151
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Deoxythymidylate kinase, DTYMK, is a novel gene for mitochondrial DNA depletion syndrome. Clin Chim Acta 2019; 496:93-99. [DOI: 10.1016/j.cca.2019.06.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 12/12/2022]
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152
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Ruebel ML, Schall PZ, Midic U, Vincent KA, Goheen B, VandeVoort CA, Latham KE. Transcriptome analysis of rhesus monkey failed-to-mature oocytes: deficiencies in transcriptional regulation and cytoplasmic maturation of the oocyte mRNA population. Mol Hum Reprod 2019; 24:478-494. [PMID: 30085220 DOI: 10.1093/molehr/gay032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
STUDY QUESTION Which different pathways and functions are altered in rhesus monkey oocytes that fail to mature after an ovulatory stimulus? SUMMARY ANSWER Failed to mature (FTM) oocytes complete a large portion of the transition in transcriptome composition associated with normal maturation, but also manifest numerous differences that indicate incomplete transcriptional repression and cytoplasmic maturation affecting multiple processes. WHAT IS KNOWN ALREADY Oocyte maturation defects contribute to unexplained female infertility. Failure of some oocytes to undergo germinal vesicle breakdown or progress to second meiotic metaphase in response to an ovulatory stimulus can limit the number of high quality oocytes available for ART. STUDY DESIGN, SIZE, DURATION The transcriptome of rhesus monkey oocytes that failed to mature (FTM; n = 11, 5 donors) in response to an ovulatory stimulus in vivo was compared to those of normal germinal vesicle stage (GV, n = 7, 2 donors) and metaphase II stage (MII, n = 7, 5 donors) oocytes by RNA-sequencing (RNAseq). PARTICIPANTS/MATERIALS, SETTING, METHODS Female rhesus monkeys of normal breeding age (6-12 years old) and with regular menstrual cycles were used. Animals underwent a controlled ovarian stimulation protocol for the collection of oocytes by ultrasound-guided needle aspiration of follicles. MAIN RESULTS AND THE ROLE OF CHANCE We obtained a high quality RNAseq dataset consisting of n = 7, n = 7, and n = 11 libraries for normal GV, normal MII and FTM oocytes, respectively. Total reads acquired were an average of 34 million for each GV sample, 41 million for each FTM sample and 59 million for each MII oocyte sample. Approximately 44% of the total reads were exonic reads that successfully aligned to the rhesus monkey genome as unique non-rRNA gene transcript sequences, providing high depth of coverage. Approximately 44% of the mRNAs that undergo changes in abundance during normal maturation display partial modulations to intermediate abundances, and 9.2% fail to diverge significantly from GV stage oocytes. Additionally, a small group of mRNAs are grossly mis-regulated in the FTM oocyte. Differential expression was seen for mRNAs associated with mitochondrial functions, fatty acid beta oxidation, lipid accumulation, meiosis, zona pellucida formation, Hippo pathway signaling, and maternal mRNA regulation. A deficiency DNA methyltransferase one mRNA expression indicates a potential defect in transcriptional silencing. LARGE SCALE DATA All RNAseq data are published in the Gene Expression Omnibus Database (GSE112536). LIMITATIONS, REASONS FOR CAUTION These results do not establish cause of maturation failure but reveal novel correlates of incompetence to mature. Transcriptome studies likely do not capture all post-transcriptional or post-translational events that inhibit maturation, but do reveal mRNA expression changes that lie downstream of such events or that are related to effects on upstream regulators. The use of an animal model allows the study of oocyte maturation failure independent of covariates and confounders, such as pre-existing conditions of the female, which is a significant concern in human studies. Depending on the legislation, it may not be possible to collect and study oocytes from healthy women; and using surplus oocytes from patients undergoing ART may introduce confounders that vary from case to case. FTM oocytes were at various stages of meiotic progression, so correlates of specific times of arrest are not revealed. All the FTM oocytes failed to respond appropriately to an ovulatory stimulus in vivo. Therefore, this analysis informs us about common transcriptome features associated with meiotic incompetence. WIDER IMPLICATIONS OF THE FINDINGS These results reveal that some diagnostic markers of oocyte quality may not reflect developmental competence because even meiotically incompetent oocytes display many normal gene expression features. The results also reveal potential mechanisms by which maternal and environmental factors may impact transcriptional repression and cytoplasmic maturation, and prevent oocyte maturation. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by grants from the National Institutes of Health Office of Research Infrastructure Programs Division of Comparative Medicine Grants R24 [OD012221 to K.E.L., OD011107/RR00169 (California National Primate Research Center), and OD010967/RR025880 to C.A.V.]; the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health under the award number T32HD087166; MSU AgBioResearch, Michigan State University. Authors have nothing to disclose.
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Affiliation(s)
- Meghan L Ruebel
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Peter Z Schall
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Uros Midic
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Kailey A Vincent
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Benjamin Goheen
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Keith E Latham
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
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153
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Appendicular skeletal muscle mass: A more sensitive biomarker of disease severity than BMI in adults with mitochondrial diseases. PLoS One 2019; 14:e0219628. [PMID: 31344055 PMCID: PMC6657836 DOI: 10.1371/journal.pone.0219628] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 06/27/2019] [Indexed: 02/06/2023] Open
Abstract
The study aimed to evaluate the body composition of patients with mitochondrial diseases (MD) and correlate it with disease severity. Overall, 89 patients (age ≥ 18 years) with MD were recruited, including 49 with chronic progressive external ophthalmoplegia (CPEO) and 40 with mitochondrial encephalomyopathy with lactate acidosis and stroke-like episodes (MELAS). Body composition, including fat mass index (FMI), fat-free mass index (FFMI), skeletal muscle mass index (SMI), and appendicular skeletal muscle mass index (ASMI), were examined using multifrequency bioelectric impedance analysis. Clinical assessments, including muscle strength, usual gait speed, and disease severity determined by the Newcastle Mitochondrial Disease Adult Scale score (NMDAS), were performed. The comparisons between patients group and age- and gender-matched healthy controls, as well as the correlations between anthropometric measurements, body composition, and disease severity were analyzed. Height, weight, body mass index (BMI), FFMI, SMI, and ASMI were significantly lower in patients with MD than in healthy controls. Notably, low muscle mass was noted in 69.7% (62/89) of MD patients, with 22 patients also presenting with compromised physical performance as indicated by decreased gait speed, resulting in 24.7% satisfied the sarcopenia diagnostic criteria. Disease severity was more negatively correlated with ASMI than it was with height, weight, and BMI. Subgroup analysis showed that in the MELAS subgroup, disease severity was negatively correlated with height, weight, and ASMI; whereas in the CPEO subgroup, it was only negatively correlated with ASMI and SMI. Additionally, ASMI was positively associated with muscle strength. Altogether, compared with BMI, ASMI is a more sensitive biomarker predicting disease severity of MD, both in MELAS and CPEO patients.
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154
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Souza PVS, Bortholin T, Teixeira CAC, Seneor DD, Marin VDGB, Dias RB, Farias IB, Badia BML, Silva LHL, Pinto WBVR, Oliveira ASB, DiMauro S. Leigh syndrome caused by mitochondrial DNA-maintenance defects revealed by whole exome sequencing. Mitochondrion 2019; 49:25-34. [PMID: 31271879 DOI: 10.1016/j.mito.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/17/2018] [Accepted: 06/24/2019] [Indexed: 01/30/2023]
Abstract
Leigh syndrome represents a complex inherited neurometabolic and neurodegenerative disorder associated with different clinical, genetic and neuroimaging findings in the context of bilateral symmetrical lesions involving the brainstem and basal ganglia. Heterogeneous neurological manifestations such as spasticity, cerebellar ataxia, dystonia, choreoathetosis and parkinsonism are associated with multisystemic and ophthalmological abnormalities due to >75 different monogenic causes. Here, we describe the clinical and genetic features of a Brazilian cohort of patients with Leigh Syndrome in which muscle biopsy analysis showed mitochondrial DNA defects and determine the utility of whole exome sequencing for a final genetic diagnostic in this cohort.
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Affiliation(s)
- P V S Souza
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil.
| | - Thiago Bortholin
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Carlos Alberto Castro Teixeira
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Daniel Delgado Seneor
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Vitor Dias Gomes Barrios Marin
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Renan Braido Dias
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Igor Braga Farias
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - B M L Badia
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Luiz Henrique Libardi Silva
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - W B V R Pinto
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Acary Souza Bulle Oliveira
- Division of Neuromuscular Diseases, Department of Neurology, Department of Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
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155
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Carreño-Gago L, Blázquez-Bermejo C, Díaz-Manera J, Cámara Y, Gallardo E, Martí R, Torres-Torronteras J, García-Arumí E. Identification and Characterization of New RNASEH1 Mutations Associated With PEO Syndrome and Multiple Mitochondrial DNA Deletions. Front Genet 2019; 10:576. [PMID: 31258551 PMCID: PMC6588129 DOI: 10.3389/fgene.2019.00576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/31/2019] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial DNA (mtDNA) depletion and deletion syndrome encompasses a group of disorders caused by mutations in genes involved in mtDNA replication and maintenance. The clinical phenotype ranges from fatal infantile hepatocerebral forms to mild adult onset progressive external ophthalmoplegia (PEO). We report the case of a patient with PEO and multiple mtDNA deletions, with two new homozygous mutations in RNASEH1. The first mutation (c.487T>C) is located in the same catalytic domain as the four previously reported mutations, and the second (c.258_260del) is located in the connection domain, where no mutations have been reported. In silico study of the mutations predicted only the first mutation as pathogenic, but functional studies showed that both mutations cause loss of ribonuclease H1 activity. mtDNA replication dysfunction was demonstrated in patient fibroblasts, which were unable to recover normal mtDNA copy number after ethidium bromide-induced mtDNA depletion. Our results demonstrate the pathogenicity of two new RNASEH1 variants found in a patient with PEO syndrome, multiple deletions, and mild mitochondrial myopathy.
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Affiliation(s)
- Lidia Carreño-Gago
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Cora Blázquez-Bermejo
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Jordi Díaz-Manera
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain.,Servei de Neurologia, Malalties Neuromusculars, Hospital de la Santa Creu i Sant Pau i Institut de Recerca de HSCSP, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yolanda Cámara
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Eduard Gallardo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain.,Servei de Neurologia, Malalties Neuromusculars, Hospital de la Santa Creu i Sant Pau i Institut de Recerca de HSCSP, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ramon Martí
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Javier Torres-Torronteras
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Elena García-Arumí
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain.,Àrea de Genètica Clínica i Molecular, Hospital Universitari Vall d'Hebron, Barcelona, Spain
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156
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Sênos Demarco R, Uyemura BS, D'Alterio C, Jones DL. Mitochondrial fusion regulates lipid homeostasis and stem cell maintenance in the Drosophila testis. Nat Cell Biol 2019; 21:710-720. [PMID: 31160709 DOI: 10.1038/s41556-019-0332-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 04/23/2019] [Indexed: 01/02/2023]
Abstract
The capacity of stem cells to self-renew or differentiate has been attributed to distinct metabolic states. A genetic screen targeting regulators of mitochondrial dynamics revealed that mitochondrial fusion is required for the maintenance of male germline stem cells (GSCs) in Drosophila melanogaster. Depletion of Mitofusin (dMfn) or Opa1 led to dysfunctional mitochondria, activation of Target of rapamycin (TOR) and a marked accumulation of lipid droplets. Enhancement of lipid utilization by the mitochondria attenuated TOR activation and rescued the loss of GSCs that was caused by inhibition of mitochondrial fusion. Moreover, constitutive activation of the TOR-pathway target and lipogenesis factor Sterol regulatory element binding protein (SREBP) also resulted in GSC loss, whereas inhibition of SREBP rescued GSC loss triggered by depletion of dMfn. Our findings highlight a critical role for mitochondrial fusion and lipid homeostasis in GSC maintenance, providing insight into the potential impact of mitochondrial and metabolic diseases on the function of stem and/or germ cells.
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Affiliation(s)
- Rafael Sênos Demarco
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bradley S Uyemura
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cecilia D'Alterio
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - D Leanne Jones
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
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157
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Duraisamy AJ, Mohammad G, Kowluru RA. Mitochondrial fusion and maintenance of mitochondrial homeostasis in diabetic retinopathy. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1617-1626. [PMID: 30922813 DOI: 10.1016/j.bbadis.2019.03.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/11/2019] [Accepted: 03/22/2019] [Indexed: 01/01/2023]
Abstract
Mitochondria are dynamic in structure, and undergo continuous fusion-fission to maintain their homeostasis. In diabetes, retinal mitochondria are swollen, their membrane is damaged and mitochondrial fusion protein, mitofusin 2 (Mfn2), is decreased. DNA methylation machinery is also activated and methylation status of genes implicated in mitochondrial damage and biogenesis is altered. This study aims to investigate the role of mitochondrial fusion in the development of diabetic retinopathy, and to illustrate the molecular mechanism responsible for Mfn2 suppression. Using human retinal endothelial cells, manipulated for Mfn2, we investigated the role of fusion in mitochondrial structural and functional damage in diabetes. The molecular mechanism of its suppression in diabetic milieu was determined by investigating Mfn2 promoter DNA methylation, and confirmed using molecular and pharmacological inhibitors of DNA methylation. Similar studies were performed in the retinal microvasculature (prepared by hypotonic shock method) of diabetic rats, and human donors with documented diabetic retinopathy. Overexpression of Mfn2 prevented glucose-induced increase in mitochondrial fragmentation, decrease in complex III activity and increase in membrane permeability, mtDNA damage and apoptosis. High glucose hypermethylated Mfn2 promoter and decreased transcription factor (SP1) binding, and Dnmt inhibition protected Mfn2 promoter from these changes. In streptozotocin-induced diabetic rats, intravitreal administration of Dnmt1-siRNA attenuated Mfn2 promoter hypermethylation and restored its expression. Human donors with diabetic retinopathy confirmed Mfn2 promoter DNA hypermethylation. Thus, regulating Mfn2 and its epigenetic modifications by molecular/pharmacological means will protect mitochondrial homeostasis in diabetes, and could attenuate the development of retinopathy in diabetic patients.
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MESH Headings
- Adult
- Aged
- Animals
- Cell Line
- DNA (Cytosine-5-)-Methyltransferase 1/antagonists & inhibitors
- DNA (Cytosine-5-)-Methyltransferase 1/genetics
- DNA (Cytosine-5-)-Methyltransferase 1/metabolism
- DNA Methylation
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Diabetic Retinopathy/genetics
- Diabetic Retinopathy/metabolism
- Diabetic Retinopathy/pathology
- Endothelial Cells/metabolism
- Endothelial Cells/pathology
- Epigenesis, Genetic
- GTP Phosphohydrolases/genetics
- GTP Phosphohydrolases/metabolism
- Homeostasis/genetics
- Humans
- Male
- Middle Aged
- Mitochondria/genetics
- Mitochondria/metabolism
- Mitochondria/pathology
- Mitochondrial Dynamics
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Promoter Regions, Genetic
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Rats
- Rats, Wistar
- Retina/metabolism
- Retina/pathology
- Signal Transduction
- Sp1 Transcription Factor/genetics
- Sp1 Transcription Factor/metabolism
- Streptozocin/administration & dosage
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Affiliation(s)
- Arul J Duraisamy
- Kresge Eye Institute, Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, MI, United States of America
| | - Ghulam Mohammad
- Kresge Eye Institute, Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, MI, United States of America
| | - Renu A Kowluru
- Kresge Eye Institute, Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, MI, United States of America.
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158
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Domínguez-González C, Hernández-Laín A, Rivas E, Hernández-Voth A, Sayas Catalán J, Fernández-Torrón R, Fuiza-Luces C, García García J, Morís G, Olivé M, Miralles F, Díaz-Manera J, Caballero C, Méndez-Ferrer B, Martí R, García Arumi E, Badosa MC, Esteban J, Jimenez-Mallebrera C, Encinar AB, Arenas J, Hirano M, Martin MÁ, Paradas C. Late-onset thymidine kinase 2 deficiency: a review of 18 cases. Orphanet J Rare Dis 2019; 14:100. [PMID: 31060578 PMCID: PMC6501326 DOI: 10.1186/s13023-019-1071-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/17/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND TK2 gene encodes for mitochondrial thymidine kinase, which phosphorylates the pyrimidine nucleosides thymidine and deoxycytidine. Recessive mutations in the TK2 gene are responsible for the 'myopathic form' of the mitochondrial depletion/multiple deletions syndrome, with a wide spectrum of severity. METHODS We describe 18 patients with mitochondrial myopathy due to mutations in the TK2 gene with absence of clinical symptoms until the age of 12. RESULTS The mean age of onset was 31 years. The first symptom was muscle limb weakness in 10/18, eyelid ptosis in 6/18, and respiratory insufficiency in 2/18. All patients developed variable muscle weakness during the evolution of the disease. Half of patients presented difficulty in swallowing. All patients showed evidence of respiratory muscle weakness, with need for non-invasive Mechanical Ventilation in 12/18. Four patients had deceased, all of them due to respiratory insufficiency. We identified common radiological features in muscle magnetic resonance, where the most severely affected muscles were the gluteus maximus, semitendinosus and sartorius. On muscle biopsies typical signs of mitochondrial dysfunction were associated with dystrophic changes. All mutations identified were previously reported, being the most frequent the in-frame deletion p.Lys202del. All cases showed multiple mtDNA deletions but mtDNA depletion was present only in two patients. CONCLUSIONS The late-onset is the less frequent form of presentation of the TK2 deficiency and its natural history is not well known. Patients with late onset TK2 deficiency have a consistent and recognizable clinical phenotype and a poor prognosis, due to the high risk of early and progressive respiratory insufficiency.
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Affiliation(s)
- Cristina Domínguez-González
- Neurology department, Neuromuscular disorders Unit, 12 de Octubre Hospital, Madrid, Spain.,Research Institute i+12, 12 de Octubre Hospital, Madrid, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Aurelio Hernández-Laín
- Neuropathology, Pathology Department, Neuromuscular disorders Unit, 12 de Octubre Hospital, Madrid, Spain
| | - Eloy Rivas
- Pathological Anatomic Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U. Virgen del Rocío, CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Ana Hernández-Voth
- Neumology department, Neuromuscular disorders Unit, 12 de Octubre Hospital, Madrid, Spain
| | - Javier Sayas Catalán
- Neumology department, Neuromuscular disorders Unit, 12 de Octubre Hospital, Madrid, Spain
| | | | - Carmen Fuiza-Luces
- Research Institute i+12, 12 de Octubre Hospital, Madrid, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Mitochondrial and Neuromuscular Diseases Laboratory, Research Institute of Hospital '12 de Octubre' ('i+12'), Madrid, Spain
| | | | - Germán Morís
- Neurology Department, Neuromuscular disorders Unit, Hospital Central de Asturias, Oviedo, Spain
| | - Montse Olivé
- Pathological Anatomy Department, Neuromuscular disorders unit, IDIBELL-Hospital de Bellvitge, Barcelona, Spain
| | - Frances Miralles
- Neurology department, Neuromuscular disorders unit, Hospital Universitari Son Espases, Palma, Spain
| | - Jordi Díaz-Manera
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Neurology department, Neuromuscular disorders unit, Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
| | - Candela Caballero
- Respiratory Department, Instituto de Biomedicina de Sevilla, Hospital U. Virgen del Rocío, CSIC, CIBERES, Universidad de Sevilla, Sevilla, Spain
| | | | - Ramon Martí
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Neuromuscular Unit, Neurology Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Elena García Arumi
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Research group on Neuromuscular and Mitochondrial Diseases, Valld'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Carmen Badosa
- Neuromuscular Unit, Neurology Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jesús Esteban
- Neurology department, Neuromuscular disorders Unit, 12 de Octubre Hospital, Madrid, Spain.,Research Institute i+12, 12 de Octubre Hospital, Madrid, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Cecilia Jimenez-Mallebrera
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Neuromuscular Unit, Neurology Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Alberto Blazquez Encinar
- Research Institute i+12, 12 de Octubre Hospital, Madrid, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Mitochondrial and Neuromuscular Diseases Laboratory, Research Institute of Hospital '12 de Octubre' ('i+12'), Madrid, Spain
| | - Joaquín Arenas
- Research Institute i+12, 12 de Octubre Hospital, Madrid, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Mitochondrial and Neuromuscular Diseases Laboratory, Research Institute of Hospital '12 de Octubre' ('i+12'), Madrid, Spain
| | - Michio Hirano
- Department of Neurology, H. Houston Merritt Center, Columbia University Medical Center, New York, New York, USA
| | - Miguel Ángel Martin
- Research Institute i+12, 12 de Octubre Hospital, Madrid, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Mitochondrial and Neuromuscular Diseases Laboratory, Research Institute of Hospital '12 de Octubre' ('i+12'), Madrid, Spain
| | - Carmen Paradas
- Neurology Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U. Virgen del Rocío, CSIC, Universidad de Sevilla, Avd. Manuel Siurot s/n, 41013, Sevilla, Spain. .,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
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159
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Blázquez-Bermejo C, Carreño-Gago L, Molina-Granada D, Aguirre J, Ramón J, Torres-Torronteras J, Cabrera-Pérez R, Martín MÁ, Domínguez-González C, de la Cruz X, Lombès A, García-Arumí E, Martí R, Cámara Y. Increased dNTP pools rescue mtDNA depletion in human POLG-deficient fibroblasts. FASEB J 2019; 33:7168-7179. [PMID: 30848931 DOI: 10.1096/fj.201801591r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Polymerase γ catalytic subunit (POLG) gene encodes the enzyme responsible for mitochondrial DNA (mtDNA) synthesis. Mutations affecting POLG are the most prevalent cause of mitochondrial disease because of defective mtDNA replication and lead to a wide spectrum of clinical phenotypes characterized by mtDNA deletions or depletion. Enhancing mitochondrial deoxyribonucleoside triphosphate (dNTP) synthesis effectively rescues mtDNA depletion in different models of defective mtDNA maintenance due to dNTP insufficiency. In this study, we studied mtDNA copy number recovery rates following ethidium bromide-forced depletion in quiescent fibroblasts from patients harboring mutations in different domains of POLG. Whereas control cells spontaneously recovered initial mtDNA levels, POLG-deficient cells experienced a more severe depletion and could not repopulate mtDNA. However, activation of deoxyribonucleoside (dN) salvage by supplementation with dNs plus erythro-9-(2-hydroxy-3-nonyl) adenine (inhibitor of deoxyadenosine degradation) led to increased mitochondrial dNTP pools and promoted mtDNA repopulation in all tested POLG-mutant cells independently of their specific genetic defect. The treatment did not compromise POLG fidelity because no increase in multiple deletions or point mutations was detected. Our study suggests that physiologic dNTP concentration limits the mtDNA replication rate. We thus propose that increasing mitochondrial dNTP availability could be of therapeutic interest for POLG deficiency and other conditions in which mtDNA maintenance is challenged.-Blázquez-Bermejo, C., Carreño-Gago, L., Molina-Granada, D., Aguirre, J., Ramón, J., Torres-Torronteras, J., Cabrera-Pérez, R., Martín, M. Á., Domínguez-González, C., de la Cruz, X., Lombès, A., García-Arumí, E., Martí, R., Cámara, Y. Increased dNTP pools rescue mtDNA depletion in human POLG-deficient fibroblasts.
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Affiliation(s)
- Cora Blázquez-Bermejo
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lidia Carreño-Gago
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - David Molina-Granada
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Josu Aguirre
- Translational Bioinformatics Group, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Ramón
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Torres-Torronteras
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Cabrera-Pérez
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel Ángel Martín
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Laboratorio de Enfermedades Mitocondriales, Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Cristina Domínguez-González
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Unidad de Neuromuscular, Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Xavier de la Cruz
- Translational Bioinformatics Group, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; and
| | - Anne Lombès
- Institut Cochin, INSERM Unité 1016-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8104-Service de Biochimie Métabolique et Centre de Génétique Moléculaire et Chromosomique, Groupement Hospitalier Universitaire (GHU) Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP)-Université Paris Descartes, Paris, France
| | - Elena García-Arumí
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ramon Martí
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Yolanda Cámara
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca-Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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160
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Munro B, Horvath R, Müller JS. Nucleoside supplementation modulates mitochondrial DNA copy number in the dguok -/- zebrafish. Hum Mol Genet 2019; 28:796-803. [PMID: 30428046 PMCID: PMC6381312 DOI: 10.1093/hmg/ddy389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023] Open
Abstract
Deoxyguanosine kinase (dGK) is an essential rate-limiting component of the mitochondrial purine nucleotide salvage pathway, encoded by the nuclear gene encoding deoxyguanosine kinase (DGUOK). Mutations in DGUOK lead to mitochondrial DNA (mtDNA) depletion typically in the liver and brain, causing a hepatocerebral phenotype. Previous work has shown that in cultured DGUOK patient cells it is possible to rescue mtDNA depletion by increasing substrate amounts for dGK. In this study we developed a mutant dguok zebrafish (Danio rerio) line using CRISPR/Cas9 mediated mutagenesis; dguok-/- fish have significantly reduced mtDNA levels compared with wild-type (wt) fish. When supplemented with only one purine nucleoside (dGuo), mtDNA copy number in both mutant and wt juvenile animals was significantly reduced, contrasting with previous cell culture studies, possibly because of nucleotide pool imbalance. However, in adult dguok-/- fish we detected a significant increase in liver mtDNA copy number when supplemented with both purine nucleosides. This study further supports the idea that nucleoside supplementation has a potential therapeutic benefit in mtDNA depletion syndromes by substrate enhancement of the purine nucleoside salvage pathway and might improve the liver pathology in patients.
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Affiliation(s)
- Benjamin Munro
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- Department of Clinical Neurosciences, University of Cambridge, John Van Geest Centre for Brain Repair, The ED Adrian Building, Forvie Site, Robinson Way, Cambridge, CB2 0PY, UK
| | - Rita Horvath
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- Department of Clinical Neurosciences, University of Cambridge, John Van Geest Centre for Brain Repair, The ED Adrian Building, Forvie Site, Robinson Way, Cambridge, CB2 0PY, UK
| | - Juliane S Müller
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- Department of Clinical Neurosciences, University of Cambridge, John Van Geest Centre for Brain Repair, The ED Adrian Building, Forvie Site, Robinson Way, Cambridge, CB2 0PY, UK
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161
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Ballout RA, Al Alam C, Bonnen PE, Huemer M, El-Hattab AW, Shbarou R. FBXL4-Related Mitochondrial DNA Depletion Syndrome 13 (MTDPS13): A Case Report With a Comprehensive Mutation Review. Front Genet 2019; 10:39. [PMID: 30804983 PMCID: PMC6370620 DOI: 10.3389/fgene.2019.00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/18/2019] [Indexed: 01/28/2023] Open
Abstract
Mitochondrial DNA depletion syndromes (MTDPS) are a group of rare genetic disorders caused by defects in multiple genes involved in mitochondrial DNA (mtDNA) maintenance. Among those, FBXL4 mutations result in the encephalomyopathic mtDNA depletion syndrome 13 (MTDPS13; OMIM #615471), which commonly presents as a combination of failure to thrive, neurodevelopmental delays, encephalopathy, hypotonia, and persistent lactic acidosis. We report here the case of a Lebanese infant presenting to us with profound neurodevelopmental delays, generalized hypotonia, facial dysmorphic features, and extreme emaciation. Whole-exome sequencing (WES) showed the girl as having MTDPS13 with an underlying FBXL4 missense mutation that has been previously reported only twice in unrelated individuals (c.1303C > T). Comprehensive literature search marked our patient as being the 94th case of MTDPS13 reported to date worldwide, and the first from Lebanon. We include at the end of this report a comprehensive mutation review table of all the pathological FBXL4 mutations reported in the literature, using it to highlight, for the first time, a possible founder effect of Arab origins to the disorder, being most prevalent in patients of Arab descent as shown in our mutation table. Finally, we provide a direct comparison of the disorder's clinical manifestations across two unrelated patients harboring the same disease-causing mutation as our patient, emphasizing the remarkable variability in genotype-to-phenotype correlation characteristic of the disease.
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Affiliation(s)
- Rami A Ballout
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Chadi Al Alam
- Division of Pediatric Neurology, Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Martina Huemer
- Department of Pediatrics, Landeskrankenhaus Bregenz, Bregenz, Austria.,Division of Metabolism, University Children's Hospital Zürich, Zurich, Switzerland
| | - Ayman W El-Hattab
- Genetics Clinic, KidsHeart Medical Center, Dubai, United Arab Emirates
| | - Rolla Shbarou
- Division of Pediatric Neurology, Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
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162
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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163
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El-Hattab AW, Suleiman J, Almannai M, Scaglia F. Mitochondrial dynamics: Biological roles, molecular machinery, and related diseases. Mol Genet Metab 2018; 125:315-321. [PMID: 30361041 DOI: 10.1016/j.ymgme.2018.10.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/15/2018] [Indexed: 01/09/2023]
Abstract
Mitochondria are dynamic organelles that undergo fusion, fission, movement, and mitophagy. These processes are essential to maintain the normal mitochondrial morphology, distribution, and function. Mitochondrial fusion allows the exchange of intramitochondrial material, whereas the fission process is required to replicate the mitochondria during cell division, facilitate the transport and distribution of mitochondria, and allow the isolation of damaged organelles. Mitochondrial mobility is essential for mitochondrial distribution depending on the cellular metabolic demands. Mitophagy is needed for the elimination of dysfunctional and damaged mitochondria to maintain a healthy mitochondrial population. The mitochondrial dynamic processes are mediated by a number of nuclear-encoded proteins that function in mitochondrial transport, fusion, fission, and mitophagy. Disorders of mitochondrial dynamics are caused by pathogenic variants in the genes encoding these proteins. These diseases have a high clinical variability, and range in severity from isolated optic atrophy to lethal encephalopathy. These disorders include defects in mitochondrial fusion (caused by pathogenic variants in MFN2, OPA1, YME1L1, MSTO1, and FBXL4), mitochondrial fission (caused by pathogenic variants in DNM1L and MFF), and mitochondrial autophagy (caused by pathogenic variants in PINK1 and PRKN). In this review, the molecular machinery and biological roles of mitochondrial dynamic processes are discussed. Subsequently, the currently known diseases related to mitochondrial dynamic defects are presented.
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Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Jehan Suleiman
- Division of Neurology, Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates
| | - Mohammed Almannai
- Medical Genetics Division, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, Hong Kong Special Administrative Region.
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164
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Goudenège D, Bris C, Hoffmann V, Desquiret-Dumas V, Jardel C, Rucheton B, Bannwarth S, Paquis-Flucklinger V, Lebre AS, Colin E, Amati-Bonneau P, Bonneau D, Reynier P, Lenaers G, Procaccio V. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 2018; 21:1407-1416. [PMID: 30393377 DOI: 10.1038/s41436-018-0350-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/17/2018] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Accurate detection of mitochondrial DNA (mtDNA) alterations is essential for the diagnosis of mitochondrial diseases. The development of high-throughput sequencing technologies has enhanced the detection sensitivity of mtDNA pathogenic variants, but the detection of mtDNA rearrangements, especially multiple deletions, is still poorly processed. Here, we present eKLIPse, a sensitive and specific tool allowing the detection and quantification of large mtDNA rearrangements from single and paired-end sequencing data. METHODS The methodology was first validated using a set of simulated data to assess the detection sensitivity and specificity, and second with a series of sequencing data from mitochondrial disease patients carrying either single or multiple deletions, related to pathogenic variants in nuclear genes involved in mtDNA maintenance. RESULTS eKLIPse provides the precise breakpoint positions and the cumulated percentage of mtDNA rearrangements at a given gene location with a detection sensitivity lower than 0.5% mutant. eKLIPse software is available either as a script to be integrated in a bioinformatics pipeline, or as user-friendly graphical interface to visualize the results through a Circos representation ( https://github.com/dooguypapua/eKLIPse ). CONCLUSION Thus, eKLIPse represents a useful resource to study the causes and consequences of mtDNA rearrangements, for further genotype/phenotype correlations in mitochondrial disorders.
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Affiliation(s)
- David Goudenège
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Celine Bris
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Virginie Hoffmann
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Valerie Desquiret-Dumas
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Claude Jardel
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Benoit Rucheton
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | | | - Anne Sophie Lebre
- CHU Reims, Hôpital Maison Blanche, Pole de biologie, Service de génétique, Reims, France
| | - Estelle Colin
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Pascal Reynier
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France. .,Biochemistry and Genetics Department, Angers Hospital, Angers, France.
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165
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Almannai M, Wang J, Dai H, El-Hattab AW, Faqeih EA, Saleh MA, Al Asmari A, Alwadei AH, Aljadhai YI, AlHashem A, Tabarki B, Lines MA, Grange DK, Benini R, Alsaman AS, Mahmoud A, Katsonis P, Lichtarge O, Wong LJC. FARS2 deficiency; new cases, review of clinical, biochemical, and molecular spectra, and variants interpretation based on structural, functional, and evolutionary significance. Mol Genet Metab 2018; 125:281-291. [PMID: 30177229 DOI: 10.1016/j.ymgme.2018.07.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023]
Abstract
An increasing number of mitochondrial diseases are found to be caused by pathogenic variants in nuclear encoded mitochondrial aminoacyl-tRNA synthetases. FARS2 encodes mitochondrial phenylalanyl-tRNA synthetase (mtPheRS) which transfers phenylalanine to its cognate tRNA in mitochondria. Since the first case was reported in 2012, a total of 21 subjects with FARS2 deficiency have been reported to date with a spectrum of disease severity that falls between two phenotypes; early onset epileptic encephalopathy and a less severe phenotype characterized by spastic paraplegia. In this report, we present an additional 15 individuals from 12 families who are mostly Arabs homozygous for the pathogenic variant Y144C, which is associated with the more severe early onset phenotype. The total number of unique pathogenic FARS2 variants known to date is 21 including three different partial gene deletions reported in four individuals. Except for the large deletions, all variants but two (one in-frame deletion of one amino acid and one splice-site variant) are missense. All large deletions and the single splice-site variant are in trans with a missense variant. This suggests that complete loss of function may be incompatible with life. In this report, we also review structural, functional, and evolutionary significance of select FARS2 pathogenic variants reported here.
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Affiliation(s)
- Mohammed Almannai
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Julia Wang
- Medical Scientist Training Program and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatric Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Mohammed A Saleh
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Al Asmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali H Alwadei
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Yaser I Aljadhai
- Department of Neuroimaging and Intervention, Medical Imaging Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Amal AlHashem
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Divisions of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Matthew A Lines
- Division of Metabolics and Newborn Screening, Children's Hospital of Eastern Ontario, Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Dorothy K Grange
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ruba Benini
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulaziz S Alsaman
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Adel Mahmoud
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lee-Jun C Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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166
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Gilberti M, Baruffini E, Donnini C, Dallabona C. Pathological alleles of MPV17 modeled in the yeast Saccharomyces cerevisiae orthologous gene SYM1 reveal their inability to take part in a high molecular weight complex. PLoS One 2018; 13:e0205014. [PMID: 30273399 PMCID: PMC6166979 DOI: 10.1371/journal.pone.0205014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/18/2018] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA depletion syndromes (MDDS) are a genetically and clinically heterogeneous group of human diseases caused by mutations in nuclear genes and characterized by a severe reduction in mitochondrial DNA (mtDNA) copy number leading to impaired energy production in affected tissues and organs. Mutations in the MPV17 gene, whose role is still elusive, were described as cause of the hepatocerebral form of MDDS and Navajo neuro-hepathopathy. The high degree of conservation observed between MPV17 and its yeast homolog SYM1 made the latter a good model for the study of the pathology. Here, we used Saccharomyces cerevisiae to elucidate the molecular consequences of seven MPV17 missense mutations identified in patients and localized in different protein domains. The phenotypic analysis of the appropriate sym1 mutant strains created demonstrated deleterious effect for all mutations regarding OXPHOS metabolism and mtDNA stability. We deepened the pathogenic effect of the mutations by investigating whether they prevented the correct protein localization into the mitochondria or affected the stability of the proteins. All the Sym1 mutant proteins correctly localized into the mitochondria and only one mutation predominantly affects protein stability. All the other mutations compromised the formation of the high molecular weight complex of unknown composition, previously identified both in yeast, cell cultures and mouse tissues, as demonstrated by the consistent fraction of the Sym1 mutant proteins found free or in not fully assembled complex, strengthening its role as protein forming part of a high molecular weight complex.
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Affiliation(s)
- Micol Gilberti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- * E-mail:
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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167
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Arrázola MS, Andraini T, Szelechowski M, Mouledous L, Arnauné-Pelloquin L, Davezac N, Belenguer P, Rampon C, Miquel MC. Mitochondria in Developmental and Adult Neurogenesis. Neurotox Res 2018; 36:257-267. [PMID: 30215161 DOI: 10.1007/s12640-018-9942-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/18/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
Abstract
Generation of new neurons is a tightly regulated process that involves several intrinsic and extrinsic factors. Among them, a metabolic switch from glycolysis to oxidative phosphorylation, together with mitochondrial remodeling, has emerged as crucial actors of neurogenesis. However, although accumulating data raise the importance of mitochondrial morphology and function in neural stem cell proliferation and differentiation during development, information regarding the contribution of mitochondria to adult neurogenesis processes remains limited. In the present review, we discuss recent evidence covering the importance of mitochondrial morphology, function, and energy metabolism in the regulation of neuronal development and adult neurogenesis, and their impact on memory processes.
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Affiliation(s)
- Macarena S Arrázola
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France. .,Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
| | - Trinovita Andraini
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France.,Department of Physiology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Marion Szelechowski
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lionel Mouledous
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laetitia Arnauné-Pelloquin
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Noélie Davezac
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pascale Belenguer
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claire Rampon
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Christine Miquel
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France.
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Mendelsohn BA, Bennett NK, Darch MA, Yu K, Nguyen MK, Pucciarelli D, Nelson M, Horlbeck MA, Gilbert LA, Hyun W, Kampmann M, Nakamura JL, Nakamura K. A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure. PLoS Biol 2018; 16:e2004624. [PMID: 30148842 PMCID: PMC6110572 DOI: 10.1371/journal.pbio.2004624] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
Insufficient or dysregulated energy metabolism may underlie diverse inherited and degenerative diseases, cancer, and even aging itself. ATP is the central energy carrier in cells, but critical pathways for regulating ATP levels are not systematically understood. We combined a pooled clustered regularly interspaced short palindromic repeats interference (CRISPRi) library enriched for mitochondrial genes, a fluorescent biosensor, and fluorescence-activated cell sorting (FACS) in a high-throughput genetic screen to assay ATP concentrations in live human cells. We identified genes not known to be involved in energy metabolism. Most mitochondrial ribosomal proteins are essential in maintaining ATP levels under respiratory conditions, and impaired respiration predicts poor growth. We also identified genes for which coenzyme Q10 (CoQ10) supplementation rescued ATP deficits caused by knockdown. These included CoQ10 biosynthetic genes associated with human disease and a subset of genes not linked to CoQ10 biosynthesis, indicating that increasing CoQ10 can preserve ATP in specific genetic contexts. This screening paradigm reveals mechanisms of metabolic control and genetic defects responsive to energy-based therapies.
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Affiliation(s)
- Bryce A. Mendelsohn
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
- Department of Pediatrics, University of California, San Francisco, California, United States of America
| | - Neal K. Bennett
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
| | - Maxwell A. Darch
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
| | - Katharine Yu
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
| | - Mai K. Nguyen
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
| | - Daniela Pucciarelli
- Department of Radiation Oncology, University of California, San Francisco, California, United States of America
| | - Maxine Nelson
- Graduate Program in Biomedical Sciences, University of California, San Francisco, California, United States of America
| | - Max A. Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Luke A. Gilbert
- Department of Urology, University of California, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, United States of America
| | - William Hyun
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
| | - Martin Kampmann
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jean L. Nakamura
- Department of Radiation Oncology, University of California, San Francisco, California, United States of America
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
- Graduate Program in Biomedical Sciences, University of California, San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco, California, United States of America
- Graduate Program in Neuroscience, University of California, San Francisco, California, United States of America
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169
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Mitochondrial DNA replication: clinical syndromes. Essays Biochem 2018; 62:297-308. [PMID: 29950321 DOI: 10.1042/ebc20170101] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/17/2018] [Accepted: 05/23/2018] [Indexed: 02/08/2023]
Abstract
Each nucleated cell contains several hundreds of mitochondria, which are unique organelles in being under dual genome control. The mitochondria contain their own DNA, the mtDNA, but most of mitochondrial proteins are encoded by nuclear genes, including all the proteins required for replication, transcription, and repair of mtDNA. MtDNA replication is a continuous process that requires coordinated action of several enzymes that are part of the mtDNA replisome. It also requires constant supply of deoxyribonucleotide triphosphates(dNTPs) and interaction with other mitochondria for mixing and unifying the mitochondrial compartment. MtDNA maintenance defects are a growing list of disorders caused by defects in nuclear genes involved in different aspects of mtDNA replication. As a result of defects in these genes, mtDNA depletion and/or multiple mtDNA deletions develop in affected tissues resulting in variable manifestations that range from adult-onset mild disease to lethal presentation early in life.
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170
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Shimada E, Ahsan FM, Nili M, Huang D, Atamdede S, TeSlaa T, Case D, Yu X, Gregory BD, Perrin BJ, Koehler CM, Teitell MA. PNPase knockout results in mtDNA loss and an altered metabolic gene expression program. PLoS One 2018; 13:e0200925. [PMID: 30024931 PMCID: PMC6053217 DOI: 10.1371/journal.pone.0200925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is an essential mitochondria-localized exoribonuclease implicated in multiple biological processes and human disorders. To reveal role(s) for PNPase in mitochondria, we established PNPase knockout (PKO) systems by first shifting culture conditions to enable cell growth with defective respiration. Interestingly, PKO established in mouse embryonic fibroblasts (MEFs) resulted in the loss of mitochondrial DNA (mtDNA). The transcriptional profile of PKO cells was similar to rho0 mtDNA deleted cells, with perturbations in cholesterol (FDR = 6.35 x 10-13), lipid (FDR = 3.21 x 10-11), and secondary alcohol (FDR = 1.04x10-12) metabolic pathway gene expression compared to wild type parental (TM6) MEFs. Transcriptome analysis indicates processes related to axonogenesis (FDR = 4.49 x 10-3), axon development (FDR = 4.74 x 10-3), and axonal guidance (FDR = 4.74 x 10-3) were overrepresented in PKO cells, consistent with previous studies detailing causative PNPase mutations in delayed myelination, hearing loss, encephalomyopathy, and chorioretinal defects in humans. Overrepresentation analysis revealed alterations in metabolic pathways in both PKO and rho0 cells. Therefore, we assessed the correlation of genes implicated in cell cycle progression and total metabolism and observed a strong positive correlation between PKO cells and rho0 MEFs compared to TM6 MEFs. We quantified the normalized biomass accumulation rate of PKO clones at 1.7% (SD ± 2.0%) and 2.4% (SD ± 1.6%) per hour, which was lower than TM6 cells at 3.3% (SD ± 3.5%) per hour. Furthermore, PKO in mouse inner ear hair cells caused progressive hearing loss that parallels human familial hearing loss previously linked to mutations in PNPase. Combined, our study reports that knockout of a mitochondrial nuclease results in mtDNA loss and suggests that mtDNA maintenance could provide a unifying connection for the large number of biological activities reported for PNPase.
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Affiliation(s)
- Eriko Shimada
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Fasih M. Ahsan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Mahta Nili
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dian Huang
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sean Atamdede
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tara TeSlaa
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dana Case
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Benjamin J. Perrin
- Department of Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Carla M. Koehler
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
| | - Michael A. Teitell
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
- Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
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171
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El-Hattab AW, Wang J, Wong LJ. Extra-muscular manifestations of TK2 deficiency. Mol Genet Metab Rep 2018; 16:30. [PMID: 30013933 PMCID: PMC6019690 DOI: 10.1016/j.ymgmr.2018.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 11/06/2022] Open
Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Julia Wang
- Medical Scientist Training Program, Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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172
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Wang J, Kim E, Dai H, Stefans V, Vogel H, Al Jasmi F, Schrier Vergano SA, Castro D, Bernes S, Bhambhani V, Long C, El-Hattab AW, Wong LJ. Clinical and molecular spectrum of thymidine kinase 2-related mtDNA maintenance defect. Mol Genet Metab 2018; 124:124-130. [PMID: 29735374 DOI: 10.1016/j.ymgme.2018.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA maintenance (mtDNA) defects have a wide range of causes, each with a set of phenotypes that overlap with many other neurological or muscular diseases. Clinicians face the challenge of narrowing down a long list of differential diagnosis when encountered with non-specific neuromuscular symptoms. Biallelic pathogenic variants in the Thymidine Kinase 2 (TK2) gene cause a myopathic form of mitochondrial DNA maintenance defect. Since the first description in 2001, there have been 71 patients reported with 42 unique pathogenic variants. Here we are reporting 11 new cases with 5 novel pathogenic variants. We describe and analyze a total of 82 cases with 47 unique TK2 pathogenic variants in effort to formulate a comprehensive molecular and clinical spectrum of TK2-related mtDNA maintenance disorders.
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Affiliation(s)
- Julia Wang
- Medical Scientist Training Program, Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States.
| | - Emily Kim
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, United States
| | - Honzheng Dai
- Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Vikki Stefans
- UAMS College of Medicine, Arkansas Children's Hospital, 1 Children's Way, Little Rock, AR 72202, United States
| | - Hannes Vogel
- Pathology, Stanford University School of Medicine, R241 Edwards Building, 300 Pasteur Drive, Palo Alto, CA 94305, United States
| | - Fatma Al Jasmi
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, 601 Children's Lane, Norfolk, VA 23507, United States
| | - Diana Castro
- Department of Pediatric, Neurology and Neurotherapeutics, Children's Health Dallas, University of Texas Southwestern, 2350 N Stemmons Freeway, Dallas, TX 75207, United States
| | - Saunder Bernes
- Department of Neurology, Phoenix Children's Hospital, Barrows Neurological Institute, 1919 East Thomas Road, Phoenix, AZ 85016, United States
| | - Vikas Bhambhani
- Genomics Medicine Program, Children's Hospital Minnesota, 2525 Chicago Ave S, Minneapolis, MN 55404, United States
| | - Catherine Long
- Genomics Medicine Program, Children's Hospital Minnesota, 2525 Chicago Ave S, Minneapolis, MN 55404, United States
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Lee-Jun Wong
- Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States.
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173
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Mauney CH, Hollis T. SAMHD1: Recurring roles in cell cycle, viral restriction, cancer, and innate immunity. Autoimmunity 2018; 51:96-110. [PMID: 29583030 PMCID: PMC6117824 DOI: 10.1080/08916934.2018.1454912] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/16/2018] [Indexed: 12/24/2022]
Abstract
Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) is a deoxynucleotide triphosphate (dNTP) hydrolase that plays an important role in the homeostatic balance of cellular dNTPs. Its emerging role as an effector of innate immunity is affirmed by mutations in the SAMHD1 gene that cause the severe autoimmune disease, Aicardi-Goutieres syndrome (AGS) and that are linked to cancer. Additionally, SAMHD1 functions as a restriction factor for retroviruses, such as HIV. Here, we review the current biochemical and biological properties of the enzyme including its structure, activity, and regulation by post-translational modifications in the context of its cellular function. We outline open questions regarding the biology of SAMHD1 whose answers will be important for understanding its function as a regulator of cell cycle progression, genomic integrity, and in autoimmunity.
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Affiliation(s)
- Christopher H Mauney
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
| | - Thomas Hollis
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
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174
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Buj R, Aird KM. Deoxyribonucleotide Triphosphate Metabolism in Cancer and Metabolic Disease. Front Endocrinol (Lausanne) 2018; 9:177. [PMID: 29720963 PMCID: PMC5915462 DOI: 10.3389/fendo.2018.00177] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/03/2018] [Indexed: 12/22/2022] Open
Abstract
The maintenance of a healthy deoxyribonucleotide triphosphate (dNTP) pool is critical for the proper replication and repair of both nuclear and mitochondrial DNA. Temporal, spatial, and ratio imbalances of the four dNTPs have been shown to have a mutagenic and cytotoxic effect. It is, therefore, essential for cell homeostasis to maintain the balance between the processes of dNTP biosynthesis and degradation. Multiple oncogenic signaling pathways, such as c-Myc, p53, and mTORC1 feed into dNTP metabolism, and there is a clear role for dNTP imbalances in cancer initiation and progression. Additionally, multiple chemotherapeutics target these pathways to inhibit nucleotide synthesis. Less is understood about the role for dNTP levels in metabolic disorders and syndromes and whether alterations in dNTP levels change cancer incidence in these patients. For instance, while deficiencies in some metabolic pathways known to play a role in nucleotide synthesis are pro-tumorigenic (e.g., p53 mutations), others confer an advantage against the onset of cancer (G6PD). More recent evidence indicates that there are changes in nucleotide metabolism in diabetes, obesity, and insulin resistance; however, whether these changes play a mechanistic role is unclear. In this review, we will address the complex network of metabolic pathways, whereby cells can fuel dNTP biosynthesis and catabolism in cancer, and we will discuss the potential role for this pathway in metabolic disease.
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Affiliation(s)
| | - Katherine M. Aird
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States
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175
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Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria. Nat Commun 2018; 9:1202. [PMID: 29572490 PMCID: PMC5865154 DOI: 10.1038/s41467-018-03552-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/21/2018] [Indexed: 12/17/2022] Open
Abstract
Replication of mammalian mitochondrial DNA (mtDNA) is an essential process that requires high fidelity and control at multiple levels to ensure proper mitochondrial function. Mutations in the mitochondrial genome maintenance exonuclease 1 (MGME1) gene were recently reported in mitochondrial disease patients. Here, to study disease pathophysiology, we generated Mgme1 knockout mice and report that homozygous knockouts develop depletion and multiple deletions of mtDNA. The mtDNA replication stalling phenotypes vary dramatically in different tissues of Mgme1 knockout mice. Mice with MGME1 deficiency accumulate a long linear subgenomic mtDNA species, similar to the one found in mtDNA mutator mice, but do not develop progeria. This finding resolves a long-standing debate by showing that point mutations of mtDNA are the main cause of progeria in mtDNA mutator mice. We also propose a role for MGME1 in the regulation of replication and transcription termination at the end of the control region of mtDNA. It has been debated whether premature ageing in mitochondrial DNA mutator mice is driven by point mutations or deletions of mtDNA. Matic et al generate Mgme1 knockout mice and show here that these mice have tissue-specific replication stalling and accumulate deleted mtDNA, without developing progeria.
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176
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Abstract
Mitochondrial DNA (mtDNA), which is essential for mitochondrial and cell function, is replicated and transcribed in the organelle by proteins that are entirely coded in the nucleus. Replication of mtDNA is challenged not only by threats related to the replication machinery and orchestration of DNA synthesis, but also by factors linked to the peculiarity of this genome. Indeed the architecture, organization, copy number, and location of mtDNA, which are markedly distinct from the nuclear genome, require ad hoc and complex regulation to ensure coordinated replication. As a consequence sub-optimal mtDNA replication, which results from compromised regulation of these factors, is generally associated with mitochondrial dysfunction and disease. Mitochondrial DNA replication should be considered in the context of the organelle and the whole cell, and not just a single genome or a single replication event. Major threats to mtDNA replication are linked to its dependence on both mitochondrial and nuclear factors, which require exquisite coordination of these crucial subcellular compartments. Moreover, regulation of replication events deals with a dynamic population of multiple mtDNA molecules rather than with a fixed number of genome copies, as it is the case for nuclear DNA. Importantly, the mechanistic aspects of mtDNA replication are still debated. We describe here major challenges for human mtDNA replication, the mechanistic aspects of the process that are to a large extent original, and their consequences on disease.
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Affiliation(s)
- Miria Ricchetti
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Stem Cells and Development, 75724 Cedex15, Paris, France; Team Stability of Nuclear and Mitochondrial DNA, CNRS UMR 3738, 75724, Cedex15, Paris, France.
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177
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Ogawa K, Itami N, Ueda M, Kansaku K, Shirasuna K, Kuwayama T, Iwata H. Non-esterified fatty acid-associated ability of follicular fluid to support porcine oocyte maturation and development. Reprod Med Biol 2018; 17:155-163. [PMID: 29692673 PMCID: PMC5902458 DOI: 10.1002/rmb2.12084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/15/2017] [Indexed: 12/19/2022] Open
Abstract
Purpose The effect of supplementing maturation medium with follicular fluid (FF) was examined according to its non‐esterified fatty acid (NEFA) content or with a fatty acid mixture (FA‐Mix) on the developmental competence of oocytes, as well as the mitochondrial quality and quantity in the oocytes and cumulus cells. Method Porcine oocytes from a slaughterhouse were used. Results The FF or FA‐Mix in maturation medium increased the lipid content in both the oocytes and the cumulus cells, but the adenosine triphosphate content was differentially affected. The FF supplementation increased the mitochondrial DNA copy number, survival of cumulus cells, and rate of oocyte development to the blastocyst stage, whereas the FA‐Mix supplementation did not show these effects. The expression levels of GPC4,PFKP,PRDX3, and TFAM in the cumulus cells increased after FF supplementation, but the expression of GJA1 decreased, compared with the cells that were cultured without FF. Conclusion Adding FF and FA‐Mix to the maturation medium increased the lipid content in the oocytes and cumulus cells. The effects of FF on the cumulus cells and oocytes were not observed after FA‐Mix supplementation, indicating that the concentration of the NEFAs in the FF are closely associated with an ability to support oocyte maturation and the metabolism of cumulus cells and oocytes.
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Affiliation(s)
- Kaori Ogawa
- Department of Animal Science Tokyo University of Agriculture Funako Japan
| | - Nobuhiko Itami
- Department of Animal Science Tokyo University of Agriculture Funako Japan
| | - Manami Ueda
- Department of Animal Science Tokyo University of Agriculture Funako Japan
| | - Kazuki Kansaku
- Department of Animal Science Tokyo University of Agriculture Funako Japan
| | - Koumei Shirasuna
- Department of Animal Science Tokyo University of Agriculture Funako Japan
| | - Takehito Kuwayama
- Department of Animal Science Tokyo University of Agriculture Funako Japan
| | - Hisataka Iwata
- Department of Animal Science Tokyo University of Agriculture Funako Japan
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178
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El-Hattab AW, Wang J, Dai H, Almannai M, Staufner C, Alfadhel M, Gambello MJ, Prasun P, Raza S, Lyons HJ, Afqi M, Saleh MAM, Faqeih EA, Alzaidan HI, Alshenqiti A, Flore LA, Hertecant J, Sacharow S, Barbouth DS, Murayama K, Shah AA, Lin HC, Wong LJC. MPV17-related mitochondrial DNA maintenance defect: New cases and review of clinical, biochemical, and molecular aspects. Hum Mutat 2018; 39:461-470. [PMID: 29282788 DOI: 10.1002/humu.23387] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/04/2017] [Accepted: 12/15/2017] [Indexed: 02/02/2023]
Abstract
Mitochondrial DNA (mtDNA) maintenance defects are a group of diseases caused by deficiency of proteins involved in mtDNA synthesis, mitochondrial nucleotide supply, or mitochondrial dynamics. One of the mtDNA maintenance proteins is MPV17, which is a mitochondrial inner membrane protein involved in importing deoxynucleotides into the mitochondria. In 2006, pathogenic variants in MPV17 were first reported to cause infantile-onset hepatocerebral mtDNA depletion syndrome and Navajo neurohepatopathy. To date, 75 individuals with MPV17-related mtDNA maintenance defect have been reported with 39 different MPV17 pathogenic variants. In this report, we present an additional 25 affected individuals with nine novel MPV17 pathogenic variants. We summarize the clinical features of all 100 affected individuals and review the total 48 MPV17 pathogenic variants. The vast majority of affected individuals presented with an early-onset encephalohepatopathic disease characterized by hepatic and neurological manifestations, failure to thrive, lactic acidemia, and mtDNA depletion detected mainly in liver tissue. Rarely, MPV17 deficiency can cause a late-onset neuromyopathic disease characterized by myopathy and peripheral neuropathy with no or minimal liver involvement. Approximately half of the MPV17 pathogenic variants are missense. A genotype with biallelic missense variants, in particular homozygous p.R50Q, p.P98L, and p.R41Q, can carry a relatively better prognosis.
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Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatric Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Julia Wang
- Medical Scientist Training Program and Program in Developmental Biology, Baylor College of Medicine, Houston, Texas
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mohammed Almannai
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Christian Staufner
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, University Hospital Heidelberg, Heidelberg, Germany
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Michael J Gambello
- Division of Medical Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Pankaj Prasun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Saleem Raza
- Department of Pediatrics, St John Hospital and Medical Center and Wayne State University School of Medicine, Detroit, Michigan
| | - Hernando J Lyons
- Department of Pediatrics, St John Hospital and Medical Center and Wayne State University School of Medicine, Detroit, Michigan
| | - Manal Afqi
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Mohammed A M Saleh
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Eissa A Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Hamad I Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abduljabbar Alshenqiti
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Leigh Anne Flore
- Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan and Wayne State University, Detroit, Michigan
| | - Jozef Hertecant
- Division of Clinical Genetics and Metabolic Disorders, Pediatric Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Stephanie Sacharow
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Deborah S Barbouth
- Division of Clinical and Translational Genetics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Amit A Shah
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Henry C Lin
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lee-Jun C Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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179
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Kalsbeek AMF, Chan EKF, Grogan J, Petersen DC, Jaratlerdsiri W, Gupta R, Lyons RJ, Haynes AM, Horvath LG, Kench JG, Stricker PD, Hayes VM. Altered mitochondrial genome content signals worse pathology and prognosis in prostate cancer. Prostate 2018; 78:25-31. [PMID: 29134670 DOI: 10.1002/pros.23440] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/29/2017] [Indexed: 01/24/2023]
Abstract
BACKGROUND Mitochondrial genome (mtDNA) content is depleted in many cancers. In prostate cancer, there is intra-glandular as well as inter-patient mtDNA copy number variation. In this study, we determine if mtDNA content can be used as a predictor for prostate cancer staging and outcomes. METHODS Fresh prostate cancer biopsies from 115 patients were obtained at time of surgery. All cores underwent pathological review, followed by isolation of cancer and normal tissue. DNA was extracted and qPCR performed to quantify the total amount of mtDNA as a ratio to genomic DNA. Differences in mtDNA content were compared for prostate cancer pathology features and disease outcomes. RESULTS We showed a significantly reduced mtDNA content in prostate cancer compared with normal adjacent prostate tissue (mean difference 1.73-fold, P-value <0.001). Prostate cancer with increased mtDNA content showed unfavorable pathologic characteristics including, higher disease stage (PT2 vs PT3 P-value = 0.018), extracapsular extension (P-value = 0.02) and a trend toward an increased Gleason score (P-value = 0.064). No significant association was observed between changes in mtDNA content and biochemical recurrence (median follow up of 107 months). CONCLUSIONS Contrary to other cancer types, prostate cancer tissue shows no universally depleted mtDNA content. Rather, the change in mtDNA content is highly variable, mirroring known prostate cancer genome heterogeneity. Patients with high mtDNA content have an unfavorable pathology, while a high mtDNA content in normal adjacent prostate tissue is associated with worse prognosis.
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Affiliation(s)
- Anton M F Kalsbeek
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
| | - Eva K F Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
| | - Judith Grogan
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Desiree C Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Ruth J Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Anne-Maree Haynes
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, New South Wales, Australia
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
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180
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Frazier AE, Thorburn DR, Compton AG. Mitochondrial energy generation disorders: genes, mechanisms, and clues to pathology. J Biol Chem 2017; 294:5386-5395. [PMID: 29233888 DOI: 10.1074/jbc.r117.809194] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Inherited disorders of oxidative phosphorylation cause the clinically and genetically heterogeneous diseases known as mitochondrial energy generation disorders, or mitochondrial diseases. Over the last three decades, mutations causing these disorders have been identified in almost 290 genes, but many patients still remain without a molecular diagnosis. Moreover, while our knowledge of the genetic causes is continually expanding, our understanding into how these defects lead to cellular dysfunction and organ pathology is still incomplete. Here, we review recent developments in disease gene discovery, functional characterization, and shared pathogenic parameters influencing disease pathology that offer promising avenues toward the development of effective therapies.
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Affiliation(s)
- Ann E Frazier
- From the Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, and
| | - David R Thorburn
- From the Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, and.,Victorian Clinical Genetic Services, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
| | - Alison G Compton
- From the Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, and
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181
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Siegmund SE, Yang H, Sharma R, Javors M, Skinner O, Mootha V, Hirano M, Schon EA. Low-dose rapamycin extends lifespan in a mouse model of mtDNA depletion syndrome. Hum Mol Genet 2017; 26:4588-4605. [PMID: 28973153 PMCID: PMC5886265 DOI: 10.1093/hmg/ddx341] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/31/2017] [Accepted: 08/24/2017] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial disorders affecting oxidative phosphorylation (OxPhos) are caused by mutations in both the nuclear and mitochondrial genomes. One promising candidate for treatment is the drug rapamycin, which has been shown to extend lifespan in multiple animal models, and which was previously shown to ameliorate mitochondrial disease in a knock-out mouse model lacking a nuclear-encoded gene specifying an OxPhos structural subunit (Ndufs4). In that model, relatively high-dose intraperitoneal rapamycin extended lifespan and improved markers of neurological disease, via an unknown mechanism. Here, we administered low-dose oral rapamycin to a knock-in (KI) mouse model of authentic mtDNA disease, specifically, progressive mtDNA depletion syndrome, resulting from a mutation in the mitochondrial nucleotide salvage enzyme thymidine kinase 2 (TK2). Importantly, low-dose oral rapamycin was sufficient to extend Tk2KI/KI mouse lifespan significantly, and did so in the absence of detectable improvements in mitochondrial dysfunction. We found no evidence that rapamycin increased survival by acting through canonical pathways, including mitochondrial autophagy. However, transcriptomics and metabolomics analyses uncovered systemic metabolic changes pointing to a potential 'rapamycin metabolic signature.' These changes also implied that rapamycin may have enabled the Tk2KI/KI mice to utilize alternative energy reserves, and possibly triggered indirect signaling events that modified mortality through developmental reprogramming. From a therapeutic standpoint, our results support the possibility that low-dose rapamycin, while not targeting the underlying mtDNA defect, could represent a crucial therapy for the treatment of mtDNA-driven, and some nuclear DNA-driven, mitochondrial diseases.
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Affiliation(s)
| | | | - Rohit Sharma
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Martin Javors
- Department of Psychiatry, University of Texas, San Antonio, TX 78229, USA
| | - Owen Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vamsi Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Eric A Schon
- Department of Neurology
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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182
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El-Hattab AW, Zarante AM, Almannai M, Scaglia F. Therapies for mitochondrial diseases and current clinical trials. Mol Genet Metab 2017; 122:1-9. [PMID: 28943110 PMCID: PMC5773113 DOI: 10.1016/j.ymgme.2017.09.009] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 01/10/2023]
Abstract
Mitochondrial diseases are a clinically and genetically heterogeneous group of disorders that result from dysfunction of the mitochondrial oxidative phosphorylation due to molecular defects in genes encoding mitochondrial proteins. Despite the advances in molecular and biochemical methodologies leading to better understanding of the etiology and mechanism of these diseases, there are still no satisfactory therapies available for mitochondrial disorders. Treatment for mitochondrial diseases remains largely symptomatic and does not significantly alter the course of the disease. Based on limited number of clinical trials, several agents aiming at enhancing mitochondrial function or treating the consequences of mitochondrial dysfunction have been used. Several agents are currently being evaluated for mitochondrial diseases. Therapeutic strategies for mitochondrial diseases include the use of agents enhancing electron transfer chain function (coenzyme Q10, idebenone, riboflavin, dichloroacetate, and thiamine), agents acting as energy buffer (creatine), antioxidants (vitamin C, vitamin E, lipoic acid, cysteine donors, and EPI-743), amino acids restoring nitric oxide production (arginine and citrulline), cardiolipin protector (elamipretide), agents enhancing mitochondrial biogenesis (bezafibrate, epicatechin, and RTA 408), nucleotide bypass therapy, liver transplantation, and gene therapy. Although, there is a lack of curative therapies for mitochondrial disorders at the current time, the increased number of clinical research evaluating agents that target different aspects of mitochondrial dysfunction is promising and is expected to generate more therapeutic options for these diseases in the future.
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Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | | | - Mohammed Almannai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA.
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183
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El-Hattab AW, Dai H, Almannai M, Wang J, Faqeih EA, Al Asmari A, Saleh MAM, Elamin MAO, Alfadhel M, Alkuraya FS, Hashem M, Aldosary MS, Almass R, Almutairi FB, Alsagob M, Al-Owain M, Al-Sharfa S, Al-Hassnan ZN, Rahbeeni Z, Al-Muhaizea MA, Makhseed N, Foskett GK, Stevenson DA, Gomez-Ospina N, Lee C, Boles RG, Schrier Vergano SA, Wortmann SB, Sperl W, Opladen T, Hoffmann GF, Hempel M, Prokisch H, Alhaddad B, Mayr JA, Chan W, Kaya N, Wong LJC. Molecular and clinical spectra of FBXL4 deficiency. Hum Mutat 2017; 38:1649-1659. [DOI: 10.1002/humu.23341] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ayman W. El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatric Department; Tawam Hospital; Al-Ain United Arab Emirates
| | - Hongzheng Dai
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Mohammed Almannai
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Julia Wang
- Medical Scientist Training Program and Program in Developmental Biology; Baylor College of Medicine; Houston Texas
| | - Eissa A. Faqeih
- Section of Medical Genetics, Children's Hospital; King Fahad Medical City; Riyadh Saudi Arabia
| | - Ali Al Asmari
- Section of Medical Genetics, Children's Hospital; King Fahad Medical City; Riyadh Saudi Arabia
| | - Mohammed A. M. Saleh
- Section of Medical Genetics, Children's Hospital; King Fahad Medical City; Riyadh Saudi Arabia
| | - Mohammed A. O. Elamin
- Section of Medical Genetics, Children's Hospital; King Fahad Medical City; Riyadh Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre; King Saud bin Abdulaziz University for Health Sciences; Riyadh Saudi Arabia
- Division of Genetics, Department of Pediatrics; King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA); Riyadh Saudi Arabia
| | - Fowzan S. Alkuraya
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine; Alfaisal University; Riyadh Saudi Arabia
| | - Mais Hashem
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
| | - Mazhor S. Aldosary
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
| | - Rawan Almass
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
| | - Faten B. Almutairi
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
| | - Maysoon Alsagob
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics; King Faisal Specialist Hospital and Research Centre; Riyadh Saudi Arabia
| | - Shirin Al-Sharfa
- Department of Medical Genetics; King Faisal Specialist Hospital and Research Centre; Riyadh Saudi Arabia
| | - Zuhair N. Al-Hassnan
- Department of Medical Genetics; King Faisal Specialist Hospital and Research Centre; Riyadh Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics; King Faisal Specialist Hospital and Research Centre; Riyadh Saudi Arabia
| | - Mohammed A. Al-Muhaizea
- Department of Anatomy and Cell Biology, College of Medicine; Alfaisal University; Riyadh Saudi Arabia
- Department of Neurosciences; King Faisal Specialist Hospital and Research Centre; Riyadh Saudi Arabia
| | - Nawal Makhseed
- Department of Pediatrics, Al-Jahra Hospital; Ministry of Health; Al-Jahra City Kuwait
| | - Gretchen K. Foskett
- Department of Pediatrics; Stanford University School of Medicine; Stanford California
| | - David A. Stevenson
- Department of Pediatrics; Stanford University School of Medicine; Stanford California
| | - Natalia Gomez-Ospina
- Department of Pediatrics; Stanford University School of Medicine; Stanford California
| | - Chung Lee
- Department of Pediatrics; Stanford University School of Medicine; Stanford California
| | | | | | - Saskia B. Wortmann
- Department of Pediatrics, Salzburger Landeskliniken; Paracelsus Medical University; Salzburg Austria
- Institute of Human Genetics; Technische Universität München; Munich Germany
- Institute of Human Genetics; Helmholtz Zentrum München; Neuherberg Germany
| | - Wolfgang Sperl
- Department of Pediatrics, Salzburger Landeskliniken; Paracelsus Medical University; Salzburg Austria
| | - Thomas Opladen
- Centre for Child and Adolescent Medicine, Divisions of General Pediatrics, Neuropediatrics, and Metabolic Medicine; University Hospital; Heidelberg Germany
| | - Georg F. Hoffmann
- Centre for Child and Adolescent Medicine, Divisions of General Pediatrics, Neuropediatrics, and Metabolic Medicine; University Hospital; Heidelberg Germany
| | - Maja Hempel
- Institute of Human Genetics; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Holger Prokisch
- Institute of Human Genetics; Technische Universität München; Munich Germany
- Institute of Human Genetics; Helmholtz Zentrum München; Neuherberg Germany
| | - Bader Alhaddad
- Institute of Human Genetics; Technische Universität München; Munich Germany
- Institute of Human Genetics; Helmholtz Zentrum München; Neuherberg Germany
| | - Johannes A. Mayr
- Department of Pediatrics; Paracelsus Medical University Salzburg; Salzburg Austria
| | - Wenyaw Chan
- Department of Biostatistics, School of Public Health; University of Texas-Health Science Center at Houston; Houston Texas
| | - Namik Kaya
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
| | - Lee-Jun C. Wong
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
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184
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Finsterer J, Zarrouk-Mahjoub S. Axonal hyperexcitability due to Schwann cell involvement in chronic progressive external ophthalmoplegia. Clin Neurophysiol 2017; 128:2096-2097. [PMID: 28811105 DOI: 10.1016/j.clinph.2017.06.260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/14/2017] [Indexed: 01/07/2023]
Affiliation(s)
| | - Sinda Zarrouk-Mahjoub
- University of Tunis El Manar and Genomics Platform, Pasteur Institute of Tunis, Tunisia
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185
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Nicassio L, Fracasso F, Sirago G, Musicco C, Picca A, Marzetti E, Calvani R, Cantatore P, Gadaleta MN, Pesce V. Dietary supplementation with acetyl-l-carnitine counteracts age-related alterations of mitochondrial biogenesis, dynamics and antioxidant defenses in brain of old rats. Exp Gerontol 2017; 98:99-109. [PMID: 28807823 DOI: 10.1016/j.exger.2017.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/31/2017] [Accepted: 08/11/2017] [Indexed: 12/21/2022]
Abstract
We previously reported the ability of dietary supplementation with acetyl-l-carnitine (ALCAR) to prevent age-related decreases of mitochondrial biogenesis in skeletal muscle and liver of old rats. Here, we investigate the effects of ALCAR supplementation in cerebral hemispheres and cerebellum of old rats by analyzing several parameters linked to mitochondrial biogenesis, mitochondrial dynamics and antioxidant defenses. We measured the level of the coactivators PGC-1α and PGC-1β and of the factors regulating mitochondrial biogenesis, finding an age-related decrease of PGC-1β, whereas PGC-1α level was unvaried. Twenty eight-month old rats supplemented with ALCAR for one and two months showed increased levels of both factors. Accordingly, the expression of the two transcription factors NRF-1 and TFAM followed the same trend of PGC-1β. The level of mtDNA, ND1 and the activity of citrate synthase, were decreased with aging and increased following ALCAR treatment. Furthermore, ALCAR counteracted the age-related increase of deleted mtDNA. We also analyzed the content of proteins involved in mitochondrial dynamics (Drp1, Fis1, OPA1 and MNF2) and found an age-dependent increase of MFN2 and of the long form of OPA1. ALCAR treatment restored the content of the two proteins to the level of the young rats. No changes with aging and ALCAR were observed for Drp1 and Fis1. ALCAR reduced total cellular levels of oxidized PRXs and counteracted the age-related decrease of PRX3 and SOD2. Overall, our findings indicate a systemic positive effect of ALCAR dietary treatment and a tissue specific regulation of mitochondrial homeostasis in brain of old rats. Moreover, it appears that ALCAR acts as a nutrient since in most cases its effects were almost completely abolished one month after treatment suspension. Dietary supplementation of old rats with this compound seems a valuable approach to prevent age-related mitochondrial dysfunction and might ultimately represent a strategy to delay age-associated negative consequences in mitochondrial homeostasis.
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Affiliation(s)
- Luigi Nicassio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Flavio Fracasso
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Giuseppe Sirago
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Clara Musicco
- Institute of Biomembranes and Bioenergetics (IBBE), National Research Council of Italy (CNR), Bari, Italy
| | - Anna Picca
- Department of Geriatrics, Neuroscience and Orthopedics, Catholic University of the Sacred Heart School of Medicine, Rome, Italy
| | - Emanuele Marzetti
- Department of Geriatrics, Neuroscience and Orthopedics, Catholic University of the Sacred Heart School of Medicine, Rome, Italy
| | - Riccardo Calvani
- Department of Geriatrics, Neuroscience and Orthopedics, Catholic University of the Sacred Heart School of Medicine, Rome, Italy
| | - Palmiro Cantatore
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Maria Nicola Gadaleta
- Institute of Biomembranes and Bioenergetics (IBBE), National Research Council of Italy (CNR), Bari, Italy
| | - Vito Pesce
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.
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