1
|
Yazdani M. Cellular and Molecular Responses to Mitochondrial DNA Deletions in Kearns-Sayre Syndrome: Some Underlying Mechanisms. Mol Neurobiol 2024; 61:5665-5679. [PMID: 38224444 DOI: 10.1007/s12035-024-03938-7] [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] [Indexed: 01/16/2024]
Abstract
Kearns-Sayre syndrome (KSS) is a rare multisystem mitochondrial disorder. It is caused by mitochondrial DNA (mtDNA) rearrangements, mostly large-scale deletions of 1.1-10 kb. These deletions primarily affect energy supply through impaired oxidative phosphorylation and reduced ATP production. This impairment gives rise to dysfunction of several tissues, in particular those with high energy demand like brain and muscles. Over the past decades, changes in respiratory chain complexes and energy metabolism have been emphasized, whereas little attention has been paid to other reports on ROS overproduction, protein synthesis inhibition, myelin vacuolation, demyelination, autophagy, apoptosis, and involvement of lipid raft and oligodendrocytes in KSS. Therefore, this paper draws attention towards these relatively underemphasized findings that might further clarify the pathologic cascades following deletions in the mtDNA.
Collapse
Affiliation(s)
- Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Oslo, 0027, Norway.
| |
Collapse
|
2
|
Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 PMCID: PMC11346376 DOI: 10.1042/bcj20230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
Collapse
Affiliation(s)
- Tiago M. Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E. Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E. Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B. Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| |
Collapse
|
3
|
Pereira CV, Gitschlag BL, Patel MR. Cellular mechanisms of mtDNA heteroplasmy dynamics. Crit Rev Biochem Mol Biol 2021; 56:510-525. [PMID: 34120542 DOI: 10.1080/10409238.2021.1934812] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant mtDNA levels can vary and change in a nonrandom fashion across generations and amongst tissues of an individual. However, our lack of understanding of the basic cellular and molecular mechanisms of mtDNA heteroplasmy dynamics has made it difficult to predict who will inherit or develop mtDNA-associated diseases. More recently, with the advances in technology and the establishment of tractable model systems, insights into the mechanisms underlying the selection forces that modulate heteroplasmy dynamics are beginning to emerge. In this review, we summarize evidence from different organisms, showing that mutant mtDNA can experience both positive and negative selection. We also review the recently identified mechanisms that modulate heteroplasmy dynamics. Taken together, this is an opportune time to survey the literature and to identify key cellular pathways that can be targeted to develop therapies for diseases caused by heteroplasmic mtDNA mutations.
Collapse
Affiliation(s)
- Claudia V Pereira
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| |
Collapse
|
4
|
Oliveira MT, Pontes CDB, Ciesielski GL. Roles of the mitochondrial replisome in mitochondrial DNA deletion formation. Genet Mol Biol 2020; 43:e20190069. [PMID: 32141473 PMCID: PMC7197994 DOI: 10.1590/1678-4685-gmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are a common cause of human mitochondrial
diseases. Mutations in the genes encoding components of the mitochondrial
replisome, such as DNA polymerase gamma (Pol γ) and the mtDNA helicase Twinkle,
have been associated with the accumulation of such deletions and the development
of pathological conditions in humans. Recently, we demonstrated that changes in
the level of wild-type Twinkle promote mtDNA deletions, which implies that not
only mutations in, but also dysregulation of the stoichiometry between the
replisome components is potentially pathogenic. The mechanism(s) by which
alterations to the replisome function generate mtDNA deletions is(are) currently
under debate. It is commonly accepted that stalling of the replication fork at
sites likely to form secondary structures precedes the deletion formation. The
secondary structural elements can be bypassed by the replication-slippage
mechanism. Otherwise, stalling of the replication fork can generate single- and
double-strand breaks, which can be repaired through recombination leading to the
elimination of segments between the recombination sites. Here, we discuss
aberrances of the replisome in the context of the two debated outcomes, and
suggest new mechanistic explanations based on replication restart and template
switching that could account for all the deletion types reported for
patients.
Collapse
Affiliation(s)
- Marcos T Oliveira
- Universidade Estadual Paulista Júlio de Mesquita Filho, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | | | | |
Collapse
|
5
|
Chen Z, Zhang F, Xu H. Human mitochondrial DNA diseases and Drosophila models. J Genet Genomics 2019; 46:201-212. [DOI: 10.1016/j.jgg.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/05/2019] [Accepted: 03/25/2019] [Indexed: 01/06/2023]
|
6
|
Goudenège D, Bris C, Hoffmann V, Desquiret-Dumas V, Jardel C, Rucheton B, Bannwarth S, Paquis-Flucklinger V, Lebre AS, Colin E, Amati-Bonneau P, Bonneau D, Reynier P, Lenaers G, Procaccio V. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 2018; 21:1407-1416. [PMID: 30393377 DOI: 10.1038/s41436-018-0350-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/17/2018] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Accurate detection of mitochondrial DNA (mtDNA) alterations is essential for the diagnosis of mitochondrial diseases. The development of high-throughput sequencing technologies has enhanced the detection sensitivity of mtDNA pathogenic variants, but the detection of mtDNA rearrangements, especially multiple deletions, is still poorly processed. Here, we present eKLIPse, a sensitive and specific tool allowing the detection and quantification of large mtDNA rearrangements from single and paired-end sequencing data. METHODS The methodology was first validated using a set of simulated data to assess the detection sensitivity and specificity, and second with a series of sequencing data from mitochondrial disease patients carrying either single or multiple deletions, related to pathogenic variants in nuclear genes involved in mtDNA maintenance. RESULTS eKLIPse provides the precise breakpoint positions and the cumulated percentage of mtDNA rearrangements at a given gene location with a detection sensitivity lower than 0.5% mutant. eKLIPse software is available either as a script to be integrated in a bioinformatics pipeline, or as user-friendly graphical interface to visualize the results through a Circos representation ( https://github.com/dooguypapua/eKLIPse ). CONCLUSION Thus, eKLIPse represents a useful resource to study the causes and consequences of mtDNA rearrangements, for further genotype/phenotype correlations in mitochondrial disorders.
Collapse
Affiliation(s)
- David Goudenège
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Celine Bris
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Virginie Hoffmann
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Valerie Desquiret-Dumas
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Claude Jardel
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Benoit Rucheton
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | | | - Anne Sophie Lebre
- CHU Reims, Hôpital Maison Blanche, Pole de biologie, Service de génétique, Reims, France
| | - Estelle Colin
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Pascal Reynier
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France. .,Biochemistry and Genetics Department, Angers Hospital, Angers, France.
| |
Collapse
|
7
|
Khan NA, Govindaraj P, Meena AK, Thangaraj K. Mitochondrial disorders: challenges in diagnosis & treatment. Indian J Med Res 2016; 141:13-26. [PMID: 25857492 PMCID: PMC4405934 DOI: 10.4103/0971-5916.154489] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial dysfunctions are known to be responsible for a number of heterogenous clinical presentations with multi-systemic involvement. Impaired oxidative phosphorylation leading to a decrease in cellular energy (ATP) production is the most important cause underlying these disorders. Despite significant progress made in the field of mitochondrial medicine during the last two decades, the molecular mechanisms underlying these disorders are not fully understood. Since the identification of first mitochondrial DNA (mtDNA) mutation in 1988, there has been an exponential rise in the identification of mtDNA and nuclear DNA mutations that are responsible for mitochondrial dysfunction and disease. Genetic complexity together with ever widening clinical spectrum associated with mitochondrial dysfunction poses a major challenge in diagnosis and treatment. Effective therapy has remained elusive till date and is mostly efficient in relieving symptoms. In this review, we discuss the important clinical and genetic features of mitochondrials disorders with special emphasis on diagnosis and treatment.
Collapse
Affiliation(s)
| | | | | | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular & Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, India
| |
Collapse
|
8
|
Kalifa L, Gewandter JS, Staversky RJ, Sia EA, Brookes PS, O'Reilly MA. DNA double-strand breaks activate ATM independent of mitochondrial dysfunction in A549 cells. Free Radic Biol Med 2014; 75:30-9. [PMID: 25048973 PMCID: PMC4171189 DOI: 10.1016/j.freeradbiomed.2014.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 10/25/2022]
Abstract
Excessive nuclear or mitochondrial DNA damage can lead to mitochondrial dysfunction, decreased energy production, and increased generation of reactive oxygen species (ROS). Although numerous cell signaling pathways are activated when cells are injured, the ataxia telangiectasia mutant (ATM) protein has emerged as a major regulator of the response to both mitochondrial dysfunction and nuclear DNA double-strand breaks (DSBs). Because mitochondrial dysfunction is often a response to excessive DNA damage, it has been difficult to determine whether nuclear and/or mitochondrial DNA DSBs activate ATM independent of mitochondrial dysfunction. In this study, mitochondrial and nuclear DNA DSBs were generated in the A549 human lung adenocarcinoma cell line by infecting with retroviruses expressing the restriction endonuclease PstI fused to a mitochondrial targeting sequence (MTS) or nuclear localization sequence (NLS) and a hemagglutinin antigen epitope tag (HA). Expression of MTS-PstI-HA or NLS-PstI-HA activated the DNA damage response defined by phosphorylation of ATM, the tumor suppressor protein p53 (TP53), KRAB-associated protein (KAP)-1, and structural maintenance of chromosomes (SMC)-1. Phosphorylated ATM and SMC1 were detected in nuclear fractions, whereas phosphorylated TP53 and KAP1 were detected in both mitochondrial and nuclear fractions. PstI also enhanced expression of the cyclin-dependent kinase inhibitor p21 and inhibited cell growth. This response to DNA damage occurred in the absence of detectable mitochondrial dysfunction and excess production of ROS. These findings reveal that DNA DSBs are sufficient to activate ATM independent of mitochondrial dysfunction and suggest that the activated form of ATM and some of its substrates are restricted to the nuclear compartment, regardless of the site of DNA damage.
Collapse
Affiliation(s)
- Lidza Kalifa
- Department of Environmental Medicine, The University of Rochester, Rochester, NY 14642, USA
| | - Jennifer S Gewandter
- Department of Anesthesiology, The University of Rochester, Rochester, NY 14642, USA
| | - Rhonda J Staversky
- Department of Pediatrics, The University of Rochester, Rochester, NY 14642, USA
| | - Elaine A Sia
- Department of Biology, The University of Rochester, Rochester, NY 14642, USA
| | - Paul S Brookes
- Department of Anesthesiology, The University of Rochester, Rochester, NY 14642, USA
| | - Michael A O'Reilly
- Department of Pediatrics, The University of Rochester, Rochester, NY 14642, USA.
| |
Collapse
|
9
|
Pathak D, Berthet A, Nakamura K. Energy failure: does it contribute to neurodegeneration? Ann Neurol 2013; 74:506-16. [PMID: 24038413 PMCID: PMC4092015 DOI: 10.1002/ana.24014] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/09/2013] [Accepted: 08/16/2013] [Indexed: 12/11/2022]
Abstract
Energy failure from mitochondrial dysfunction is proposed to be a central mechanism leading to neuronal death in a range of neurodegenerative diseases. However, energy failure has never been directly demonstrated in affected neurons in these diseases, nor has it been proved to produce degeneration in disease models. Therefore, despite considerable indirect evidence, it is not known whether energy failure truly occurs in susceptible neurons, and whether this failure is responsible for their death. This limited understanding results primarily from a lack of sensitivity and resolution of available tools and assays and the inherent limitations of in vitro model systems. Major advances in these methodologies and approaches should greatly enhance our understanding of the relationship between energy failure, neuronal dysfunction, and death, and help us to determine whether boosting bioenergetic function would be an effective therapeutic approach. Here we review the current evidence that energy failure occurs in and contributes to neurodegenerative disease, and consider new approaches that may allow us to better address this central issue.
Collapse
Affiliation(s)
- Divya Pathak
- Gladstone Institute of Neurological Disease, University of California, San Francisco, San Francisco, CA
| | | | | |
Collapse
|
10
|
Benard G, Trian T, Bellance N, Berger P, Lavie J, Espil-Taris C, Rocher C, Eimer-Bouillot S, Goizet C, Nouette-Gaulain K, Letellier T, Lacombe D, Rossignol R. Adaptative capacity of mitochondrial biogenesis and of mitochondrial dynamics in response to pathogenic respiratory chain dysfunction. Antioxid Redox Signal 2013; 19:350-65. [PMID: 22369111 DOI: 10.1089/ars.2011.4244] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
AIMS Cellular energy homeostasy relies on mitochondrial plasticity, the molecular determinants of which are multiple. Yet, the relative contribution of and possible cooperation between mitochondrial biogenesis and morphogenesis to cellular energy homeostasy remains elusive. Here we analyzed the adaptative capacity of mitochondrial content and dynamics in muscle biopsies of patients with a complex IV defect, and in skin fibroblasts challenged with complex IV inhibition. RESULTS We observed a biphasic variation of the mitochondrial content upon complex IV inhibition in muscle biopsies and in skin fibroblasts. Adjustment of mitochondrial content for respiratory maintenance was blocked by using a dominant negative form of CREB (CREB-M1) and by L-NAME, a blocker of NO production. Accordingly, cells treated with KCN 6 μM showed higher levels of phospho-CREB, PGC1α mRNA, eNOS mRNA, and mtTFA mRNA. We also observed the increased expression of the fission protein DRP1 during fibroblasts adaptation, as well as mitochondrial ultrastructural defects indicative of increased fission in patients muscle micrographs. Accordingly, the expression of a dominant negative form of DRP1 (K38A mutant) reduced the biogenic response in fibroblasts challenged with 6 μM KCN. INNOVATION Our findings indicate that mitochondrial biogenesis and mitochondrial fission cooperate to promote cellular adaptation to respiratory chain inhibition. CONCLUSIONS Our data show for the first time that DRP1 intervenes during the initiation of the mitochondrial adaptative response to respiratory chain defects. The evidenced pathway of mitochondrial adaptation to respiratory chain deficiency provides a safety mechanism against mitochondrial dysfunction.
Collapse
Affiliation(s)
- Giovanni Benard
- Université Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), EA 4576, F-33000 Bordeaux, France
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Gendron SP, Bastien N, Mallet JD, Rochette PJ. The 3895-bp mitochondrial DNA deletion in the human eye: a potential involvement in corneal ageing and macular degeneration. Mutagenesis 2013; 28:197-204. [DOI: 10.1093/mutage/ges071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
12
|
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.
Collapse
|
13
|
Wen Q, Hu Y, Ji F, Qian G. Mitochondrial DNA alterations of peripheral lymphocytes in acute lymphoblastic leukemia patients undergoing total body irradiation therapy. Radiat Oncol 2011; 6:133. [PMID: 21978541 PMCID: PMC3198693 DOI: 10.1186/1748-717x-6-133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 10/06/2011] [Indexed: 11/28/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) alterations, including mtDNA copy number and mtDNA 4977 bp common deletion (CD), are key indicators of irradiation-induced damage. The relationship between total body irradiation (TBI) treatment and mtDNA alterations in vivo, however, has not been postulated yet. The aim of this study is to analyze mtDNA alterations in irradiated human peripheral lymphocytes from acute lymphoblastic leukemia (ALL) patients as well as to take them as predictors for radiation toxicity. Methods Peripheral blood lymphocytes were isolated from 26 ALL patients 24 hours after TBI preconditioning (4.5 and 9 Gy, respectively). Extracted DNA was analyzed by real-time PCR method. Results Average 2.31 times mtDNA and 0.53 fold CD levels were observed after 4.5 Gy exposure compared to their basal levels. 9 Gy TBI produced a greater response of both mtDNA and CD levels than 4.5 Gy. Significant inverse correlation was found between mtDNA content and CD level at 4.5 and 9 Gy (P = 0.037 and 0.048). Moreover, mtDNA content of lymphocytes without irradiation was found to be correlated to age. Conclusions mtDNA and CD content may be considered as predictive factors to radiation toxicity.
Collapse
Affiliation(s)
- Quan Wen
- Third Department of Oncology, The second affiliated hospital, Third Military Medical University, Chongqing 400037, China
| | | | | | | |
Collapse
|
14
|
Mitochondrial DNA mutations and human disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:113-28. [PMID: 19761752 DOI: 10.1016/j.bbabio.2009.09.005] [Citation(s) in RCA: 417] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 09/04/2009] [Accepted: 09/09/2009] [Indexed: 01/07/2023]
Abstract
Mitochondrial disorders are a group of clinically heterogeneous diseases, commonly defined by a lack of cellular energy due to oxidative phosphorylation (OXPHOS) defects. Since the identification of the first human pathological mitochondrial DNA (mtDNA) mutations in 1988, significant efforts have been spent in cataloguing the vast array of causative genetic defects of these disorders. Currently, more than 250 pathogenic mtDNA mutations have been identified. An ever-increasing number of nuclear DNA mutations are also being reported as the majority of proteins involved in mitochondrial metabolism and maintenance are nuclear-encoded. Understanding the phenotypic diversity and elucidating the molecular mechanisms at the basis of these diseases has however proved challenging. Progress has been hampered by the peculiar features of mitochondrial genetics, an inability to manipulate the mitochondrial genome, and difficulties in obtaining suitable models of disease. In this review, we will first outline the unique features of mitochondrial genetics before detailing the diseases and their genetic causes, focusing specifically on primary mtDNA genetic defects. The functional consequences of mtDNA mutations that have been characterised to date will also be discussed, along with current and potential future diagnostic and therapeutic advances.
Collapse
|
15
|
Prigione A, Cortopassi G. Mitochondrial DNA deletions induce the adenosine monophosphate-activated protein kinase energy stress pathway and result in decreased secretion of some proteins. Aging Cell 2007; 6:619-30. [PMID: 17651460 DOI: 10.1111/j.1474-9726.2007.00323.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) deletions occur sporadically in zygotic and somatic tissues and reach their highest concentration in substantia nigra. Previously, we noted the increase of the adenosine monophosphate (AMP)-activated protein kinase (AMPK) transcript by microarray in multiple cells and tissues bearing deletions. In this work, we demonstrate that the induction of AMPK transcript is dependent on deletions by quantitative polymerase chain reaction, and also demonstrate a deficiency in adenosine triphosphate (ATP) synthesis in the same cells. Consistent with AMPK induction, its known targets SREBF1 (sterol regulatory element binding protein-1) and ATG12 were inhibited and induced, respectively. AMPK induction is known to decrease secretory processes in some cells, and the secretion of both osteoprotegerin (OPG) and fibronectin (FN) proteins to the extracellular space was significantly deficient. Deletions caused a defect in the adenosine diphosphate (ADP)-ribosylation factor-like 2 (ARL2) transcript, which is known to be important in secretion and interacts with protein phosphatase 2A (PP2A) and thus AMPK. The deletion-dependent dysfunctions occurred even in cells bearing less than 30% deletions, suggesting that the concept of a high biological 'threshold' for deletions should be further revised downward. The defects in ATP synthesis, induction of the AMPK and SREBF1 transcripts, and decreased expression of ARL2 and secretion of OPG and FN were recapitulated by low doses of rotenone, demonstrating that they were a specific consequence of electron transport chain inhibition. Thus, mtDNA deletions result in cellular energy depletion, which causes the induction of AMPK and its regulated targets, and inhibit secretion of some proteins. We integrate these observations into a pathophysiological model for how mitochondrial deletions cause disease.
Collapse
Affiliation(s)
- Alessandro Prigione
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, Monza, Italy
| | | |
Collapse
|
16
|
Alemi M, Prigione A, Wong A, Schoenfeld R, DiMauro S, Hirano M, Taroni F, Cortopassi G. Mitochondrial DNA deletions inhibit proteasomal activity and stimulate an autophagic transcript. Free Radic Biol Med 2007; 42:32-43. [PMID: 17157191 PMCID: PMC1927835 DOI: 10.1016/j.freeradbiomed.2006.09.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 07/29/2006] [Accepted: 09/14/2006] [Indexed: 01/01/2023]
Abstract
Deletions within the mitochondrial DNA (mtDNA) cause Kearns Sayre syndrome (KSS) and chronic progressive external opthalmoplegia (CPEO). The clinical signs of KSS include muscle weakness, heart block, pigmentary retinopathy, ataxia, deafness, short stature, and dementia. The identical deletions occur and rise exponentially as humans age, particularly in substantia nigra. Deletions at >30% concentration cause deficits in basic bioenergetic parameters, including membrane potential and ATP synthesis, but it is poorly understood how these alterations cause the pathologies observed in patients. To better understand the consequences of mtDNA deletions, we microarrayed six cell types containing mtDNA deletions from KSS and CPEO patients. There was a prominent inhibition of transcripts encoding ubiquitin-mediated proteasome activity, and a prominent induction of transcripts involved in the AMP kinase pathway, macroautophagy, and amino acid degradation. In mutant cells, we confirmed a decrease in proteasome biochemical activity, significantly lower concentration of several amino acids, and induction of an autophagic transcript. An interpretation consistent with the data is that mtDNA deletions increase protein damage, inhibit the ubiquitin-proteasome system, decrease amino acid salvage, and activate autophagy. This provides a novel pathophysiological mechanism for these diseases, and suggests potential therapeutic strategies.
Collapse
Affiliation(s)
- Mansour Alemi
- Department of Molecular Biosciences, 1311 Haring Hall, University of California, Davis, CA 95616, USA
| | - Alessandro Prigione
- Department of Molecular Biosciences, 1311 Haring Hall, University of California, Davis, CA 95616, USA
| | - Alice Wong
- Department of Molecular Biosciences, 1311 Haring Hall, University of California, Davis, CA 95616, USA
| | - Robert Schoenfeld
- Department of Molecular Biosciences, 1311 Haring Hall, University of California, Davis, CA 95616, USA
| | - Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, 630 West 168 Street, New York, NY 10032
| | - Michio Hirano
- Department of Neurology, Columbia University Medical Center, 630 West 168 Street, New York, NY 10032
| | - Franco Taroni
- Division of Biochemistry and Genetics, Istituto Nazionale Neurologico Carlo Besta, Milan, Italy
| | - Gino Cortopassi
- Department of Molecular Biosciences, 1311 Haring Hall, University of California, Davis, CA 95616, USA
| |
Collapse
|
17
|
Williams SL, Moraes CT. Microdissection and Analytical PCR for the Investigation of mtDNA Lesions. Methods Cell Biol 2007; 80:481-501. [PMID: 17445710 DOI: 10.1016/s0091-679x(06)80024-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Sion L Williams
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | |
Collapse
|
18
|
Giese A, Kirschner-Schwabe R, Blumchen K, Wronski L, Shalapour S, Prada J, Driever PH, Brauer M, Schuelke M, Henze G, Seeger K. Prenatal manifestation of pancytopenia in Pearson marrow-pancreas syndrome caused by a mitochondrial DNA deletion. Am J Med Genet A 2007; 143A:285-8. [PMID: 17219391 DOI: 10.1002/ajmg.a.31493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Almut Giese
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Wong A, Cortopassi G. Mitochondrial Genetic Diseases. Neurobiol Dis 2007. [DOI: 10.1016/b978-012088592-3/50016-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
20
|
Kolesnikova O, Entelis N, Kazakova H, Brandina I, Martin RP, Tarassov I. Targeting of tRNA into yeast and human mitochondria: the role of anticodon nucleotides. Mitochondrion 2005; 2:95-107. [PMID: 16120312 DOI: 10.1016/s1567-7249(02)00013-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2002] [Revised: 03/29/2002] [Accepted: 03/29/2002] [Indexed: 12/27/2022]
Abstract
In vivo, yeast mitochondria import a single cytoplasmic tRNA, tRNA(CUU)Lys, while human mitochondria do not import any cytoplasmic tRNA. We have previously demonstrated that both yeast and human isolated mitochondria can specifically internalize tRNA(CUU)Lys, several of its mutant versions and some mutant versions of yeast cytosolic tRNA(UUU)Lys (not imported in vivo). Aminoacylation of tRNA(CUU)Lys by the cytoplasmic lysyl-tRNA synthetase was a prerequisite for its import. Here we are studying the influence of one-base replacements in the anticodon of tRNAs(Lys) on their aminoacylation, on binding to the precursor of the mitochondrial lysyl-tRNA synthetase (carrier protein directing the import), and on the efficiency of import into isolated yeast and human mitochondria. We show that the base U35 is the main identity element for the yeast cytoplasmic lysyl-tRNA synthetase. The single replacement that abolished import was C34G, while all the others only modulated the import efficiency. The need of aminoacylation for import and for interaction with the carrier protein was shown only for a subset of mutant versions, while the others could be recognized and internalized without aminoacylation or in misacylated forms.
Collapse
Affiliation(s)
- O Kolesnikova
- FRE 2375 CNRS Modèles Levures de Pathologies Humaines, Institut de Physiologie et Chimie Biologique, 21 rue René Descartes 67084, Strasbourg, France
| | | | | | | | | | | |
Collapse
|
21
|
Krishnan KJ, Harbottle A, Birch-Machin MA. The Use of a 3895 bp Mitochondrial DNA Deletion as a Marker for Sunlight Exposure in Human Skin. J Invest Dermatol 2004; 123:1020-4. [PMID: 15610508 DOI: 10.1111/j.0022-202x.2004.23457.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous work has examined the use of mitochondrial DNA (mtDNA) damage as a biomarker of cumulative sun exposure in human skin. These studies have simply compared mtDNA damage between sun-protected and sun exposed skin. This approach is limited because non-melanoma skin cancer (NMSC) is predominantly formed on body sites which are 'usually' sun exposed as opposed to sites which are 'occasionally' sun exposed and as such they differ in their cumulative ultraviolet (UV) exposure. This study addresses this limitation by investigating the frequency of occurrence of a rarely reported 3895 bp mtDNA deletion in 104 age-matched human skin samples taken from different sun-exposed body sites. There was a significant increase in the deletion frequency with increasing UV exposure (p<0.0001). Furthermore there was a significantly greater deletion frequency in 'usually' sun exposed compared with 'occasionally' sun-exposed body sites in both the dermis (p=0.0018) and epidermis (p<0.0001). Investigation of the 3895 bp deletion in the same NMSC samples used in a previous study of the 4977 bp common deletion, showed a greater frequency of the 3895 bp deletion (8/10 vs 4/10, respectively). Additionally, we have linked the 3895 bp deletion with the UVR component of sunlight by inducing the deletion in vitro with repetitive sub-lethal doses of a UVA+UVB light source.
Collapse
Affiliation(s)
- Kim J Krishnan
- Dermatological Sciences, University of Newcastle, Newcastle upon Tyne, UK
| | | | | |
Collapse
|
22
|
Abstract
The quantitative relationship between deleted mitochondrial DNA and the clinical course of patients with Kearns-Sayre syndrome is poorly understood. We investigated this point using tissue samples obtained at age 10 years when the patient was diagnosed as Kearns-Sayre syndrome and at age 20 years when he died of disseminated intravascular coagulation. By long polymerase chain reaction, a shortened mitochondrial genome (8.8 kb; normal, 16.6 kb) was detected in the patient. By quantitative competitive polymerase chain reaction, the percentage of deletion-carrying mitochondrial DNA was not increased as expected and did not differ significantly by tissue type or sampling time or correlate with clinical course. Although we could not demonstrate that the amounts of wild-type mitochondrial DNA decreased with accelerating progression, it was emphasized that such a reduction of mitochondrial DNA in various tissues, including those of the central nervous system, could play a significant pathogenetic role, since only wild-type mitochondrial DNA is functional in patients with large-scale deletions of mitochondrial DNA.
Collapse
Affiliation(s)
- Y Ishikawa
- Department of Pediatrics, National Yakumo Hospital, Hokkaido, Japan.
| | | | | | | |
Collapse
|
23
|
Chapter 9 The Role of Mitochondrial Genome Mutations in Neurodegenerative Disease. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1566-3124(08)60029-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
24
|
Cantatore P, Petruzzella V, Nicoletti C, Papadia F, Fracasso F, Rustin P, Gadaleta MN. Alteration of mitochondrial DNA and RNA level in human fibroblasts with impaired vitamin B12 coenzyme synthesis. FEBS Lett 1998; 432:173-8. [PMID: 9720919 DOI: 10.1016/s0014-5793(98)00857-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Alterations of mitochondrial (mt) nucleic acid metabolism in methylmalonic aciduria (MMA) were studied in two cell lines from skin fibroblasts of patients with mitochondrial (GM00595) or cytosolic (GM10011) defects in the biosynthesis pathways of cobalamin coenzymes. The mtDNA level increased two-fold in GM00595 cells, which carry a mt defect in the adenosylcobalamin synthesis, whereas no appreciable change was found in GM10011 cells. The content of the two rRNAs 16S and 12S mtRNAs, normalized for the mtDNA copy number, decreased by 70% and 50% in GM00595 and GM10011, respectively. The normalized content of ND1, ND2 and CO I mRNAs decreased in GM00595, but was unchanged in GM10011. Respiratory chain complex activities measured in these two cell lines were not different from control activities. These data suggest that the maintenance of the mt function is due to doubling of mtDNA and that this compensatory response takes place only in those cells in which the greater reduction of the level of rRNA might have brought the content of these transcripts below the threshold value for optimal expression of the mt genome.
Collapse
Affiliation(s)
- P Cantatore
- Department of Biochemistry and Molecular Biology, University of Bari and Centro Studi sui Mitocondri e Metabolismo Energetico, CNR, Italy
| | | | | | | | | | | | | |
Collapse
|
25
|
Birch-Machin MA, Tindall M, Turner R, Haldane F, Rees JL. Mitochondrial DNA deletions in human skin reflect photo- rather than chronologic aging. J Invest Dermatol 1998; 110:149-52. [PMID: 9457910 DOI: 10.1046/j.1523-1747.1998.00099.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have examined the use of mitochondrial DNA (mtDNA) as a molecular marker to study the relation between chronologic aging and photoageing in human skin. Using a 3-primer quantitative polymerase chain reaction method we have studied changes in the ratio of the 4977 bp deleted to wild-type mtDNA in relation to sun exposure and chronologic age of human skin. Based on previous studies, samples showing greater than 1% deleted mtDNA were classed as abnormal. There was a significant increase in the incidence of high levels (i.e., >1%) of the 4977 bp deleted mtDNA in sun-exposed sites (27%, 27 of 100) compared with sun-protected sites (1.1%, one of 90) (Fisher's exact test, p < 0.0001). There appeared to be no relation between the frequency of the mtDNA deletion and age. Analysis of split skin samples showed that most deletions (93%, n = 27) were confined to the dermal rather than the epidermal component, and in keeping with this deletions were found in three of six primary cultures of fibroblasts from sun-exposed sites. Deletions were not seen in the epidermal component of several epidermal tumors nor were deletions seen in fibroblasts cultured from an individual with Werner's syndrome. We propose that deletions or mutations of mitochondrial DNA may be useful as a marker of cumulative ultraviolet radiation exposure.
Collapse
Affiliation(s)
- M A Birch-Machin
- Department of Dermatology, Medical School, University of Newcastle upon Tyne, UK
| | | | | | | | | |
Collapse
|
26
|
Abstract
Rapid progress has been made in the identification of mitochondrial DNA mutations which are typically associated with diseases of the nervous system and muscle. The well established mitochondrial disorders are maternally inherited and males and females are equally affected. An exception is Leber's hereditary optic atrophy (LHON) which is observed much more frequently in males than in females. There are three common point mutations in LHON which can be homoplasmic or heteroplasmic. In mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) most mutations are single base changes and lie within the tRNA-Leu gene. Point mutations in myoclonic epilepsy with ragged red fibres (MERRF) usually occur within the tRNA-Lys gene but mutations of the tRNA-Leu gene are also observed. MELAS and MERRF mutations are heteroplasmic and there is considerable clinical overlap between these diseases. Point mutations within the ATPase6 gene result in either neuropathy, ataxia and retinitis pigmentosa (NARP) or in Leigh's syndrome. The latter occurs if the mutation is present in the majority of mitochondria (extreme heteroplasmy). Finally, mitochondrial DNA deletions are the cause underlying Kearns-Sayre syndrome (KSS). Apart from the well-established mitochondrial diseases, there is increasing evidence that mitochondrial mutations may also play a role in the neurodegenerative disorders Parkinson, Alzheimer and Huntington disease. The complex I defect found in Parkinson disease is especially interesting in this respect. However, no causative mitochondrial mutation has as yet been established in any of these three common disorders.
Collapse
Affiliation(s)
- M B Graeber
- Department of Neuromorphology, Max-Planck-Institute of Psychiatry, Martinsried, Germany.
| | | |
Collapse
|
27
|
Hirt L, Magistretti PJ, Hirt L, Bogousslavsky J, Boulat O, Borruat FX. Large deletion (7.2 kb) of mitochondrial DNA with novel boundaries in a case of progressive external ophthalmoplegia. J Neurol Neurosurg Psychiatry 1996; 61:422-3. [PMID: 8890791 PMCID: PMC486594 DOI: 10.1136/jnnp.61.4.422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|