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Aleo SJ, Del Dotto V, Romagnoli M, Fiorini C, Capirossi G, Peron C, Maresca A, Caporali L, Capristo M, Tropeano CV, Zanna C, Ross-Cisneros FN, Sadun AA, Pignataro MG, Giordano C, Fasano C, Cavaliere A, Porcelli AM, Tioli G, Musiani F, Catania A, Lamperti C, Marzoli SB, De Negri A, Cascavilla ML, Battista M, Barboni P, Carbonelli M, Amore G, La Morgia C, Smirnov D, Vasilescu C, Farzeen A, Blickhaeuser B, Prokisch H, Priglinger C, Livonius B, Catarino CB, Klopstock T, Tiranti V, Carelli V, Ghelli AM. Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy. Cell Rep Med 2024; 5:101383. [PMID: 38272025 PMCID: PMC10897523 DOI: 10.1016/j.xcrm.2023.101383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 07/03/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Idebenone, the only approved treatment for Leber hereditary optic neuropathy (LHON), promotes recovery of visual function in up to 50% of patients, but we can neither predict nor understand the non-responders. Idebenone is reduced by the cytosolic NAD(P)H oxidoreductase I (NQO1) and directly shuttles electrons to respiratory complex III, bypassing complex I affected in LHON. We show here that two polymorphic variants drastically reduce NQO1 protein levels when homozygous or compound heterozygous. This hampers idebenone reduction. In its oxidized form, idebenone inhibits complex I, decreasing respiratory function in cells. By retrospectively analyzing a large cohort of idebenone-treated LHON patients, classified by their response to therapy, we show that patients with homozygous or compound heterozygous NQO1 variants have the poorest therapy response, particularly if carrying the m.3460G>A/MT-ND1 LHON mutation. These results suggest consideration of patient NQO1 genotype and mitochondrial DNA mutation in the context of idebenone therapy.
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Affiliation(s)
- Serena Jasmine Aleo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valentina Del Dotto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Giada Capirossi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Camille Peron
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Mariantonietta Capristo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | | | - Claudia Zanna
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | | | - Alfredo A Sadun
- Doheny Eye Institute, Pasadena, CA, USA; Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Maria Gemma Pignataro
- Departments of Radiology, Oncology, and Pathology, Sapienza, University of Rome, Rome, Italy
| | - Carla Giordano
- Departments of Radiology, Oncology, and Pathology, Sapienza, University of Rome, Rome, Italy
| | - Chiara Fasano
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Andrea Cavaliere
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Anna Maria Porcelli
- Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gaia Tioli
- Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Francesco Musiani
- Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Stefania Bianchi Marzoli
- Neuro-Ophthalmology Center and Ocular Electrophysiology Laboratory, IRCCS Istituto Auxologico Italiano, Capitanio Hospital, Milan, Italy
| | | | | | | | | | - Michele Carbonelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Giulia Amore
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Dmitrii Smirnov
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Catalina Vasilescu
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Aiman Farzeen
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Beryll Blickhaeuser
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Claudia Priglinger
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Bettina Livonius
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Claudia B Catarino
- Department of Neurology, Friedrich Baur Institute, LMU Klinikum, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich Baur Institute, LMU Klinikum, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Valeria Tiranti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
| | - Anna Maria Ghelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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Brockmann SJ, Buck E, Casoli T, Meirelles JL, Ruf WP, Fabbietti P, Holzmann K, Weishaupt JH, Ludolph AC, Conti F, Danzer KM. Mitochondrial genome study in blood of maternally inherited ALS cases. Hum Genomics 2023; 17:70. [PMID: 37507754 PMCID: PMC10375681 DOI: 10.1186/s40246-023-00516-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND ALS is a heterogeneous disease in which different factors such as mitochondrial phenotypes act in combination with a genetic predisposition. This study addresses the question of whether homoplasmic (total mitochondrial genome of a sample is affected) and/or heteroplasmic mutations (wildtype and mutant mitochondrial DNA molecules coexist) might play a role in familial ALS. Blood was drawn from familial ALS patients with a possible maternal pattern of inheritance according to their pedigrees, which was compared to blood of ALS patients without maternal association as well as age-matched controls. In two cohorts, we analyzed the mitochondrial genome from whole blood or isolated white blood cells and platelets using a resequencing microarray (Affymetrix MitoChip v2.0) that is able to detect homoplasmic and heteroplasmic mitochondrial DNA mutations and allows the assessment of low-level heteroplasmy. RESULTS We identified an increase in homoplasmic ND5 mutations, a subunit of respiratory chain complex I, in whole blood of ALS patients that allowed maternal inheritance. This effect was more pronounced in patients with bulbar onset. Heteroplasmic mutations were significantly increased in different mitochondrial genes in platelets of patients with possible maternal inheritance. No increase of low-level heteroplasmy was found in maternal ALS patients. CONCLUSION Our results indicate a contribution of homoplasmic ND5 mutations to maternally associated ALS with bulbar onset. Therefore, it might be conceivable that specific maternally transmitted rather than randomly acquired mitochondrial DNA mutations might contribute to the disease process. This stands in contrast with observations from Alzheimer's and Parkinson's diseases showing an age-dependent accumulation of unspecific mutations in mitochondrial DNA.
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Affiliation(s)
- Sarah J Brockmann
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
| | - Eva Buck
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany
| | - Tiziana Casoli
- Center for Neurobiology of Aging, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - João L Meirelles
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany
| | - Wolfgang P Ruf
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
| | - Paolo Fabbietti
- Unit of Geriatric Pharmacoepidemiology, IRCCS INRCA, Ancona, Italy
| | | | - Jochen H Weishaupt
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
- Division for Neurodegenerative Diseases, Neurology Department, University Medicine Mannheim, Heidelberg University, Mannheim, Germany
| | - Albert C Ludolph
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany
| | - Fiorenzo Conti
- Center for Neurobiology of Aging, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
- Section of Neuroscience and Cell Biology, Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, Ancona, Italy
| | - Karin M Danzer
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany.
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Abstract
Mitochondrial optic neuropathies have a leading role in the field of mitochondrial medicine ever since 1988, when the first mutation in mitochondrial DNA was associated with Leber's hereditary optic neuropathy (LHON). Autosomal dominant optic atrophy (DOA) was subsequently associated in 2000 with mutations in the nuclear DNA affecting the OPA1 gene. LHON and DOA are both characterized by selective neurodegeneration of retinal ganglion cells (RGCs) triggered by mitochondrial dysfunction. This is centered on respiratory complex I impairment in LHON and defective mitochondrial dynamics in OPA1-related DOA, leading to distinct clinical phenotypes. LHON is a subacute, rapid, severe loss of central vision involving both eyes within weeks or months, with age of onset between 15 and 35 years old. DOA is a more slowly progressive optic neuropathy, usually apparent in early childhood. LHON is characterized by marked incomplete penetrance and a clear male predilection. The introduction of next-generation sequencing has greatly expanded the genetic causes for other rare forms of mitochondrial optic neuropathies, including recessive and X-linked, further emphasizing the exquisite sensitivity of RGCs to compromised mitochondrial function. All forms of mitochondrial optic neuropathies, including LHON and DOA, can manifest either as pure optic atrophy or as a more severe multisystemic syndrome. Mitochondrial optic neuropathies are currently at the forefront of a number of therapeutic programs, including gene therapy, with idebenone being the only approved drug for a mitochondrial disorder.
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Affiliation(s)
- Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy; IRCCS Istituto di Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy.
| | - Chiara La Morgia
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy; IRCCS Istituto di Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Patrick Yu-Wai-Man
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom; Institute of Ophthalmology, University College London, London, United Kingdom
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The role of mtDNA haplogroups on metabolic features in narcolepsy type 1. Mitochondrion 2022; 63:37-42. [PMID: 35051655 DOI: 10.1016/j.mito.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 11/24/2022]
Abstract
Narcolepsy type 1 (NT1) is due to selective loss of hypocretin (hcrt)-producing-neurons. Hcrt is a neuropeptide regulating the sleep/wake cycle, as well as feeding behavior. A subset of NT1 patients become overweight/obese, with a dysmetabolic phenotype. We hypothesized that mitochondrial DNA (mtDNA) sequence variation might contribute to the metabolic features in NT1 and we undertook an exploratory survey of mtDNA haplogroups in a cohort of well-characterized patients. We studied 246 NT1 Italian patients, fully defined for their metabolic features, including obesity, hypertension, low HDL, hypertriglyceridemia and hyperglycemia. For haplogroup assignment, the mtDNA control region was sequenced in combination with an assessment of diagnostic markers in the coding region. NT1 patients displayed the same mtDNA haplogroups (H, HV, J, K, T, U) frequency as those reported in the general Italian population. The majority of NT1 patients (64%) were overweight: amongst these, 35% were obese, 48% had low HDL cholesterol levels, and 31% had hypertriglyceridemia. We identified an association between haplogroups J, K and hypertriglyceridemia (P=0.03, 61.5% and 61.5%, respectively vs. 31.3% of the whole sample) and after correction for age and sex, we observed a reduction of these associations (OR=3.65, 95%CI=0.76-17.5, p=0.106 and 1.73, 0.52-5.69, p=0.368, respectively). The low HDL level showed a trend for association with haplogroup J (P=0.09, 83.3% vs. 47.4% of the whole sample) and after correction we observed an OR=6.73, 95%CI=0.65-69.9, p=0.110. Our study provides the first indication that mtDNA haplogroups J and K can modulate metabolic features of NT1 patients, linking mtDNA variation to the dysmetabolic phenotype in NT1.
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Jones SW, Ball AL, Chadwick AE, Alfirevic A. The Role of Mitochondrial DNA Variation in Drug Response: A Systematic Review. Front Genet 2021; 12:698825. [PMID: 34484295 PMCID: PMC8416105 DOI: 10.3389/fgene.2021.698825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/14/2021] [Indexed: 01/11/2023] Open
Abstract
Background: The triad of drug efficacy, toxicity and resistance underpins the risk-benefit balance of all therapeutics. The application of pharmacogenomics has the potential to improve the risk-benefit balance of a given therapeutic via the stratification of patient populations based on DNA variants. A growth in the understanding of the particulars of the mitochondrial genome, alongside the availability of techniques for its interrogation has resulted in a growing body of literature examining the impact of mitochondrial DNA (mtDNA) variation upon drug response. Objective: To critically evaluate and summarize the available literature, across a defined period, in a systematic fashion in order to map out the current landscape of the subject area and identify how the field may continue to advance. Methods: A systematic review of the literature published between January 2009 and December 2020 was conducted using the PubMed database with the following key inclusion criteria: reference to specific mtDNA polymorphisms or haplogroups, a core objective to examine associations between mtDNA variants and drug response, and research performed using human subjects or human in vitro models. Results: Review of the literature identified 24 articles reporting an investigation of the association between mtDNA variant(s) and drug efficacy, toxicity or resistance that met the key inclusion criteria. This included 10 articles examining mtDNA variations associated with antiretroviral therapy response, 4 articles examining mtDNA variants associated with anticancer agent response and 4 articles examining mtDNA variants associated with antimicrobial agent response. The remaining articles covered a wide breadth of medications and were therefore grouped together and referred to as "other." Conclusions: Investigation of the impact of mtDNA variation upon drug response has been sporadic to-date. Collective assessment of the associations identified in the articles was inconclusive due to heterogeneous methods and outcomes, limited racial/ethnic groups, lack of replication and inadequate statistical power. There remains a high degree of idiosyncrasy in drug response and this area has the potential to explain variation in drug response in a clinical setting, therefore further research is likely to be of clinical benefit.
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Affiliation(s)
- Samantha W. Jones
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, United Kingdom
| | - Amy L. Ball
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, United Kingdom
| | - Amy E. Chadwick
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, United Kingdom
| | - Ana Alfirevic
- Department of Pharmacology and Therapeutics, Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool, United Kingdom
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Gutiérrez Cortés N, Pertuiset C, Dumon E, Börlin M, Da Costa B, Le Guédard M, Stojkovic T, Loundon N, Rouillon I, Nadjar Y, Letellier T, Jonard L, Marlin S, Rocher C. Mutation m.3395A > G in MT-ND1 leads to variable pathologic manifestations. Hum Mol Genet 2021; 29:980-989. [PMID: 32011699 DOI: 10.1093/hmg/ddaa020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 11/12/2022] Open
Abstract
A non-synonymous mtDNA mutation, m.3395A > G, which changes tyrosine in position 30 to cysteine in p.MT-ND1, was found in several patients with a wide range of clinical phenotypes such as deafness, diabetes and cerebellar syndrome but no Leber's hereditary optic neuropathy. Although this mutation has already been described, its pathogenicity has not been demonstrated. Here, it was found isolated for the first time, allowing a study to investigate its pathogenicity. To do so, we constructed cybrid cell lines and carried out a functional study to assess the possible consequences of the mutation on mitochondrial bioenergetics. Results obtained demonstrated that this mutation causes an important dysfunction of the mitochondrial respiratory chain with a decrease in both activity and quantity of complex I due to a diminution of p.MT-ND1 quantity. However, no subcomplexes were found in cybrids carrying the mutation, indicating that the quality of the complex I assembly is not affected. Moreover, based on the crystal structure of p.MT-ND1 and the data found in the literature, we propose a hypothesis for the mechanism of the degradation of p.MT-ND1. Our study provides new insights into the pathophysiology of mitochondrial diseases and in particular of MT-ND1 mutations.
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Affiliation(s)
- Nicolás Gutiérrez Cortés
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Claire Pertuiset
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Elodie Dumon
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Marine Börlin
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Barbara Da Costa
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Marina Le Guédard
- Laboratoire de Biogenèse Membranaire, CNRS UMR 5200, Université de Bordeaux, INRA Bordeaux Aquitaine, Villenave d'Ornon, France.,LEB Aquitaine Transfert-ADERA, FR-33883 Villenave d'Ornon, Cedex, France
| | - Tanya Stojkovic
- APHP, Centre de Référence des Maladies Neuromusculaires Ile de France Nord Est, G-H Pitié-Salpêtrière, 75013 Paris, France
| | - Natalie Loundon
- Otorhinolaryngologie Pédiatrique, Centre de Référence des Surdités Génétiques, Hôpital Necker, AP-HP, Paris, France
| | - Isabelle Rouillon
- Otorhinolaryngologie Pédiatrique, Centre de Référence des Surdités Génétiques, Hôpital Necker, AP-HP, Paris, France
| | - Yann Nadjar
- Neurologie, GH Pitié Salpêtrière, 75013 Paris, France
| | - Thierry Letellier
- Equipe de Médecine Evolutive, AMIS, UMR 5288 CNRS/Université Paul Sabatier, 31073 Toulouse, France
| | - Laurence Jonard
- Service de Génétique Moléculaire, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Sandrine Marlin
- Service de Génétique Moléculaire, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.,Centre de Référence des Surdités Génétiques, Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.,UMR 1163, Université Paris Descartes, Sorbonne Paris Cité, Institut IMAGINE, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Christophe Rocher
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
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Shuai J, Shi J, Liang Y, Ji F, Gu L, Yuan Z. Mutational analysis of mitochondrial tRNA genes in 138 patients with Leber's hereditary optic neuropathy. Ir J Med Sci 2021; 191:865-876. [PMID: 34053002 DOI: 10.1007/s11845-021-02656-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Mutations in mitochondrial DNA (mtDNA) are the most important causes for Leber's hereditary optic neuropathy (LHON). Of these, three primary mtDNA mutations account for more than 90% cases of this disease. However, to date, little is known regarding the relationship between mitochondrial tRNA (mt-tRNA) variants and LHON. AIM In this study, we aimed to investigate the association between mt-tRNA variants and LHON. METHODOLOGY One hundred thirty-eight LHON patients lacking three primary mutations (ND1 3460G > A, ND4 11778Gxs > A, and ND6 14484 T > C), as well as 266 controls were enrolled in this study. PCR-Sanger sequencing was performed to screen the mt-tRNA variants. Moreover, the phylogenetic analysis, pathogenicity scoring system, as well as mitochondrial functions were performed. RESULTS We identified 8 possible pathogenic variants: tRNAPhe 593 T > C, tRNALeu(UUR) 3275C > T, tRNAGln 4363 T > C, tRNAMet 4435A > G, tRNAAla 5587 T > C, tRNAGlu 14693A > G, tRNAThr 15927G > A, and 15951A > G, which may change the structural and functional impact on the corresponding tRNAs, and subsequently lead to a failure in tRNA metabolism. Furthermore, significant reductions in mitochondrial ATP and MMP levels and an overproduction of ROS were observed in cybrid cells containing these mt-tRNA variants, suggesting that these variants may lead to mitochondrial dysfunction which was responsible for LHON. CONCLUSION Our study indicated that mt-tRNA variants were associated with LHON, and screening for mt-tRNA variants were recommended for early detection, diagnosis, and prevention of maternally inherited LHON.
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Affiliation(s)
- Jie Shuai
- Department of Ophthalmology, the Affiliated Hospital of Nantong University, Nantong, China
| | - Jian Shi
- Department of Ophthalmology, the Affiliated Hospital of Nantong University, Nantong, China
| | - Ya Liang
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Fangfang Ji
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Luo Gu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Zhilan Yuan
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
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Macken WL, Vandrovcova J, Hanna MG, Pitceathly RDS. Applying genomic and transcriptomic advances to mitochondrial medicine. Nat Rev Neurol 2021; 17:215-230. [PMID: 33623159 DOI: 10.1038/s41582-021-00455-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2021] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has increased our understanding of the molecular basis of many primary mitochondrial diseases (PMDs). Despite this progress, many patients with suspected PMD remain without a genetic diagnosis, which restricts their access to in-depth genetic counselling, reproductive options and clinical trials, in addition to hampering efforts to understand the underlying disease mechanisms. Although they represent a considerable improvement over their predecessors, current methods for sequencing the mitochondrial and nuclear genomes have important limitations, and molecular diagnostic techniques are often manual and time consuming. However, recent advances in genomics and transcriptomics offer realistic solutions to these challenges. In this Review, we discuss the current genetic testing approach for PMDs and the opportunities that exist for increased use of whole-genome NGS of nuclear and mitochondrial DNA (mtDNA) in the clinical environment. We consider the possible role for long-read approaches in sequencing of mtDNA and in the identification of novel nuclear genomic causes of PMDs. We examine the expanding applications of RNA sequencing, including the detection of cryptic variants that affect splicing and gene expression and the interpretation of rare and novel mitochondrial transfer RNA variants.
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Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK.
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Maresca A, Carelli V. Molecular Mechanisms behind Inherited Neurodegeneration of the Optic Nerve. Biomolecules 2021; 11:496. [PMID: 33806088 PMCID: PMC8064499 DOI: 10.3390/biom11040496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 01/01/2023] Open
Abstract
Inherited neurodegeneration of the optic nerve is a paradigm in neurology, as many forms of isolated or syndromic optic atrophy are encountered in clinical practice. The retinal ganglion cells originate the axons that form the optic nerve. They are particularly vulnerable to mitochondrial dysfunction, as they present a peculiar cellular architecture, with axons that are not myelinated for a long intra-retinal segment, thus, very energy dependent. The genetic landscape of causative mutations and genes greatly enlarged in the last decade, pointing to common pathways. These mostly imply mitochondrial dysfunction, which leads to a similar outcome in terms of neurodegeneration. We here critically review these pathways, which include (1) complex I-related oxidative phosphorylation (OXPHOS) dysfunction, (2) mitochondrial dynamics, and (3) endoplasmic reticulum-mitochondrial inter-organellar crosstalk. These major pathogenic mechanisms are in turn interconnected and represent the target for therapeutic strategies. Thus, their deep understanding is the basis to set and test new effective therapies, an urgent unmet need for these patients. New tools are now available to capture all interlinked mechanistic intricacies for the pathogenesis of optic nerve neurodegeneration, casting hope for innovative therapies to be rapidly transferred into the clinic and effectively cure inherited optic neuropathies.
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Affiliation(s)
- Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy;
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy;
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy
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10
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Ball AL, Bloch KM, Rainbow L, Liu X, Kenny J, Lyon JJ, Gregory R, Alfirevic A, Chadwick AE. Assessment of the impact of mitochondrial genotype upon drug-induced mitochondrial dysfunction in platelets derived from healthy volunteers. Arch Toxicol 2021; 95:1335-1347. [PMID: 33585966 PMCID: PMC8032628 DOI: 10.1007/s00204-021-02988-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/21/2021] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA (mtDNA) is highly polymorphic and encodes 13 proteins which are critical to the production of ATP via oxidative phosphorylation. As mtDNA is maternally inherited and undergoes negligible recombination, acquired mutations have subdivided the human population into several discrete haplogroups. Mitochondrial haplogroup has been found to significantly alter mitochondrial function and impact susceptibility to adverse drug reactions. Despite these findings, there are currently limited models to assess the effect of mtDNA variation upon susceptibility to adverse drug reactions. Platelets offer a potential personalised model of this variation, as their anucleate nature offers a source of mtDNA without interference from the nuclear genome. This study, therefore, aimed to determine the effect of mtDNA variation upon mitochondrial function and drug-induced mitochondrial dysfunction in a platelet model. The mtDNA haplogroup of 383 healthy volunteers was determined using next-generation mtDNA sequencing (Illumina MiSeq). Subsequently, 30 of these volunteers from mitochondrial haplogroups H, J, T and U were recalled to donate fresh, whole blood from which platelets were isolated. Platelet mitochondrial function was tested at basal state and upon treatment with compounds associated with both mitochondrial dysfunction and adverse drug reactions, flutamide, 2-hydroxyflutamide and tolcapone (10–250 μM) using extracellular flux analysis. This study has demonstrated that freshly-isolated platelets are a practical, primary cell model, which is amenable to the study of drug-induced mitochondrial dysfunction. Specifically, platelets from donors of haplogroup J have been found to have increased susceptibility to the inhibition of complex I-driven respiration by 2-hydroxyflutamide. At a time when individual susceptibility to adverse drug reactions is not fully understood, this study provides evidence that inter-individual variation in mitochondrial genotype could be a factor in determining sensitivity to mitochondrial toxicants associated with costly adverse drug reactions.
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Affiliation(s)
- Amy L Ball
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Katarzyna M Bloch
- The Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Lucille Rainbow
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Xuan Liu
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - John Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | | | - Richard Gregory
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ana Alfirevic
- The Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Amy E Chadwick
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK.
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11
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Jiang Z, Teng L, Zhang S, Ding Y. Mitochondrial ND1 T4216C and ND2 C5178A mutations are associated with maternally transmitted diabetes mellitus. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 32:59-65. [PMID: 33284036 DOI: 10.1080/24701394.2020.1856101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mutations in mitochondrial DNA (mtDNA) are important causes for type 2 diabetes mellitus (T2DM). To investigate the association between mtDNA mutations/variants and diabetes, we reported here clinical, genetic and biochemical characterization of a Chinese pedigree with maternally transmitted T2DM. Using PCR and direct sequencing analysis of mitochondrial genomes from the matrilineal relatives, we identified two potential pathogenic mutations, m.T4216C (p.Y304H) and m.C5178A (p.L237M) in the ND1 and ND2 genes, respectively, together with a set of genetic polymorphisms belonging to the human mitochondrial haplogroup D4b. Moreover, by isolating and analyzing polymononuclear leukocytes generated from the T2DM patients and controls, we identified lower levels of mitochondrial membrane potential and ATP production in T2DM patients than in the controls, in contrast, a significantly higher level of reactive oxygen species was observed in the T2DM patients carrying both of the m.T4216C and m.C5178A mutations (p < 0.05 for all). In addition, the plasma levels of malondialdehyde and 8-hydroxydeoxyguanosine in the T2DM patients markedly increased, while the level of superoxide dismutase decreased (p < 0.05 for all). Taken together, our data indicated that the ND1 T4216C and ND2 C5178A mutations may lead to oxidative stress and impair the mitochondrial function, and this, in turn, might have been involved in the pathogenesis and progression of T2DM in this pedigree. Thus, our study provides novel insight into the pathophysiology of T2DM that is manifested by mitochondrial dysfunction.
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Affiliation(s)
- Zhaochang Jiang
- Department of Pathology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lili Teng
- Department of Geriatric Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shunrong Zhang
- Department of Gerontology, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Ding
- Central Laboratory, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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12
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Toncheva D, Serbezov D, Karachanak-Yankova S, Nesheva D. Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease. PLoS One 2020; 15:e0233666. [PMID: 32970680 PMCID: PMC7514063 DOI: 10.1371/journal.pone.0233666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.
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Affiliation(s)
- Draga Toncheva
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
- Bulgarian Academy of Sciences–BAS, Sofia, Bulgaria
- * E-mail:
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
- Department of Genetics, Faculty of biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
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Whole Mitochondrial Genome Analysis in Serbian Cases of Leber's Hereditary Optic Neuropathy. Genes (Basel) 2020; 11:genes11091037. [PMID: 32887465 PMCID: PMC7565519 DOI: 10.3390/genes11091037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON) is a maternally inherited disorder that affects central vision in young adults and is typically associated with mitochondrial DNA (mtDNA) mutations. This study is based on a mutational screening of entire mtDNA in eight Serbian probands clinically and genetically diagnosed with LHON and four of their family members, who are asymptomatic mutation carriers. All obtained sequence variants were compared to human mtDNA databases, and their potential pathogenic characteristics were assessed by bioinformatics tools. Mitochondrial haplogroup analysis was performed by MITOMASTER. Our study revealed two well-known primary LHON mutations, m.11778G>A and m.3460G>A, and one rare LHON mutation, m.8836A>G. Various secondary mutations were detected in association with the primary mutations. MITOMASTER analysis showed that the two well-known primary mutations belong to the R haplogroup, while the rare LHON m.8836A>G was detected within the N1b haplogroup. Our results support the need for further studies of genetic background and its role in the penetrance and severity of LHON.
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Zhou L, Chan JCY, Chupin S, Gueguen N, Desquiret-Dumas V, Koh SK, Li J, Gao Y, Deng L, Verma C, Beuerman RW, Chan ECY, Milea D, Reynier P. Increased Protein S-Glutathionylation in Leber's Hereditary Optic Neuropathy (LHON). Int J Mol Sci 2020; 21:ijms21083027. [PMID: 32344771 PMCID: PMC7215361 DOI: 10.3390/ijms21083027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/11/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON, MIM#535000) is the most common form of inherited optic neuropathies and mitochondrial DNA-related diseases. The pathogenicity of mutations in genes encoding components of mitochondrial Complex I is well established, but the underlying pathomechanisms of the disease are still unclear. Hypothesizing that oxidative stress related to Complex I deficiency may increase protein S-glutathionylation, we investigated the proteome-wide S-glutathionylation profiles in LHON (n = 11) and control (n = 7) fibroblasts, using the GluICAT platform that we recently developed. Glutathionylation was also studied in healthy fibroblasts (n = 6) after experimental Complex I inhibition. The significantly increased reactive oxygen species (ROS) production in the LHON group by Complex I was shown experimentally. Among the 540 proteins which were globally identified as glutathionylated, 79 showed a significantly increased glutathionylation (p < 0.05) in LHON and 94 in Complex I-inhibited fibroblasts. Approximately 42% (33/79) of the altered proteins were shared by the two groups, suggesting that Complex I deficiency was the main cause of increased glutathionylation. Among the 79 affected proteins in LHON fibroblasts, 23% (18/79) were involved in energetic metabolism, 31% (24/79) exhibited catalytic activity, 73% (58/79) showed various non-mitochondrial localizations, and 38% (30/79) affected the cell protein quality control. Integrated proteo-metabolomic analysis using our previous metabolomic study of LHON fibroblasts also revealed similar alterations of protein metabolism and, in particular, of aminoacyl-tRNA synthetases. S-glutathionylation is mainly known to be responsible for protein loss of function, and molecular dynamics simulations and 3D structure predictions confirmed such deleterious impacts on adenine nucleotide translocator 2 (ANT2), by weakening its affinity to ATP/ADP. Our study reveals a broad impact throughout the cell of Complex I-related LHON pathogenesis, involving a generalized protein stress response, and provides a therapeutic rationale for targeting S-glutathionylation by antioxidative strategies.
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Affiliation(s)
- Lei Zhou
- Ocular Proteomics, Singapore Eye Research Institute, Singapore 169856, Singapore; (S.K.K.); (J.L.); (Y.G.); (R.W.B.)
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
- Correspondence: (L.Z.); (D.M.); (P.R.)
| | - James Chun Yip Chan
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore; (J.C.Y.C.); (E.C.Y.C.)
| | - Stephanie Chupin
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (S.C.); (N.G.); (V.D.-D.)
| | - Naïg Gueguen
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (S.C.); (N.G.); (V.D.-D.)
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d’Angers, 49933 Angers, France
| | - Valérie Desquiret-Dumas
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (S.C.); (N.G.); (V.D.-D.)
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d’Angers, 49933 Angers, France
| | - Siew Kwan Koh
- Ocular Proteomics, Singapore Eye Research Institute, Singapore 169856, Singapore; (S.K.K.); (J.L.); (Y.G.); (R.W.B.)
| | - Jianguo Li
- Ocular Proteomics, Singapore Eye Research Institute, Singapore 169856, Singapore; (S.K.K.); (J.L.); (Y.G.); (R.W.B.)
- Atomistic Simulations and Design in Biology, Bioinformatics Institute, 30 Biopolis Street, #07–01 Matrix, Singapore 138671, Singapore;
| | - Yan Gao
- Ocular Proteomics, Singapore Eye Research Institute, Singapore 169856, Singapore; (S.K.K.); (J.L.); (Y.G.); (R.W.B.)
| | - Lu Deng
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore 117546, Singapore;
| | - Chandra Verma
- Atomistic Simulations and Design in Biology, Bioinformatics Institute, 30 Biopolis Street, #07–01 Matrix, Singapore 138671, Singapore;
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singpaore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Roger W Beuerman
- Ocular Proteomics, Singapore Eye Research Institute, Singapore 169856, Singapore; (S.K.K.); (J.L.); (Y.G.); (R.W.B.)
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Eric Chun Yong Chan
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore; (J.C.Y.C.); (E.C.Y.C.)
- Singapore Institute for Clinical Sciences, Brenner Centre for Molecular Medicine, 30 Medical Drive, Singapore 117609, Singapore
| | - Dan Milea
- Ocular Proteomics, Singapore Eye Research Institute, Singapore 169856, Singapore; (S.K.K.); (J.L.); (Y.G.); (R.W.B.)
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France
- Neuro-Ophthalmology Department, Singapore National Eye Centre, Singapore 168751, Singpaore
- Correspondence: (L.Z.); (D.M.); (P.R.)
| | - Pascal Reynier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (S.C.); (N.G.); (V.D.-D.)
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d’Angers, 49933 Angers, France
- Correspondence: (L.Z.); (D.M.); (P.R.)
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15
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Casagrande FV, Amadeo A, Cartelli D, Calogero AM, Modena D, Costa I, Cantele F, Onelli E, Moscatelli A, Ascagni M, Pezzoli G, Cappelletti G. The imbalance between dynamic and stable microtubules underlies neurodegeneration induced by 2,5-hexanedione. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165581. [DOI: 10.1016/j.bbadis.2019.165581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/17/2019] [Accepted: 10/12/2019] [Indexed: 01/10/2023]
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16
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Starikovskaya E, Shalaurova S, Dryomov S, Nazhmidenova A, Volodko N, Bychkov I, Mazunin I, Sukernik R. Mitochondrial DNA Variation of Leber's Hereditary Optic Neuropathy in Western Siberia. Cells 2019; 8:E1574. [PMID: 31817256 PMCID: PMC6953113 DOI: 10.3390/cells8121574] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 12/24/2022] Open
Abstract
Our data first represent the variety of Leber's hereditary optic neuropathy (LHON) mutations in Western Siberia. LHON is a disorder caused by pathogenic mutations in mitochondrial DNA (mtDNA), inherited maternally and presents mainly in young adults, predominantly males. Clinically, LHON manifests itself as painless central vision loss, resulting in early onset of disability. The epidemiology of LHON has not been fully investigated yet. In this study, we report 44 genetically unrelated families with LHON manifestation. We performed whole mtDNA genome sequencing and provided genealogical and molecular genetic data on mutations and haplogroup background of LHON patients. Known "primary" pathogenic mtDNA mutations (MITOMAP) were found in 32 families: m.11778G>A represents 53.10% (17/32), m.3460G>A-21.90% (7/32), m.14484T>C-18.75% (6/32), and rare m.10663T>C and m.3635G>A represent 6.25% (2/32). We describe potentially pathogenic m.4659G>A in one subject without known pathogenic mutations, and potentially pathogenic m.6261G>A, m.8412T>C, m.8551T>C, m.9444C>T, m.9921G>A, and m.15077G>A in families with known pathogenic mutations confirmed. We suppose these mutations could contribute to the pathogenesis of optic neuropathy development. Our results indicate that haplogroup affiliation and mutational spectrum of the Western Siberian LHON cohort substantially deviate from those of European populations.
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Affiliation(s)
- Elena Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Sofia Shalaurova
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Azhar Nazhmidenova
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Natalia Volodko
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Igor Bychkov
- Novosibirsk Branch of S.N. Fedorov NMRC “MNTK Eye Microsurgery”, Moscow 127486, Russia
| | - Ilia Mazunin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
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Patel TH, Norman L, Chang S, Abedi S, Liu C, Chwa M, Atilano SR, Thaker K, Lu S, Jazwinski SM, Miceli MV, Udar N, Bota D, Kenney MC. European mtDNA Variants Are Associated With Differential Responses to Cisplatin, an Anticancer Drug: Implications for Drug Resistance and Side Effects. Front Oncol 2019; 9:640. [PMID: 31380278 PMCID: PMC6659439 DOI: 10.3389/fonc.2019.00640] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/01/2019] [Indexed: 01/02/2023] Open
Abstract
Background: Cisplatin, a powerful antitumor agent, causes formation of DNA adducts, and activation of apoptotic pathways. Presently, cisplatin resistance develops in up to 70% of patients but the underlying molecular mechanism(s) are unclear and there are no markers to determine which patients will become resistant. Mitochondria play a significant role not only in energy metabolism but also retrograde signaling (mitochondria to nucleus) that modulates inflammation, complement, and apoptosis pathways. Maternally inherited mitochondrial (mt) DNA can be classified into haplogroups representing different ethnic populations that have diverse susceptibilities to diseases and medications. Methods: Transmitochondrial cybrids, where all cell lines possess identical nuclear genomes but either the H (Southern European) or J (Northern European) mtDNA haplogroups, were treated with cisplatin and analyzed for differential responses related to viability, oxidative stress, and expression levels of genes associated with cancer, cisplatin-induced nephrotoxicity and resistance, apoptosis and signaling pathways. Results: The cisplatin-treated-J cybrids showed greater loss of cell viability along with lower levels of reactive oxygen species and mitochondrial membrane potential compared to cisplatin-treated-H cybrids. After cisplatin treatment, J cybrids showed increased gene expression of BAX, CASP3, and CYP51A, but lower levels of SFRP1 compared to untreated-J cybrids. The cisplatin-treated-H cybrids had elevated expression of CDKN1A/P21, which has a role in cisplatin toxicity, compared to untreated-H cybrids. The cisplatin-treated H had higher transcription levels of ABCC1, DHRS2/HEP27, and EFEMP1 compared to cisplatin-treated-J cybrids. Conclusions: Cybrid cell lines that contain identical nuclei but either H mtDNA mitochondria or J mtDNA mitochondria respond differently to cisplatin treatments suggesting involvement of the retrograde signaling (from mitochondria to nucleus) in the drug-induced cell death. Varying toxicities and transcription levels of the H vs. J cybrids after cisplatin treatment support the hypothesis that mtDNA variants play a role in the expression of genes affecting resistance and side effects of cisplatin.
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Affiliation(s)
- Tej H Patel
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Lucas Norman
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Steven Chang
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Sina Abedi
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Catherine Liu
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States.,Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL, United States
| | - Marilyn Chwa
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Shari R Atilano
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Kunal Thaker
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Stephanie Lu
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States.,VA Medical Center Long Beach Hospital, Long Beach, CA, United States
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University, New Orleans, LA, United States
| | - Michael V Miceli
- Tulane Center for Aging and Department of Medicine, Tulane University, New Orleans, LA, United States
| | - Nitin Udar
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Daniela Bota
- Department of Neurology, Neuro-Oncology Division, University of California, Irvine, Irvine, CA, United States
| | - M Cristina Kenney
- Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States.,Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, United States
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18
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Dobler R, Dowling DK, Morrow EH, Reinhardt K. A systematic review and meta-analysis reveals pervasive effects of germline mitochondrial replacement on components of health. Hum Reprod Update 2019; 24:519-534. [PMID: 29757366 DOI: 10.1093/humupd/dmy018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 05/03/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Mitochondrial replacement, a form of nuclear transfer, has been proposed as a germline therapy to prevent the transmission of mitochondrial diseases. Mitochondrial replacement therapy has been licensed for clinical application in the UK, and already carried out in other countries, but little is known about negative or unintended effects on the health of offspring born using this technique. OBJECTIVE AND RATIONALE Studies in invertebrate models have used techniques that achieve mitochondrial replacement to create offspring with novel combinations of mitochondrial and nuclear genotype. These have demonstrated that the creation of novel mitochondrial-nuclear interactions can lead to alterations in offspring characteristics, such as development rates, fertility and longevity. However, it is currently unclear whether such interactions could similarly affect the outcomes of vertebrate biomedical studies, which have sought to assess the efficacy of the replacement therapy. SEARCH METHODS This systematic review addresses whether the effects of mitochondrial replacement on offspring characteristics differ in magnitude between biological (conducted on invertebrate models, with an ecological or evolutionary focus) and biomedical studies (conducted on vertebrate models, with a clinical focus). Studies were selected based on a key-word search in 'Web of Science', complemented by backward searches of reviews on the topic of mitochondrial-nuclear (mito-nuclear) interactions. In total, 43 of the resulting 116 publications identified in the search contained reliable data to estimate effect sizes of mitochondrial replacement. We found no evidence of publication bias when examining effect-size estimates across sample sizes. OUTCOMES Mitochondrial replacement consistently altered the phenotype, with significant effects at several levels of organismal performance and health, including gene expression, anatomy, metabolism and life-history. Biomedical and biological studies, while differing in the methods used to achieve mitochondrial replacement, showed only marginally significant differences in effect-size estimates (-0.233 [CI: -0.495 to -0.011]), with larger effect-size estimates in biomedical studies (0.697 [CI: 0.450-0.956]) than biological studies (0.462 [CI: 0.287-0.688]). Humans showed stronger effects than other species. Effects of mitochondrial replacement were also stronger in species with a higher basal metabolic rate. Based on our results, we conducted the first formal risk analysis of mitochondrial replacement, and conservatively estimate negative effects in at least one in every 130 resulting offspring born to the therapy. WIDER IMPLICATIONS Our findings suggest that mitochondrial replacement may routinely affect offspring characteristics across a wide array of animal species, and that such effects are likely to extend to humans. Studies in invertebrate models have confirmed mito-nuclear interactions as the underpinning cause of organismal effects following mitochondrial replacement. This therefore suggests that mito-nuclear interactions are also likely to be contributing to effects seen in biomedical studies, on vertebrate models, whose effect sizes exceeded those of biological studies. Our results advocate the use of safeguards that could offset any negative effects (defining any unintended effect as being negative) mediated by mito-nuclear interactions following mitochondrial replacement in humans, such as mitochondrial genetic matching between donor and recipient. Our results also suggest that further research into the molecular nature of mito-nuclear interactions would be beneficial in refining the clinical application of mitochondrial replacement, and in establishing what degree of variation between donor and patient mitochondrial DNA haplotypes is acceptable to ensure 'haplotype matching'.
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Affiliation(s)
- Ralph Dobler
- Applied Zoology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Edward H Morrow
- Evolution, Behaviour and Environment Group, School of Life Sciences, University of Sussex, Brighton, UK
| | - Klaus Reinhardt
- Applied Zoology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, Germany
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19
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Bris C, Goudenege D, Desquiret-Dumas V, Charif M, Colin E, Bonneau D, Amati-Bonneau P, Lenaers G, Reynier P, Procaccio V. Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing. Front Genet 2018; 9:632. [PMID: 30619459 PMCID: PMC6297213 DOI: 10.3389/fgene.2018.00632] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 11/13/2022] Open
Abstract
The development of next generation sequencing (NGS) has greatly enhanced the diagnosis of mitochondrial disorders, with a systematic analysis of the whole mitochondrial DNA (mtDNA) sequence and better detection sensitivity. However, the exponential growth of sequencing data renders complex the interpretation of the identified variants, thereby posing new challenges for the molecular diagnosis of mitochondrial diseases. Indeed, mtDNA sequencing by NGS requires specific bioinformatics tools and the adaptation of those developed for nuclear DNA, for the detection and quantification of mtDNA variants from sequence alignment to the calling steps, in order to manage the specific features of the mitochondrial genome including heteroplasmy, i.e., coexistence of mutant and wildtype mtDNA copies. The prioritization of mtDNA variants remains difficult, relying on a limited number of specific resources: population and clinical databases, and in silico tools providing a prediction of the variant pathogenicity. An evaluation of the most prominent bioinformatics tools showed that their ability to predict the pathogenicity was highly variable indicating that special efforts should be directed at developing new bioinformatics tools dedicated to the mitochondrial genome. In addition, massive parallel sequencing raised several issues related to the interpretation of very low mtDNA mutational loads, discovery of variants of unknown significance, and mutations unrelated to patient phenotype or the co-occurrence of mtDNA variants. This review provides an overview of the current strategies and bioinformatics tools for accurate annotation, prioritization and reporting of mtDNA variations from NGS data, in order to carry out accurate genetic counseling in individuals with primary mitochondrial diseases.
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Affiliation(s)
- Céline Bris
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - David Goudenege
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Valérie Desquiret-Dumas
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Majida Charif
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Estelle Colin
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Pascal Reynier
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Vincent Procaccio
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
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20
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López-Gallardo E, Emperador S, Hernández-Ainsa C, Montoya J, Bayona-Bafaluy MP, Ruiz-Pesini E. Food derived respiratory complex I inhibitors modify the effect of Leber hereditary optic neuropathy mutations. Food Chem Toxicol 2018; 120:89-97. [PMID: 29991444 DOI: 10.1016/j.fct.2018.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/21/2018] [Accepted: 07/05/2018] [Indexed: 01/14/2023]
Abstract
Mitochondrial DNA mutations in genes encoding respiratory complex I polypeptides can cause Leber hereditary optic neuropathy. Toxics affecting oxidative phosphorylation system can also cause mitochondrial optic neuropathy. Some complex I inhibitors found in edible plants might differentially interact with these pathologic mutations and modify their penetrance. To analyze this interaction, we have compared the effect of rotenone, capsaicin and rolliniastatin-1 on cybrids harboring the most frequent Leber hereditary optic neuropathy mutations and found that m.3460G > A mutation increases rotenone resistance but capsaicin and rolliniastatin-1 susceptibility. Thus, to explain the pathogenicity of mitochondrial diseases due to mitochondrial DNA mutations, their potential interactions with environment factors will have to be considered.
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Affiliation(s)
- Ester López-Gallardo
- Departamento de Bioquímica, Biología Molecular y Celular. Universidad de Zaragoza, Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigaciones Biomédicas En Red de Enfermedades Raras (CIBERER), Zaragoza, Spain.
| | - Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular. Universidad de Zaragoza, Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigaciones Biomédicas En Red de Enfermedades Raras (CIBERER), Zaragoza, Spain.
| | - Carmen Hernández-Ainsa
- Departamento de Bioquímica, Biología Molecular y Celular. Universidad de Zaragoza, Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain.
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular. Universidad de Zaragoza, Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigaciones Biomédicas En Red de Enfermedades Raras (CIBERER), Zaragoza, Spain.
| | - M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular. Universidad de Zaragoza, Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigaciones Biomédicas En Red de Enfermedades Raras (CIBERER), Zaragoza, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular. Universidad de Zaragoza, Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigaciones Biomédicas En Red de Enfermedades Raras (CIBERER), Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain.
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21
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The Oncojanus Paradigm of Respiratory Complex I. Genes (Basel) 2018; 9:genes9050243. [PMID: 29735924 PMCID: PMC5977183 DOI: 10.3390/genes9050243] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/09/2018] [Accepted: 05/03/2018] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial respiratory function is now recognized as a pivotal player in all the aspects of cancer biology, from tumorigenesis to aggressiveness and chemotherapy resistance. Among the enzymes that compose the respiratory chain, by contributing to energy production, redox equilibrium and oxidative stress, complex I assumes a central role. Complex I defects may arise from mutations in mitochondrial or nuclear DNA, in both structural genes or assembly factors, from alteration of the expression levels of its subunits, or from drug exposure. Since cancer cells have a high-energy demand and require macromolecules for proliferation, it is not surprising that severe complex I defects, caused either by mutations or treatment with specific inhibitors, prevent tumor progression, while contributing to resistance to certain chemotherapeutic agents. On the other hand, enhanced oxidative stress due to mild complex I dysfunction drives an opposite phenotype, as it stimulates cancer cell proliferation and invasiveness. We here review the current knowledge on the contribution of respiratory complex I to cancer biology, highlighting the double-edged role of this metabolic enzyme in tumor progression, metastasis formation, and response to chemotherapy.
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22
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Giorgio V, Schiavone M, Galber C, Carini M, Da Ros T, Petronilli V, Argenton F, Carelli V, Acosta Lopez MJ, Salviati L, Prato M, Bernardi P. The idebenone metabolite QS10 restores electron transfer in complex I and coenzyme Q defects. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:901-908. [PMID: 29694828 DOI: 10.1016/j.bbabio.2018.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/03/2018] [Accepted: 04/18/2018] [Indexed: 12/11/2022]
Abstract
Idebenone is a hydrophilic short-chain coenzyme (Co) Q analogue, which has been used as a potential bypass of defective complex I in both Leber Hereditary Optic Neuropathy and OPA1-dependent Dominant Optic Atrophy. Based on its potential antioxidant effects, it has also been tested in degenerative disorders such as Friedreich's ataxia, Huntington's and Alzheimer's diseases. Idebenone is rapidly modified but the biological effects of its metabolites have been characterized only partially. Here we have studied the effects of quinones generated during in vivo metabolism of idebenone with specific emphasis on 6-(9-carboxynonyl)-2,3-dimethoxy-5-methyl-1,4-benzoquinone (QS10). QS10 partially restored respiration in cells deficient of complex I or of CoQ without inducing the mitochondrial permeability transition, a detrimental effect of idebenone that may offset its potential benefits [Giorgio et al. (2012) Biochim. Biophys. Acta 1817: 363-369]. Remarkably, respiration was largely rotenone-insensitive in complex I deficient cells and rotenone-sensitive in CoQ deficient cells. These findings indicate that, like idebenone, QS10 can provide a bypass to defective complex I; and that, unlike idebenone, QS10 can partially replace endogenous CoQ. In zebrafish (Danio rerio) treated with rotenone, QS10 was more effective than idebenone in allowing partial recovery of respiration (to 40% and 20% of the basal respiration of untreated embryos, respectively) and allowing zebrafish survival (80% surviving embryos at 60 h post-fertilization, a time point at which all rotenone-treated embryos otherwise died). We conclude that QS10 is potentially more active than idebenone in the treatment of diseases caused by complex I defects, and that it could also be used in CoQ deficiencies of genetic and acquired origin.
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Affiliation(s)
- Valentina Giorgio
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Marco Schiavone
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Chiara Galber
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Marco Carini
- INSTM Trieste Unit, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Tatiana Da Ros
- INSTM Trieste Unit, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Valeria Petronilli
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Valerio Carelli
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy; Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Manuel J Acosta Lopez
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, IRP Città della Speranza, Padova, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, IRP Città della Speranza, Padova, Italy
| | - Maurizio Prato
- INSTM Trieste Unit, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy; Carbon Nanobiotechnology Laboratory CIC biomaGUNE, Donostia-San Sebastián, Spain; Basque Fdn Sci, Ikerbasque, Bilbao, Spain
| | - Paolo Bernardi
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, Padova, Italy.
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23
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Guimarães‐Costa R, Schoindre Y, Metlaine A, Lefaucheur J, Camdessanché J, Maisonobe T, Léger J. N‐hexane exposure: a cause of small fiber neuropathy. J Peripher Nerv Syst 2018. [DOI: 10.1111/jns.12261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raquel Guimarães‐Costa
- National Referral Center for Neuromuscular Diseases Institut Hospitalo‐Universitaire (IHU) de Neurosciences, University Hospital Pitié Salpêtrière Paris France
| | - Yoland Schoindre
- Internal Medicine Department, Foch Hospital Versailles Saint‐Quentin‐en‐Yvelines University Suresnes France
| | - Arnaud Metlaine
- Sleep Disorders Center University Hospital Hôtel Dieu Paris France
| | | | | | - Thierry Maisonobe
- Clinical Neurophysiology Department, IHU de Neurosciences University Hospital Pitié Salpêtrière Paris France
| | - Jean‐Marc Léger
- National Referral Center for Neuromuscular Diseases Institut Hospitalo‐Universitaire (IHU) de Neurosciences, University Hospital Pitié Salpêtrière Paris France
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24
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Strobbe D, Caporali L, Iommarini L, Maresca A, Montopoli M, Martinuzzi A, Achilli A, Olivieri A, Torroni A, Carelli V, Ghelli A. Haplogroup J mitogenomes are the most sensitive to the pesticide rotenone: Relevance for human diseases. Neurobiol Dis 2018; 114:129-139. [PMID: 29486301 DOI: 10.1016/j.nbd.2018.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/30/2018] [Accepted: 02/21/2018] [Indexed: 12/21/2022] Open
Abstract
There is growing evidence that the sequence variation of mitochondrial DNA (mtDNA), which clusters in population- and/or geographic-specific haplogroups, may result in functional effects that, in turn, become relevant in disease predisposition or protection, interaction with environmental factors and ultimately in modulating longevity. To unravel functional differences between mtDNA haplogroups we here employed transmitochondrial cytoplasmic hybrid cells (cybrids) grown in galactose medium, a culture condition that forces oxidative phosphorylation, and in the presence of rotenone, the classic inhibitor of respiratory Complex I. Under this experimental paradigm we assessed functional parameters such as cell viability and respiration, ATP synthesis, reactive oxygen species production and mtDNA copy number. Our analyses show that haplogroup J1, which is common in western Eurasian populations, is the most sensitive to rotenone, whereas K1 mitogenomes orchestrate the best compensation, possibly because of the haplogroup-specific missense variants impinging on Complex I function. Remarkably, haplogroups J1 and K1 fit the genetic associations previously established with Leber's hereditary optic neuropathy (LHON) for J1, as a penetrance enhancer, and with Parkinson's disease (PD) for K1, as a protective background. Our findings provide functional evidences supporting previous well-established genetic associations of specific haplogroups with two neurodegenerative pathologies, LHON and PD. Our experimental paradigm is instrumental to highlighting the subtle functional differences characterizing mtDNA haplogroups, which will be increasingly needed to dissect the role of mtDNA genetic variation in health, disease and longevity.
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Affiliation(s)
- Daniela Strobbe
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine-University of Padua, Italy
| | | | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | | | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine-University of Padua, Italy
| | - Andrea Martinuzzi
- IRCCS "E. Medea" Scientific Institute Conegliano-Pieve di Soligo Research Center, Pieve di Soligo, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Valerio Carelli
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.
| | - Anna Ghelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy.
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25
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Caporali L, Iommarini L, La Morgia C, Olivieri A, Achilli A, Maresca A, Valentino ML, Capristo M, Tagliavini F, Del Dotto V, Zanna C, Liguori R, Barboni P, Carbonelli M, Cocetta V, Montopoli M, Martinuzzi A, Cenacchi G, De Michele G, Testa F, Nesti A, Simonelli F, Porcelli AM, Torroni A, Carelli V. Peculiar combinations of individually non-pathogenic missense mitochondrial DNA variants cause low penetrance Leber's hereditary optic neuropathy. PLoS Genet 2018; 14:e1007210. [PMID: 29444077 PMCID: PMC5828459 DOI: 10.1371/journal.pgen.1007210] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/27/2018] [Accepted: 01/21/2018] [Indexed: 12/23/2022] Open
Abstract
We here report on the existence of Leber’s hereditary optic neuropathy (LHON) associated with peculiar combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I. The pathogenic potential of these mtDNA haplotypes is supported by multiple evidences: first, the LHON phenotype is strictly inherited along the maternal line in one very large family; second, the combinations of mtDNA variants are unique to the two maternal lineages that are characterized by recurrence of LHON; third, the Complex I-dependent respiratory and oxidative phosphorylation defect is co-transferred from the proband’s fibroblasts into the cybrid cell model. Finally, all but one of these missense mtDNA variants cluster along the same predicted fourth E-channel deputed to proton translocation within the transmembrane domain of Complex I, involving the ND1, ND4L and ND6 subunits. Hence, the definition of the pathogenic role of a specific mtDNA mutation becomes blurrier than ever and only an accurate evaluation of mitogenome sequence variation data from the general population, combined with functional analyses using the cybrid cell model, may lead to final validation. Our study conclusively shows that even in the absence of a clearly established LHON primary mutation, unprecedented combinations of missense mtDNA variants, individually known as polymorphisms, may lead to reduced OXPHOS efficiency sufficient to trigger LHON. In this context, we introduce a new diagnostic perspective that implies the complete sequence analysis of mitogenomes in LHON as mandatory gold standard diagnostic approach. Leber’s hereditary optic neuropathy (LHON) is a common cause of maternally inherited vision loss. In the large majority of cases LHON is due to mitochondrial DNA (mtDNA) point mutations, clearly distinct from common polymorphisms normally found in the general population, affecting the mitochondrial function, thus defined as pathogenic. For the first time, we here demonstrate, on the genetic and functional ground, that unusual combinations of otherwise polymorphic and non-pathogenic mtDNA variants are sufficient for causing low-penetrance maternally inherited optic neuropathy in pedigrees fitting the LHON clinical diagnosis. Our findings bridge the blurry border between “pathogenic” and “neutral” mutations in an overall continuum that truly depends on the specific and sometime unique combination of variants characterizing each mitogenome. As a result, we conclude that, for an accurate diagnosis of LHON and possibly of other mitochondrial diseases, the only approach that can disclose all possible causative sources is complete mitogenome sequencing.
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Affiliation(s)
- Leonardo Caporali
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandra Maresca
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Maria Lucia Valentino
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Francesca Tagliavini
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Valentina Del Dotto
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Rocco Liguori
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Michele Carbonelli
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Studio Oculistico D’Azeglio, Bologna, Italy
| | - Veronica Cocetta
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Andrea Martinuzzi
- IRCCS "E. Medea" Scientific Institute Conegliano-Pieve di Soligo Research Center, Pieve di Soligo, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Giuseppe De Michele
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Anna Nesti
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
- Health Sciences & Technologies (HST) CIRI, University of Bologna, Bologna, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Valerio Carelli
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- * E-mail:
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26
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Caporali L, Maresca A, Capristo M, Del Dotto V, Tagliavini F, Valentino ML, La Morgia C, Carelli V. Incomplete penetrance in mitochondrial optic neuropathies. Mitochondrion 2017; 36:130-137. [PMID: 28716668 DOI: 10.1016/j.mito.2017.07.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 06/27/2017] [Accepted: 07/13/2017] [Indexed: 01/06/2023]
Abstract
Incomplete penetrance characterizes the two most frequent inherited optic neuropathies, Leber's Hereditary Optic Neuropathy (LHON) and dominant optic atrophy (DOA), due to genetic errors in the mitochondrial DNA (mtDNA) and the nuclear DNA (nDNA), respectively. For LHON, compelling evidence has accumulated on the complex interplay of mtDNA haplogroups and environmental interacting factors, whereas the nDNA remains essentially non informative. However, a compensatory mechanism of activated mitochondrial biogenesis and increased mtDNA copy number, possibly driven by a permissive nDNA background, is documented in LHON; when successful it maintains unaffected the mutation carriers, but in some individuals it might be hampered by tobacco smoking or other environmental factors, resulting in disease onset. In females, mitochondrial biogenesis is promoted and maintained within the compensatory range by estrogens, partially explaining the gender bias in LHON. Concerning DOA, none of the above mechanisms has been fully explored, thus mtDNA haplogroups, environmental factors such as tobacco and alcohol, and further nDNA variants may all participate as protective factors or, on the contrary, favor disease expression and severity. Next generation sequencing, complemented by transcriptomics and proteomics, may provide some answers in the next future, even if the multifactorial model that seems to apply to incomplete penetrance in mitochondrial optic neuropathies remains problematic, and careful stratification of patients will play a key role for data interpretation. The deep understanding of which factors impinge on incomplete penetrance may shed light on the pathogenic mechanisms leading to optic nerve atrophy, on their possible compensation and, thus, on development of therapeutic strategies.
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Affiliation(s)
- Leonardo Caporali
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
| | | | - Valentina Del Dotto
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Francesca Tagliavini
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
| | - Maria Lucia Valentino
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Chiara La Morgia
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Valerio Carelli
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.
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Bi R, Logan I, Yao YG. Leber Hereditary Optic Neuropathy: A Mitochondrial Disease Unique in Many Ways. Handb Exp Pharmacol 2017; 240:309-336. [PMID: 27787713 DOI: 10.1007/164_2016_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Leber hereditary optic neuropathy (LHON) was the first mitochondrial disease to be identified as being caused by mutations in the mitochondrial DNA (mtDNA). This disease has been studied extensively in the past two decades, particularly in Brazilian, Chinese and European populations; and many primary mutations have been reported. However, the disease is enigmatic with many unique features, and there still are several important questions to be resolved. The incomplete penetrance, the male-biased disease expression and the prevalence in young adults all defy a proper explanation. It has been reported that the development of LHON is affected by the interaction between mtDNA mutations, mtDNA haplogroup background, nuclear genes, environmental factors and epigenetics. Furthermore, with the help of new animal models for LHON that have been created in recent years, we are continuing to learn more about the mechanism of this disease. The stage has now been reached at which there is a good understanding of both the genetic basis of the disease and its epidemiology, but just how the blindness that follows from the death of cells in the optic nerve can be prevented remains to be a pharmacological challenge. In this chapter, we summarize the progress that has been made in various recent studies on LHON, focusing on the molecular pathogenic mechanisms, clinical features, biochemical effects, the pharmacology and its treatment.
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Affiliation(s)
- Rui Bi
- Division of Medical Genetics & Evolutionary Medicine, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | - Yong-Gang Yao
- Division of Medical Genetics & Evolutionary Medicine, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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28
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Clima R, Preste R, Calabrese C, Diroma MA, Santorsola M, Scioscia G, Simone D, Shen L, Gasparre G, Attimonelli M. HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor. Nucleic Acids Res 2016; 45:D698-D706. [PMID: 27899581 PMCID: PMC5210550 DOI: 10.1093/nar/gkw1066] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 11/04/2016] [Indexed: 11/14/2022] Open
Abstract
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.
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Affiliation(s)
- Rosanna Clima
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy.,Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, 40126 Bologna, Italy
| | - Roberto Preste
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Claudia Calabrese
- European Bioinformatics Institute EMBL Outstation - Hinxton, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Mariangela Santorsola
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Gaetano Scioscia
- IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab Bari, Italy
| | - Domenico Simone
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
| | - Lishuang Shen
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, CA 90027, USA
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, 40126 Bologna, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
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29
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Investigating Leber's hereditary optic neuropathy: Cell models and future perspectives. Mitochondrion 2016; 32:19-26. [PMID: 27847334 DOI: 10.1016/j.mito.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/19/2023]
Abstract
Leber's hereditary optic neuropathy (LHON) was the first human disease found to be associated with a mitochondrial DNA (mtDNA) point mutation. The most common LHON mutations are 11778G>A, 3460G>A or 14484T>C. The most common clinical features of LHON are optic nerve and retina atrophy. The affected tissue is not available for studies, therefore a variety of other cell types are used. However, all models face difficulties and limitations in mitochondrial disease research. The advantages and disadvantages of different cell models used to study LHON, recent advances in animal model generation and novel approaches in this field are discussed.
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30
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Collins DW, Gudiseva HV, Trachtman B, Bowman AS, Sagaser A, Sankar P, Miller-Ellis E, Lehman A, Addis V, O'Brien JM. Association of primary open-angle glaucoma with mitochondrial variants and haplogroups common in African Americans. Mol Vis 2016; 22:454-71. [PMID: 27217714 PMCID: PMC4872278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/13/2016] [Indexed: 11/06/2022] Open
Abstract
PURPOSE To estimate the population frequencies of all common mitochondrial variants and ancestral haplogroups among 1,999 subjects recruited for the Primary Open-Angle African American Glaucoma Genetics (POAAGG) Study, including 1,217 primary open-angle glaucoma (POAG) cases and 782 controls, and to identify ancestral subpopulations and mitochondrial mutations as potential risk factors for POAG susceptibility. METHODS Subject classification by characteristic glaucomatous optic nerve findings and corresponding visual field defects, as defined by enrolling glaucoma specialists, stereo disc photography, phlebotomy, extraction of total DNA from peripheral blood or saliva, DNA quantification and normalization, PCR amplification of whole mitochondrial genomes, Ion Torrent deep semiconductor DNA sequencing on DNA pools ("Pool-seq"), Sanger sequencing of 3,479 individual mitochondrial DNAs, and bioinformatic analysis. RESULTS The distribution of common African haplogroups within the POAAGG study population was broadly similar to prior surveys of African Americans. However, the POAG case population was found to be enriched in L1c2 haplogroups, which are defined in part by missense mutations m.6150G>A (Val83Ile, odds ratio [OR] 1.8, p=0.01), m.6253C>T (Met117Thr, rs200165736, OR 1.6, p=0.04), and m.6480G>A (Val193Ile, rs199476128, OR 4.6, p=0.04) in the cytochrome c oxidase subunit 1 (MT-CO1) gene and by a variant, m.2220A>G (OR 2.0, p=0.01), in MT-RNR2, which encodes the mitochondrial ribosomal 16s RNA gene. L2 haplogroups were predicted to be overrepresented in the POAG case population by Pool-seq, and the difference was confirmed to be significant with Sanger sequencing, that targeted the L2-associated variants m.2416T>C (rs28358580, OR 1.2, p=0.02) and m.2332C>T (OR 1.2, p=.02) in MT-RNR2. Another variant within MT-RNR2, m.3010G>A (rs3928306), previously implicated in sensitivity to the optic neuropathy-associated antibiotic linezolid, and arising on D4 and J1 lineages, associated with Leber hereditary optic neuropathy (LHON) severity, was confirmed to be common (>5%) but was not significantly enriched in the POAG cases. Two variants linked to the composition of the gut microbiome, m.15784T>C (rs527236194, haplogroup L2a1) and m.16390G>A (rs41378955, L2 haplogroups), were also enriched in the case DNA pools. CONCLUSIONS These results implicate African mtDNA haplogroups L1c2, L1c2b, and L2 as risk factors for POAG. Approximately one in four African Americans have these mitochondrial ancestries, which may contribute to their elevated glaucoma risk. These haplogroups are defined in part by ancestral variants in the MT-RNR2 and/or MT-CO1 genes, several of which have prior disease associations, such as MT-CO1 missense variants that have been implicated in prostate cancer.
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Affiliation(s)
- David W Collins
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | | | | | - Anita S Bowman
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Anna Sagaser
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Prithvi Sankar
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | | | - Amanda Lehman
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Victoria Addis
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Joan M O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
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31
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Giordano L, Deceglie S, d'Adamo P, Valentino ML, La Morgia C, Fracasso F, Roberti M, Cappellari M, Petrosillo G, Ciaravolo S, Parente D, Giordano C, Maresca A, Iommarini L, Del Dotto V, Ghelli AM, Salomao SR, Berezovsky A, Belfort R, Sadun AA, Carelli V, Loguercio Polosa P, Cantatore P. Cigarette toxicity triggers Leber's hereditary optic neuropathy by affecting mtDNA copy number, oxidative phosphorylation and ROS detoxification pathways. Cell Death Dis 2015; 6:e2021. [PMID: 26673666 PMCID: PMC4720897 DOI: 10.1038/cddis.2015.364] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/15/2023]
Abstract
Leber's hereditary optic neuropathy (LHON), the most frequent mitochondrial disease, is associated with mitochondrial DNA (mtDNA) point mutations affecting Complex I subunits, usually homoplasmic. This blinding disorder is characterized by incomplete penetrance, possibly related to several genetic modifying factors. We recently reported that increased mitochondrial biogenesis in unaffected mutation carriers is a compensatory mechanism, which reduces penetrance. Also, environmental factors such as cigarette smoking have been implicated as disease triggers. To investigate this issue further, we first assessed the relationship between cigarette smoke and mtDNA copy number in blood cells from large cohorts of LHON families, finding that smoking was significantly associated with the lowest mtDNA content in affected individuals. To unwrap the mechanism of tobacco toxicity in LHON, we exposed fibroblasts from affected individuals, unaffected mutation carriers and controls to cigarette smoke condensate (CSC). CSC decreased mtDNA copy number in all cells; moreover, it caused significant reduction of ATP level only in mutated cells including carriers. This implies that the bioenergetic compensation in carriers is hampered by exposure to smoke derivatives. We also observed that in untreated cells the level of carbonylated proteins was highest in affected individuals, whereas the level of several detoxifying enzymes was highest in carriers. Thus, carriers are particularly successful in reactive oxygen species (ROS) scavenging capacity. After CSC exposure, the amount of detoxifying enzymes increased in all cells, but carbonylated proteins increased only in LHON mutant cells, mostly from affected individuals. All considered, it appears that exposure to smoke derivatives has a more deleterious effect in affected individuals, whereas carriers are the most efficient in mitigating ROS rather than recovering bioenergetics. Therefore, the identification of genetic modifiers that modulate LHON penetrance must take into account also the exposure to environmental triggers such as tobacco smoke.
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MESH Headings
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Female
- Humans
- Male
- Optic Atrophy, Hereditary, Leber/etiology
- Optic Atrophy, Hereditary, Leber/genetics
- Optic Atrophy, Hereditary, Leber/metabolism
- Optic Atrophy, Hereditary, Leber/pathology
- Oxidative Phosphorylation
- Reactive Oxygen Species/metabolism
- Smoking/adverse effects
- Smoking/genetics
- Smoking/metabolism
- Smoking/pathology
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Affiliation(s)
- L Giordano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - S Deceglie
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - P d'Adamo
- Department of Reproductive Sciences, Medical Genetics, Development and Public Health, University of Trieste, Trieste, Italy
- IRCCS-Burlo Garofolo Children Hospital, Trieste, Italy
| | - M L Valentino
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), Neurology Unit, University of Bologna, Bologna, Italy
| | - C La Morgia
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), Neurology Unit, University of Bologna, Bologna, Italy
| | - F Fracasso
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - M Roberti
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - M Cappellari
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - G Petrosillo
- Institute of Biomembranes and Bioenergetics (IBBE) National Research Council (CNR), Bari, Italy
| | - S Ciaravolo
- Vectis s.r.l. Cava dei Tirreni (Salerno), Italy
| | - D Parente
- Vectis s.r.l. Cava dei Tirreni (Salerno), Italy
| | - C Giordano
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - A Maresca
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), Neurology Unit, University of Bologna, Bologna, Italy
| | - L Iommarini
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), Neurology Unit, University of Bologna, Bologna, Italy
| | - V Del Dotto
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - A M Ghelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - S R Salomao
- Department of Ophthalmology, and Visual Sciences, Paulista School of Medicine Federal University of Sao Paulo—UNIFESP, Sao Paulo, Brazil
| | - A Berezovsky
- Department of Ophthalmology, and Visual Sciences, Paulista School of Medicine Federal University of Sao Paulo—UNIFESP, Sao Paulo, Brazil
| | - R Belfort
- Department of Ophthalmology, and Visual Sciences, Paulista School of Medicine Federal University of Sao Paulo—UNIFESP, Sao Paulo, Brazil
| | - A A Sadun
- Doheny Eye Institute, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - V Carelli
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), Neurology Unit, University of Bologna, Bologna, Italy
| | - P Loguercio Polosa
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - P Cantatore
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
- Institute of Biomembranes and Bioenergetics (IBBE) National Research Council (CNR), Bari, Italy
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Carelli V, d'Adamo P, Valentino ML, La Morgia C, Ross-Cisneros FN, Caporali L, Maresca A, Loguercio Polosa P, Barboni P, De Negri A, Sadun F, Karanjia R, Salomao SR, Berezovsky A, Chicani F, Moraes M, Moraes Filho M, Belfort R, Sadun AA. Parsing the differences in affected with LHON: genetic versus environmental triggers of disease conversion. Brain 2015; 139:e17. [PMID: 26657166 DOI: 10.1093/brain/awv339] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Valerio Carelli
- 1 IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy 2 Neurology Unit, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Pio d'Adamo
- 3 Medical Genetics, Department of Reproductive Sciences, Development and Public Health, University of Trieste, Trieste, Italy 4 IRCCS-Burlo Garofolo Children Hospital, Trieste, Italy
| | - Maria Lucia Valentino
- 1 IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy 2 Neurology Unit, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- 1 IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy 2 Neurology Unit, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Leonardo Caporali
- 1 IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
| | - Alessandra Maresca
- 1 IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy 2 Neurology Unit, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Paola Loguercio Polosa
- 6 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Piero Barboni
- 7 IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | | | | | - Rustum Karanjia
- 10 Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Solange R Salomao
- 11 Department of Ophthalmology, Federal University of Sao Paulo (UNIFESP) and IPEPO (Instituto da Visão), Sao Paulo, Brazil
| | - Adriana Berezovsky
- 11 Department of Ophthalmology, Federal University of Sao Paulo (UNIFESP) and IPEPO (Instituto da Visão), Sao Paulo, Brazil
| | - Filipe Chicani
- 11 Department of Ophthalmology, Federal University of Sao Paulo (UNIFESP) and IPEPO (Instituto da Visão), Sao Paulo, Brazil
| | | | | | - Rubens Belfort
- 11 Department of Ophthalmology, Federal University of Sao Paulo (UNIFESP) and IPEPO (Instituto da Visão), Sao Paulo, Brazil
| | - Alfredo A Sadun
- 5 Doheny Eye Institute, Los Angeles, CA, USA 10 Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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33
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Santorsola M, Calabrese C, Girolimetti G, Diroma MA, Gasparre G, Attimonelli M. A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest. Hum Genet 2015; 135:121-36. [PMID: 26621530 PMCID: PMC4698288 DOI: 10.1007/s00439-015-1615-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/12/2015] [Indexed: 02/07/2023]
Abstract
Assigning a pathogenic role to mitochondrial DNA (mtDNA) variants and unveiling the potential involvement of the mitochondrial genome in diseases are challenging tasks in human medicine. Assuming that rare variants are more likely to be damaging, we designed a phylogeny-based prioritization workflow to obtain a reliable pool of candidate variants for further investigations. The prioritization workflow relies on an exhaustive functional annotation through the mtDNA extraction pipeline MToolBox and includes Macro Haplogroup Consensus Sequences to filter out fixed evolutionary variants and report rare or private variants, the nucleotide variability as reported in HmtDB and the disease score based on several predictors of pathogenicity for non-synonymous variants. Cutoffs for both the disease score as well as for the nucleotide variability index were established with the aim to discriminate sequence variants contributing to defective phenotypes. The workflow was validated on mitochondrial sequences from Leber’s Hereditary Optic Neuropathy affected individuals, successfully identifying 23 variants including the majority of the known causative ones. The application of the prioritization workflow to cancer datasets allowed to trim down the number of candidate for subsequent functional analyses, unveiling among these a high percentage of somatic variants. Prioritization criteria were implemented in both standalone (http://sourceforge.net/projects/mtoolbox/) and web version (https://mseqdr.org/mtoolbox.php) of MToolBox.
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Affiliation(s)
- Mariangela Santorsola
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E.Orabona 4, 70126, Bari, Italy.,Department of Science and Technologies, University of Sannio, Via Port'Arsa 11, 82100, Benevento, Italy
| | - Claudia Calabrese
- Department of Medical and Surgical Sciences, Medical Genetics, University of Bologna Medical School, via Massarenti 9, 40138, Bologna, Italy
| | - Giulia Girolimetti
- Department of Medical and Surgical Sciences, Medical Genetics, University of Bologna Medical School, via Massarenti 9, 40138, Bologna, Italy
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E.Orabona 4, 70126, Bari, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences, Medical Genetics, University of Bologna Medical School, via Massarenti 9, 40138, Bologna, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E.Orabona 4, 70126, Bari, Italy.
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34
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Pisano A, Preziuso C, Iommarini L, Perli E, Grazioli P, Campese AF, Maresca A, Montopoli M, Masuelli L, Sadun AA, d'Amati G, Carelli V, Ghelli A, Giordano C. Targeting estrogen receptor β as preventive therapeutic strategy for Leber's hereditary optic neuropathy. Hum Mol Genet 2015; 24:6921-31. [PMID: 26410888 DOI: 10.1093/hmg/ddv396] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 11/13/2022] Open
Abstract
Leber's hereditary optic neuropathy (LHON) is a maternally inherited blinding disease characterized by degeneration of retinal ganglion cells (RGCs) and consequent optic nerve atrophy. Peculiar features of LHON are incomplete penetrance and gender bias, with a marked male prevalence. Based on the different hormonal metabolism between genders, we proposed that estrogens play a protective role in females and showed that these hormones ameliorate mitochondrial dysfunction in LHON through the estrogen receptors (ERs). We also showed that ERβ localize to the mitochondria of RGCs. Thus, targeting ERβ may become a therapeutic strategy for LHON specifically aimed at avoiding or delaying the onset of disease in mutation carriers. Here, we tested the effects of ERβ targeting on LHON mitochondrial defective metabolism by treating LHON cybrid cells carrying the m.11778G>A mutation with a combination of natural estrogen-like compounds that bind ERβ with high selectivity. We demonstrated that these molecules improve cell viability by reducing apoptosis, inducing mitochondrial biogenesis and strongly reducing the levels of reactive oxygen species in LHON cells. These effects were abolished in cells with ERβ knockdown by silencing receptor expression or by using specific receptor antagonists. Our observations support the hypothesis that estrogen-like molecules may be useful in LHON prophylactic therapy. This is particularly important for lifelong disease prevention in unaffected LHON mutation carriers. Current strategies attempting to combat degeneration of RGCs during the acute phase of LHON have not been very effective. Implementing a different and preemptive approach with a low risk profile may be very helpful.
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Affiliation(s)
- Annalinda Pisano
- Department of Radiological, Oncological and Pathological Sciences
| | - Carmela Preziuso
- Department of Radiological, Oncological and Pathological Sciences
| | | | - Elena Perli
- Department of Radiological, Oncological and Pathological Sciences
| | | | | | - Alessandra Maresca
- Neurology Unit, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy, IRCCS Institute of Neurologic Science of Bologna, Bellaria Hospital, Bologna, Italy
| | - Monica Montopoli
- Department of Pharmacology and Anesthesiology, University of Padua, Padua, Italy and
| | - Laura Masuelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alfredo A Sadun
- Doheny Eye Institute, University of California Los Angeles, Los Angeles, USA
| | - Giulia d'Amati
- Department of Radiological, Oncological and Pathological Sciences
| | - Valerio Carelli
- Neurology Unit, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy, IRCCS Institute of Neurologic Science of Bologna, Bellaria Hospital, Bologna, Italy
| | - Anna Ghelli
- Department of Pharmacy and Biotechnology (FABIT),
| | - Carla Giordano
- Department of Radiological, Oncological and Pathological Sciences,
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Yang H, Liu R, Wang CC. Searching the co-occurrence of pathogenic mutations for Leber's hereditary optic neuropathy and hearing loss in more than 26,000 whole mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3399-402. [PMID: 25714144 DOI: 10.3109/19401736.2015.1018239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The co-occurrence of pathogenic or candidate mutations for Leber's hereditary optic neuropathy (LHON) and hearing loss has long been suggested to be a rare incident. The "rare" is probably caused by inadequate database searches. In this study, we created and released a comprehensive database with detailed information of haplogroup, variants, coding sites, and potential pathogenic mutations for more than 26,000 whole mitochondrial genomes. We found the co-occurrence in more than 200 individuals including not only LHON or hearing loss patients but also individuals sampled from general populations with various haplogroup backgrounds. The results highlighted the significant importance of adequate database searching in the genetic analysis of mitochondrial disorders.
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Affiliation(s)
- Haixin Yang
- a Department of Neurology , Liaocheng People's Hospital , Liaocheng , Shandong , P.R. China and
| | - Rui Liu
- b State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology , Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai , P.R. China
| | - Chuan-Chao Wang
- b State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology , Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai , P.R. China
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Alsmadi O, John SE, Thareja G, Hebbar P, Antony D, Behbehani K, Thanaraj TA. Genome at juncture of early human migration: a systematic analysis of two whole genomes and thirteen exomes from Kuwaiti population subgroup of inferred Saudi Arabian tribe ancestry. PLoS One 2014; 9:e99069. [PMID: 24896259 PMCID: PMC4045902 DOI: 10.1371/journal.pone.0099069] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 05/10/2014] [Indexed: 01/19/2023] Open
Abstract
Population of the State of Kuwait is composed of three genetic subgroups of inferred Persian, Saudi Arabian tribe and Bedouin ancestry. The Saudi Arabian tribe subgroup traces its origin to the Najd region of Saudi Arabia. By sequencing two whole genomes and thirteen exomes from this subgroup at high coverage (>40X), we identify 4,950,724 Single Nucleotide Polymorphisms (SNPs), 515,802 indels and 39,762 structural variations. Of the identified variants, 10,098 (8.3%) exomic SNPs, 139,923 (2.9%) non-exomic SNPs, 5,256 (54.3%) exomic indels, and 374,959 (74.08%) non-exomic indels are 'novel'. Up to 8,070 (79.9%) of the reported novel biallelic exomic SNPs are seen in low frequency (minor allele frequency <5%). We observe 5,462 known and 1,004 novel potentially deleterious nonsynonymous SNPs. Allele frequencies of common SNPs from the 15 exomes is significantly correlated with those from genotype data of a larger cohort of 48 individuals (Pearson correlation coefficient, 0.91; p <2.2×10-16). A set of 2,485 SNPs show significantly different allele frequencies when compared to populations from other continents. Two notable variants having risk alleles in high frequencies in this subgroup are: a nonsynonymous deleterious SNP (rs2108622 [19:g.15990431C>T] from CYP4F2 gene [MIM:*604426]) associated with warfarin dosage levels [MIM:#122700] required to elicit normal anticoagulant response; and a 3' UTR SNP (rs6151429 [22:g.51063477T>C]) from ARSA gene [MIM:*607574]) associated with Metachromatic Leukodystrophy [MIM:#250100]. Hemoglobin Riyadh variant (identified for the first time in a Saudi Arabian woman) is observed in the exome data. The mitochondrial haplogroup profiles of the 15 individuals are consistent with the haplogroup diversity seen in Saudi Arabian natives, who are believed to have received substantial gene flow from Africa and eastern provenance. We present the first genome resource imperative for designing future genetic studies in Saudi Arabian tribe subgroup. The full-length genome sequences and the identified variants are available at ftp://dgr.dasmaninstitute.org and http://dgr.dasmaninstitute.org/DGR/gb.html.
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Affiliation(s)
- Osama Alsmadi
- Dasman Diabetes Institute, Dasman, Kuwait
- * E-mail: (TAT); (OA)
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Romero P, Fernández V, Slabaugh M, Seleme N, Reyes N, Gallardo P, Herrera L, Peña L, Pezo P, Moraga M. Pan-American mDNA haplogroups in Chilean patients with Leber's hereditary optic neuropathy. Mol Vis 2014; 20:334-40. [PMID: 24672219 PMCID: PMC3962688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/12/2014] [Indexed: 11/23/2022] Open
Abstract
PURPOSE The clinical impact of mDNA mutations on the development of Leber hereditary optic neuropathy (LHON) may be modulated by mitochondrial haplogroups, which vary across populations. The aim of this research was to determine the clinical spectrum and molecular characteristics, including the haplogroup, of 15 South American families with LHON. METHODS This study was a prospective, observational study conducted between March 2006 and August 2012. All patients were referred to the Clinical Hospital of the University of Chile, where the clinical study was conducted. Molecular studies were conducted at the Biomedical Sciences Institute (ICBM) of the University of Chile. Fifteen index cases were identified with molecular analysis after initial neuroophthalmic examination at different centers throughout Chile. Clinical features of patients with LHON and maternal relatives of the 15 families (75 individuals: 26 affected and 49 healthy carriers) were evaluated. The primary mDNA mutations (m.3460G>A, m.11778G>A, or m.14484T>C) were determined with restriction fragment length polymorphism analysis in all individuals. Mitochondrial haplogroups were determined with direct sequencing of two hypervariable regions (HV1 and HV2) and compared with reference sequences. RESULTS The m.11778G>A mutation was found in 59 subjects (78.7%), the m.14484T>C mutation was found in 12 subjects (16.0%), and the m.3460G>A mutation was found in four (5.3%) subjects. The average age of onset of symptoms in affected subjects was 22.2 years old (range 3 to 53 years); 21 (80.7%) were male, and five (19.3%) were female. Twelve families (80%) had Amerindian haplogroups: One family had the A2 haplogroup, four families had the B2i2 haplogroup, six families had the C1b haplogroup, and one family had the D1g haplogroup. CONCLUSIONS In this limited sample size, the Amerindian haplogroup A2 was associated with delayed onset of disease in this population. Patients with haplogroup C retained better vision than the patients with other haplogroups in this population. Disease in subjects with haplogroup D appeared to be underrepresented compared to the population at large.
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Affiliation(s)
- Pablo Romero
- Departamento de Oftalmología, Hospital Clínico “José Joaquín Aguirre,” Universidad de Chile, Santiago, Chile,Department of Ophthalmology, University of Washington, Seattle, WA
| | - Verónica Fernández
- Departamento de Neuro-oftalmología Instituto Chileno de Neurocirugía, Santiago, Chile
| | - Mark Slabaugh
- Department of Ophthalmology, University of Washington, Seattle, WA
| | - Nicolás Seleme
- Departamento de Oftalmología, Hospital Clínico “José Joaquín Aguirre,” Universidad de Chile, Santiago, Chile
| | - Nury Reyes
- Servicio de Oftalmología, Hospital Regional de Concepción, Santiago, Chile
| | - Patricia Gallardo
- Departamento de Oftalmología, Hospital Clínico “José Joaquín Aguirre,” Universidad de Chile, Santiago, Chile
| | - Luisa Herrera
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Luis Peña
- Departamento de Oftalmología. Universidad Católica de Chile, Santiago, Chile
| | - Patricio Pezo
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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Perli E, Giordano C, Pisano A, Montanari A, Campese AF, Reyes A, Ghezzi D, Nasca A, Tuppen HA, Orlandi M, Di Micco P, Poser E, Taylor RW, Colotti G, Francisci S, Morea V, Frontali L, Zeviani M, d'Amati G. The isolated carboxy-terminal domain of human mitochondrial leucyl-tRNA synthetase rescues the pathological phenotype of mitochondrial tRNA mutations in human cells. EMBO Mol Med 2014; 6:169-82. [PMID: 24413190 PMCID: PMC3927953 DOI: 10.1002/emmm.201303198] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/16/2013] [Accepted: 10/17/2013] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial (mt) diseases are multisystem disorders due to mutations in nuclear or mtDNA genes. Among the latter, more than 50% are located in transfer RNA (tRNA) genes and are responsible for a wide range of syndromes, for which no effective treatment is available at present. We show that three human mt aminoacyl-tRNA syntethases, namely leucyl-, valyl-, and isoleucyl-tRNA synthetase are able to improve both viability and bioenergetic proficiency of human transmitochondrial cybrid cells carrying pathogenic mutations in the mt-tRNA(Ile) gene. Importantly, we further demonstrate that the carboxy-terminal domain of human mt leucyl-tRNA synthetase is both necessary and sufficient to improve the pathologic phenotype associated either with these "mild" mutations or with the "severe" m.3243A>G mutation in the mt-tRNA(L)(eu(UUR)) gene. Furthermore, we provide evidence that this small, non-catalytic domain is able to directly and specifically interact in vitro with human mt-tRNA(Leu(UUR)) with high affinity and stability and, with lower affinity, with mt-tRNA(Ile). Taken together, our results sustain the hypothesis that the carboxy-terminal domain of human mt leucyl-tRNA synthetase can be used to correct mt dysfunctions caused by mt-tRNA mutations.
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Affiliation(s)
- Elena Perli
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
| | - Carla Giordano
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
| | - Annalinda Pisano
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Department of Internal Medicine and Medical Specialties, Sapienza University of RomeRome, Italy
| | - Arianna Montanari
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of RomeRome, Italy
| | - Antonio F Campese
- Department of Molecular Medicine, Sapienza University of RomeRome, Italy
| | | | - Daniele Ghezzi
- Unit of Molecular Neurogenetics, The Foundation “Carlo Besta” Institute of Neurology IRCCSMilan, Italy
| | - Alessia Nasca
- Unit of Molecular Neurogenetics, The Foundation “Carlo Besta” Institute of Neurology IRCCSMilan, Italy
| | - Helen A Tuppen
- Wellcome Trust Center for Mitochondrial Research, Institute for Ageing and Health, Newcastle UniversityNewcastle upon Tyne, UK
| | - Maurizia Orlandi
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Department of Molecular Medicine, Sapienza University of RomeRome, Italy
| | - Patrizio Di Micco
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of RomeRome, Italy
| | - Elena Poser
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of RomeRome, Italy
| | - Robert W Taylor
- Wellcome Trust Center for Mitochondrial Research, Institute for Ageing and Health, Newcastle UniversityNewcastle upon Tyne, UK
| | - Gianni Colotti
- National Research Council of Italy, Institute of Molecular Biology and PathologyRome, Italy
| | - Silvia Francisci
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of RomeRome, Italy
| | - Veronica Morea
- National Research Council of Italy, Institute of Molecular Biology and PathologyRome, Italy
| | - Laura Frontali
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of RomeRome, Italy
| | | | - Giulia d'Amati
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
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Collins DW, Gudiseva HV, Trachtman BT, Jerrehian M, Gorry T, Merritt III WT, Rhodes AL, Sankar PS, Regina M, Miller-Ellis E, O’Brien JM. Mitochondrial sequence variation in African-American primary open-angle glaucoma patients. PLoS One 2013; 8:e76627. [PMID: 24146900 PMCID: PMC3798711 DOI: 10.1371/journal.pone.0076627] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 08/23/2013] [Indexed: 01/21/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is a major cause of blindness and results from irreversible retinal ganglion cell damage and optic nerve degeneration. In the United States, POAG is most prevalent in African-Americans. Mitochondrial genetics and dysfunction have been implicated in POAG, and potentially pathogenic sequence variations, in particular novel transversional base substitutions, are reportedly common in mitochondrial genomes (mtDNA) from POAG patient blood. The purpose of this study was to ascertain the spectrum of sequence variation in mtDNA from African-American POAG patients and determine whether novel nonsynonymous, transversional or other potentially pathogenic sequence variations are observed more commonly in POAG cases than controls. mtDNA from African-American POAG cases (n = 22) and age-matched controls (n = 22) was analyzed by deep sequencing of a single 16,487 base pair PCR amplicon by Ion Torrent, and candidate novel variants were validated by Sanger sequencing. Sequence variants were classified and interpreted using the MITOMAP compendium of polymorphisms. 99.8% of the observed variations had been previously reported. The ratio of novel variants to POAG cases was 7-fold lower than a prior estimate. Novel mtDNA variants were present in 3 of 22 cases, novel nonsynonymous changes in 1 of 22 cases and novel transversions in 0 of 22 cases; these proportions are significantly lower (p<.0005, p<.0004, p<.0001) than estimated previously for POAG, and did not differ significantly from controls. Although it is possible that mitochondrial genetics play a role in African-Americans' high susceptibility to POAG, it is unlikely that any mitochondrial respiratory dysfunction is due to an abnormally high incidence of novel mutations that can be detected in mtDNA from peripheral blood.
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Affiliation(s)
- David W. Collins
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Harini V. Gudiseva
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Benjamin T. Trachtman
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Matthew Jerrehian
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Thomasine Gorry
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - William T. Merritt III
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Allison L. Rhodes
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Prithvi S. Sankar
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Meredith Regina
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Eydie Miller-Ellis
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joan M. O’Brien
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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Kim HL, Schuster SC. Poor Man's 1000 Genome Project: Recent Human Population Expansion Confounds the Detection of Disease Alleles in 7,098 Complete Mitochondrial Genomes. Front Genet 2013; 4:13. [PMID: 23450075 PMCID: PMC3584485 DOI: 10.3389/fgene.2013.00013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/28/2013] [Indexed: 01/29/2023] Open
Abstract
Rapid growth of the human population has caused the accumulation of rare genetic variants that may play a role in the origin of genetic diseases. However, it is challenging to identify those rare variants responsible for specific diseases without genetic data from an extraordinarily large population sample. Here we focused on the accumulated data from the human mitochondrial (mt) genome sequences because this data provided 7,098 whole genomes for analysis. In this dataset we identified 6,110 single nucleotide variants (SNVs) and their frequency and determined that the best-fit demographic model for the 7,098 genomes included severe population bottlenecks and exponential expansions of the non-African population. Using this model, we simulated the evolution of mt genomes in order to ascertain the behavior of deleterious mutations. We found that such deleterious mutations barely survived during population expansion. We derived the threshold frequency of a deleterious mutation in separate African, Asian, and European populations and used it to identify pathogenic mutations in our dataset. Although threshold frequency was very low, the proportion of variants showing a lower frequency than that threshold was 82, 83, and 91% of the total variants for the African, Asian, and European populations, respectively. Within these variants, only 18 known pathogenic mutations were detected in the 7,098 genomes. This result showed the difficulty of detecting a pathogenic mutation within an abundance of rare variants in the human population, even with a large number of genomes available for study.
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Affiliation(s)
- Hie Lim Kim
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University University Park, PA, USA
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41
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Mitochondrial DNA variations in Madras motor neuron disease. Mitochondrion 2013; 13:721-8. [PMID: 23419391 DOI: 10.1016/j.mito.2013.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 11/20/2022]
Abstract
Although the Madras motor neuron disease (MMND) was found three decades ago, its genetic basis has not been elucidated, so far. The symptom at onset was impaired hearing, upper limb weakness and atrophy. Since some clinical features of MMND overlap with mitochondrial disorders, we analyzed the complete mitochondrial genome of 45 MMND patients and found 396 variations, including 13 disease-associated, 2 mt-tRNA and 33 non-synonymous (16 MT-ND, 10 MT-CO, 3 MT-CYB and 4 MT-ATPase). A rare variant (m.8302A>G) in mt-tRNA(Leu) was found in three patients. We predict that these variation(s) may influence the disease pathogenesis along with some unknown factor(s).
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Abstract
Mutations in the human mitochondrial genome are known to cause an array of diverse disorders, most of which are maternally inherited, and all of which are associated with defects in oxidative energy metabolism. It is now emerging that somatic mutations in mitochondrial DNA (mtDNA) are also linked to other complex traits, including neurodegenerative diseases, ageing and cancer. Here we discuss insights into the roles of mtDNA mutations in a wide variety of diseases, highlighting the interesting genetic characteristics of the mitochondrial genome and challenges in studying its contribution to pathogenesis.
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Iglesias E, Llobet L, Pacheu-Grau D, Gómez-Durán A, Ruiz-Pesini E. Cybrids for Mitochondrial DNA Pharmacogenomics. Drug Dev Res 2012. [DOI: 10.1002/ddr.21037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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44
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Bellizzi D, D'Aquila P, Giordano M, Montesanto A, Passarino G. Global DNA methylation levels are modulated by mitochondrial DNA variants. Epigenomics 2012; 4:17-27. [PMID: 22332655 DOI: 10.2217/epi.11.109] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
AIM In the present study, we investigated whether global DNA methylation levels are affected by mitochondrial DNA (mtDNA) variants, which are known to modulate mitochondrial functions. MATERIALS & METHODS Global DNA methylation levels were evaluated in peripheral blood DNA collected from adult subjects and in vitro using the DNA of cybrid cells harboring mtDNAs of different haplogroups. In these cells, mRNA expression of genes involved in DNA methylation processes, and ATP and reactive oxygen species levels were also analyzed. RESULTS The analysis revealed that methylation levels were higher in the subjects carrying the J haplogroup than in non-J carriers. Consistently, cybrids with J haplogroup mtDNA showed higher methylation levels than other cybrids. Interestingly, we observed overexpression of the MAT1A gene and low ATP and ROS levels in J cybrids. CONCLUSION Our findings indicate that mtDNA-specific interactions between mitochondria and the nucleus regulate epigenetic changes, possibly by affecting oxidative phosphorylation efficiency.
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Affiliation(s)
- Dina Bellizzi
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
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Petruzzella V, Carrozzo R, Calabrese C, Dell'Aglio R, Trentadue R, Piredda R, Artuso L, Rizza T, Bianchi M, Porcelli AM, Guerriero S, Gasparre G, Attimonelli M. Deep sequencing unearths nuclear mitochondrial sequences under Leber's hereditary optic neuropathy-associated false heteroplasmic mitochondrial DNA variants. Hum Mol Genet 2012; 21:3753-64. [PMID: 22589247 DOI: 10.1093/hmg/dds182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Leber's hereditary optic neuropathy (LHON) is associated with mitochondrial DNA (mtDNA) ND mutations that are mostly homoplasmic. However, these mutations are not sufficient to explain the peculiar features of penetrance and the tissue-specific expression of the disease and are believed to be causative in association with unknown environmental or other genetic factors. Discerning between clear-cut pathogenetic variants, such as those that appear to be heteroplasmic, and less penetrant variants, such as the homoplasmic, remains a challenging issue that we have addressed here using next-generation sequencing approach. We set up a protocol to quantify MTND5 heteroplasmy levels in a family in which the proband manifests a LHON phenotype. Furthermore, to study this mtDNA haplotype, we applied the cybridization protocol. The results demonstrate that the mutations are mostly homoplasmic, whereas the suspected heteroplasmic feature of the observed mutations is due to the co-amplification of Nuclear mitochondrial Sequences.
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Grzybowska-Szatkowska L, Slaska B. Polymorphisms in genes encoding mt-tRNA in female breast cancer in Poland. ACTA ACUST UNITED AC 2012; 23:106-11. [PMID: 22397379 DOI: 10.3109/19401736.2012.660925] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Recently, there have been indications of participation of mitochondria in the carcinogenic process and the role of polymorphisms in increasing the risk of cancer. The aim of the study was to detect possible changes in the sequence of 22 genes encoding mitochondrial tRNA in breast cancer carcinoma, which take part in protein synthesis in the translation process. The analysis of tumour tissue and blood material sampled from 50 patients revealed that few mutations have been found. It cannot be excluded that, through their impact on the secondary and tertiary tRNA structure, polymorphisms may cause mitochondrial dysfunction and contribute to appearance of other changes in mtDNA. Mutations in tRNA genes in breast cancer may affect the cell and cause its dysfunction, as in mitochondrial diseases.
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Abstract
Mutations that arise in mitochondrial DNA (mtDNA) may be sporadic, maternally inherited, or Mendelian in character and include mtDNA rearrangements such as deletions, inversions or duplications, point mutations, or copy number depletion. Primary mtDNA mutations occur sporadically or exhibit maternal inheritance and arise due in large part to the high mutation rate of mtDNA. mtDNA mutations may also occur because of defects in the biogenesis or maintenance of mtDNA, reflecting the contribution of nuclear-encoded genes to these processes, and in this case exhibit Mendelian inheritance. Whether maternally inherited, sporadic, or Mendelian, mtDNA mutations can exhibit a complex and broad spectrum of disease manifestations due to the central role mitochondria play in a variety of cellular functions. In addition, because there exist hundreds to thousands of copies of mtDNA in each cell, the proportion of mutant mtDNA molecules can have a profound effect on the cellular and clinical phenotype. This chapter reviews the classification of mtDNA mutations and the clinical features that determine the diagnosis of a primary mtDNA disorder.
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Affiliation(s)
- William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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Zhang AM, Jia X, Bi R, Salas A, Li S, Xiao X, Wang P, Guo X, Kong QP, Zhang Q, Yao YG. Mitochondrial DNA haplogroup background affects LHON, but not suspected LHON, in Chinese patients. PLoS One 2011; 6:e27750. [PMID: 22110754 PMCID: PMC3216987 DOI: 10.1371/journal.pone.0027750] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 10/24/2011] [Indexed: 02/07/2023] Open
Abstract
Recent studies have shown that mtDNA background could affect the clinical expression of Leber hereditary optic neuropathy (LHON). We analyzed the mitochondrial DNA (mtDNA) variation of 304 Chinese patients with m.11778G>A (sample #1) and of 843 suspected LHON patients who lack the three primary mutations (sample #2) to discern mtDNA haplogroup effect on disease onset. Haplogroup frequencies in the patient group was compared to frequencies in the general Han Chinese population (n = 1,689; sample #3). The overall matrilineal composition of the suspected LHON population resembles that of the general Han Chinese population, suggesting no association with mtDNA haplogroup. In contrast, analysis of these LHON patients confirms mtDNA haplogroup effect on LHON. Specifically, the LHON sample significantly differs from the general Han Chinese and suspected LHON populations by harboring an extremely lower frequency of haplogroup R9, in particular of its main sub-haplogroup F (#1 vs. #3, P-value = 1.46×10−17, OR = 0.051, 95% CI: 0.016–0.162; #1 vs. #2, P-value = 4.44×10−17, OR = 0.049, 95% CI: 0.015–0.154; in both cases, adjusted P-value <10−5) and higher frequencies of M7b (#1 vs. #3, adjusted P-value = 0.001 and #1 vs. #2, adjusted P-value = 0.004). Our result shows that mtDNA background affects LHON in Chinese patients with m.11778G>A but not suspected LHON. Haplogroup F has a protective effect against LHON, while M7b is a risk factor.
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Affiliation(s)
- A-Mei Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiangming Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
- * E-mail: (QZ); (Y-GY)
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
- * E-mail: (QZ); (Y-GY)
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49
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Giorgio V, Petronilli V, Ghelli A, Carelli V, Rugolo M, Lenaz G, Bernardi P. The effects of idebenone on mitochondrial bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:363-9. [PMID: 22086148 PMCID: PMC3265671 DOI: 10.1016/j.bbabio.2011.10.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 12/17/2022]
Abstract
We have studied the effects of idebenone on mitochondrial function in cybrids derived from one normal donor (HQB17) and one patient harboring the G3460A/MT-ND1 mutation of Leber's Hereditary Optic Neuropathy (RJ206); and in XTC.UC1 cells bearing a premature stop codon at aminoacid 101 of MT-ND1 that hampers complex I assembly. Addition of idebenone to HQB17 cells caused mitochondrial depolarization and NADH depletion, which were inhibited by cyclosporin (Cs) A and decylubiquinone, suggesting an involvement of the permeability transition pore (PTP). On the other hand, addition of dithiothreitol together with idebenone did not cause PTP opening and allowed maintenance of the mitochondrial membrane potential even in the presence of rotenone. Addition of dithiothreitol plus idebenone, or of idebenol, to HQB17, RJ206 and XTC.UC1 cells sustained membrane potential in intact cells and ATP synthesis in permeabilized cells even in the presence of rotenone and malonate, and restored a good level of coupled respiration in complex I-deficient XTC.UC1 cells. These findings demonstrate that idebenol can feed electrons at complex III. If the quinone is maintained in the reduced state, a task that in some cell types appears to be performed by dicoumarol-sensitive NAD(P)H:quinone oxidoreductase 1 [Haefeli et al. (2011) PLoS One 6, e17963], electron transfer to complex III may allow reoxidation of NADH in complex I deficiencies.
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Affiliation(s)
- Valentina Giorgio
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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50
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Pierron D, Letellier T, Grossman LI. Mitogroup: continent-specific clusters of mitochondrial OXPHOS complexes based on nuclear non-synonymous polymorphisms. Mitochondrion 2011; 12:237-41. [PMID: 21968253 DOI: 10.1016/j.mito.2011.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/05/2011] [Accepted: 09/16/2011] [Indexed: 11/20/2022]
Abstract
OXPHOS polymorphisms are known to be population specific and to influence disease. Previous studies have focused on mtDNA polymorphisms. Based on a world sampling of 629 unrelated individuals, we have now studied the polymorphisms of the 80 genes encoding OXPHOS nuclear subunits. We have shown that (i) amino-acid replacement frequencies are significantly correlated with their pathogenicity probability, and (ii) populations can be distinguished based only on amino-acid replacements in nuclear encoded OXPHOS subunits. These results are congruent with the major mtDNA haplogroups, which suggests that OXPHOS complexes are different across the populations in both nuclear and in mitochondrial encoded subunits.
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Affiliation(s)
- Denis Pierron
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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