement of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish a TARS2 zebrafish model as an important tool to study variant pathogenicity.
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Affiliation(s)
- Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | | | - Sung-Hoon Kim
- Goodman Cancer Institute, McGill University, Montreal, Canada; Department of Biochemistry, McGill University, Montreal, Canada
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Megan Landsverk
- University of South Dakota Sanford School of Medicine Sioux Falls, SD; Sanford Research, Pediatrics and Rare Diseases Group, Sioux Falls, SD
| | - Maha S Zaki
- Human Genetics and Genome Research Institute, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman; Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | | | - Khalid Al-Thihli
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman; Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - G Bradly Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Monica Davis
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Davide Tonduti
- Unit of Pediatric Neurology, COALA (Center for Diagnosis and Treatment of Leukodystrophies), V. Buzzi Children's Hospital, Milan, Italy; Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Chiara Doneda
- Pediatric Radiology and Neuroradiology Department, Children's Hospital Vittore Buzzi, Milan, Italy
| | - Lara M Marten
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Germany
| | - Chris Mühlhausen
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Germany
| | - Maria Gomez
- Centro de Obsetricia y Ginecologia & Centro Medico Moderno, Santo Domingo, Dominican Republic
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Rafael Mena
- Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Centro de Obsetricia y Ginecologia, Santo Domingo, Dominican Republic
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU de Nantes, Nantes Université, Nantes, France; Nantes Université, CNRS, INSERM, l'Institut du Thorax, Nantes, France
| | - Vincent Procaccio
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France; Department of Genetics, CHU Angers, Angers, France
| | | | | | | | - Heidi L Schulz
- Human Genetic center Tübingen, Baden-Württemberg, Germany
| | - Julia Mohr
- Human Genetic center Tübingen, Baden-Württemberg, Germany
| | - Saskia Biskup
- Human Genetic center Tübingen, Baden-Württemberg, Germany; CeGaT GmbH, Germany
| | - Mariana Amina Loos
- Department of Neurology, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Hilda Verónica Aráoz
- Genomics Laboratory, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Laura Davis Keppen
- University of South Dakota Sanford School of Medicine Sioux Falls, SD; Sanford Research, Pediatrics and Rare Diseases Group, Sioux Falls, SD
| | - Manali Chitre
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Lucy Raymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women and Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Lindsey B Sawyer
- Children's Hospital of the King's Daughters, Norfolk, Virginia, VA
| | - Alice A Basinger
- Children's Hospital of the King's Daughters, Norfolk, Virginia, VA
| | - Signe Vandal Pedersen
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Toni S Pearson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO; Center for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO
| | | | - Paige McDunnah
- Division of Medical Genetics, Nemours/A I duPont Hospital for Children, Wilmington, DE
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin Cognè
- Service de Génétique Médicale, CHU de Nantes, Nantes Université, Nantes, France; Nantes Université, CNRS, INSERM, l'Institut du Thorax, Nantes, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes Université, Nantes, France
| | - Andreas Hahn
- Department of Child Neurology, University Hospital, Gießen, Germany
| | - Karen W Gripp
- Division of Medical Genetics, Nemours/A I duPont Hospital for Children, Wilmington, DE
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Carlos E Prada
- Division of Genetics, Genomics, and Metabolism, Ann & Robert Lurie Children's Hospital of Chicago, Chicago; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago; Fundacion Cardiovascular de Colombia, Floridablanca, Colombia
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | | | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialized Service for Rare Mitochondrial Disorders of Adults and Children, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nahum Sonenberg
- Goodman Cancer Institute, McGill University, Montreal, Canada; Department of Biochemistry, McGill University, Montreal, Canada
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Marie Sissler
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK.
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom.
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10
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Kong LY, Wu YZ, Cheng RQ, Wang PH, Peng BW. Role of Mutations of Mitochondrial Aminoacyl-tRNA Synthetases Genes on Epileptogenesis. Mol Neurobiol 2023; 60:5482-5492. [PMID: 37316759 DOI: 10.1007/s12035-023-03429-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Mitochondria are the structures in cells that are responsible for producing energy. They contain a specific translation unit for synthesizing mitochondria-encoded respiratory chain components: the mitochondrial DNA (mt DNA). Recently, a growing number of syndromes associated with the dysfunction of mt DNA translation have been reported. However, the functions of these diseases still need to be precise and thus attract much attention. Mitochondrial tRNAs (mt tRNAs) are encoded by mt DNA; they are the primary cause of mitochondrial dysfunction and are associated with a wide range of pathologies. Previous research has shown the role of mt tRNAs in the epileptic mechanism. This review will focus on the function of mt tRNA and the role of mitochondrial aminoacyl-tRNA synthetase (mt aaRS) in order to summarize some common relevant mutant genes of mt aaRS that cause epilepsy and the specific symptoms of the disease they cause.
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Affiliation(s)
- Ling-Yue Kong
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yi-Ze Wu
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Run-Qi Cheng
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Pei-Han Wang
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Bi-Wen Peng
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.
- Department of Physiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Donghu Rd185#, Wuhan, 430071, Hubei, China.
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11
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Guang S, O'Brien BM, Fine AS, Ying M, Fatemi A, Nemeth CL. Mutations in DARS2 result in global dysregulation of mRNA metabolism and splicing. Sci Rep 2023; 13:13042. [PMID: 37563224 PMCID: PMC10415389 DOI: 10.1038/s41598-023-40107-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023] Open
Abstract
Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) is a rare neurological disorder caused by the mutations in the DARS2 gene, which encodes the mitochondrial aspartyl-tRNA synthetase. The objective of this study was to understand the impact of DARS2 mutations on cell processes through evaluation of LBSL patient stem cell derived cerebral organoids and neurons. We generated human cerebral organoids (hCOs) from induced pluripotent stem cells (iPSCs) of seven LBSL patients and three healthy controls using an unguided protocol. Single cells from 70-day-old hCOs were subjected to SMART-seq2 sequencing and bioinformatic analysis to acquire high-resolution gene and transcript expression datasets. Global gene expression analysis demonstrated dysregulation of a number of genes involved in mRNA metabolism and splicing processes within LBSL hCOs. Importantly, there were distinct and divergent gene expression profiles based on the nature of the DARS2 mutation. At the transcript level, pervasive differential transcript usage and differential spliced exon events that are involved in protein translation and metabolism were identified in LBSL hCOs. Single-cell analysis of DARS2 (exon 3) showed that some LBSL cells exclusively express transcripts lacking exon 3, indicating that not all LBSL cells can benefit from the "leaky" nature common to splice site mutations. At the gene- and transcript-level, we uncovered that dysregulated RNA splicing, protein translation and metabolism may underlie at least some of the pathophysiological mechanisms in LBSL. To confirm hCO findings, iPSC-derived neurons (iNs) were generated by overexpressing Neurogenin 2 using lentiviral vector to study neuronal growth, splicing of DARS2 exon 3 and DARS2 protein expression. Live cell imaging revealed neuronal growth defects of LBSL iNs, which was consistent with the finding of downregulated expression of genes related to neuronal differentiation in LBSL hCOs. DARS2 protein was downregulated in iNs compared to iPSCs, caused by increased exclusion of exon 3. The scope and complexity of our data imply that DARS2 is potentially involved in transcription regulation beyond its canonical role of aminoacylation. Nevertheless, our work highlights transcript-level dysregulation as a critical, and relatively unexplored, mechanism linking genetic data with neurodegenerative disorders.
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Affiliation(s)
- S Guang
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - B M O'Brien
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA
| | - A S Fine
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA
| | - M Ying
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, USA
| | - A Fatemi
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - C L Nemeth
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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López-Soldado I, Torres AG, Ventura R, Martínez-Ruiz I, Díaz-Ramos A, Planet E, Cooper D, Pazderska A, Wanic K, O'Hanlon D, O'Gorman DJ, Carbonell T, de Pouplana LR, Nolan JJ, Zorzano A, Hernández-Alvarez MI. Decreased expression of mitochondrial aminoacyl-tRNA synthetases causes downregulation of OXPHOS subunits in type 2 diabetic muscle. Redox Biol 2023; 61:102630. [PMID: 36796135 PMCID: PMC9958393 DOI: 10.1016/j.redox.2023.102630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Type 2 diabetes mellitus (T2D) affects millions of people worldwide and is one of the leading causes of morbidity and mortality. The skeletal muscle (SKM) is one of the most important tissues involved in maintaining glucose homeostasis and substrate oxidation, and it undergoes insulin resistance in T2D. In this study, we identify the existence of alterations in the expression of mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in skeletal muscle from two different forms of T2D: early-onset type 2 diabetes (YT2) (onset of the disease before 30 years of age) and the classical form of the disease (OT2). GSEA analysis from microarray studies revealed the repression of mitochondrial mt-aaRSs independently of age, which was validated by real-time PCR assays. In agreement with this, a reduced expression of several encoding mt-aaRSs was also detected in skeletal muscle from diabetic (db/db) mice but not in obese ob/ob mice. In addition, the expression of the mt-aaRSs proteins most relevant in the synthesis of mitochondrial proteins, threonyl-tRNA, and leucyl-tRNA synthetases (TARS2 and LARS2) were also repressed in muscle from db/db mice. It is likely that these alterations participate in the reduced expression of proteins synthesized in the mitochondria detected in db/db mice. We also document an increased iNOS abundance in mitochondrial-enriched muscle fractions from diabetic mice that may inhibit aminoacylation of TARS2 and LARS2 by nitrosative stress. Our results indicate a reduced expression of mt-aaRSs in skeletal muscle from T2D patients, which may participate in the reduced expression of proteins synthesized in mitochondria. An enhanced mitochondrial iNOS could play a regulatory role in diabetes.
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Affiliation(s)
- Iliana López-Soldado
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raúl Ventura
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain
| | - Inma Martínez-Ruiz
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain
| | - Angels Díaz-Ramos
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain
| | - Evarist Planet
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diane Cooper
- National Institute for Cellular Biotechnology, 3U Diabetes Partnership & School of Health and Human Performance, Dublin City University, Dublin, Ireland
| | - Agnieszka Pazderska
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Krzysztof Wanic
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Declan O'Hanlon
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Donal J O'Gorman
- National Institute for Cellular Biotechnology, 3U Diabetes Partnership & School of Health and Human Performance, Dublin City University, Dublin, Ireland
| | - Teresa Carbonell
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biologia, 08028, Barcelona, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - John J Nolan
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Antonio Zorzano
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain.
| | - María Isabel Hernández-Alvarez
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain.
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13
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Guang S, O'Brien B, Fine AS, Ying M, Fatemi A, Nemeth C. Mutations in DARS2 result in global dysregulation of mRNA metabolism and splicing. RESEARCH SQUARE 2023:rs.3.rs-2603446. [PMID: 36909591 PMCID: PMC10002802 DOI: 10.21203/rs.3.rs-2603446/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation (LBSL) is a rare neurological disorder caused by the mutations in the DARS2 gene, which encodes the mitochondrial aspartyl-tRNA synthetase. The objective of this study was to understand the impact of DARS2 mutations on cell processes through evaluation of LBSL patient stem cell derived cerebral organoids and neurons. We generated human cerebral organoids (hCOs) from induced pluripotent stem cells (iPSCs) of seven LBSL patients and three healthy controls using an unguided protocol. Single cells from 70-day-old hCOs underwent SMART-seq2 sequencing and multiple bioinformatic analysis tools were applied to high-resolution gene and transcript expression analyses. To confirm hCO findings, iPSC-derived neurons (iNs) were generated by overexpressing Neurogenin 2 using lentiviral vector to study neuronal growth, splicing of DARS2 exon 3 and DARS2 protein expression. Global gene expression analysis demonstrated dysregulation of a number of genes involved in mRNA metabolism and splicing processes within LBSL hCOs. Importantly, there were distinct and divergent gene expression profiles based on the nature of the DARS2 mutation. At the transcript level, pervasive differential transcript usage and differential spliced exon events that are involved in protein translation and metabolism were identified in LBSL hCOs. Single-cell analysis of DARS2 (exon 3) showed that some LBSL cells exclusively express transcripts lacking exon 3, indicating that not all LBSL cells can benefit from the "leaky" nature common to splice site mutations. Live cell imaging revealed neuronal growth defects of LBSL iNs, which was consistent with the finding of downregulated expression of genes related to neuronal differentiation in LBSL hCOs. DARS2 protein was downregulated in iNs compared to iPSCs, caused by increased exclusion of exon 3. At the gene- and transcript-level, we uncovered that dysregulated RNA splicing, protein translation and metabolism may underlie at least some of the pathophysiological mechanisms in LBSL. The scope and complexity of our data imply that DARS2 is potentially involved in transcription regulation beyond its canonical role of aminoacylation. Nevertheless, our work highlights transcript-level dysregulation as a critical, and relatively unexplored, mechanism linking genetic data with neurodegenerative disorders.
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Affiliation(s)
- Shiqi Guang
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | - Brett O'Brien
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | - Amena Smith Fine
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | | | - Ali Fatemi
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | - Christina Nemeth
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
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14
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He P, Wang Q, Hong X, Yuan H. Novel TARS2 variant identified in a Chinese patient with mitochondrial encephalomyopathy and a systematic review. Am J Med Genet A 2023; 191:70-76. [PMID: 36218002 DOI: 10.1002/ajmg.a.62988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/15/2022] [Accepted: 09/24/2022] [Indexed: 12/14/2022]
Abstract
Biallelic pathogenic variants in the TARS2 gene cause combined oxidative phosphorylation deficiency, subtype 21 (COXPD21, MIM #615918), which is a rare mitochondrial encephalomyopathy (ME) characterized by early-onset severe axial hypotonia, limb hypertonia, delayed psychomotor development, epilepsy, and brain anomalies. Currently, eight COXPD21 patients have been reported in the literature, and 11 pathogenic variants in TARS2 have been identified. Here, we report a 2-year-6-month-old Chinese female who presented with severe dystonia, developmental regression, absent speech, and intractable epilepsy. Laboratory examination showed persistently increased serum lactate. Brain MRI showed that the head of the caudate and partial lenticular nucleus were bilateral symmetrical T2-weighted imaging (T2WI) hyperintense and the corpus callosum was very thin. The clinical characteristics pointed to a ME. Trio-based whole-exome sequencing (WES) was employed to detect the causative variants. WES revealed novel compound heterozygous variants, c.470G>C (p.Thr157Arg) and c.2051C>T (p.Arg684Gln), in TARS2 in our patient that were inherited from the mother and father, respectively. Next, we systematically reviewed the available clinical features of COXPD21 patients and noticed that the reduced fetal movement observed in our patient may be a novel phenotype of COXPD21. These findings expand the mutation spectrum of TARS2 and provide insights into the genotype-phenotype relationship in COXPD21 as well as a foundation for its genetic counseling, diagnosis and treatment.
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Affiliation(s)
- Peiqing He
- Affiliated Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, China.,Dongguan Institute of Reproductive and Genetic Research, Dongguan, China
| | - Qingming Wang
- Affiliated Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, China.,Dongguan Institute of Reproductive and Genetic Research, Dongguan, China
| | - Xiaochun Hong
- Affiliated Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, China
| | - Haiming Yuan
- Affiliated Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, China.,Dongguan Institute of Reproductive and Genetic Research, Dongguan, China
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15
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Peng GX, Mao XL, Cao Y, Yao SY, Li QR, Chen X, Wang ED, Zhou XL. RNA granule-clustered mitochondrial aminoacyl-tRNA synthetases form multiple complexes with the potential to fine-tune tRNA aminoacylation. Nucleic Acids Res 2022; 50:12951-12968. [PMID: 36503967 PMCID: PMC9825176 DOI: 10.1093/nar/gkac1141] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/23/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial RNA metabolism is suggested to occur in identified compartmentalized foci, i.e. mitochondrial RNA granules (MRGs). Mitochondrial aminoacyl-tRNA synthetases (mito aaRSs) catalyze tRNA charging and are key components in mitochondrial gene expression. Mutations of mito aaRSs are associated with various human disorders. However, the suborganelle distribution, interaction network and regulatory mechanism of mito aaRSs remain largely unknown. Here, we found that all mito aaRSs partly colocalize with MRG, and this colocalization is likely facilitated by tRNA-binding capacity. A fraction of human mitochondrial AlaRS (hmtAlaRS) and hmtSerRS formed a direct complex via interaction between catalytic domains in vivo. Aminoacylation activities of both hmtAlaRS and hmtSerRS were fine-tuned upon complex formation in vitro. We further established a full spectrum of interaction networks via immunoprecipitation and mass spectrometry for all mito aaRSs and discovered interactions between hmtSerRS and hmtAsnRS, between hmtSerRS and hmtTyrRS and between hmtThrRS and hmtArgRS. The activity of hmtTyrRS was also influenced by the presence of hmtSerRS. Notably, hmtSerRS utilized the same catalytic domain in mediating several interactions. Altogether, our results systematically analyzed the suborganelle localization and interaction network of mito aaRSs and discovered several mito aaRS-containing complexes, deepening our understanding of the functional and regulatory mechanisms of mito aaRSs.
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Affiliation(s)
| | | | - Yating Cao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shi-Ying Yao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qing-Run Li
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Xin Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - En-Duo Wang
- Correspondence may also be addressed to En-Duo Wang. Tel: +86 21 5492 1241; Fax: +86 21 5492 1011;
| | - Xiao-Long Zhou
- To whom correspondence should be addressed. Tel: +86 21 5492 1247; Fax: +86 21 5492 1011;
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16
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Yu T, Zhang Y, Zheng WQ, Wu S, Li G, Zhang Y, Li N, Yao R, Fang P, Wang J, Zhou XL. Selective degradation of tRNASer(AGY) is the primary driver for mitochondrial seryl-tRNA synthetase-related disease. Nucleic Acids Res 2022; 50:11755-11774. [PMID: 36350636 PMCID: PMC9723649 DOI: 10.1093/nar/gkac1028] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022] Open
Abstract
Mitochondrial translation is of high significance for cellular energy homeostasis. Aminoacyl-tRNA synthetases (aaRSs) are crucial translational components. Mitochondrial aaRS variants cause various human diseases. However, the pathogenesis of the vast majority of these diseases remains unknown. Here, we identified two novel SARS2 (encoding mitochondrial seryl-tRNA synthetase) variants that cause a multisystem disorder. c.654-14T > A mutation induced mRNA mis-splicing, generating a peptide insertion in the active site; c.1519dupC swapped a critical tRNA-binding motif in the C-terminus due to stop codon readthrough. Both mutants exhibited severely diminished tRNA binding and aminoacylation capacities. A marked reduction in mitochondrial tRNASer(AGY) was observed due to RNA degradation in patient-derived induced pluripotent stem cells (iPSCs), causing impaired translation and comprehensive mitochondrial function deficiencies. These impairments were efficiently rescued by wild-type SARS2 overexpression. Either mutation caused early embryonic fatality in mice. Heterozygous mice displayed reduced muscle tissue-specific levels of tRNASers. Our findings elucidated the biochemical and cellular consequences of impaired translation mediated by SARS2, suggesting that reduced abundance of tRNASer(AGY) is a key determinant for development of SARS2-related diseases.
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Affiliation(s)
| | | | - Wen-Qiang Zheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Siqi Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Guoqiang Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Yong Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jian Wang
- Correspondence may also be addressed to Jian Wang. Tel: +86 21 3808 7371;
| | - Xiao-Long Zhou
- To whom correspondence should be addressed. Tel: +86 21 5492 1247; Fax: +86 21 5492 1011;
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17
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Turvey AK, Horvath GA, Cavalcanti ARO. Aminoacyl-tRNA synthetases in human health and disease. Front Physiol 2022; 13:1029218. [PMID: 36330207 PMCID: PMC9623071 DOI: 10.3389/fphys.2022.1029218] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/04/2022] [Indexed: 11/29/2022] Open
Abstract
The Aminoacyl-tRNA Synthetases (aaRSs) are an evolutionarily ancient family of enzymes that catalyze the esterification reaction linking a transfer RNA (tRNA) with its cognate amino acid matching the anticodon triplet of the tRNA. Proper functioning of the aaRSs to create aminoacylated (or “charged”) tRNAs is required for efficient and accurate protein synthesis. Beyond their basic canonical function in protein biosynthesis, aaRSs have a surprisingly diverse array of non-canonical functions that are actively being defined. The human genome contains 37 genes that encode unique aaRS proteins. To date, 56 human genetic diseases caused by damaging variants in aaRS genes have been described: 46 are autosomal recessive biallelic disorders and 10 are autosomal dominant monoallelic disorders. Our appreciation of human diseases caused by damaging genetic variants in the aaRSs has been greatly accelerated by the advent of next-generation sequencing, with 89% of these gene discoveries made since 2010. In addition to these genetic disorders of the aaRSs, anti-synthetase syndrome (ASSD) is a rare autoimmune inflammatory myopathy that involves the production of autoantibodies that disrupt aaRS proteins. This review provides an overview of the basic biology of aaRS proteins and describes the rapidly growing list of human diseases known to be caused by genetic variants or autoimmune targeting that affect both the canonical and non-canonical functions of these essential proteins.
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Affiliation(s)
- Alexandra K. Turvey
- Department of Biology, Pomona College, Claremont, CA, United States
- *Correspondence: Alexandra K. Turvey,
| | - Gabriella A. Horvath
- Division of Biochemical Genetics, Department of Pediatrics, University of British Columbia, BC Children’s Hospital, Vancouver, BC, Canada
- Adult Metabolic Diseases Clinic, Vancouver General Hospital, Vancouver, BC, Canada
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18
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Vafaee-Shahi M, Farhadi M, Razmara E, Morovvati S, Ghasemi S, Abedini SS, Bagher Z, Alizadeh R, Falah M. Novel phenotype and genotype spectrum of NARS2 and literature review of previous mutations. Ir J Med Sci 2022; 191:1877-1890. [PMID: 34374940 DOI: 10.1007/s11845-021-02736-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/30/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Mutations in NARS2 (MIM: 612803) are associated with combined oxidative phosphorylation deficiency 24 (COXPD24; MIM: 616239) that is a rare mitochondrial and a multisystem autosomal recessive disorder. AIMS We aimed to detect the underlying genetic factors in two siblings with progressive ataxia, epilepsy, and severe-to-profound hearing impairment. METHODS After doing medical assessments and pertinent tests (i.e., auditory brainstem responses, pure tone otoacoustic emission test, cardiac examinations, computed tomography, and electroencephalogram), because of the clinical and probable genetic heterogeneity, whole-exome sequencing was performed, and co-segregation analysis was confirmed by Sanger sequencing. Biological impacts of the novel variant were evaluated using sequence-to-function bioinformatics tools. RESULTS A novel homozygous missense variant, NM_024678.6:c.545 T > A; p.(Ile182Lys), in exon 5 of NARS2 was identified in both patients and verified by Sanger sequencing. In silico analyses introduced this variant as pathogenic. Mitral valve prolapses with mild regurgitation, brachymetatarsia, severe hallux valgus, and clubbed fingers were reported as novel manifestations in association with NARS2 gene. By doing a literature review, we also underscored the high heterogeneity of disease phenotype. CONCLUSIONS Herein, we report some novel phenotype and genotype features of two female patients in an Iranian consanguineous family with COXPD24, caused by a variant in NARS2-NM_024678.6: c.545 T > A; p.(Ile182Lys). Moreover, our data expanded the phenotype and genotype spectrum of NARS2-related disorder and confirmed an unpredictable nature of genotype-phenotype correlation in COXPD24.
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Affiliation(s)
- Mohammad Vafaee-Shahi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
- Pediatric Growth and Development Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhadi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeid Morovvati
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saeide Ghasemi
- Ali Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Bagher
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Rafieh Alizadeh
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
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19
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Mitochondrial Neurodegeneration. Cells 2022; 11:cells11040637. [PMID: 35203288 PMCID: PMC8870525 DOI: 10.3390/cells11040637] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/28/2022] [Accepted: 02/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mitochondria are cytoplasmic organelles, which generate energy as heat and ATP, the universal energy currency of the cell. This process is carried out by coupling electron stripping through oxidation of nutrient substrates with the formation of a proton-based electrochemical gradient across the inner mitochondrial membrane. Controlled dissipation of the gradient can lead to production of heat as well as ATP, via ADP phosphorylation. This process is known as oxidative phosphorylation, and is carried out by four multiheteromeric complexes (from I to IV) of the mitochondrial respiratory chain, carrying out the electron flow whose energy is stored as a proton-based electrochemical gradient. This gradient sustains a second reaction, operated by the mitochondrial ATP synthase, or complex V, which condensates ADP and Pi into ATP. Four complexes (CI, CIII, CIV, and CV) are composed of proteins encoded by genes present in two separate compartments: the nuclear genome and a small circular DNA found in mitochondria themselves, and are termed mitochondrial DNA (mtDNA). Mutations striking either genome can lead to mitochondrial impairment, determining infantile, childhood or adult neurodegeneration. Mitochondrial disorders are complex neurological syndromes, and are often part of a multisystem disorder. In this paper, we divide the diseases into those caused by mtDNA defects and those that are due to mutations involving nuclear genes; from a clinical point of view, we discuss pediatric disorders in comparison to juvenile or adult-onset conditions. The complementary genetic contributions controlling organellar function and the complexity of the biochemical pathways present in the mitochondria justify the extreme genetic and phenotypic heterogeneity of this new area of inborn errors of metabolism known as ‘mitochondrial medicine’.
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20
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Li JL, Lee NC, Chen PS, Lee GH, Wu RM. Leukoencephalopathy with Brainstem and Spinal Cord Involvement and Lactate Elevation: A Novel DARS2 Mutation and Intra-Familial Heterogeneity. Mov Disord Clin Pract 2021; 8:1116-1122. [PMID: 34631948 PMCID: PMC8485606 DOI: 10.1002/mdc3.13281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/28/2021] [Accepted: 06/27/2021] [Indexed: 11/06/2022] Open
Abstract
Background Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) is characterized by slowly progressive spastic gait, cerebellar symptoms, and posterior cord dysfunction. DARS2, which encodes mitochondrial aspartyl tRNA synthase, is associated with the rare disease. Cases The proband had gait disturbance since age 56, while her younger brother had the gait problem since his 20s and needed cane‐assistance at age 45. Both cases showed typical demyelinating features of LBSL on the magnetic resonance imaging (MRI) involving the periventricular white matter, brainstem, cerebellum and spinal cord. Sequencing of both cases showed compound heterozygous mutations: c.228‐16C>A and c.508C>T in DARS2. The c.228‐16C>A is a common mutation in splicing site of intron 2, which causes alternative splicing defect of exon 3, while the c.508C>T at the exon 6 is novel. Our patients are unique in the relative late onset and the apparent difference in disease progression. Literature Review Literatures from PubMed were reviewed. Five families showed intra‐familial heterogeneity on age at onset or clinical severity. Conclusion We identified a family of LBSL with compound heterozygous mutations, and c.508C>T at the exon 6 is a novel one. Clinical heterogeneity was observed in the family and other literatures. Further research for underlying mechanism is required.
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Affiliation(s)
- Jeng-Lin Li
- Department of Neurology National Taiwan University Hospital Taipei Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics National Taiwan University Hospital Taipei Taiwan
| | - Pin-Shiuan Chen
- Department of Neurology National Taiwan University Hospital Taipei Taiwan
| | - Gin Hoong Lee
- Department of Neurology National Taiwan University Hospital Taipei Taiwan.,Department of Medical Education National Taiwan University Hospital Taipei Taiwan
| | - Ruey-Meei Wu
- Department of Neurology National Taiwan University Hospital Taipei Taiwan.,Department of Neurology, College of Medicine National Taiwan University Taipei Taiwan
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21
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Li B, Chen K, Liu F, Zhang J, Chen X, Chen T, Chen Q, Yao Y, Hu W, Wang L, Wu Y. Developmental Angiogenesis Requires the Mitochondrial Phenylalanyl-tRNA Synthetase. Front Cardiovasc Med 2021; 8:724846. [PMID: 34540921 PMCID: PMC8440837 DOI: 10.3389/fcvm.2021.724846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/04/2021] [Indexed: 12/03/2022] Open
Abstract
Background: Mitochondrial aminoacyl-tRNA synthetases (mtARSs) catalyze the binding of specific amino acids to their cognate tRNAs and play an essential role in the synthesis of proteins encoded by mitochondrial DNA. Defects in mtARSs have been linked to human diseases, but their tissue-specific pathophysiology remains elusive. Here we examined the role of mitochondrial phenylalanyl-tRNA synthetase (FARS2) in developmental angiogenesis and its potential contribution to the pathogenesis of cardiovascular disease. Methods: Morpholinos were injected into fertilized zebrafish ova to establish an in vivo fars2 knock-down model. A visualization of the vasculature was achieved by using Tg (fli1: EGFP)y1 transgenic zebrafish. In addition, small interference RNAs (siRNAs) were transferred into human umbilical vein endothelial cells (HUVECs) to establish an in vitro FARS2 knock-down model. Cell motility, proliferation, and tubulogenesis were determined using scratch-wound CCK8, transwell-based migration, and tube formation assays. In addition, mitochondria- and non-mitochondria-related respiration were evaluated using a Seahorse XF24 analyzer and flow cytometry assays. Analyses of the expression levels of transcripts and proteins were performed using qRT-PCR and western blotting, respectively. Results: The knock-down of fars2 hampered the embryonic development in zebrafish and delayed the formation of the vasculature in Tg (fli1: EGFP)y1 transgenic zebrafish. In addition, the siRNA-mediated knock-down of FARS2 impaired angiogenesis in HUVECs as indicated by decreased cell motility and tube formation capacity. The knock-down of FARS2 also produced variable decreases in mitochondrial- and non-mitochondrial respiration in HUVECs and disrupted the regulatory pathways of angiogenesis in both HUVECs and zebrafish. Conclusion: Our current work offers novel insights into angiogenesis defects and cardiovascular diseases induced by FARS2 deficiency.
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Affiliation(s)
- Bowen Li
- Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, China
| | - Kun Chen
- Department of Anatomy, Histology and Embryology and K.K. Leung Brain Research Centre, Air Force Medical University, Xi'an, China
| | - Fangfang Liu
- Department of Neurosciences, Air Force Medical University, Xi'an, China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Northwest University, Xi'an, China
| | - Xihui Chen
- Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, China
| | - Tangdong Chen
- Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, China
| | - Qi Chen
- Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, China
| | - Yan Yao
- Department of Clinical Medicine, Yan'an University, Yan'an, China
| | - Weihong Hu
- Department of Clinical Medicine, Yan'an University, Yan'an, China
| | - Li Wang
- Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, China.,School of Aerospace Medicine, Air Force Medical University, Xi'an, China
| | - Yuanming Wu
- Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, China
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22
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Zheng WQ, Pedersen SV, Thompson K, Bellacchio E, French CE, Munro B, Pearson TS, Vogt J, Diodato D, Diemer T, Ernst A, Horvath R, Chitre M, Ek J, Wibrand F, Grange DK, Raymond L, Zhou XL, Taylor RW, Ostergaard E. Elucidating the molecular mechanisms associated with TARS2-related mitochondrial disease. Hum Mol Genet 2021; 31:523-534. [PMID: 34508595 DOI: 10.1093/hmg/ddab257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/12/2022] Open
Abstract
TARS2 encodes human mitochondrial threonyl tRNA-synthetase that is responsible for generating mitochondrial Thr-tRNAThr and clearing mischarged Ser-tRNAThr during mitochondrial translation. Pathogenic variants in TARS2 have hitherto been reported in a pair of siblings and an unrelated patient with an early onset mitochondrial encephalomyopathy and a combined respiratory chain enzyme deficiency in muscle. We here report five additional unrelated patients with TARS2-related mitochondrial diseases, expanding the clinical phenotype to also include epilepsy, dystonia, hyperhidrosis and severe hearing impairment. Additionally, we document seven novel TARS2 variants-one nonsense variant and six missense variants-that we demonstrate are pathogenic and causal of the disease presentation based on population frequency, homology modelling and functional studies that show the effects of the pathogenic variants on TARS2 stability and/or function.
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Affiliation(s)
- Wen-Qiang Zheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Signe Vandal Pedersen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emanuele Bellacchio
- Area di Ricerca Genetica e Malattie Rare, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Courtney E French
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Benjamin Munro
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Toni S Pearson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham Women's Hospital, Birmingham, UK
| | - Daria Diodato
- Neuromuscular and Neurodegenerative Disease Unit, Children Hospital Bambino Gesù, Rome, Italy
| | - Tue Diemer
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Anja Ernst
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Manali Chitre
- Department of Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Jakob Ek
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Flemming Wibrand
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Dorothy K Grange
- Department of Pediatrics, Division Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucy Raymond
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Elsebet Ostergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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23
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Parrot C, Moulinier L, Bernard F, Hashem Y, Dupuy D, Sissler M. Peculiarities of aminoacyl-tRNA synthetases from trypanosomatids. J Biol Chem 2021; 297:100913. [PMID: 34175310 PMCID: PMC8319005 DOI: 10.1016/j.jbc.2021.100913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 10/28/2022] Open
Abstract
Trypanosomatid parasites are responsible for various human diseases, such as sleeping sickness, animal trypanosomiasis, or cutaneous and visceral leishmaniases. The few available drugs to fight related parasitic infections are often toxic and present poor efficiency and specificity, and thus, finding new molecular targets is imperative. Aminoacyl-tRNA synthetases (aaRSs) are essential components of the translational machinery as they catalyze the specific attachment of an amino acid onto cognate tRNA(s). In trypanosomatids, one gene encodes both cytosolic- and mitochondrial-targeted aaRSs, with only three exceptions. We identify here a unique specific feature of aaRSs from trypanosomatids, which is that most of them harbor distinct insertion and/or extension sequences. Among the 26 identified aaRSs in the trypanosome Leishmania tarentolae, 14 contain an additional domain or a terminal extension, confirmed in mature mRNAs by direct cDNA nanopore sequencing. Moreover, these RNA-Seq data led us to address the question of aaRS dual localization and to determine splice-site locations and the 5'-UTR lengths for each mature aaRS-encoding mRNA. Altogether, our results provided evidence for at least one specific mechanism responsible for mitochondrial addressing of some L. tarentolae aaRSs. We propose that these newly identified features of trypanosomatid aaRSs could be developed as relevant drug targets to combat the diseases caused by these parasites.
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Affiliation(s)
- Camila Parrot
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Luc Moulinier
- CSTB Complex Systems and Translational Bioinformatics, ICube laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Florian Bernard
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Yaser Hashem
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Denis Dupuy
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Marie Sissler
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France.
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24
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Figuccia S, Degiorgi A, Ceccatelli Berti C, Baruffini E, Dallabona C, Goffrini P. Mitochondrial Aminoacyl-tRNA Synthetase and Disease: The Yeast Contribution for Functional Analysis of Novel Variants. Int J Mol Sci 2021; 22:ijms22094524. [PMID: 33926074 PMCID: PMC8123711 DOI: 10.3390/ijms22094524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
In most eukaryotes, mitochondrial protein synthesis is essential for oxidative phosphorylation (OXPHOS) as some subunits of the respiratory chain complexes are encoded by the mitochondrial DNA (mtDNA). Mutations affecting the mitochondrial translation apparatus have been identified as a major cause of mitochondrial diseases. These mutations include either heteroplasmic mtDNA mutations in genes encoding for the mitochondrial rRNA (mtrRNA) and tRNAs (mttRNAs) or mutations in nuclear genes encoding ribosomal proteins, initiation, elongation and termination factors, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (mtARSs). Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to their cognate tRNAs. Differently from most mttRNAs, which are encoded by mitochondrial genome, mtARSs are encoded by nuclear genes and then imported into the mitochondria after translation in the cytosol. Due to the extensive use of next-generation sequencing (NGS), an increasing number of mtARSs variants associated with large clinical heterogeneity have been identified in recent years. Being most of these variants private or sporadic, it is crucial to assess their causative role in the disease by functional analysis in model systems. This review will focus on the contributions of the yeast Saccharomyces cerevisiae in the functional validation of mutations found in mtARSs genes associated with human disorders.
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Affiliation(s)
| | | | | | | | - Cristina Dallabona
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
| | - Paola Goffrini
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
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25
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Hathazi D, Griffin H, Jennings MJ, Giunta M, Powell C, Pearce SF, Munro B, Wei W, Boczonadi V, Poulton J, Pyle A, Calabrese C, Gomez‐Duran A, Schara U, Pitceathly RDS, Hanna MG, Joost K, Cotta A, Paim JF, Navarro MM, Duff J, Mattman A, Chapman K, Servidei S, Della Marina A, Uusimaa J, Roos A, Mootha V, Hirano M, Tulinius M, Giri M, Hoffmann EP, Lochmüller H, DiMauro S, Minczuk M, Chinnery PF, Müller JS, Horvath R. Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency. EMBO J 2020; 39:e105364. [PMID: 33128823 PMCID: PMC7705457 DOI: 10.15252/embj.2020105364] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/31/2020] [Accepted: 09/09/2020] [Indexed: 12/23/2022] Open
Abstract
Reversible infantile respiratory chain deficiency (RIRCD) is a rare mitochondrial myopathy leading to severe metabolic disturbances in infants, which recover spontaneously after 6-months of age. RIRCD is associated with the homoplasmic m.14674T>C mitochondrial DNA mutation; however, only ~ 1/100 carriers develop the disease. We studied 27 affected and 15 unaffected individuals from 19 families and found additional heterozygous mutations in nuclear genes interacting with mt-tRNAGlu including EARS2 and TRMU in the majority of affected individuals, but not in healthy carriers of m.14674T>C, supporting a digenic inheritance. Our transcriptomic and proteomic analysis of patient muscle suggests a stepwise mechanism where first, the integrated stress response associated with increased FGF21 and GDF15 expression enhances the metabolism modulated by serine biosynthesis, one carbon metabolism, TCA lipid oxidation and amino acid availability, while in the second step mTOR activation leads to increased mitochondrial biogenesis. Our data suggest that the spontaneous recovery in infants with digenic mutations may be modulated by the above described changes. Similar mechanisms may explain the variable penetrance and tissue specificity of other mtDNA mutations and highlight the potential role of amino acids in improving mitochondrial disease.
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26
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Garin S, Levi O, Cohen B, Golani-Armon A, Arava YS. Localization and RNA Binding of Mitochondrial Aminoacyl tRNA Synthetases. Genes (Basel) 2020; 11:genes11101185. [PMID: 33053729 PMCID: PMC7600831 DOI: 10.3390/genes11101185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria contain a complete translation machinery that is used to translate its internally transcribed mRNAs. This machinery uses a distinct set of tRNAs that are charged with cognate amino acids inside the organelle. Interestingly, charging is executed by aminoacyl tRNA synthetases (aaRS) that are encoded by the nuclear genome, translated in the cytosol, and need to be imported into the mitochondria. Here, we review import mechanisms of these enzymes with emphasis on those that are localized to both mitochondria and cytosol. Furthermore, we describe RNA recognition features of these enzymes and their interaction with tRNA and non-tRNA molecules. The dual localization of mitochondria-destined aaRSs and their association with various RNA types impose diverse impacts on cellular physiology. Yet, the breadth and significance of these functions are not fully resolved. We highlight here possibilities for future explorations.
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27
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Felhi R, Charif M, Sfaihi L, Mkaouar-Rebai E, Desquiret-Dumas V, Kallel R, Bris C, Goudenège D, Guichet A, Bonneau D, Procaccio V, Reynier P, Amati-Bonneau P, Hachicha M, Fakhfakh F, Lenaers G. Mutations in aARS genes revealed by targeted next-generation sequencing in patients with mitochondrial diseases. Mol Biol Rep 2020; 47:3779-3787. [PMID: 32319008 DOI: 10.1007/s11033-020-05425-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/03/2020] [Indexed: 11/29/2022]
Abstract
Mitochondrial diseases are a clinically heterogeneous group of multisystemic disorders that arise as a result of various mitochondrial dysfunctions. Autosomal recessive aARS deficiencies represent a rapidly growing group of severe rare inherited mitochondrial diseases, involving multiple organs, and currently without curative option. They might be related to defects of mitochondrial aminoacyl t-RNA synthetases (mtARS) that are ubiquitous enzymes involved in mitochondrial aminoacylation and the translation process. Here, using NGS analysis of 281 nuclear genes encoding mitochondrial proteins, we identified 4 variants in different mtARS in three patients from unrelated Tunisian families, with clinical features of mitochondrial disorders. Two homozygous variants were found in KARS (c.683C>T) and AARS2 (c.1150-4C>G), respectively in two patients, while two heterozygous variants in EARS2 (c.486-7C>G) and DARS2 (c.1456C>T) were concomitantly found in the third patient. Bio-informatics investigations predicted their pathogenicity and deleterious effects on pre-mRNA splicing and on protein stability. Thus, our results suggest that mtARS mutations are common in Tunisian patients with mitochondrial diseases.
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Affiliation(s)
- Rahma Felhi
- Molecular and Functional Genetics Laboratory, Faculty of Science of Sfax, University of Sfax, Route Soukra, Km 3, Sfax, Tunisia.
| | - Majida Charif
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Genetics and Immuno-Cell Therapy Team, Mohammed First University, Oujda, Morocco
| | - Lamia Sfaihi
- Departments of Pediatry, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Emna Mkaouar-Rebai
- Molecular and Functional Genetics Laboratory, Faculty of Science of Sfax, University of Sfax, Route Soukra, Km 3, Sfax, Tunisia
| | - Valerie Desquiret-Dumas
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Rim Kallel
- Departments of Pathology, University Hospital Habib Bourguiba, Sfax, Tunisia
| | - Céline Bris
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - David Goudenège
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Agnès Guichet
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Dominique Bonneau
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Vincent Procaccio
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Pascal Reynier
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France.,Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Mongia Hachicha
- Departments of Pediatry, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Faiza Fakhfakh
- Molecular and Functional Genetics Laboratory, Faculty of Science of Sfax, University of Sfax, Route Soukra, Km 3, Sfax, Tunisia.
| | - Guy Lenaers
- MitoLab Team, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers University, Angers, France
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Peretz M, Tworowski D, Kartvelishvili E, Livingston J, Chrzanowska-Lightowlers Z, Safro M. Breaking a single hydrogen bond in the mitochondrial tRNA Phe -PheRS complex leads to phenotypic pleiotropy of human disease. FEBS J 2020; 287:3814-3826. [PMID: 32115907 PMCID: PMC7540514 DOI: 10.1111/febs.15268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/09/2020] [Accepted: 02/27/2020] [Indexed: 01/19/2023]
Abstract
Various pathogenic variants in both mitochondrial tRNAPhe and Phenylalanyl‐tRNA synthetase mitochondrial protein coding gene (FARS2) gene encoding for the human mitochondrial PheRS have been identified and associated with neurological and/or muscle‐related pathologies. An important Guanine‐34 (G34)A anticodon mutation associated with myoclonic epilepsy with ragged red fibers (MERRF) syndrome has been reported in hmit‐tRNAPhe. The majority of G34 contacts in available aaRSs‐tRNAs complexes specifically use that base as an important tRNA identity element. The network of intermolecular interactions providing its specific recognition also largely conserved. However, their conservation depends also on the invariance of the residues in the anticodon binding domain (ABD) of human mitochondrial Phenylalanyl‐tRNA synthetase (hmit‐PheRS). A defect in recognition of the anticodon of tRNAPhe may happen not only because of G34A mutation, but also due to mutations in the ABD. Indeed, a pathogenic mutation in FARS2 has been recently reported in a 9‐year‐old female patient harboring a p.Asp364Gly mutation. Asp364 is hydrogen bonded (HB) to G34 in WT hmit‐PheRS. Thus, there are two pathogenic variants disrupting HB between G34 and Asp364: one is associated with G34A mutation, and the other with Asp364Gly mutation. We have measured the rates of tRNAPhe aminoacylation catalyzed by WT hmit‐PheRS and mutant enzymes. These data ranked the residues making a HB with G34 according to their contribution to activity and the signal transduction pathway in the hmit‐PheRS‐tRNAPhe complex. Furthermore, we carried out extensive MD simulations to reveal the interdomain contact topology on the dynamic trajectories of the complex, and gaining insight into the structural and dynamic integrity effects of hmit‐PheRS complexed with tRNAPhe. Database Structural data are available in PDB database under the accession number(s): 3CMQ, 3TUP, 5MGH, 5MGV.
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Affiliation(s)
- Moshe Peretz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dmitry Tworowski
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Mark Safro
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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29
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Mitochondrial aminoacyl-tRNA synthetases. Enzymes 2020. [PMID: 33837704 DOI: 10.1016/bs.enz.2020.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
In all eukaryotic cells, protein synthesis occurs not only in the cytosol, but also in the mitochondria. Translation of mitochondrial genes requires a set of aminoacyl-tRNA synthetases, many of which are often specialized for organellar function. These enzymes have evolved unique mechanisms for tRNA recognition and for ensuring fidelity of translation. Mutations of human mitochondrial synthetases are associated with a wide range of pathogenic phenotypes, both highlighting the importance of their role in maintaining the cellular "powerhouse" and suggesting additional cellular roles.
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30
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Fine AS, Nemeth CL, Kaufman ML, Fatemi A. Mitochondrial aminoacyl-tRNA synthetase disorders: an emerging group of developmental disorders of myelination. J Neurodev Disord 2019; 11:29. [PMID: 31839000 PMCID: PMC6913031 DOI: 10.1186/s11689-019-9292-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The mitochondrial aminoacyl-tRNA synthetase proteins (mt-aaRSs) are a group of nuclear-encoded enzymes that facilitate conjugation of each of the 20 amino acids to its cognate tRNA molecule. Mitochondrial diseases are a large, clinically heterogeneous group of disorders with diverse etiologies, ages of onset, and involved organ systems. Diseases related to mt-aaRS mutations are associated with specific syndromes that affect the central nervous system and produce highly characteristic MRI patterns, prototypically the DARS2, EARS, and AARS2 leukodystrophies, which are caused by mutations in mitochondrial aspartyl-tRNA synthetase, mitochondria glutamate tRNA synthetase, and mitochondrial alanyl-tRNA synthetase, respectively. BODY: The disease patterns emerging for these leukodystrophies are distinct in terms of the age of onset, nature of disease progression, and predominance of involved white matter tracts. In DARS2 and EARS2 disorders, earlier disease onset is typically correlated with more significant brain abnormalities, rapid neurological decline, and greater disability. In AARS2 leukodystrophy cases reported thus far, there is nearly invariable progression to severe disability and atrophy of involved brain regions, often within a decade. Although most mutations are compound heterozygous inherited in an autosomal recessive fashion, homozygous variants are found in each disorder and demonstrate high phenotypic variability. Affected siblings manifest disease on a wide spectrum. CONCLUSION The syndromic nature and selective vulnerability of white matter tracts in these disorders suggests there may be a shared mechanism of mitochondrial dysfunction to target for study. There is evidence that the clinical variability and white matter tract specificity of each mt-aaRS leukodystrophy depend on both canonical and non-canonical effects of the mutations on the process of mitochondrial translation. Furthermore, different sensitivities to the mt-aaRS mutations have been observed based on cell type. Most mutations result in at least partial retention of mt-aaRS enzyme function with varied effects on the mitochondrial respiratory chain complexes. In EARS2 and AARS2 cells, this appears to result in cumulative impairment of respiration. Mt-aaRS mutations may also affect alternative biochemical pathways such as the integrated stress response, a homeostatic program in eukaryotic cells that typically confers cytoprotection, but can lead to cell death when abnormally activated in response to pathologic states. Systematic review of this group of disorders and further exploration of disease mechanisms in disease models and neural cells are warranted.
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Affiliation(s)
- Amena Smith Fine
- Moser Center for Leukodystrophies at the Kennedy Krieger Institute, Baltimore, MD 21205 USA
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205 USA
| | - Christina L. Nemeth
- Moser Center for Leukodystrophies at the Kennedy Krieger Institute, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Miriam L. Kaufman
- Moser Center for Leukodystrophies at the Kennedy Krieger Institute, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Ali Fatemi
- Moser Center for Leukodystrophies at the Kennedy Krieger Institute, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
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31
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Rand DM, Mossman JA. Mitonuclear conflict and cooperation govern the integration of genotypes, phenotypes and environments. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190188. [PMID: 31787039 PMCID: PMC6939372 DOI: 10.1098/rstb.2019.0188] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mitonuclear genome is the most successful co-evolved mutualism in the history of life on Earth. The cross-talk between the mitochondrial and nuclear genomes has been shaped by conflict and cooperation for more than 1.5 billion years, yet this system has adapted to countless genomic reorganizations by each partner, and done so under changing environments that have placed dramatic biochemical and physiological pressures on evolving lineages. From putative anaerobic origins, mitochondria emerged as the defining aerobic organelle. During this transition, the two genomes resolved rules for sex determination and transmission that made uniparental inheritance the dominant, but not a universal pattern. Mitochondria are much more than energy-producing organelles and play crucial roles in nutrient and stress signalling that can alter how nuclear genes are expressed as phenotypes. All of these interactions are examples of genotype-by-environment (GxE) interactions, gene-by-gene (GxG) interactions (epistasis) or more generally context-dependent effects on the link between genotype and phenotype. We provide evidence from our own studies in Drosophila, and from those of other systems, that mitonuclear interactions—either conflicting or cooperative—are common features of GxE and GxG. We argue that mitonuclear interactions are an important model for how to better understand the pervasive context-dependent effects underlying the architecture of complex phenotypes. Future research in this area should focus on the quantitative genetic concept of effect size to place mitochondrial links to phenotype in a proper context. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
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32
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Chakraborty S, Ibba M, Banerjee R. Biophysical characterization Of Alpers encephalopathy associated mutants of human mitochondrial phenylalanyl-tRNA synthetase. IUBMB Life 2019; 71:1141-1149. [PMID: 31241862 DOI: 10.1002/iub.2114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Abstract
Mutations in nucleus-encoded mitochondrial aminoacyl-tRNA synthetases (mitaaRSs) lead to defects in mitochondrial translation affecting the expression and function of 13 subunits of the respiratory chain complex leading to diverse pathological conditions. Mutations in the FARS2 gene encoding human mitochondrial phenylalanyl-tRNA synthetase (HsmitPheRS) have been found to be associated with two different clinical representations, infantile Alpers encephalopathy and spastic paraplegia. Here we have studied three pathogenic mutants (Tyr144Cys, Ile329Thr, and Asp391Val) associated with Alpers encephalopathy to understand how these variants affect the biophysical properties of the enzyme. These mutants have already been reported to have reduced aminoacylation activity. Our study established that the mutants are significantly more thermolabile compared to the wild-type enzyme with reduced solubility in vitro. The presence of aggregation-prone insoluble HsmitPheRS variants could have a detrimental impact on organellar translation, and potentially impact normal mitochondrial function. © 2019 IUBMB Life, 71(8): 1141-1149, 2019 © 2019 IUBMB Life, 71(8):1141-1149, 2019.
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Affiliation(s)
- Shruti Chakraborty
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, Ohio
| | - Rajat Banerjee
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
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33
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Scheidecker S, Bär S, Stoetzel C, Geoffroy V, Lannes B, Rinaldi B, Fischer F, Becker HD, Pelletier V, Pagan C, Acquaviva-Bourdain C, Kremer S, Mirande M, Tranchant C, Muller J, Friant S, Dollfus H. Mutations in KARS cause a severe neurological and neurosensory disease with optic neuropathy. Hum Mutat 2019; 40:1826-1840. [PMID: 31116475 DOI: 10.1002/humu.23799] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/25/2019] [Accepted: 05/15/2019] [Indexed: 11/09/2022]
Abstract
Mutations in genes encoding aminoacyl-tRNA synthetases have been reported in several neurological disorders. KARS is a dual localized lysyl-tRNA synthetase and its cytosolic isoform belongs to the multiple aminoacyl-tRNA synthetase complex (MSC). Biallelic mutations in the KARS gene were described in a wide phenotypic spectrum ranging from nonsyndromic deafness to complex impairments. Here, we report on a patient with severe neurological and neurosensory disease investigated by whole-exome sequencing and found to carry biallelic mutations c.683C>T (p.Pro228Leu) and c.871T>G (p.Phe291Val), the second one being novel, in the KARS gene. The patient presented with an atypical clinical presentation with an optic neuropathy not previously reported. At the cellular level, we show that cytoplasmic KARS was expressed at a lower level in patient cells and displayed decreased interaction with MSC. In vitro, these two KARS variants have a decreased aminoacylation activity compared with wild-type KARS, the p.Pro228Leu being the most affected. Our data suggest that dysfunction of cytoplasmic KARS resulted in a decreased level of translation of the nuclear-encoded lysine-rich proteins belonging to the respiratory chain complex, thus impairing mitochondria functions.
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Affiliation(s)
- Sophie Scheidecker
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Séverine Bär
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Corinne Stoetzel
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France
| | - Béatrice Lannes
- Service d'Anatomo-pathologie, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Bruno Rinaldi
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Frédéric Fischer
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Hubert D Becker
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Valérie Pelletier
- Centre de Référence pour les affections rares en génétique ophtalmologique, CARGO, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Cécile Pagan
- Service de Biochimie et Biologie Moléculaire, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Cécile Acquaviva-Bourdain
- Service de Biochimie et Biologie Moléculaire, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Stéphane Kremer
- Service de Neuroradiologie/Imagerie 2, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Marc Mirande
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Christine Tranchant
- Service de Neurologie Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sylvie Friant
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France.,Centre de Référence pour les affections rares en génétique ophtalmologique, CARGO, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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34
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Florentz C, Giegé R. History of tRNA research in strasbourg. IUBMB Life 2019; 71:1066-1087. [PMID: 31185141 DOI: 10.1002/iub.2079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/06/2019] [Indexed: 01/03/2023]
Abstract
The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl-tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two-way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health-focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1066-1087, 2019.
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Affiliation(s)
- Catherine Florentz
- Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, F-67084, 15 rue René Descartes, Strasbourg, France.,Direction de la Recherche et de la Valorisation, Université de Strasbourg, F-67084, 4 rue Blaise Pascal, Strasbourg, France
| | - Richard Giegé
- Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, F-67084, 15 rue René Descartes, Strasbourg, France
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35
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González-Serrano LE, Chihade JW, Sissler M. When a common biological role does not imply common disease outcomes: Disparate pathology linked to human mitochondrial aminoacyl-tRNA synthetases. J Biol Chem 2019; 294:5309-5320. [PMID: 30647134 PMCID: PMC6462531 DOI: 10.1074/jbc.rev118.002953] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are essential components of the mitochondrial translation machinery. The correlation of mitochondrial disorders with mutations in these enzymes has raised the interest of the scientific community over the past several years. Most surprising has been the wide-ranging presentation of clinical manifestations in patients with mt-aaRS mutations, despite the enzymes' common biochemical role. Even among cases where a common physiological system is affected, phenotypes, severity, and age of onset varies depending on which mt-aaRS is mutated. Here, we review work done thus far and propose a categorization of diseases based on tissue specificity that highlights emerging patterns. We further discuss multiple in vitro and in cellulo efforts to characterize the behavior of WT and mutant mt-aaRSs that have shaped hypotheses about the molecular causes of these pathologies. Much remains to do in order to complete our understanding of these proteins. We expect that futher work is likely to result in the discovery of new roles for the mt-aaRSs in addition to their fundamental function in mitochondrial translation, informing the development of treatment strategies and diagnoses.
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Affiliation(s)
- Ligia Elena González-Serrano
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France and
| | - Joseph W Chihade
- the Department of Chemistry, Carleton College, Northfield, Minnesota 55057
| | - Marie Sissler
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France and
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36
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Tang Y, Qin Q, Xing Y, Guo D, Di L, Jia J. AARS2 leukoencephalopathy: A new variant of mitochondrial encephalomyopathy. Mol Genet Genomic Med 2019; 7:e00582. [PMID: 30706699 PMCID: PMC6465728 DOI: 10.1002/mgg3.582] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/23/2018] [Accepted: 01/02/2019] [Indexed: 01/27/2023] Open
Abstract
Background Mutations in the mitochondrial alanyl‐transfer (t)RNA synthetase 2 (AARS2,OMIM:612035) have been linked to leukoencephalopathy recently. Till now, there have been 19 cases reported so far. However, the clinical and genetic characteristics of this disease are not fully understood. We reported an adult‐onset male leukoencephalopathy patient related to novel AARS2 gene mutations and reviewed all previous cases regarding the clinical and genetic features of AARS2 leukoencephalopathy. Methods The spectrum of clinical symptoms and the genetic analysis of the presented patient were identified and investigated. Besides this case, we assessed previously reported cases with AARS2 gene mutations. Results Here, we present a 30‐year‐old man with progressive motor deficits in the right lower limb and severe cerebellar ataxia for one year. MRI revealed extensive white matter lesions in periventricular regions and along the corticospinal tract. Genetic analysis revealed two new heterogeneous missense mutations in AARS2: c.179C>A and c.1703_1704del. We described the ragged red fiber (RRF) for the first time, suggesting that AARS2‐related leukoencephalopathy be a new variant of mitochondrial encephalomyopathy. Gradual improvement in motor function was observed with intravenous coenzyme complex treatment. We also summarized our case and all previously reported cases to provide an overview of AARS2‐related late‐onset leukoencephalopathy. Then, we compared clinical and neuroimaging features of AARS2‐related leukoencephalopathy with three other frequently diagnosed types of adult‐onset leukoencephalopathy to provide insight into diagnostic strategies. Conclusion The characteristic MRI abnormalities and clinical symptoms described here may help to distinguish AARS2‐related leukoencephalopathy from other adult‐onset leukoencephalopathies. The combination of encephalopathy and myopathy strongly suggest that AARS2‐related leukoencephalopathy is a new variant of mitochondrial encephalomyopathy. The response to coenzyme complex will shed light on future therapy investigation.
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Affiliation(s)
- Yi Tang
- Innovation Center for Neurological Disorders, Department of Neurology, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Qi Qin
- Innovation Center for Neurological Disorders, Department of Neurology, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Yi Xing
- Innovation Center for Neurological Disorders, Department of Neurology, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Dongmei Guo
- Innovation Center for Neurological Disorders, Department of Neurology, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Li Di
- Innovation Center for Neurological Disorders, Department of Neurology, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Jianping Jia
- Innovation Center for Neurological Disorders, Department of Neurology, Xuan Wu Hospital, Capital Medical University, Beijing, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing Key Laboratory of Geriatric Cognitive Disorders, Neurodegenerative Laboratory of Ministry of Education of the People's Republic of China, Beijing, China
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Ruzzenente B, Assouline Z, Barcia G, Rio M, Boddaert N, Munnich A, Rötig A, Metodiev MD. Inhibition of mitochondrial translation in fibroblasts from a patient expressing the KARS p.(Pro228Leu) variant and presenting with sensorineural deafness, developmental delay, and lactic acidosis. Hum Mutat 2018; 39:2047-2059. [PMID: 30252186 DOI: 10.1002/humu.23657] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 09/03/2018] [Accepted: 09/22/2018] [Indexed: 01/12/2023]
Abstract
Aminoacyl-tRNA synthetases are ubiquitous enzymes, which universally charge tRNAs with their cognate amino acids for use in cytosolic or organellar translation. In humans, mutations in mitochondrial tRNA synthetases have been linked to different tissue-specific pathologies. Mutations in the KARS gene, which encodes both the cytosolic and mitochondrial isoform of lysyl-tRNA synthetase, cause predominantly neurological diseases that often involve deafness, but have also been linked to cardiomyopathy, developmental delay, and lactic acidosis. Using whole exome sequencing, we identified two compound heterozygous mutations, NM_001130089.1:c.683C>T p.(Pro228Leu) and NM_001130089.1:c.1438del p.(Leu480TrpfsX3), in a patient presenting with sensorineural deafness, developmental delay, hypotonia, and lactic acidosis. Nonsense-mediated mRNA decay eliminated the truncated mRNA transcript, rendering the patient hemizygous for the missense mutation. The c.683C>T mutation was previously described, but its pathogenicity remained unexamined. Molecular characterization of patient fibroblasts revealed a multiple oxidative phosphorylation deficiency due to impaired mitochondrial translation, but no evidence of inhibition of cytosolic translation. Reintroduction of wild-type mitochondrial KARS, but not the cytosolic isoform, rescued this phenotype confirming the disease-causing nature of p.(Pro228Leu) exchange and demonstrating the mitochondrial etiology of the disease. We propose that mitochondrial translation deficiency is the probable disease culprit in this and possibly other patients with mutations in KARS.
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Affiliation(s)
- Benedetta Ruzzenente
- INSERM UMR1163, Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Zahra Assouline
- Departments of Pediatrics, Neurology and Genetics, Hôpital Necker-Enfants-Malades, Paris, France
| | - Giulia Barcia
- Departments of Pediatrics, Neurology and Genetics, Hôpital Necker-Enfants-Malades, Paris, France
| | - Marlène Rio
- Departments of Pediatrics, Neurology and Genetics, Hôpital Necker-Enfants-Malades, Paris, France
| | - Nathalie Boddaert
- Department of pediatric radiology, INSERM 1000 and INSERM UMR1136, Hôpital Necker-Enfants-Malades AP-HP, Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Arnold Munnich
- INSERM UMR1163, Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, Paris, France.,Departments of Pediatrics, Neurology and Genetics, Hôpital Necker-Enfants-Malades, Paris, France
| | - Agnès Rötig
- INSERM UMR1163, Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Metodi D Metodiev
- INSERM UMR1163, Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, Paris, France
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González-Serrano LE, Karim L, Pierre F, Schwenzer H, Rötig A, Munnich A, Sissler M. Three human aminoacyl-tRNA synthetases have distinct sub-mitochondrial localizations that are unaffected by disease-associated mutations. J Biol Chem 2018; 293:13604-13615. [PMID: 30006346 PMCID: PMC6120215 DOI: 10.1074/jbc.ra118.003400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/12/2018] [Indexed: 01/04/2023] Open
Abstract
Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are key enzymes in the mitochondrial protein translation system and catalyze the charging of amino acids on their cognate tRNAs. Mutations in their nuclear genes are associated with pathologies having a broad spectrum of clinical phenotypes, but with no clear molecular mechanism(s). For example, mutations in the nuclear genes encoding mt-AspRS and mt-ArgRS are correlated with the moderate neurodegenerative disorder leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) and with the severe neurodevelopmental disorder pontocerebellar hypoplasia type 6 (PCH6), respectively. Previous studies have shown no or only minor impacts of these mutations on the canonical properties of these enzymes, indicating that the role of the mt-aaRSs in protein synthesis is mostly not affected by these mutations, but their effects on the mitochondrial localizations of aaRSs remain unclear. Here, we demonstrate that three human aaRSs, mt-AspRS, mt-ArgRS, and LysRS, each have a specific sub-mitochondrial distribution, with mt-ArgRS being exclusively localized in the membrane, LysRS exclusively in the soluble fraction, and mt-AspRS being present in both. Chemical treatments revealed that mt-AspRs is anchored in the mitochondrial membrane through electrostatic interactions, whereas mt-ArgRS uses hydrophobic interactions. We also report that novel mutations in mt-AspRS and mt-ArgRS genes from individuals with LBSL and PCH6, respectively, had no significant impact on the mitochondrial localizations of mt-AspRS and mt-ArgRS. The variable sub-mitochondrial locations for these three mt-aaRSs strongly suggest the existence of additional enzyme properties, requiring further investigation to unravel the mechanisms underlying the two neurodegenerative disorders.
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Affiliation(s)
- Ligia Elena González-Serrano
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67084 Strasbourg, France and
| | - Loukmane Karim
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67084 Strasbourg, France and
| | - Florian Pierre
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67084 Strasbourg, France and
| | - Hagen Schwenzer
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67084 Strasbourg, France and
| | - Agnès Rötig
- the INSERM UMR 1163, Laboratory of Genetics of Mitochondrial Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, F-75015 Paris, France
| | - Arnold Munnich
- the INSERM UMR 1163, Laboratory of Genetics of Mitochondrial Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, F-75015 Paris, France
| | - Marie Sissler
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67084 Strasbourg, France and
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Sissler M, González-Serrano LE, Westhof E. Recent Advances in Mitochondrial Aminoacyl-tRNA Synthetases and Disease. Trends Mol Med 2017; 23:693-708. [DOI: 10.1016/j.molmed.2017.06.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/08/2017] [Accepted: 06/14/2017] [Indexed: 01/02/2023]
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Moulinier L, Ripp R, Castillo G, Poch O, Sissler M. MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease-causing mutations in human mitochondrial aminoacyl-tRNA synthetases. Hum Mutat 2017; 38:1316-1324. [PMID: 28608363 PMCID: PMC5638098 DOI: 10.1002/humu.23277] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 11/25/2022]
Abstract
Numerous mutations in each of the mitochondrial aminoacyl‐tRNA synthetases (aaRSs) have been implicated in human diseases. The mutations are autosomal and recessive and lead mainly to neurological disorders, although with pleiotropic effects. The processes and interactions that drive the etiology of the disorders associated with mitochondrial aaRSs (mt‐aaRSs) are far from understood. The complexity of the clinical, genetic, and structural data requires concerted, interdisciplinary efforts to understand the molecular biology of these disorders. Toward this goal, we designed MiSynPat, a comprehensive knowledge base together with an ergonomic Web server designed to organize and access all pertinent information (sequences, multiple sequence alignments, structures, disease descriptions, mutation characteristics, original literature) on the disease‐linked human mt‐aaRSs. With MiSynPat, a user can also evaluate the impact of a possible mutation on sequence‐conservation‐structure in order to foster the links between basic and clinical researchers and to facilitate future diagnosis. The proposed integrated view, coupled with research on disease‐related mt‐aaRSs, will help to reveal new functions for these enzymes and to open new vistas in the molecular biology of the cell. The purpose of MiSynPat, freely available at http://misynpat.org, is to constitute a reference and a converging resource for scientists and clinicians.
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Affiliation(s)
- Luc Moulinier
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Raymond Ripp
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Gaston Castillo
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France.,Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, Strasbourg, France
| | - Olivier Poch
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie Sissler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, Strasbourg, France
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