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Boopathy S, Luce BE, Lugo CM, Hakim P, McDonald J, Kim HL, Ponce J, Ueberheide BM, Chao LH. Identification of SLC25A46 interaction interfaces with mitochondrial membrane fusogens Opa1 and Mfn2. J Biol Chem 2024; 300:107740. [PMID: 39222684 DOI: 10.1016/j.jbc.2024.107740] [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: 12/31/2023] [Revised: 07/27/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
Mitochondrial fusion requires the sequential merger of four bilayers to two. The outer-membrane solute carrier family 25 member (SLC25A46) interacts with both the outer and inner membrane dynamin family GTPases mitofusin 1/2 and optic atrophy 1 (Opa1). While SLC25A46 levels are known to affect mitochondrial morphology, how SLC25A46 interacts with mitofusin 1/2 and Opa1 to regulate membrane fusion is not understood. In this study, we use crosslinking mass spectrometry and AlphaFold 2 modeling to identify interfaces mediating an SLC25A46 interaction with Opa1 and Mfn2. We reveal that the bundle signaling element of Opa1 interacts with SLC25A46, and present evidence of an Mfn2 interaction involving the SLC25A46 cytosolic face. We validate these newly identified interaction interfaces and show that they play a role in mitochondrial network maintenance.
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Affiliation(s)
- Sivakumar Boopathy
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston Massachusetts, USA
| | - Bridget E Luce
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Camila Makhlouta Lugo
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Pusparanee Hakim
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Julie McDonald
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Ha Lin Kim
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Jackeline Ponce
- Proteomics Resource Center, Division of Advanced Research Technologies, New York University Langone Health Center, New York New York, USA
| | - Beatrix M Ueberheide
- Proteomics Resource Center, Division of Advanced Research Technologies, New York University Langone Health Center, New York New York, USA; Department of Biochemistry and Molecular Pharmacology, New York University Langone Health Center, New York New York, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston Massachusetts, USA.
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2
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Boopathy S, Luce BE, Lugo CM, Hakim P, McDonald J, Kim HL, Ponce J, Ueberheide BM, Chao LH. Identification of SLC25A46 interaction interfaces with mitochondrial membrane fusogens Opa1 and Mfn2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573615. [PMID: 38234813 PMCID: PMC10793391 DOI: 10.1101/2023.12.29.573615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Mitochondrial fusion requires the sequential merger of four bilayers to two. The outer-membrane solute carrier protein SLC25A46 interacts with both the outer and inner-membrane dynamin family GTPases Mfn1/2 and Opa1. While SLC25A46 levels are known to affect mitochondrial morphology, how SLC25A46 interacts with Mfn1/2 and Opa1 to regulate membrane fusion is not understood. In this study, we use crosslinking mass-spectrometry and AlphaFold 2 modeling to identify interfaces mediating a SLC25A46 interactions with Opa1 and Mfn2. We reveal that the bundle signaling element of Opa1 interacts with SLC25A46, and present evidence of a Mfn2 interaction involving the SLC25A46 cytosolic face. We validate these newly identified interaction interfaces and show that they play a role in mitochondrial network maintenance.
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3
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Guillaume A, Stejskal V, Smits G, Kelen D. A novel homozygous variant in SLC25A46 gene associated with pontocerebellar hypoplasia type 1E: a case report. Front Pediatr 2024; 12:1303772. [PMID: 38464896 PMCID: PMC10920260 DOI: 10.3389/fped.2024.1303772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
Neonatal encephalopathy (NE) is a complex clinical condition with diverse etiologies. Hypoxic-ischemic encephalopathy (HIE) is a major contributor to NE cases. However, distinguishing NE subtypes, such as pontocerebellar hypoplasia type 1E (PCH1E), from HIE can be challenging due to overlapping clinical features. Here, we present a case of PCH1E in a neonate with a homozygous mutation c.72delT p. (Phe24LeufsTer20) in the SLC25A46 gene. The severity of PCH1E associated NE highlighted the significance of early recognition to guide appropriate clinical management.
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Affiliation(s)
- Adrien Guillaume
- Neonatal Intensive Care Unit, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Guillaume Smits
- Center of Human Genetics, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Dorottya Kelen
- Neonatal Intensive Care Unit, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles (ULB), Brussels, Belgium
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4
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Nguyen T, Shabot S, Yngve D, Abouleish A. Anesthetic Management for a Child With a Newly Identified Mitochondrial Disease SLC25A46 Mutation: A Case Report. Cureus 2023; 15:e47076. [PMID: 38021708 PMCID: PMC10645459 DOI: 10.7759/cureus.47076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2023] [Indexed: 12/01/2023] Open
Abstract
SLC25A46 mutation is a newly recognized mitochondrial mutation causing neurological and muscular abnormalities. We describe a first-ever report of the anesthetic management of a seven-year-old boy with an SLC25A46 mutation during a major orthopedic procedure. The patient was nonverbal and presented with cerebral visual impairment, torticollis, and lower extremity contractures. Because of his new diagnosis of mitochondrial disease and history of delayed awakening after anesthesia, we performed general anesthesia with sevoflurane, a low-dose ketamine infusion, and small doses of fentanyl while avoiding propofol and maintaining normoglycemia and normothermia. No postoperative complications were noted during the recovery period.
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Affiliation(s)
- Thong Nguyen
- Anesthesiology and Perioperative Medicine, Texas Children's Hospital, Houston, USA
| | - Sarah Shabot
- Anesthesiology and Perioperative Medicine, University of Texas Medical Branch, Galveston, USA
| | - David Yngve
- Orthopedic Surgery and Rehabilitation, University of Texas Medical Branch, Galveston, USA
| | - Amr Abouleish
- Anesthesiology and Perioperative Medicine, University of Texas Medical Branch, Galveston, USA
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5
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Schuettpelz J, Janer A, Antonicka H, Shoubridge EA. The role of the mitochondrial outer membrane protein SLC25A46 in mitochondrial fission and fusion. Life Sci Alliance 2023; 6:e202301914. [PMID: 36977595 PMCID: PMC10052876 DOI: 10.26508/lsa.202301914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Mutations in SLC25A46 underlie a wide spectrum of neurodegenerative diseases associated with alterations in mitochondrial morphology. We established an SLC25A46 knock-out cell line in human fibroblasts and studied the pathogenicity of three variants (p.T142I, p.R257Q, and p.E335D). Mitochondria were fragmented in the knock-out cell line and hyperfused in all pathogenic variants. The loss of SLC25A46 led to abnormalities in the mitochondrial cristae ultrastructure that were not rescued by the expression of the variants. SLC25A46 was present in discrete puncta at mitochondrial branch points and tips of mitochondrial tubules, co-localizing with DRP1 and OPA1. Virtually, all fission/fusion events were demarcated by a SLC25A46 focus. SLC25A46 co-immunoprecipitated with the fusion machinery, and loss of function altered the oligomerization state of OPA1 and MFN2. Proximity interaction mapping identified components of the ER membrane, lipid transfer proteins, and mitochondrial outer membrane proteins, indicating that it is present at interorganellar contact sites. SLC25A46 loss of function led to altered mitochondrial lipid composition, suggesting that it may facilitate interorganellar lipid flux or play a role in membrane remodeling associated with mitochondrial fusion and fission.
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Affiliation(s)
- Jana Schuettpelz
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Alexandre Janer
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Hana Antonicka
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Eric A Shoubridge
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Canada
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6
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Santo-Domingo J, Lassueur S, Galindo AN, Alvarez-Illera P, Romero-Sanz S, Caldero-Escudero E, de la Fuente S, Dayon L, Wiederkehr A. SLC25A46 promotes mitochondrial fission and mediates resistance to lipotoxic stress in INS-1E insulin-secreting cells. J Cell Sci 2023; 136:jcs260049. [PMID: 36942724 DOI: 10.1242/jcs.260049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Glucose sensing in pancreatic β-cells depends on oxidative phosphorylation and mitochondria-derived signals that promote insulin secretion. Using mass spectrometry-based phosphoproteomics to search for downstream effectors of glucose-dependent signal transduction in INS-1E insulinoma cells, we identified the outer mitochondrial membrane protein SLC25A46. Under resting glucose concentrations, SLC25A46 was phosphorylated on a pair of threonine residues (T44/T45) and was dephosphorylated in response to glucose-induced Ca2+ signals. Overexpression of SLC25A46 in INS-1E cells caused complete mitochondrial fragmentation, resulting in a mild mitochondrial defect associated with lowered glucose-induced insulin secretion. In contrast, inactivation of the Slc25a46 gene resulted in dramatic mitochondrial hyperfusion, without affecting respiratory activity or insulin secretion. Consequently, SLC25A46 is not essential for metabolism-secretion coupling under normal nutrient conditions. Importantly, insulin-secreting cells lacking SLC25A46 had an exacerbated sensitivity to lipotoxic conditions, undergoing massive apoptosis when exposed to palmitate. Therefore, in addition to its role in mitochondrial dynamics, SLC25A46 plays a role in preventing mitochondria-induced apoptosis in INS-E cells exposed to nutrient stress. By protecting mitochondria, SLC25A46 might help to maintain β-cell mass essential for blood glucose control.
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Affiliation(s)
- Jaime Santo-Domingo
- Department of Cell Biology, Nestlé Institute of Health Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Steve Lassueur
- Department of Cell Biology, Nestlé Institute of Health Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Pilar Alvarez-Illera
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Silvia Romero-Sanz
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Elena Caldero-Escudero
- Department of Biochemistry and Molecular Biology, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Faculty of Medicine, 47003 Valladolid, Spain
| | - Sergio de la Fuente
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Andreas Wiederkehr
- Department of Cell Biology, Nestlé Institute of Health Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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7
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Horvath R, Medina J, Reilly MM, Shy ME, Zuchner S. Peripheral neuropathy in mitochondrial disease. HANDBOOK OF CLINICAL NEUROLOGY 2023; 194:99-116. [PMID: 36813324 DOI: 10.1016/b978-0-12-821751-1.00014-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Mitochondria are essential for the health and viability of both motor and sensory neurons and their axons. Processes that disrupt their normal distribution and transport along axons will likely cause peripheral neuropathies. Similarly, mutations in mtDNA or nuclear encoded genes result in neuropathies that either stand alone or are part of multisystem disorders. This chapter focuses on the more common genetic forms and characteristic clinical phenotypes of "mitochondrial" peripheral neuropathies. We also explain how these various mitochondrial abnormalities cause peripheral neuropathy. In a patient with a neuropathy either due to a mutation in a nuclear or an mtDNA gene, clinical investigations aim to characterize the neuropathy and make an accurate diagnosis. In some patients, this may be relatively straightforward, where a clinical assessment and nerve conduction studies followed by genetic testing is all that is needed. In others, multiple investigations including a muscle biopsy, CNS imaging, CSF analysis, and a wide range of metabolic and genetic tests in blood and muscle may be needed to establish diagnosis.
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Affiliation(s)
- Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, John van Geest Centre for Brain Repair, Cambridge, United Kingdom.
| | - Jessica Medina
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Michael E Shy
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
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8
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Kodal LS, Hammer-Hansen S, Holm-Yildiz S, Grønskov K, Karstensen HG, Dysgaard T. Case report: A novel variant in SLC25A46 causing sensorimotor polyneuropathy and optic atrophy. Front Neurol 2022; 13:1066040. [PMID: 36578309 PMCID: PMC9790965 DOI: 10.3389/fneur.2022.1066040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Abstract
SLC25A46 is a mitochondrial protein involved in mitochondrial dynamics. Recently, bi-allelic variants have been identified as a pathogenic cause in a spectrum of neurological syndromes. We report a novel homozygous SLC25A46 variant in two siblings, originating from Iraq. Both presented with optic atrophy and varying neurological symptoms. The neurological examination and nerve conduction studies were consistent with sensorimotor polyneuropathy, one having mild polyneuropathy and the other pronounced polyneuropathy. The cases illustrate the disease spectrum and provide substantial information to the knowledge of polyneuropathy caused by SLC25A46 variants. It further highlights the diagnostic potentials of whole exome sequencing which can improve future understanding of disease mechanisms.
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Affiliation(s)
- Louise Sloth Kodal
- Department of Neurology, Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark,*Correspondence: Louise Sloth Kodal
| | - Sophia Hammer-Hansen
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sonja Holm-Yildiz
- Department of Neurology, Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Tina Dysgaard
- Department of Neurology, Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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9
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Elsherbini AM, Alsamman AM, Elsherbiny NM, El-Sherbiny M, Ahmed R, Ebrahim HA, Bakkach J. Decoding Diabetes Biomarkers and Related Molecular Mechanisms by Using Machine Learning, Text Mining, and Gene Expression Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13890. [PMID: 36360783 PMCID: PMC9656783 DOI: 10.3390/ijerph192113890] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 05/13/2023]
Abstract
The molecular basis of diabetes mellitus is yet to be fully elucidated. We aimed to identify the most frequently reported and differential expressed genes (DEGs) in diabetes by using bioinformatics approaches. Text mining was used to screen 40,225 article abstracts from diabetes literature. These studies highlighted 5939 diabetes-related genes spread across 22 human chromosomes, with 112 genes mentioned in more than 50 studies. Among these genes, HNF4A, PPARA, VEGFA, TCF7L2, HLA-DRB1, PPARG, NOS3, KCNJ11, PRKAA2, and HNF1A were mentioned in more than 200 articles. These genes are correlated with the regulation of glycogen and polysaccharide, adipogenesis, AGE/RAGE, and macrophage differentiation. Three datasets (44 patients and 57 controls) were subjected to gene expression analysis. The analysis revealed 135 significant DEGs, of which CEACAM6, ENPP4, HDAC5, HPCAL1, PARVG, STYXL1, VPS28, ZBTB33, ZFP37 and CCDC58 were the top 10 DEGs. These genes were enriched in aerobic respiration, T-cell antigen receptor pathway, tricarboxylic acid metabolic process, vitamin D receptor pathway, toll-like receptor signaling, and endoplasmic reticulum (ER) unfolded protein response. The results of text mining and gene expression analyses used as attribute values for machine learning (ML) analysis. The decision tree, extra-tree regressor and random forest algorithms were used in ML analysis to identify unique markers that could be used as diabetes diagnosis tools. These algorithms produced prediction models with accuracy ranges from 0.6364 to 0.88 and overall confidence interval (CI) of 95%. There were 39 biomarkers that could distinguish diabetic and non-diabetic patients, 12 of which were repeated multiple times. The majority of these genes are associated with stress response, signalling regulation, locomotion, cell motility, growth, and muscle adaptation. Machine learning algorithms highlighted the use of the HLA-DQB1 gene as a biomarker for diabetes early detection. Our data mining and gene expression analysis have provided useful information about potential biomarkers in diabetes.
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Affiliation(s)
- Amira M. Elsherbini
- Department of Oral Biology, Faculty of Dentistry, Mansoura University, Mansoura 35116, Egypt
| | - Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Nehal M. Elsherbiny
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35116, Egypt
| | - Mohamed El-Sherbiny
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh 71666, Saudi Arabia
- Department of Anatomy, Mansoura Faculty of Medicine, Mansoura University, Mansoura 35116, Egypt
| | - Rehab Ahmed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan
| | - Hasnaa Ali Ebrahim
- Department of Basic Medical Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Joaira Bakkach
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaâdi University Morocco, Tétouan 93000, Morocco
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10
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Wang L, Yang Z, He X, Pu S, Yang C, Wu Q, Zhou Z, Cen X, Zhao H. Mitochondrial protein dysfunction in pathogenesis of neurological diseases. Front Mol Neurosci 2022; 15:974480. [PMID: 36157077 PMCID: PMC9489860 DOI: 10.3389/fnmol.2022.974480] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Mitochondria are essential organelles for neuronal function and cell survival. Besides the well-known bioenergetics, additional mitochondrial roles in calcium signaling, lipid biogenesis, regulation of reactive oxygen species, and apoptosis are pivotal in diverse cellular processes. The mitochondrial proteome encompasses about 1,500 proteins encoded by both the nuclear DNA and the maternally inherited mitochondrial DNA. Mutations in the nuclear or mitochondrial genome, or combinations of both, can result in mitochondrial protein deficiencies and mitochondrial malfunction. Therefore, mitochondrial quality control by proteins involved in various surveillance mechanisms is critical for neuronal integrity and viability. Abnormal proteins involved in mitochondrial bioenergetics, dynamics, mitophagy, import machinery, ion channels, and mitochondrial DNA maintenance have been linked to the pathogenesis of a number of neurological diseases. The goal of this review is to give an overview of these pathways and to summarize the interconnections between mitochondrial protein dysfunction and neurological diseases.
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Affiliation(s)
- Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Ziyun Yang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Xiumei He
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Shiming Pu
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Cheng Yang
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Qiong Wu
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Zuping Zhou
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Xiaobo Cen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Hongxia Zhao
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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11
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Holling T, Nampoothiri S, Tarhan B, Schneeberger PE, Vinayan KP, Yesodharan D, Roy AG, Radhakrishnan P, Alawi M, Rhodes L, Girisha KM, Kang PB, Kutsche K. Novel biallelic variants expand the SLC5A6-related phenotypic spectrum. Eur J Hum Genet 2022; 30:439-449. [PMID: 35013551 PMCID: PMC8747999 DOI: 10.1038/s41431-021-01033-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022] Open
Abstract
The sodium (Na+):multivitamin transporter (SMVT), encoded by SLC5A6, belongs to the sodium:solute symporter family and is required for the Na+-dependent uptake of biotin (vitamin B7), pantothenic acid (vitamin B5), the vitamin-like substance α-lipoic acid, and iodide. Compound heterozygous SLC5A6 variants have been reported in individuals with variable multisystemic disorder, including failure to thrive, developmental delay, seizures, cerebral palsy, brain atrophy, gastrointestinal problems, immunodeficiency, and/or osteopenia. We expand the phenotypic spectrum associated with biallelic SLC5A6 variants affecting function by reporting five individuals from three families with motor neuropathies. We identified the homozygous variant c.1285 A > G [p.(Ser429Gly)] in three affected siblings and a simplex patient and the maternally inherited c.280 C > T [p.(Arg94*)] variant and the paternally inherited c.485 A > G [p.(Tyr162Cys)] variant in the simplex patient of the third family. Both missense variants were predicted to affect function by in silico tools. 3D homology modeling of the human SMVT revealed 13 transmembrane helices (TMs) and Tyr162 and Ser429 to be located at the cytoplasmic facing region of TM4 and within TM11, respectively. The SLC5A6 missense variants p.(Tyr162Cys) and p.(Ser429Gly) did not affect plasma membrane localization of the ectopically expressed multivitamin transporter suggesting reduced but not abolished function, such as lower catalytic activity. Targeted therapeutic intervention yielded clinical improvement in four of the five patients. Early molecular diagnosis by exome sequencing is essential for timely replacement therapy in affected individuals.
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Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Bedirhan Tarhan
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Pauline E Schneeberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Amedes MVZ Wagnerstibbe für Laboratoriumsmedizin, Hämostaseologie, Humangenetik und Mikrobiologie Hannover, 30159, Hannover, Germany
| | | | - Dhanya Yesodharan
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Arun Grace Roy
- Department of Neurology, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Periyasamy Radhakrishnan
- Suma Genomics Pvt. Ltd, Manipal Universal Technology Business Incubator (MUTBI), Manipal, 576104, India
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, 576104, India
| | - Peter B Kang
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, 32610, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
- Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
- Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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12
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Yamada M, Suzuki H, Adachi H, Noguchi A, Miya F, Takahashi T, Kosaki K. Diagnosis of SLC25A46-related pontocerebellar hypoplasia in two siblings with fulminant neonatal course: role of postmortem CT and whole genomic analysis: a case report. BMC Neurol 2022; 22:20. [PMID: 35012485 PMCID: PMC8750809 DOI: 10.1186/s12883-021-02540-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Pontocerebellar hypoplasia (PCH) is increasingly known as a degenerative disease rather than simple “hypoplasia”. At least 21 disease-causing genes have been identified for PCH so far. Because PCH is very heterogenous, prognostic prediction based solely on clinical or radiologic findings is not feasible. Case presentation Here, we report two siblings who had a fulminant neonatal course. The documentation of pontocerebellar hypoplasia by postmortem brain CT imaging in one of the siblings and a subsequent complex and comprehensive whole genome analysis established that both siblings had bi-allelic compound heterozygous variants (a splicing variant and a deletion) in the SLC25A46 gene which encodes a solute carrier protein essential for mitochondrial function. Long-read whole genome sequencing was required to confirm the presence of the deletion. The fulminant courses suggest that SLC25A46-related PCH is an acutely progressive degenerative condition starting in utero, rather than a simple static hypoplasia. Conclusion The genomic analysis was instrumental and essential to solving the enigma of the unexplained neonatal deaths of these two siblings and to provide accurate genetic counseling.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroyuki Adachi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tsutomu Takahashi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
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13
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Perivolidi VI, Violitzi F, Ioannidou E, Rinotas V, Stamatakis G, Samiotaki M, Panayotou G, Douni E. Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG. J Proteome Res 2022; 21:375-394. [PMID: 34983179 DOI: 10.1021/acs.jproteome.1c00728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The outer mitochondrial membrane protein SLC25A46 has been recently identified as a novel genetic cause of a wide spectrum of neurological diseases. The aim of the present work was to elucidate the physiological role of SLC25A46 through the identification of its interactome with immunoprecipitation and proteomic analysis in whole cell extracts from the cerebellum, cerebrum, heart, and thymus of transgenic mice expressing ubiquitously SLC25A46-FLAG. Our analysis identified 371 novel putative interactors of SLC25A46 and confirmed 17 known ones. A total of 79 co-immunoprecipitated proteins were common in two or more tissues, mainly participating in mitochondrial activities such as oxidative phosphorylation (OXPHOS) and ATP production, active transport of ions or molecules, and the metabolism. Tissue-specific co-immunoprecipitated proteins were enriched for synapse annotated proteins in the cerebellum and cerebrum for metabolic processes in the heart and for nuclear processes and proteasome in the thymus. Our proteomic approach confirmed known mitochondrial interactors of SLC25A46 including MICOS complex subunits and also OPA1 and VDACs, while we identified novel interactors including the ADP/ATP translocases SLC25A4 and SLC25A5, subunits of the OXPHOS complexes and F1Fo-ATP synthase, and components of the mitochondria-ER contact sites. Our results show that SLC25A46 interacts with a large number of proteins and protein complexes involved in the mitochondria architecture, energy production, and flux and also in inter-organellar contacts.
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Affiliation(s)
- Vasiliki-Iris Perivolidi
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.,Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Foteini Violitzi
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.,Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Elisavet Ioannidou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Vagelis Rinotas
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - George Stamatakis
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Eleni Douni
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.,Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
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14
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Zeviani M, Carelli V. Mitochondrial Retinopathies. Int J Mol Sci 2021; 23:210. [PMID: 35008635 PMCID: PMC8745158 DOI: 10.3390/ijms23010210] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 12/13/2022] Open
Abstract
The retina is an exquisite target for defects of oxidative phosphorylation (OXPHOS) associated with mitochondrial impairment. Retinal involvement occurs in two ways, retinal dystrophy (retinitis pigmentosa) and subacute or chronic optic atrophy, which are the most common clinical entities. Both can present as isolated or virtually exclusive conditions, or as part of more complex, frequently multisystem syndromes. In most cases, mutations of mtDNA have been found in association with mitochondrial retinopathy. The main genetic abnormalities of mtDNA include mutations associated with neurogenic muscle weakness, ataxia and retinitis pigmentosa (NARP) sometimes with earlier onset and increased severity (maternally inherited Leigh syndrome, MILS), single large-scale deletions determining Kearns-Sayre syndrome (KSS, of which retinal dystrophy is a cardinal symptom), and mutations, particularly in mtDNA-encoded ND genes, associated with Leber hereditary optic neuropathy (LHON). However, mutations in nuclear genes can also cause mitochondrial retinopathy, including autosomal recessive phenocopies of LHON, and slowly progressive optic atrophy caused by dominant or, more rarely, recessive, mutations in the fusion/mitochondrial shaping protein OPA1, encoded by a nuclear gene on chromosome 3q29.
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Affiliation(s)
- Massimo Zeviani
- Department of Neurosciences, The Clinical School, University of Padova, 35128 Padova, Italy
- Veneto Institute of Molecular Medicine, Via Orus 2, 35128 Padova, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy
- Programma di Neurogenetica, IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura 6, 40139 Bologna, Italy
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15
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Li Q, Madden JA, Lin J, Shi J, Rosen SM, Schmitz-Abe K, Agrawal PB. Reanalysis of Exome Data Identifies Novel SLC25A46 Variants Associated with Leigh Syndrome. J Pers Med 2021; 11:jpm11121277. [PMID: 34945750 PMCID: PMC8703603 DOI: 10.3390/jpm11121277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
SLC25A46 (solute carrier family 25 member 46) mutations have been linked to various neurological diseases with recessive inheritance, including Leigh syndrome, optic atrophy, and lethal congenital pontocerebellar hypoplasia. SLC25A46 is expressed in the outer membrane of mitochondria, where it plays a critical role in mitochondrial dynamics. A deceased 7-month-old female infant was suspected to have Leigh syndrome. Clinical exome sequencing was non-diagnostic, but research reanalysis of the sequencing data identified two novel variants in SLC25A46: a missense (c.1039C>T, p.Arg347Cys; NM_138773, hg19) and a donor splice region variant (c.283+5G>A) in intron 1. Both variants were predicted to be damaging. Sanger sequencing of cDNA detected a single missense allele in the patient compared to control, and the SLC25A46 transcript levels were also reduced due to the splice region variant. Additionally, Western blot analysis of whole-cell lysate showed a decrease of SLC25A46 expression in proband fibroblasts, relative to control cells. Further, analysis of mitochondrial morphology revealed evidence of increased fragmentation of the mitochondrial network in proband fibroblasts, compared to control cells. Collectively, our findings suggest that these novel variants in SLC24A46, the donor splice one and the missense variant, are the cause of the neurological phenotype in this proband.
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Affiliation(s)
- Qifei Li
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (Q.L.); (J.L.); (S.M.R.); (K.S.-A.)
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jill A. Madden
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jasmine Lin
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (Q.L.); (J.L.); (S.M.R.); (K.S.-A.)
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiahai Shi
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China;
| | - Samantha M. Rosen
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (Q.L.); (J.L.); (S.M.R.); (K.S.-A.)
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Klaus Schmitz-Abe
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (Q.L.); (J.L.); (S.M.R.); (K.S.-A.)
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (Q.L.); (J.L.); (S.M.R.); (K.S.-A.)
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-6179192153
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16
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Kunji ERS, King MS, Ruprecht JJ, Thangaratnarajah C. The SLC25 Carrier Family: Important Transport Proteins in Mitochondrial Physiology and Pathology. Physiology (Bethesda) 2021; 35:302-327. [PMID: 32783608 PMCID: PMC7611780 DOI: 10.1152/physiol.00009.2020] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Members of the mitochondrial carrier family (SLC25) transport a variety of compounds across the inner membrane of mitochondria. These transport steps provide building blocks for the cell and link the pathways of the mitochondrial matrix and cytosol. An increasing number of diseases and pathologies has been associated with their dysfunction. In this review, the molecular basis of these diseases is explained based on our current understanding of their transport mechanism.
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Affiliation(s)
- Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan J Ruprecht
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular Sciences and Biotechnology Institute, Membrane Enzymology, University of Groningen, Groningen, The Netherlands
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17
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Zou W, Chen Q, Slone J, Yang L, Lou X, Diao J, Huang T. Nanoscopic quantification of sub-mitochondrial morphology, mitophagy and mitochondrial dynamics in living cells derived from patients with mitochondrial diseases. J Nanobiotechnology 2021; 19:136. [PMID: 33985528 PMCID: PMC8120746 DOI: 10.1186/s12951-021-00882-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Abstract
SLC25A46 mutations have been found to lead to mitochondrial hyper-fusion and reduced mitochondrial respiratory function, which results in optic atrophy, cerebellar atrophy, and other clinical symptoms of mitochondrial disease. However, it is generally believed that mitochondrial fusion is attributable to increased mitochondrial oxidative phosphorylation (OXPHOS), which is inconsistent with the decreased OXPHOS of highly-fused mitochondria observed in previous studies. In this paper, we have used the live-cell nanoscope to observe and quantify the structure of mitochondrial cristae, and the behavior of mitochondria and lysosomes in patient-derived SLC25A46 mutant fibroblasts. The results show that the cristae have been markedly damaged in the mutant fibroblasts, but there is no corresponding increase in mitophagy. This study suggests that severely damaged mitochondrial cristae might be the predominant cause of reduced OXPHOS in SLC25A46 mutant fibroblasts. This study demonstrates the utility of nanoscope-based imaging for realizing the sub-mitochondrial morphology, mitophagy and mitochondrial dynamics in living cells, which may be particularly valuable for the quick evaluation of pathogenesis of mitochondrial morphological abnormalities. ![]()
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Affiliation(s)
- Weiwei Zou
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.,Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Qixin Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.,Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.,Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Li Yang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.,Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiaoting Lou
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.,School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA.
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18
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Sharma G, Pfeffer G, Shutt TE. Genetic Neuropathy Due to Impairments in Mitochondrial Dynamics. BIOLOGY 2021; 10:268. [PMID: 33810506 PMCID: PMC8066130 DOI: 10.3390/biology10040268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 12/12/2022]
Abstract
Mitochondria are dynamic organelles capable of fusing, dividing, and moving about the cell. These properties are especially important in neurons, which in addition to high energy demand, have unique morphological properties with long axons. Notably, mitochondrial dysfunction causes a variety of neurological disorders including peripheral neuropathy, which is linked to impaired mitochondrial dynamics. Nonetheless, exactly why peripheral neurons are especially sensitive to impaired mitochondrial dynamics remains somewhat enigmatic. Although the prevailing view is that longer peripheral nerves are more sensitive to the loss of mitochondrial motility, this explanation is insufficient. Here, we review pathogenic variants in proteins mediating mitochondrial fusion, fission and transport that cause peripheral neuropathy. In addition to highlighting other dynamic processes that are impacted in peripheral neuropathies, we focus on impaired mitochondrial quality control as a potential unifying theme for why mitochondrial dysfunction and impairments in mitochondrial dynamics in particular cause peripheral neuropathy.
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Affiliation(s)
- Govinda Sharma
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Gerald Pfeffer
- Departments of Clinical Neurosciences and Medical Genetics, Cumming School of Medicine, Hotchkiss Brain Institute, Alberta Child Health Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Timothy E. Shutt
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada;
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19
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Yamaguchi M, Omori K, Asada S, Yoshida H. Epigenetic Regulation of ALS and CMT: A Lesson from Drosophila Models. Int J Mol Sci 2021; 22:ijms22020491. [PMID: 33419039 PMCID: PMC7825332 DOI: 10.3390/ijms22020491] [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: 12/17/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the third most common neurodegenerative disorder and is sometimes associated with frontotemporal dementia. Charcot–Marie–Tooth disease (CMT) is one of the most commonly inherited peripheral neuropathies causing the slow progression of sensory and distal muscle defects. Of note, the severity and progression of CMT symptoms markedly vary. The phenotypic heterogeneity of ALS and CMT suggests the existence of modifiers that determine disease characteristics. Epigenetic regulation of biological functions via gene expression without alterations in the DNA sequence may be an important factor. The methylation of DNA, noncoding RNA, and post-translational modification of histones are the major epigenetic mechanisms. Currently, Drosophila is emerging as a useful ALS and CMT model. In this review, we summarize recent studies linking ALS and CMT to epigenetic regulation with a strong emphasis on approaches using Drosophila models.
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Affiliation(s)
- Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (K.O.); (S.A.)
- Kansai Gakken Laboratory, Kankyo Eisei Yakuhin Co. Ltd., Seika-cho, Kyoto 619-0237, Japan
- Correspondence: (M.Y.); (H.Y.)
| | - Kentaro Omori
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (K.O.); (S.A.)
| | - Satoshi Asada
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (K.O.); (S.A.)
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (K.O.); (S.A.)
- Correspondence: (M.Y.); (H.Y.)
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20
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Saneto RP. Mitochondrial diseases: expanding the diagnosis in the era of genetic testing. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2020; 4:384-428. [PMID: 33426505 PMCID: PMC7791531 DOI: 10.20517/jtgg.2020.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases are clinically and genetically heterogeneous. These diseases were initially described a little over three decades ago. Limited diagnostic tools created disease descriptions based on clinical, biochemical analytes, neuroimaging, and muscle biopsy findings. This diagnostic mechanism continued to evolve detection of inherited oxidative phosphorylation disorders and expanded discovery of mitochondrial physiology over the next two decades. Limited genetic testing hampered the definitive diagnostic identification and breadth of diseases. Over the last decade, the development and incorporation of massive parallel sequencing has identified approximately 300 genes involved in mitochondrial disease. Gene testing has enlarged our understanding of how genetic defects lead to cellular dysfunction and disease. These findings have expanded the understanding of how mechanisms of mitochondrial physiology can induce dysfunction and disease, but the complete collection of disease-causing gene variants remains incomplete. This article reviews the developments in disease gene discovery and the incorporation of gene findings with mitochondrial physiology. This understanding is critical to the development of targeted therapies.
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Affiliation(s)
- Russell P. Saneto
- Center for Integrative Brain Research, Neuroscience Institute, Seattle, WA 98101, USA
- Department of Neurology/Division of Pediatric Neurology, Seattle Children’s Hospital/University of Washington, Seattle, WA 98105, USA
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21
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Tan NB, Stapleton R, Stark Z, Delatycki MB, Yeung A, Hunter MF, Amor DJ, Brown NJ, Stutterd CA, McGillivray G, Yap P, Regan M, Chong B, Fanjul Fernandez M, Marum J, Phelan D, Pais LS, White SM, Lunke S, Tan TY. Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review. Mol Genet Genomic Med 2020; 8:e1508. [PMID: 32969205 PMCID: PMC7667328 DOI: 10.1002/mgg3.1508] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/15/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Our primary aim was to evaluate the systematic reanalysis of singleton exome sequencing (ES) data for unsolved cases referred for any indication. A secondary objective was to undertake a literature review of studies examining the reanalysis of genomic data from unsolved cases. Methods We examined data from 58 unsolved cases referred between June 2016 and March 2017. First reanalysis at 4–13 months after the initial report considered genes newly associated with disease since the original analysis; second reanalysis at 9–18 months considered all disease‐associated genes. At 25–34 months we reviewed all cases and the strategies which solved them. Results Reanalysis of existing ES data alone at two timepoints did not yield new diagnoses. Over the same timeframe, 10 new diagnoses were obtained (17%) from additional strategies, such as microarray detection of copy number variation, repeat sequencing to improve coverage, and trio sequencing. Twenty‐seven peer‐reviewed articles were identified on the literature review, with a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months. Conclusion Our findings suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. We also recommend a multi‐faceted strategy for cases remaining unsolved after singleton ES.
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Affiliation(s)
- Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rachel Stapleton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - David J Amor
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Patrick Yap
- Genetic Health Service NZ, Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Miriam Fanjul Fernandez
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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22
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Ali MS, Suda K, Kowada R, Ueoka I, Yoshida H, Yamaguchi M. Neuron-specific knockdown of solute carrier protein SLC25A46a induces locomotive defects, an abnormal neuron terminal morphology, learning disability, and shortened lifespan. IBRO Rep 2020; 8:65-75. [PMID: 32140609 PMCID: PMC7047145 DOI: 10.1016/j.ibror.2020.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/17/2020] [Indexed: 01/21/2023] Open
Abstract
Various mutations in the SLC25A46 gene have been reported in mitochondrial diseases that are sometimes classified as type 2 Charcot-Marie-Tooth disease, optic atrophy, and Leigh syndrome. Although human SLC25A46 is a well-known transporter that acts through the mitochondrial outer membrane, the relationship between neurodegeneration in these diseases and the loss-of-function of SLC25A46 remains unclear. Two Drosophila genes, CG8931 (dSLC25A46a) and CG5755 (dSLC25A46b) have been identified as candidate homologs of human SLC25A46. We previously characterized the phenotypes of pan-neuron-specific dSLC25A46b knockdown flies. In the present study, we developed pan-neuron-specific dSLC25A46a knockdown flies and examined their phenotypes. Neuron-specific dSLC25A46a knockdown resulted in reduced mobility in larvae as well as adults. An aberrant morphology for neuromuscular junctions (NMJs), such as a reduced synaptic branch length and decreased number and size of boutons, was observed in dSLC25A46a knockdown flies. Learning ability was also reduced in the larvae of knockdown flies. In dSLC25A46a knockdown flies, mitochondrial hyperfusion was detected in NMJ synapses together with the accumulation of reactive oxygen species and reductions in ATP. These phenotypes were very similar to those of dSLC25A46b knockdown flies, suggesting that dSLC25A46a and dSLC25A46b do not have redundant roles in neurons. Collectively, these results show that the depletion of SLC25A46a leads to mitochondrial defects followed by an aberrant synaptic morphology, resulting in locomotive defects and learning disability. Thus, the dSLC25A46a knockdown fly summarizes most of the phenotypes in patients with mitochondrial diseases, offering a useful tool for studying these diseases.
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Affiliation(s)
- Md Saheb Ali
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
- Faculty of Agriculture, Bangladesh Jute Research Institute, Manik Mia Ave., Dhaka, 1207, Bangladesh
| | - Kojiro Suda
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Ryosuke Kowada
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Ibuki Ueoka
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Hideki Yoshida
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
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Palmieri F, Scarcia P, Monné M. Diseases Caused by Mutations in Mitochondrial Carrier Genes SLC25: A Review. Biomolecules 2020; 10:biom10040655. [PMID: 32340404 PMCID: PMC7226361 DOI: 10.3390/biom10040655] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
In the 1980s, after the mitochondrial DNA (mtDNA) had been sequenced, several diseases resulting from mtDNA mutations emerged. Later, numerous disorders caused by mutations in the nuclear genes encoding mitochondrial proteins were found. A group of these diseases are due to defects of mitochondrial carriers, a family of proteins named solute carrier family 25 (SLC25), that transport a variety of solutes such as the reagents of ATP synthase (ATP, ADP, and phosphate), tricarboxylic acid cycle intermediates, cofactors, amino acids, and carnitine esters of fatty acids. The disease-causing mutations disclosed in mitochondrial carriers range from point mutations, which are often localized in the substrate translocation pore of the carrier, to large deletions and insertions. The biochemical consequences of deficient transport are the compartmentalized accumulation of the substrates and dysfunctional mitochondrial and cellular metabolism, which frequently develop into various forms of myopathy, encephalopathy, or neuropathy. Examples of diseases, due to mitochondrial carrier mutations are: combined D-2- and L-2-hydroxyglutaric aciduria, carnitine-acylcarnitine carrier deficiency, hyperornithinemia-hyperammonemia-homocitrillinuria (HHH) syndrome, early infantile epileptic encephalopathy type 3, Amish microcephaly, aspartate/glutamate isoform 1 deficiency, congenital sideroblastic anemia, Fontaine progeroid syndrome, and citrullinemia type II. Here, we review all the mitochondrial carrier-related diseases known until now, focusing on the connections between the molecular basis, altered metabolism, and phenotypes of these inherited disorders.
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Affiliation(s)
- Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy;
- Correspondence: (F.P.); (M.M.); Tel.: +39-0805443323 (F.P.)
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy;
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy;
- Department of Sciences, University of Basilicata, via Ateneo Lucano 10, 85100 Potenza, Italy
- Correspondence: (F.P.); (M.M.); Tel.: +39-0805443323 (F.P.)
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24
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Bitetto G, Malaguti MC, Ceravolo R, Monfrini E, Straniero L, Morini A, Di Giacopo R, Frosini D, Palermo G, Biella F, Ronchi D, Duga S, Taroni F, Corti S, Comi GP, Bresolin N, Giometto B, Di Fonzo A. SLC25A46 mutations in patients with Parkinson's Disease and optic atrophy. Parkinsonism Relat Disord 2020; 74:1-5. [PMID: 32259769 DOI: 10.1016/j.parkreldis.2020.03.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/14/2020] [Accepted: 03/22/2020] [Indexed: 12/14/2022]
Abstract
Mutations in the gene encoding the mitochondrial carrier protein SLC25A46 are known to cause optic atrophy associated with peripheral neuropathy and congenital pontocerebellar hypoplasia. We found novel biallelic SLC25A46 mutations (p.H137R, p.A401Sfs*17) in a patient with Parkinson's disease and optic atrophy. Screening of six unrelated patients with parkinsonism and optic atrophy allowed us to identify two additional mutations (p.A176V, p.K256R) in a second patient. All identified variants are predicted likely pathogenic and affect very conserved protein residues. These findings suggest for the first time a possible link between Parkinson's Disease and SLC25A46 mutations. Replication in additional studies is needed to conclusively prove this link.
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Affiliation(s)
- Giacomo Bitetto
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | | | | | - Edoardo Monfrini
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Letizia Straniero
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Alberto Morini
- Department of Neurology, Ospedale Santa Chiara, Trento, Italy
| | | | - Daniela Frosini
- Unit of Neurology, Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
| | - Giovanni Palermo
- Unit of Neurology, Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
| | - Fabio Biella
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Dario Ronchi
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefania Corti
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Giacomo P Comi
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Nereo Bresolin
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Bruno Giometto
- Department of Neurology, Ospedale Santa Chiara, Trento, Italy
| | - Alessio Di Fonzo
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.
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Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease. PLoS One 2020; 15:e0230566. [PMID: 32208444 PMCID: PMC7092968 DOI: 10.1371/journal.pone.0230566] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/03/2020] [Indexed: 12/22/2022] Open
Abstract
A phenomenon of genetic compensation is commonly observed when an organism with a disease-bearing mutation shows incomplete penetrance of the disease phenotype. Such incomplete phenotypic penetrance, or genetic compensation, is more commonly found in stable knockout models, rather than transient knockdown models. As such, these incidents present a challenge for the disease modeling field, although a deeper understanding of genetic compensation may also hold the key for novel therapeutic interventions. In our study we created a knockout model of slc25a46 gene, which is a recently discovered important player in mitochondrial dynamics, and deleterious mutations in which are known to cause peripheral neuropathy, optic atrophy and cerebellar ataxia. We report a case of genetic compensation in a stable slc25a46 homozygous zebrafish mutant (hereafter referred as “mutant”), in contrast to a penetrant disease phenotype in the first generation (F0) slc25a46 mosaic mutant (hereafter referred as “crispant”), generated with CRISPR/Cas-9 technology. We show that the crispant phenotype is specific and rescuable. By performing mRNA sequencing, we define significant changes in slc25a46 mutant’s gene expression profile, which are largely absent in crispants. We find that among the most significantly altered mRNAs, anxa6 gene stands out as a functionally relevant player in mitochondrial dynamics. We also find that our genetic compensation case does not arise from mechanisms driven by mutant mRNA decay. Our study contributes to the growing evidence of the genetic compensation phenomenon and presents novel insights about Slc25a46 function. Furthermore, our study provides the evidence for the efficiency of F0 CRISPR screens for disease candidate genes, which may be used to advance the field of functional genetics.
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26
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Diagnostic utility of transcriptome sequencing for rare Mendelian diseases. Genet Med 2019; 22:490-499. [PMID: 31607746 DOI: 10.1038/s41436-019-0672-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/25/2019] [Indexed: 01/04/2023] Open
Abstract
PURPOSE We investigated the value of transcriptome sequencing (RNAseq) in ascertaining the consequence of DNA variants on RNA transcripts to improve the diagnostic rate from exome or genome sequencing for undiagnosed Mendelian diseases spanning a wide spectrum of clinical indications. METHODS From 234 subjects referred to the Undiagnosed Diseases Network, University of California-Los Angeles clinical site between July 2014 and August 2018, 113 were enrolled for high likelihood of having rare undiagnosed, suspected genetic conditions despite thorough prior clinical evaluation. Exome or genome sequencing and RNAseq were performed, and RNAseq data was integrated with genome sequencing data for DNA variant interpretation genome-wide. RESULTS The molecular diagnostic rate by exome or genome sequencing was 31%. Integration of RNAseq with genome sequencing resulted in an additional seven cases with clear diagnosis of a known genetic disease. Thus, the overall molecular diagnostic rate was 38%, and 18% of all genetic diagnoses returned required RNAseq to determine variant causality. CONCLUSION In this rare disease cohort with a wide spectrum of undiagnosed, suspected genetic conditions, RNAseq analysis increased the molecular diagnostic rate above that possible with genome sequencing analysis alone even without availability of the most appropriate tissue type to assess.
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27
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Suda K, Muraoka Y, Ortega-Yáñez A, Yoshida H, Kizu F, Hochin T, Kimura H, Yamaguchi M. Reduction of Rpd3 suppresses defects in locomotive ability and neuronal morphology induced by the knockdown of Drosophila SLC25A46 via an epigenetic pathway. Exp Cell Res 2019; 385:111673. [PMID: 31614134 DOI: 10.1016/j.yexcr.2019.111673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023]
Abstract
Mitochondrial dysfunction causes various diseases. Mutations in the SLC25A46 gene have been identified in mitochondrial diseases that are sometimes classified as Charcot-Marie-Tooth disease type 2, optic atrophy, and Leigh syndrome. A homolog of SLC25A46 was identified in Drosophila and designated as dSLC25A46 (CG5755). We previously established mitochondrial disease model targeting of dSLC25A46, which causes locomotive dysfunction and morphological defects at neuromuscular junctions, such as reduced synaptic branch lengths and decreased numbers of boutons. The diverse symptoms of mitochondrial diseases carrying mutations in SLC25A46 may be associated with the dysregulation of some epigenetic regulators. To investigate the involvement of epigenetic regulators in mitochondrial diseases, we examined candidate epigenetic regulators that interact with human SLC25A46 by searching Gene Expression Omnibus (GEO). We discovered that HDAC1 binds to several SLC25A46 genomic regions in human cultured CD4 (+) cells, and attempted to prove this in an in vivo Drosophila model. By demonstrating that Rpd3, Drosophila HDAC1, regulates the histone H4K8 acetylation state in dSLC25A46 genomic regions, we confirmed that Rpd3 is a novel epigenetic regulator modifying the phenotypes observed with the mitochondrial disease model targeting of dSLC25A46. The functional reduction of Rpd3 rescued the deficient locomotive ability and aberrant morphology of motoneurons at presynaptic terminals induced by the dSLC25A46 knockdown. The present results suggest that the inhibition of HDAC1 suppresses the pathogenic processes that lead to the degeneration of motoneurons in mitochondrial diseases.
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Affiliation(s)
- Kojiro Suda
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Yuuka Muraoka
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Andrea Ortega-Yáñez
- Departamento de Genética del Desarrollo Y Fisiología Molecular Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico
| | - Hideki Yoshida
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Fuma Kizu
- Department of Information Science, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Teruhisa Hochin
- Department of Information Science, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
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28
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Van Laar VS, Otero PA, Hastings TG, Berman SB. Potential Role of Mic60/Mitofilin in Parkinson's Disease. Front Neurosci 2019; 12:898. [PMID: 30740041 PMCID: PMC6357844 DOI: 10.3389/fnins.2018.00898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/16/2018] [Indexed: 12/21/2022] Open
Abstract
There are currently no treatments that hinder or halt the inexorable progression of Parkinson's disease (PD). While the etiology of PD remains elusive, evidence suggests that early dysfunction of mitochondrial respiration and homeostasis play a major role in PD pathogenesis. The mitochondrial structural protein Mic60, also known as mitofilin, is critical for maintaining mitochondrial architecture and function. Loss of Mic60 is associated with detrimental effects on mitochondrial homeostasis. Growing evidence now implicates Mic60 in the pathogenesis of PD. In this review, we discuss the data supporting a role of Mic60 and mitochondrial dysfunction in PD. We will also consider the potential of Mic60 as a therapeutic target for treating neurological disorders.
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Affiliation(s)
- Victor S Van Laar
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - P Anthony Otero
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA, United States.,Division of Neuropathology, Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Cellular and Molecular Pathology (CMP) Program, Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Teresa G Hastings
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah B Berman
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA, United States.,Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, United States
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