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Orekhov AN, Nikiforov NN, Ivanova EA, Sobenin IA. Possible Role of Mitochondrial DNA Mutations in Chronification of Inflammation: Focus on Atherosclerosis. J Clin Med 2020; 9:jcm9040978. [PMID: 32244740 PMCID: PMC7230212 DOI: 10.3390/jcm9040978] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
Chronification of inflammation is the process that lies at the basis of several human diseases that make up to 80% of morbidity and mortality worldwide. It can also explain a great deal of processes related to aging. Atherosclerosis is an example of the most important chronic inflammatory pathology in terms of public health impact. Atherogenesis is based on the inflammatory response of the innate immunity arising locally or focally. The main trigger for this response appears to be modified low-density lipoprotein (LDL), although other factors may also play a role. With the quick resolution of inflammation, atherosclerotic changes in the arterial wall do not occur. However, a violation of the innate immunity response can lead to chronification of local inflammation and, as a result, to atherosclerotic lesion formation. In this review, we discuss possible mechanisms of the impaired immune response with a special focus on mitochondrial dysfunction. Some mitochondrial dysfunctions may be due to mutations in mitochondrial DNA. Several mitochondrial DNA mutations leading to defective mitophagy have been identified. The regulatory role of mitophagy in the immune response has been shown in recent studies. We suggest that defective mitophagy promoted by mutations in mitochondrial DNA can cause innate immunity disorders leading to chronification of inflammation.
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Affiliation(s)
- Alexander N. Orekhov
- Laboratory for Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Laboratory of Infection Pathology and Molecular Microecology, Institute of Human Morphology, 117418 Moscow, Russia
- Correspondence: (A.N.O.); (E.A.I.); Tel.: +7-903-169-08-66 (A.N.O.)
| | - Nikita N. Nikiforov
- Centre of Collective Usage, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, 119334 Moscow, Russia;
- Institute of Experimental Cardiology, National Medical Research Center of Cardiology, 121552 Moscow, Russia
| | - Ekaterina A. Ivanova
- Department of Basic Research, Institute for Atherosclerosis Research, 121609 Moscow, Russia
- Correspondence: (A.N.O.); (E.A.I.); Tel.: +7-903-169-08-66 (A.N.O.)
| | - Igor A. Sobenin
- Laboratory of Medical Genetics, Institute of Experimental Cardiology, National Medical Research Center of Cardiology, 121552 Moscow, Russia;
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102
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Wen JJ, Cummins CB, Radhakrishnan RS. Burn-Induced Cardiac Mitochondrial Dysfunction via Interruption of the PDE5A-cGMP-PKG Pathway. Int J Mol Sci 2020; 21:ijms21072350. [PMID: 32231130 PMCID: PMC7177322 DOI: 10.3390/ijms21072350] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022] Open
Abstract
Burn-induced heart dysfunction is a key factor for patient mortality. However, the molecular mechanisms are not yet fully elucidated. This study sought to understand whether burn-induced heart dysfunction is associated with cardiac mitochondrial dysfunction and interruption of the PDE5A-cGMP-PKG pathway. Sixty percent total body surface area (TBSA) scald burned rats (±sildenafil) were used in this study. A transmission electron microscope (TEM), real-time qPCR, O2K-respirometer, and electron transport chain assays were used to characterized molecular function. Cardiac mitochondrial morphological shapes were disfigured with a decline in mitochondrial number, area, and size, resulting in deficiency of cardiac mitochondrial replication. Burn induced a decrease in all mitDNA encoded genes. State 3 oxygen consumption was significantly decreased. Mitochondrial complex I substrate-energized or complex II substrate-energized and both of respiratory control ratio (RCRs) were decreased after burn. All mitochondrial complex activity except complex II were decreased in the burn group, correlating with decreases in mitochondrial ATP and MnSOD activity. Sildenafil, a inhibitor of the PDE5A-cGMP-PKG pathway, preserved the mitochondrial structure, respiratory chain efficiency and energy status in cardiac tissue. Furthermore, sildenafil treatment significantly restored ADP-conjugated respiration in burned groups. In conclusion, cardiac mitochondrial damage contributes to burn-induced heart dysfunction via the PDE5A-cGMP-PKG pathway.
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Affiliation(s)
- Jake J. Wen
- Correspondence: (J.J.W.); (R.S.R.); Tel.: +1-409-256-5878 (J.J.W.); +1-409-772-5666 (R.S.R.); Fax: +1-409-772-4253 (J.J.W. & R.S.R.)
| | | | - Ravi S. Radhakrishnan
- Correspondence: (J.J.W.); (R.S.R.); Tel.: +1-409-256-5878 (J.J.W.); +1-409-772-5666 (R.S.R.); Fax: +1-409-772-4253 (J.J.W. & R.S.R.)
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103
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The role of control region mitochondrial DNA mutations in cardiovascular disease: stroke and myocardial infarction. Sci Rep 2020; 10:2766. [PMID: 32066781 PMCID: PMC7026394 DOI: 10.1038/s41598-020-59631-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
Recent studies associated certain type of cardiovascular disease (CVD) with specific mitochondrial DNA (mtDNA) defects, mainly driven by the central role of mitochondria in cellular metabolism. Considering the importance of the control region (CR) on the regulation of the mtDNA gene expression, the aim of the present study was to investigate the role of mtDNA CR mutations in two CVDs: stroke and myocardial infarction (MI). MtDNA CR mutations (both fixed and in heteroplasmy) were analysed in two demographically-matched case-control samples, using 154 stroke cases, 211 MI cases and their corresponding control individuals. Significant differences were found, reporting mutations m.16145 G > A and m.16311 T > C as potential genetic risk factors for stroke (conditional logistic regression: p = 0.038 and p = 0.018, respectively), whereas the m.72 T > C, m.73 A > G and m.16356 T > C mutations could act as possible beneficial genetic factors for MI (conditional logistic regression: p = 0.001, p = 0.009 and p = 0.016, respectively). Furthermore, our findings also showed a high percentage of point heteroplasmy in MI controls (logistic regression: p = 0.046; OR = 0.209, 95% CI [0.045-0.972]). These results demonstrate the possible role of mtDNA mutations in the CR on the pathogenesis of stroke and MI, and show the importance of including this regulatory region in genetic association studies.
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104
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Mitochondrial DNA: A Key Regulator of Anti-Microbial Innate Immunity. Genes (Basel) 2020; 11:genes11010086. [PMID: 31940818 PMCID: PMC7017290 DOI: 10.3390/genes11010086] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/25/2022] Open
Abstract
During the last few years, mitochondrial DNA has attained much attention as a modulator of immune responses. Due to common evolutionary origin, mitochondrial DNA shares various characteristic features with DNA of bacteria, as it consists of a remarkable number of unmethylated DNA as 2′-deoxyribose cytidine-phosphate-guanosine (CpG) islands. Due to this particular feature, mitochondrial DNA seems to be recognized as a pathogen-associated molecular pattern by the innate immune system. Under the normal physiological situation, mitochondrial DNA is enclosed in the double membrane structure of mitochondria. However, upon pathological conditions, it is usually released into the cytoplasm. Growing evidence suggests that this cytosolic mitochondrial DNA induces various innate immune signaling pathways involving NLRP3, toll-like receptor 9, and stimulator of interferon genes (STING) signaling, which participate in triggering downstream cascade and stimulating to produce effector molecules. Mitochondrial DNA is responsible for inflammatory diseases after stress and cellular damage. In addition, it is also involved in the anti-viral and anti-bacterial innate immunity. Thus, instead of entire mitochondrial importance in cellular metabolism and energy production, mitochondrial DNA seems to be essential in triggering innate anti-microbial immunity. Here, we describe existing knowledge on the involvement of mitochondrial DNA in the anti-microbial immunity by modulating the various immune signaling pathways.
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105
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Jin X, Cheng Z, Wang B, Yau TO, Chen Z, Barker SC, Chen D, Bu W, Sun D, Gao S. Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals. RNA Biol 2020; 17:395-402. [PMID: 31905034 DOI: 10.1080/15476286.2019.1709746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
In the present study, we applied our 'precise annotation' to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5' and 3' end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.
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Affiliation(s)
- Xiufeng Jin
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Zhi Cheng
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Bo Wang
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, P.R.China
| | - Tung On Yau
- John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, P.R. China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Defu Chen
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Daqing Sun
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, P.R.China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, P.R.China
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106
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Matkarimov BT, Saparbaev MK. DNA Repair and Mutagenesis in Vertebrate Mitochondria: Evidence for Asymmetric DNA Strand Inheritance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:77-100. [DOI: 10.1007/978-3-030-41283-8_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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107
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Cao H, Salazar-García L, Gao F, Wahlestedt T, Wu CL, Han X, Cai Y, Xu D, Wang F, Tang L, Ricciardi N, Cai D, Wang H, Chin MPS, Timmons JA, Wahlestedt C, Kapranov P. Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells. Nat Commun 2019; 10:5799. [PMID: 31862872 PMCID: PMC6925131 DOI: 10.1038/s41467-019-13602-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
Single-strand breaks (SSBs) represent the major form of DNA damage, yet techniques to map these lesions genome-wide with nucleotide-level precision are limited. Here, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realms of cellular biology, not obtainable with current approaches.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lorena Salazar-García
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Thor Wahlestedt
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Chun-Lin Wu
- Department of Pathology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, China
| | - Xueer Han
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ye Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fang Wang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lu Tang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Natalie Ricciardi
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - DingDing Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifang Wang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Mario P S Chin
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - James A Timmons
- Augur Precision Medicine LTD, Scion House, Stirling University Innovation Park, Stirling, FK9 4NF, UK
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, 33136, USA.
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
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108
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Abstract
DNA replication in human mitochondria has been studied for several decades; however, its mechanism still remains unclear. During the last 15 years, many new experimental data on the mitochondrial replication have appeared, although extremely contradictory. Two asynchronous (strand displacement and RITOLS) and one synchronous (strand-coupled) replication models have been proposed. In the asynchronous models, replication from the origin in the H-chain starts earlier, so that the replication of the two chains ends at different times. The synchronous model is more traditional and implies two replication forks with leading and lagging strands initiated at the same origin. For each of the three models, both confirming and contradicting experimental data exist. Most likely, there is no single model of mitochondrial replication. It is possible that the unique mitochondrial replication machinery that has originated as a results of endosymbiosis has an unexpected variety of replication strategies to maintain the mitochondrial genome. An unusual combination of enzymes of different origin (phage, bacterial, eukaryotic) and unique features of the mitochondrial genome (existance of heavy and light chains, insertions of ribonucleotides, a variety of origins) can allow replication through different mechanisms. In human mitochondria, asynchronous replication seems to dominate; however, synchronous replication is also possible under certain conditions. In the human heart mitochondria, circular mitochondrial DNA (mtDNA) molecules can rearrange in a network of rapidly replicating linear genomes, thereby suggesting possible existence of a wide range of replication mechanisms in the mitochondria. The review describes the main stages of mtDNA replication and enzymes involved in this process, as well as discusses the prospects of mitochondrial replication studies.
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Affiliation(s)
- L A Zinovkina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.
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109
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Yoshitake K, Yoshinaga T, Tanaka C, Mizusawa N, Reza MS, Tsujimoto A, Kobayashi T, Watabe S. HaCeD-Seq: a Novel Method for Reliable and Easy Estimation About the Fish Population Using Haplotype Count from eDNA. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:813-820. [PMID: 31758428 DOI: 10.1007/s10126-019-09926-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
It is common to count the numbers of specified fish in the field after speciation of captured fish according to their morphology and to subject these counts to appropriate statistical analyses. In recent years, a non-invasive method to estimate the abundance of a particular fish species using environmental DNA (eDNA) has been developed. However, it is still difficult to determine accurate numbers of fish species using such method. We predict that the estimation of individuals of certain fish species in the field is more accurate and easier by using haplotypes of DNA in the fast evolutionary region. Therefore, we focused on the regulatory region (D-loop) in mitochondrial DNA, which is known to have a high genetic variation at the intraspecific level of the targeting eel. We investigated haplotype diversity in eel at first and then determined the number of D-loop haplotypes contained in their exfoliated cells in breeding water. Finally, we developed a novel analytical method, HaCeD-Seq, to estimate the number of individuals based on the abovementioned data.
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Affiliation(s)
- Kazutoshi Yoshitake
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
- Japan Software Management Co., Ltd., Kinko-cho, Yokohama, Kanagawa, Japan
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, Japan
| | - Tatsuki Yoshinaga
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Chikaya Tanaka
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Nanami Mizusawa
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Md Shaheed Reza
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Atsumi Tsujimoto
- Japan Software Management Co., Ltd., Kinko-cho, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
- Japan Fisheries Research and Education Agency, Minato Mirai, Nishi-ku, Yokohama, Kanagawa, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan.
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110
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Holt IJ. The mitochondrial R-loop. Nucleic Acids Res 2019; 47:5480-5489. [PMID: 31045202 PMCID: PMC6582354 DOI: 10.1093/nar/gkz277] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/11/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022] Open
Abstract
The DNA in mitochondria contributes essential components of the organelle’s energy producing machinery that is essential for life. In 1971, many mitochondrial DNA molecules were found to have a third strand of DNA that maps to a region containing critical regulatory elements for transcription and replication. Forty-five years later, a third strand of RNA in the same region has been reported. This mitochondrial R-loop is present on thousands of copies of mitochondrial DNA per cell making it potentially the most abundant R-loop in nature. Here, I assess the discovery of the mitochondrial R-loop, discuss why it remained unrecognized for almost half a century and propose for it central roles in the replication, organization and expression of mitochondrial DNA, which if compromised can lead to disease states.
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Affiliation(s)
- Ian J Holt
- Biodonostia Health Research Institute, 20014 San Sebastián, Spain & IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK.,CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), Madrid, Spain
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111
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Bailey LJ, Bianchi J, Doherty AJ. PrimPol is required for the maintenance of efficient nuclear and mitochondrial DNA replication in human cells. Nucleic Acids Res 2019; 47:4026-4038. [PMID: 30715459 PMCID: PMC6486543 DOI: 10.1093/nar/gkz056] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/14/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic Primase-Polymerase (PrimPol) is an enzyme that maintains efficient DNA duplication by repriming replication restart downstream of replicase stalling lesions and structures. To elucidate the cellular requirements for PrimPol in human cells, we generated PrimPol-deleted cell lines and show that it plays key roles in maintaining active replication in both the nucleus and mitochondrion, even in the absence of exogenous damage. Human cells lacking PrimPol exhibit delayed recovery after UV-C damage and increased mutation frequency, micronuclei and sister chromatin exchanges but are not sensitive to genotoxins. PrimPol is also required during mitochondrial replication, with PrimPol-deficient cells having increased mtDNA copy number but displaying a significant decrease in replication. Deletion of PrimPol in XPV cells, lacking functional polymerase Eta, causes an increase in DNA damage sensitivity and pronounced fork stalling after UV-C treatment. We show that, unlike canonical TLS polymerases, PrimPol is important for allowing active replication to proceed, even in the absence of exogenous damage, thus preventing the accumulation of excessive fork stalling and genetic mutations. Together, these findings highlight the importance of PrimPol for maintaining efficient DNA replication in unperturbed cells and its complementary roles, with Pol Eta, in damage tolerance in human cells.
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Affiliation(s)
- Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Julie Bianchi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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112
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Russlies J, Fähnrich A, Witte M, Yin J, Benoit S, Gläser R, Günter C, Eming R, Erdmann J, Gola D, Gupta Y, Holtsche MM, Kern JS, König IR, Kiritsi D, Lieb W, Sadik CD, Sárdy M, Schauer F, van Beek N, Weidinger A, Worm M, Zillikens D, Schmidt E, Busch H, Ibrahim SM, Hirose M. Polymorphisms in the Mitochondrial Genome Are Associated With Bullous Pemphigoid in Germans. Front Immunol 2019; 10:2200. [PMID: 31824475 PMCID: PMC6883920 DOI: 10.3389/fimmu.2019.02200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/30/2019] [Indexed: 01/06/2023] Open
Abstract
Bullous pemphigoid (BP) is the most prevalent autoimmune skin blistering disease and is characterized by the generation of autoantibodies against the hemidesmosomal proteins BP180 (type XVII collagen) and BP230. Most intriguingly, BP is distinct from other autoimmune diseases because it predominantly affects elderly individuals above the age of 75 years, raising the question why autoantibodies and the clinical lesions of BP emerges mostly in this later stage of life, even in individuals harboring known putative BP-associated germline gene variants. The mitochondrial genome (mtDNA) is a potential candidate to provide additional insights into the BP etiology; however, the mtDNA has not been extensively explored to date. Therefore, we sequenced the whole mtDNA of German BP patients (n = 180) and age- and sex-matched healthy controls (n = 188) using next generation sequencing (NGS) technology, followed by the replication study using Sanger sequencing of an additional independent BP (n = 89) and control cohort (n = 104). While the BP and control groups showed comparable mitochondrial haplogroup distributions, the haplogroup T exhibited a tendency of higher frequency in BP patients suffering from neurodegenerative diseases (ND) compared to BP patients without ND (50%; 3 in 6 BP with haplogroup T). A total of four single nucleotide polymorphisms (SNPs) in the mtDNA, namely, m.16263T>C, m.16051A>G, and m.16162A>G in the D-loop region of the mtDNA, and m.11914G>A in the mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 gene (MT-ND4), were found to be significantly associated with BP based on the meta-analysis of our NGS data and the Sanger sequencing data (p = 0.0017, p = 0.0129, p = 0.0076, and p = 0.0132, respectively, Peto's test). More specifically, the three SNPs in the D-loop region were negatively, and the SNP in the MT-ND4 gene was positively associated with BP. Our study is the first to interrogate the whole mtDNA in BP patients and controls and to implicate multiple novel mtDNA variants in disease susceptibility. Studies using larger cohorts and more diverse populations are warranted to explore the functional consequences of the mtDNA variants identified in this study on immune and skin cells to understand their contributions to BP pathology.
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Affiliation(s)
- Juliane Russlies
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
| | - Anke Fähnrich
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Mareike Witte
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Department of Dermatology, University of Luebeck, Luebeck, Germany
| | - Junping Yin
- Research Center Borstel, Leibniz-Center for Medicine and Bioscience, Borstel, Germany
| | - Sandrine Benoit
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Regine Gläser
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Claudia Günter
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, University Hospital of Dresden, Dresden, Germany
| | - Rüdiger Eming
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology and Allergology, Phillips-Universität Marburg, Marburg, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Damian Gola
- Institute of Medical Biometry and Statistics, University of Luebeck, Luebeck, Germany
| | - Yask Gupta
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
| | | | - Johannes S. Kern
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
- Dermatology Department, Faculty of Medicine, Dentistry and Health Sciences, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Inke R. König
- Institute of Medical Biometry and Statistics, University of Luebeck, Luebeck, Germany
| | - Dimitra Kiritsi
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrecht University of Kiel, Kiel, Germany
- Popgen Biobank, Christian-Albrecht University of Kiel, Kiel, Germany
| | | | - Miklós Sárdy
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany
| | - Franziska Schauer
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Nina van Beek
- Department of Dermatology, University of Luebeck, Luebeck, Germany
| | - Anke Weidinger
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Margitta Worm
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Allergology, Allergy Center Charité, Charité Medical University Berlin, Berlin, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Luebeck, Luebeck, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Enno Schmidt
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Department of Dermatology, University of Luebeck, Luebeck, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Hauke Busch
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Saleh M. Ibrahim
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Misa Hirose
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
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Mitochondrial Dysfunction in Aging and Cancer. J Clin Med 2019; 8:jcm8111983. [PMID: 31731601 PMCID: PMC6912717 DOI: 10.3390/jcm8111983] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/01/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022] Open
Abstract
Aging is a major risk factor for developing cancer, suggesting that these two events may represent two sides of the same coin. It is becoming clear that some mechanisms involved in the aging process are shared with tumorigenesis, through convergent or divergent pathways. Increasing evidence supports a role for mitochondrial dysfunction in promoting aging and in supporting tumorigenesis and cancer progression to a metastatic phenotype. Here, a summary of the current knowledge of three aspects of mitochondrial biology that link mitochondria to aging and cancer is presented. In particular, the focus is on mutations and changes in content of the mitochondrial genome, activation of mitochondria-to-nucleus signaling and the newly discovered mitochondria-telomere communication.
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114
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Duraisamy AJ, Radhakrishnan R, Seyoum B, Abrams GW, Kowluru RA. Epigenetic Modifications in Peripheral Blood as Potential Noninvasive Biomarker of Diabetic Retinopathy. Transl Vis Sci Technol 2019; 8:43. [PMID: 31871829 PMCID: PMC6924565 DOI: 10.1167/tvst.8.6.43] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Progression of diabetic retinopathy is related to the duration and severity of hyperglycemia, and after 25 years of diabetes, 90% of patients show some signs of retinopathy. Despite initiation of many retinal molecular/biochemical abnormalities, including mitochondrial damage and epigenetic modifications, the disease remains asympotomatic in the initial stages. Our goal is to examine the utility of DNA methylation as a possible biomarker of diabetic retinopathy. METHODS Genomic DNA (gDNA) was isolated from the buffy coat, isolated from blood of diabetic patients with proliferative (PDR) or no retinopathy (No-DR), and nondiabetic subjects (CONT). Methylation of mitochondrial DNA (mtDNA), especially its D-Loop (the site of mtDNA transcription/replication), was quantified by methylated DNA immunoprecipitation and methyl-specific PCR techniques. Results were confirmed in purified mtDNA. The specific D-Loop region with the highest DNA methylation was identified using five overlapping primers, and DNMT1 binding was quantified by chromatin immunoprecipitation. Promoter DNA methylation of DNA mismatch repair (MLH1) and superoxide scavenging (SOD2) enzymes were also quantified. RESULTS Compared to CONT, D-Loop methylation was higher in PDR and No-DR groups, and the D-Loop region responsible for encoding the majority of the mtDNA-encoded genes had significantly higher methylation in the PDR group versus No-DR. Similarly, compared to No-DR, the PDR group also had hypermethylated MHL1 and SOD2 promoters. CONCLUSIONS Blood from PDR patients have higher DNA methylation, than seen in diabetic patients without retinopathy. Thus, DNA methylation can be used as a possible biomarker of diabetic retinopathy. TRANSLATIONAL RELEVANCE DNA methylation status in the blood of diabetic patients could serve as a potential noninvasive biomarker of retinopathy, and also an important readout parameter for testing longitudinal outcome of novel therapeutics for this blinding disease.
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Affiliation(s)
- Arul J. Duraisamy
- Wayne State University, Department of Ophthalmology, Visual and Anatomical Sciences, Detroit, MI, USA
- PerkinElmer Health Sciences Pvt Ltd., Tharamani, India
| | - Rakesh Radhakrishnan
- Wayne State University, Department of Ophthalmology, Visual and Anatomical Sciences, Detroit, MI, USA
| | | | - Gary W. Abrams
- Wayne State University, Department of Ophthalmology, Visual and Anatomical Sciences, Detroit, MI, USA
| | - Renu A. Kowluru
- Wayne State University, Department of Ophthalmology, Visual and Anatomical Sciences, Detroit, MI, USA
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115
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Podlesniy P, Puigròs M, Serra N, Fernández-Santiago R, Ezquerra M, Tolosa E, Trullas R. Accumulation of mitochondrial 7S DNA in idiopathic and LRRK2 associated Parkinson's disease. EBioMedicine 2019; 48:554-567. [PMID: 31631040 PMCID: PMC6838390 DOI: 10.1016/j.ebiom.2019.09.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Both idiopathic and familial Parkinson's disease are associated with mitochondrial dysfunction. Mitochondria have their own mitochondrial DNA (mtDNA) and previous studies have reported that the release of mtDNA is a biomarker of Parkinson's disease. METHODS We have now investigated the relationship between mtDNA replication, transcription and release in fibroblasts from patients with idiopathic (iPD) and Leucine-rich repeat kinase 2G2019S -associated Parkinson's disease (LRRK2-PD), using Selfie-digital PCR, a method that allows absolute quantification of mtDNA genomes and transcripts. FINDINGS In comparison with healthy controls, we found that fibroblasts from patients with iPD or LRRK2-PD had a high amount of mitochondrial 7S DNA along with a low mtDNA replication rate that was associated with a reduction of cf-mtDNA release. Accumulation of 7S DNA in iPD and LRRK2-PD fibroblasts was related with an increase in H-strand mtDNA transcription. INTERPRETATION These results show that 7S DNA accumulation, low mtDNA replication, high H-strand transcription, and low mtDNA release compose a pattern of mtDNA dysfunction shared by both iPD and LRRK2-PD fibroblasts. Moreover, these results suggest that the deregulation of the genetic switch formed by 7SDNA that alternates between mtDNA replication and transcription is a fundamental pathophysiological mechanism in both idiopathic and monogenic Parkinson's disease.
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Affiliation(s)
- Petar Podlesniy
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain.
| | - Margalida Puigròs
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Núria Serra
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Rubén Fernández-Santiago
- Neurology Service, Parkinson's Disease and Movement Disorders Unit, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, University of Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Mario Ezquerra
- Neurology Service, Parkinson's Disease and Movement Disorders Unit, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, University of Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Eduardo Tolosa
- Neurology Service, Parkinson's Disease and Movement Disorders Unit, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, University of Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Ramon Trullas
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain.
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116
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Billard P, Poncet DA. Replication Stress at Telomeric and Mitochondrial DNA: Common Origins and Consequences on Ageing. Int J Mol Sci 2019; 20:ijms20194959. [PMID: 31597307 PMCID: PMC6801922 DOI: 10.3390/ijms20194959] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/12/2022] Open
Abstract
Senescence is defined as a stress-induced durable cell cycle arrest. We herein revisit the origin of two of these stresses, namely mitochondrial metabolic compromise, associated with reactive oxygen species (ROS) production, and replicative senescence, activated by extreme telomere shortening. We discuss how replication stress-induced DNA damage of telomeric DNA (telDNA) and mitochondrial DNA (mtDNA) can be considered a common origin of senescence in vitro, with consequences on ageing in vivo. Unexpectedly, mtDNA and telDNA share common features indicative of a high degree of replicative stress, such as G-quadruplexes, D-loops, RNA:DNA heteroduplexes, epigenetic marks, or supercoiling. To avoid these stresses, both compartments use similar enzymatic strategies involving, for instance, endonucleases, topoisomerases, helicases, or primases. Surprisingly, many of these replication helpers are active at both telDNA and mtDNA (e.g., RNAse H1, FEN1, DNA2, RecQ helicases, Top2α, Top2β, TOP3A, DNMT1/3a/3b, SIRT1). In addition, specialized telomeric proteins, such as TERT (telomerase reverse transcriptase) and TERC (telomerase RNA component), or TIN2 (shelterin complex), shuttle from telomeres to mitochondria, and, by doing so, modulate mitochondrial metabolism and the production of ROS, in a feedback manner. Hence, mitochondria and telomeres use common weapons and cooperate to resist/prevent replication stresses, otherwise producing common consequences, namely senescence and ageing.
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Affiliation(s)
- Pauline Billard
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France.
- Institut de Biopathologie moléculaire, Centre de Bio-Pathologie Est, Groupement hospitalier Est, Hospices Civils de Lyon, 69500 Bron, France.
| | - Delphine A Poncet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France.
- Institut de Biopathologie moléculaire, Centre de Bio-Pathologie Est, Groupement hospitalier Est, Hospices Civils de Lyon, 69500 Bron, France.
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Al Khatib I, Shutt TE. Advances Towards Therapeutic Approaches for mtDNA Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:217-246. [PMID: 31452143 DOI: 10.1007/978-981-13-8367-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondria maintain and express their own genome, referred to as mtDNA, which is required for proper mitochondrial function. While mutations in mtDNA can cause a heterogeneous array of disease phenotypes, there is currently no cure for this collection of diseases. Here, we will cover characteristics of the mitochondrial genome important for understanding the pathology associated with mtDNA mutations, and review recent approaches that are being developed to treat and prevent mtDNA disease. First, we will discuss mitochondrial replacement therapy (MRT), where mitochondria from a healthy donor replace maternal mitochondria harbouring mutant mtDNA. In addition to ethical concerns surrounding this procedure, MRT is only applicable in cases where the mother is known or suspected to carry mtDNA mutations. Thus, there remains a need for other strategies to treat patients with mtDNA disease. To this end, we will also discuss several alternative means to reduce the amount of mutant mtDNA present in cells. Such methods, referred to as heteroplasmy shifting, have proven successful in animal models. In particular, we will focus on the approach of targeting engineered endonucleases to specifically cleave mutant mtDNA. Together, these approaches offer hope to prevent the transmission of mtDNA disease and potentially reduce the impact of mtDNA mutations.
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Affiliation(s)
- Iman Al Khatib
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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118
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Hübner A, Wachsmuth M, Schröder R, Li M, Eis-Hübinger AM, Madea B, Stoneking M. Sharing of heteroplasmies between human liver lobes varies across the mtDNA genome. Sci Rep 2019; 9:11219. [PMID: 31375696 PMCID: PMC6677727 DOI: 10.1038/s41598-019-47570-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy (intra-individual variation) varies among different human tissues and increases with age, suggesting that the majority of mtDNA heteroplasmies are acquired, rather than inherited. However, the extent to which heteroplasmic sites are shared across a tissue remains an open question. We therefore investigated heteroplasmy in two liver samples (one from each primary lobe) from 83 Europeans, sampled at autopsy. Minor allele frequencies (MAF) at heteroplasmic sites were significantly correlated between the two liver samples from an individual, with significantly more sharing of heteroplasmic sites in the control region than in the non-control region. We show that this increased sharing for the control region cannot be explained by recent mutations at just a few specific heteroplasmic sites or by the possible presence of 7S DNA. Moreover, we carried out simulations to show that there is significantly more sharing than would be predicted from random genetic drift from a common progenitor cell. We also observe a significant excess of non-synonymous vs. synonymous heteroplasmies in the protein-coding region, but significantly more sharing of synonymous heteroplasmies. These contrasting patterns for the control vs. the non-control region, and for non-synonymous vs. synonymous heteroplasmies, suggest that selection plays a role in heteroplasmy sharing.
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Affiliation(s)
- Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
| | - Manja Wachsmuth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Anna Maria Eis-Hübinger
- Institut für Virologie, Universitätsklinikum Bonn, Sigmund-Freud-Str. 25, D-53105, Bonn, Germany
| | - Burkhard Madea
- Institut für Rechtsmedizin, Universitätsklinikum Bonn, Stiftsplatz 12, D-53111, Bonn, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
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119
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Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma J, Li J, Gan J. Structural insights into DNA degradation by human mitochondrial nuclease MGME1. Nucleic Acids Res 2019; 46:11075-11088. [PMID: 30247721 PMCID: PMC6237815 DOI: 10.1093/nar/gky855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/11/2018] [Indexed: 01/16/2023] Open
Abstract
Mitochondrial nucleases play important roles in accurate maintenance and correct metabolism of mtDNA, the own genetic materials of mitochondria that are passed exclusively from mother to child. MGME1 is a highly conserved DNase that was discovered recently. Mutations in MGME1-coding gene lead to severe mitochondrial syndromes characterized by external ophthalmoplegia, emaciation, and respiratory failure in humans. Unlike many other nucleases that are distributed in multiple cellular organelles, human MGME1 is a mitochondria-specific nuclease; therefore, it can serve as an ideal target for treating related syndromes. Here, we report one HsMGME1-Mn2+ complex and three different HsMGME1-DNA complex structures. In combination with in vitro cleavage assays, our structures reveal the detailed molecular basis for substrate DNA binding and/or unwinding by HsMGME1. Besides the conserved two-cation-assisted catalytic mechanism, structural analysis of HsMGME1 and comparison with homologous proteins also clarified substrate binding and cleavage directionalities of the DNA double-strand break repair complexes RecBCD and AddAB.
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Affiliation(s)
- Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ruiqi Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yanqing Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yangyang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
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Abstract
Perturbed mitochondrial bioenergetics constitute a core pillar of cancer-associated metabolic dysfunction. While mitochondrial dysfunction in cancer may result from myriad biochemical causes, a historically neglected source is that of the mitochondrial genome. Recent large-scale sequencing efforts and clinical studies have highlighted the prevalence of mutations in mitochondrial DNA (mtDNA) in human tumours and their potential roles in cancer progression. In this review we discuss the biology of the mitochondrial genome, sources of mtDNA mutations, and experimental evidence of a role for mtDNA mutations in cancer. We also propose a ‘metabolic licensing’ model for mtDNA mutation-derived dysfunction in cancer initiation and progression.
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Affiliation(s)
- Payam A Gammage
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK. .,CRUK Beatson Institute for Cancer Research, Glasgow, UK.
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121
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Identifying Pig Mitochondrial TSS: Structure and Functional Features. Mitochondrion 2019; 49:19-24. [PMID: 31279875 DOI: 10.1016/j.mito.2019.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/12/2019] [Accepted: 07/03/2019] [Indexed: 11/23/2022]
Abstract
The transcription start sites (TSSs) of porcine mitochondrial genome were firstly identified in this study, including heavy-strand promoter 1 and 2 (HSP1 and HSP2) harbored at nt 903 and nt 1369 in H strand, respectively, and light-strand promoter (LSP) located at nt 166 in L strand. HSP1 structure and expression features were investigated by analyzing mtDNA copy number, expression of 11 nucleoplasmic genes, mtDNA methylation levels, and gene expression levels of methyl-modifying enzymes, DNMT1 and TETs. The mtDNA copy number presented large differences among 15 organs/tissues, and the largest disparity, nearly 17 times, was found between pancreas (~1890 relative copy numbers) and spleen (~110 relative copy numbers, P < .01). The expression levels of HSP1 strand in these organs/tissues presented similar trends with mtDNA copy number (P < .05), and all of 11 nucleoplasmic genes (POLG, POLRMT, TERT, TFAM, TFB1M, TFB2M, NRF-1, PPARα, ESRRA, SP1 and TUFM) detected in this study displayed significantly higher expression values in pancreas than those in spleen (P < .05). Besides, bisulfite sequencing showed that all cytosine residues in the detected region (D-loop) existed methylation with different levels, and the methylation level in spleen was significantly higher than that in pancreas (P < .05). Unlike nuclear DNA, the tested region contained four types of methylation mode (CA, CC, CT, and CG). In addition, the expression of TET1 in pancreas was significantly higher than that in spleen (P < .05). Collectively, our findings indicated that mtDNA TSSs had correlation to mtDNA copy number, expression of nucleoplasmic gene, and mtDNA methylation level.
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122
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Young MJ, Jayaprakash AD, Young CKJ. Analysis of Mitochondrial DNA Polymorphisms in the Human Cell Lines HepaRG and SJCRH30. Int J Mol Sci 2019; 20:ijms20133245. [PMID: 31269646 PMCID: PMC6651321 DOI: 10.3390/ijms20133245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022] Open
Abstract
The mitochondrial DNA (mtDNA) sequences of two commonly used human cell lines, HepaRG and SJCRH30, were determined. HepaRG originates from a liver tumor obtained from a patient with hepatocarcinoma and hepatitis C while SJCRH30 originates from a rhabdomyosarcoma patient tumor. In comparison to the revised Cambridge Reference Sequence, HepaRG and SJCRH30 mtDNA each contain 14 nucleotide variations. In addition to an insertion of a cytosine at position 315 (315insC), the mtDNA sequences from both cell types share six common polymorphisms. Heteroplasmic variants were identified in both cell types and included the identification of the 315insC mtDNA variant at 42 and 75% heteroplasmy in HepaRG and SJCRH30, respectively. Additionally, a novel heteroplasmic G13633A substitution in the HepaRG ND5 gene was detected at 33%. Previously reported cancer-associated mtDNA variants T195C and T16519C were identified in SJCRH30, both at homoplasmy (100%), while HepaRG mtDNA harbors a known prostate cancer-associated T6253C substitution at near homoplasmy, 95%. Based on our sequencing analysis, HepaRG mtDNA is predicted to lie within haplogroup branch H15a1 while SJCRH30 mtDNA is predicted to localize to H27c. The catalog of polymorphisms and heteroplasmy reported here should prove useful for future investigations of mtDNA maintenance in HepaRG and SJCRH30 cell lines.
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Affiliation(s)
- Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, USA.
| | | | - Carolyn K J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, USA
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Grünewald A, Kumar KR, Sue CM. New insights into the complex role of mitochondria in Parkinson’s disease. Prog Neurobiol 2019; 177:73-93. [DOI: 10.1016/j.pneurobio.2018.09.003] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/09/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023]
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Wei W, Tuna S, Keogh MJ, Smith KR, Aitman TJ, Beales PL, Bennett DL, Gale DP, Bitner-Glindzicz MAK, Black GC, Brennan P, Elliott P, Flinter FA, Floto RA, Houlden H, Irving M, Koziell A, Maher ER, Markus HS, Morrell NW, Newman WG, Roberts I, Sayer JA, Smith KGC, Taylor JC, Watkins H, Webster AR, Wilkie AOM, Williamson C, Ashford S, Penkett CJ, Stirrups KE, Rendon A, Ouwehand WH, Bradley JR, Raymond FL, Caulfield M, Turro E, Chinnery PF. Germline selection shapes human mitochondrial DNA diversity. Science 2019; 364:eaau6520. [PMID: 31123110 DOI: 10.1126/science.aau6520] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/22/2019] [Accepted: 04/03/2019] [Indexed: 02/02/2023]
Abstract
Approximately 2.4% of the human mitochondrial DNA (mtDNA) genome exhibits common homoplasmic genetic variation. We analyzed 12,975 whole-genome sequences to show that 45.1% of individuals from 1526 mother-offspring pairs harbor a mixed population of mtDNA (heteroplasmy), but the propensity for maternal transmission differs across the mitochondrial genome. Over one generation, we observed selection both for and against variants in specific genomic regions; known variants were more likely to be transmitted than previously unknown variants. However, new heteroplasmies were more likely to match the nuclear genetic ancestry as opposed to the ancestry of the mitochondrial genome on which the mutations occurred, validating our findings in 40,325 individuals. Thus, human mtDNA at the population level is shaped by selective forces within the female germ line under nuclear genetic control, which ensures consistency between the two independent genetic lineages.
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125
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Transcription, Processing, and Decay of Mitochondrial RNA in Health and Disease. Int J Mol Sci 2019; 20:ijms20092221. [PMID: 31064115 PMCID: PMC6540609 DOI: 10.3390/ijms20092221] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Although the large majority of mitochondrial proteins are nuclear encoded, for their correct functioning mitochondria require the expression of 13 proteins, two rRNA, and 22 tRNA codified by mitochondrial DNA (mtDNA). Once transcribed, mitochondrial RNA (mtRNA) is processed, mito-ribosomes are assembled, and mtDNA-encoded proteins belonging to the respiratory chain are synthesized. These processes require the coordinated spatio-temporal action of several enzymes, and many different factors are involved in the regulation and control of protein synthesis and in the stability and turnover of mitochondrial RNA. In this review, we describe the essential steps of mitochondrial RNA synthesis, maturation, and degradation, the factors controlling these processes, and how the alteration of these processes is associated with human pathologies.
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126
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Kornienko IV, Chebotarev DA, Makhotkin MA, Grigoriev VA, Ponomareva EN, Matishov GG. Termination of Replication and Mechanisms of Heteroplasmy in Sturgeon Mitochondrial DNA. Mol Biol 2019. [DOI: 10.1134/s0026893319010060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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127
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Breton CV, Song AY, Xiao J, Kim SJ, Mehta HH, Wan J, Yen K, Sioutas C, Lurmann F, Xue S, Morgan TE, Zhang J, Cohen P. Effects of air pollution on mitochondrial function, mitochondrial DNA methylation, and mitochondrial peptide expression. Mitochondrion 2019; 46:22-29. [PMID: 30980914 DOI: 10.1016/j.mito.2019.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/25/2019] [Accepted: 04/01/2019] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA is sensitive to damage by exogenous reactive oxygen sources, including traffic-related air pollution (TRAP). Given the important role for mitochondria in human disease, we hypothesized that prenatal air pollution exposure may be associated with mitochondrial dysfunction and that mitochondrial-derived peptides (MDPs) might protect against these effects. In in vitro studies, 24-hour exposure to nanoparticulate matter (nPM) increased oxidation of mtDNA, decreased mitochondrial consumption rate (OCR), and decreased mtDNAcn in SH-SY5Y cells. Addition of MDPs rescued these effects to varying degrees. Liver tissue taken from C57Bl/6 males exposed for 10 weeks to nPM had lower OCR, lower mtDNAcn and higher MDP levels, similar to in vitro studies. In newborn cord blood, MDP levels were positively associated with prenatal TRAP exposures. Moreover, DNA methylation of two distinct regions of the D-Loop in the mitochondria genome was associated with levels of several MDPs. Our in vitro and in vivo data indicate that TRAP can directly affect mitochondrial respiratory function and mtDNAcn. Treatment of cells with MDPs can counteract TRAP induced-effects. Lastly, we present evidence that suggests MDPs may be regulated in part by mitochondrial DNA methylation in humans.
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Affiliation(s)
- Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine USC, 2001 N Soto St., Los Angeles, CA 90032, United States of America.
| | - Ashley Y Song
- Department of Preventive Medicine, Keck School of Medicine USC, 2001 N Soto St., Los Angeles, CA 90032, United States of America
| | - Jialin Xiao
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Su-Jeong Kim
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Hemal H Mehta
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Junxiang Wan
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Kelvin Yen
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Constantinos Sioutas
- USC Viterbi School of Engineering, 3620 South Vermont Ave, Los Angeles, CA 90089, United States of America
| | - Fred Lurmann
- Sonoma Technology, 1450 N. McDowell Blvd., Suite 200, Petaluma, CA 94954, United States of America
| | - Shanyan Xue
- Department of Preventive Medicine, Keck School of Medicine USC, 2001 N Soto St., Los Angeles, CA 90032, United States of America
| | - Todd E Morgan
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Junfeng Zhang
- Nicholas School of the Enviroment, Duke University, 308 Research Drive LSRC, Durham, NC 27708, United States of America
| | - Pinchas Cohen
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
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128
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Gu X, Kang X, Liu J. Mutation signatures in germline mitochondrial genome provide insights into human mitochondrial evolution and disease. Hum Genet 2019; 138:613-624. [PMID: 30968252 DOI: 10.1007/s00439-019-02009-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/02/2019] [Indexed: 01/06/2023]
Abstract
Variations in mitochondrial DNA (mtDNA) have been fundamental for understanding human evolution and are causative for a plethora of inherited mitochondrial diseases, but the mutation signatures of germline mtDNA and their value in understanding mitochondrial pathogenicity remain unknown. Here, we carried out a systematic analysis of mutation patterns in germline mtDNA based on 97,566 mtDNA variants from 45,494 full-length sequences and revealed a highly non-stochastic and replication-coupled mutation signature characterized by nucleotide-specific mutation pressure (G > T>A > C) and position-specific selection pressure, suggesting the existence of an intensive mutation-selection interplay in germline mtDNA. We provide evidence that this mutation-selection interplay has strongly shaped the mtDNA sequence during evolution, which not only manifests as an oriented alteration of amino acid compositions of mitochondrial encoded proteins, but also explains the long-lasting mystery of CpG depletion in mitochondrial genome. Finally, we demonstrated that these insights may be integrated to better understand the pathogenicity of disease-implicated mitochondrial variants.
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Affiliation(s)
- Xiwen Gu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.
| | - Xinyun Kang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
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129
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Bolognin S, Fossépré M, Qing X, Jarazo J, Ščančar J, Moreno EL, Nickels SL, Wasner K, Ouzren N, Walter J, Grünewald A, Glaab E, Salamanca L, Fleming RMT, Antony PMA, Schwamborn JC. 3D Cultures of Parkinson's Disease-Specific Dopaminergic Neurons for High Content Phenotyping and Drug Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1800927. [PMID: 30643711 PMCID: PMC6325628 DOI: 10.1002/advs.201800927] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/31/2018] [Indexed: 05/16/2023]
Abstract
Parkinson's disease (PD)-specific neurons, grown in standard 2D cultures, typically only display weak endophenotypes. The cultivation of PD patient-specific neurons, derived from induced pluripotent stem cells carrying the LRRK2-G2019S mutation, is optimized in 3D microfluidics. The automated image analysis algorithms are implemented to enable pharmacophenomics in disease-relevant conditions. In contrast to 2D cultures, this 3D approach reveals robust endophenotypes. High-content imaging data show decreased dopaminergic differentiation and branching complexity, altered mitochondrial morphology, and increased cell death in LRRK2-G2019S neurons compared to isogenic lines without using stressor agents. Treatment with the LRRK2 inhibitor 2 (Inh2) rescues LRRK2-G2019S-dependent dopaminergic phenotypes. Strikingly, a holistic analysis of all studied features shows that the genetic background of the PD patients, and not the LRRK2-G2019S mutation, constitutes the strongest contribution to the phenotypes. These data support the use of advanced in vitro models for future patient stratification and personalized drug development.
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Affiliation(s)
- Silvia Bolognin
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Braingineering Technologies SARL9 avenue des Hauts‐ForneauxEsch‐sur‐AlzetteL‐4362Luxembourg
| | - Marie Fossépré
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Braingineering Technologies SARL9 avenue des Hauts‐ForneauxEsch‐sur‐AlzetteL‐4362Luxembourg
| | - Xiaobing Qing
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Javier Jarazo
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Janez Ščančar
- Department of Environmental SciencesJožef Stefan InstituteJamova 391000LjubljanaSlovenia
| | - Edinson Lucumi Moreno
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Sarah L. Nickels
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Kobi Wasner
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Nassima Ouzren
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Jonas Walter
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Braingineering Technologies SARL9 avenue des Hauts‐ForneauxEsch‐sur‐AlzetteL‐4362Luxembourg
| | - Anne Grünewald
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Institute of NeurogeneticsUniversity of Lübeck23562LübeckGermany
| | - Enrico Glaab
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Luis Salamanca
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Ronan M. T. Fleming
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Paul M. A. Antony
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Jens C. Schwamborn
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
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130
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Posse V, Al-Behadili A, Uhler JP, Clausen AR, Reyes A, Zeviani M, Falkenberg M, Gustafsson CM. RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. PLoS Genet 2019; 15:e1007781. [PMID: 30605451 PMCID: PMC6317783 DOI: 10.1371/journal.pgen.1007781] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/23/2018] [Indexed: 11/21/2022] Open
Abstract
Human mitochondrial DNA (mtDNA) replication is first initiated at the origin of H-strand replication. The initiation depends on RNA primers generated by transcription from an upstream promoter (LSP). Here we reconstitute this process in vitro using purified transcription and replication factors. The majority of all transcription events from LSP are prematurely terminated after ~120 nucleotides, forming stable R-loops. These nascent R-loops cannot directly prime mtDNA synthesis, but must first be processed by RNase H1 to generate 3′-ends that can be used by DNA polymerase γ to initiate DNA synthesis. Our findings are consistent with recent studies of a knockout mouse model, which demonstrated that RNase H1 is required for R-loop processing and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In an RNase H1 deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. In combination with previously published in vivo data, the findings presented here suggest a model, in which R-loop processing by RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. Human mitochondria contain a double-stranded DNA genome that codes for key components of the oxidative phosphorylation system. The mitochondrial DNA (mtDNA) is replicated by a replication machinery distinct from that operating in the nucleus and mutations affecting individual replication factors have been associated with an array of rare, human diseases. In the present work, we demonstrate that RNase H1 directs origin-specific initiation of DNA replication in human mitochondria and that disease-causing mutations may impair this process. A unique feature of mtDNA replication is that primers required for initiation of leading-strand DNA replication are produced by the mitochondrial transcription machinery. A substantial fraction of all transcription events is prematurely terminated about 120 nucleotides downstream of the promoter and the RNA remains firmly associated with the genome, forming R-loops. Interestingly, the free 3′-end of these R-loops cannot directly prime initiation of DNA synthesis, but must first be processed by RNase H1. The process is stimulated by the mitochondrial single-stranded DNA binding protein and faithfully reconstitutes replication events mapped in vivo. In combination with mapping of replication events in fibroblasts derived from patients with mutations in RNASEH1, our findings point to a possible model for replication initiation in human mitochondria similar to that previously described in the E. coli plasmid, ColE1.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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131
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Novel Lines of Evidence for the Asymmetric Strand Displacement Model of Mitochondrial DNA Replication. Mol Cell Biol 2019; 39:MCB.00406-18. [PMID: 30397074 DOI: 10.1128/mcb.00406-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/20/2018] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial genome, which consists of 16,569 bp of DNA with a cytosine-rich light (L) strand and a heavy (H) strand, exists as a multicopy closed circular genome within the mitochondrial matrix. The machinery for replication of the mammalian mitochondrial genome is distinct from that for replication of the nuclear genome. Three models have been proposed for mitochondrial DNA (mtDNA) replication, and one of the key differences among them is whether extensive single-stranded regions exist on the H strand. Here, three different methods that can detect single-stranded DNA (ssDNA) are utilized to identify the presence, location, and abundance of ssDNA on mtDNA. Importantly, none of these newly described methods involve the complication of prior mtDNA fractionation. The H strand was found to have extensive single-stranded regions with a profile consistent with the strand displacement model of mtDNA replication, whereas single strandedness was predominantly absent on the L strand. These findings are consistent with the in vivo occupancy of mitochondrial single-stranded DNA binding protein reported previously and provide strong new qualitative and quantitative evidence for the asymmetric strand displacement model of mtDNA replication.
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132
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Zhao L. Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response. Enzymes 2019; 45:311-341. [PMID: 31627882 DOI: 10.1016/bs.enz.2019.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria play a central role in bioenergetics, and fulfill a plethora of functions in cell signaling, programmed cell death, and biosynthesis of key protein cofactors. Mitochondria harbor their own genomic DNA, which encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. Mitochondrial DNA (mtDNA) is essential for cellular and organismal functions, and defects in mitochondrial genome maintenance have been implicated in common human diseases and mitochondrial disorders. mtDNA repair and degradation are known pathways to cope with mtDNA damage; however, molecular factors involved in this process have remained unclear. Such knowledge is fundamental to the understanding of mitochondrial genomic maintenance and pathology, because mtDNA degradation may contribute to the etiology of mtDNA depletion syndromes and to the activation of the innate immune response by fragmented mtDNA. This article reviews the current literature regarding the importance of mitochondrial DNA degradation in mtDNA maintenance and stress response, and the recent progress in uncovering molecular factors involved in mtDNA degradation. These factors include key components of the mtDNA replication machinery, such as DNA polymerase γ, helicase Twinkle, and exonuclease MGME1, as well as a major DNA-packaging protein, mitochondrial transcription factor A (TFAM).
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
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133
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Li R, Ren X, Bi Y, Ding Q, Ho VWS, Zhao Z. Comparative mitochondrial genomics reveals a possible role of a recent duplication of NADH dehydrogenase subunit 5 in gene regulation. DNA Res 2018; 25:577-586. [PMID: 30085012 PMCID: PMC6289777 DOI: 10.1093/dnares/dsy026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 07/22/2018] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial genome (mtDNA) carries not only well-conserved protein coding, tRNA and rRNA genes, but also highly variable non-coding regions (NCRs). However, the NCRs show poor conservation across species, making their function and evolution elusive. Identification and functional characterization of NCRs across species would be critical for addressing these questions. To this end, we devised a computational pipeline and performed de novo assembly and annotation of mtDNA from 19 Caenorhabditis species using next-generation sequencing (NGS) data. The mtDNAs for 14 out of the 19 species are reported for the first time. Comparison of the 19 genomes reveals species-specific sampling of partial displacement-loop (D-loop) sequence as a novel NCR inserted into a unique tRNA cluster, suggesting an important role of the D-loop and the tRNA cluster in shaping NCR evolution. Intriguingly, RNA-Seq analysis suggests that a novel NCR resulting from a recent duplication of NADH dehydrogenase subunit 5 (ND5) could be utilized as a 3' UTR for up-regulation of its upstream gene. The expression analysis shows a species- and sex-specific expression of mitochondrial genes encoded by mtDNA and nucleus, respectively. Our analyses provide important insights into the function and evolution of mitochondrial NCRs and pave the way for further studying the function and evolution of mitochondrial genome.
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Affiliation(s)
- Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Bi
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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134
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Abstract
Epigenetics can be explored at different levels and can be divided into two major areas: epigenetics of nuclear-encoded DNA and epigenetics of mitochondrial-encoded DNA. In epigenetics of nuclear-encoded DNA, the main roles are played by DNA methylation, changes in histone structure and several types of non-coding RNAs. Mitochondrial epigenetics seems to be similar in the aspect of DNA methylation and to some extent in the role of non-coding RNAs but differs significantly in changes in components coiling DNA. Nuclear DNA is coiled around histones, but mitochondrial DNA, together with associated proteins, is located in mitochondrial pseudocompartments called nucleoids. It has been shown that mitochondrial epigenetic mechanisms influence cell fate, transcription regulation, cell division, cell cycle, physiological homeostasis, bioenergetics and even pathologies, but not all of these mechanisms have been explored in stem cells. The main issue is that most of these mechanisms have only recently been discovered in mitochondria, while improvements in methodology, especially next-generation sequencing, have enabled in-depth studies. Because studies exploring mitochondria from other aspects show that mitochondria are crucial for the normal behavior of stem cells, it is suggested that precise mitochondrial epigenetics in stem cells should be studied more intensively.
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135
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Yasukawa T, Kang D. An overview of mammalian mitochondrial DNA replication mechanisms. J Biochem 2018; 164:183-193. [PMID: 29931097 PMCID: PMC6094444 DOI: 10.1093/jb/mvy058] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/15/2018] [Indexed: 11/14/2022] Open
Abstract
While the majority of DNA is enclosed within the nucleus, the mitochondria also contain their own, separate DNA, the mitochondrial DNA (mtDNA). Mutations in mtDNA are associated with various human diseases, demonstrating the importance of mtDNA. Intensive studies over the last 18 years have demonstrated the presence of two distinct classes of mtDNA replication intermediates in mammals. One involves leading-strand DNA synthesis in the absence of synchronous lagging-strand DNA synthesis. Currently there are competing models in which the lagging-strand template is either systematically hybridized to processed mitochondrial transcripts, or coated with protein, until the lagging-strand DNA synthesis takes place. The other class of mtDNA replication intermediates has many properties of conventional, coupled leading- and lagging-strand DNA synthesis. Additionally, the highly unusual arrangement of DNA in human heart mitochondria suggests a third mechanism of replication. These findings indicate that the mtDNA replication systems of humans and other mammals are far more complex than previously thought, and thereby will require further research to understand the full picture of mtDNA replication.
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Affiliation(s)
- Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
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136
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Loutre R, Heckel AM, Smirnova A, Entelis N, Tarassov I. Can Mitochondrial DNA be CRISPRized: Pro and Contra. IUBMB Life 2018; 70:1233-1239. [PMID: 30184317 DOI: 10.1002/iub.1919] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 01/08/2023]
Abstract
Mitochondria represent a chimera of macromolecules encoded either in the organellar genome, mtDNA, or in the nuclear one. If the pathway of protein targeting to different sub-compartments of mitochondria was relatively well studied, import of small noncoding RNAs into mammalian mitochondria still awaits mechanistic explanations and its functional issues are often not understood thus raising polemics. At the same time, RNA mitochondrial import pathway has an obvious attractiveness as it appears as a unique natural mechanism permitting to address nucleic acids into the organelles. Deciphering the function(s) of imported RNAs inside the mitochondria is extremely complicated due to their relatively low abundance, which suggests their regulatory role. We previously demonstrated that mitochondrial targeting of small noncoding RNAs able to specifically anneal with the mutant mitochondrial DNA led to a decrease of the mtDNA heteroplasmy level by inhibiting mutant mtDNA replication. We then demonstrated that increasing level of expression of such antireplicative recombinant RNAs increases significantly the antireplicative effect. In this report, we present a new data investigating the possibility to establish a CRISPR-Cas9 system targeting mtDNA exploiting of the pathway of RNA import into mitochondria. Mitochondrially addressed Cas9 versions and a set of mitochondrially targeted guide RNAs were tested in vitro and in vivo and their effect on mtDNA copy number was demonstrated. So far, the system appeared as more complicated for use than previously found for nuclear DNA, because only application of a pair of guide RNAs produced the effect of mtDNA depletion. We discuss, in a critical way, these results and put them in a broader context of polemics concerning the possibilities of manipulation of mtDNA in mammalians. The findings described here prove the potential of the RNA import pathway as a tool for studying mtDNA and for future therapy of mitochondrial disorders. © The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1233-1239, 2018.
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Affiliation(s)
- Romuald Loutre
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Anne-Marie Heckel
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Anna Smirnova
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Nina Entelis
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Ivan Tarassov
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
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137
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Lima NCB, Soares AER, Almeida LGDP, Costa IRD, Sato FM, Schneider P, Aleixo A, Schneider MP, Santos FR, Mello CV, Miyaki C, Vasconcelos ATR, Prosdocimi F. Comparative mitogenomic analyses of Amazona parrots and Psittaciformes. Genet Mol Biol 2018; 41:593-604. [PMID: 30235395 PMCID: PMC6136379 DOI: 10.1590/1678-4685-gmb-2017-0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/22/2018] [Indexed: 11/21/2022] Open
Abstract
Amazon parrots are long-lived birds with highly developed cognitive skills, including vocal learning. Several parrot mitogenomes have been sequenced, but important aspects of their organization and evolution are not fully understood or have limited experimental support. The main aim of the present study was to describe the mitogenome of the blue-fronted Amazon, Amazona aestiva, and compare it to other mitogenomes from the genus Amazona and the order Psittaciformes. We observed that mitogenomes are highly conserved among Amazon parrots, and a detailed analysis of their duplicated control regions revealed conserved blocks. Population level analyses indicated that the specimen analyzed here seems to be close to A. aestiva individuals from Bahia state. Evolutionary relationships of 41 Psittaciformes species and three outgroups were inferred by BEAST. All relationships were retrieved with high support.
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Affiliation(s)
- Nicholas Costa Barroso Lima
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.,Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | | | | | - Igor Rodrigues da Costa
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Midori Sato
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Patricia Schneider
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emilio Goeldi, Belém, PA, Brazil
| | - Maria Paula Schneider
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Fabrício R Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Cristina Miyaki
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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138
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Droplet digital PCR shows the D-Loop to be an error prone locus for mitochondrial DNA copy number determination. Sci Rep 2018; 8:11392. [PMID: 30061621 PMCID: PMC6065360 DOI: 10.1038/s41598-018-29621-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/13/2018] [Indexed: 02/07/2023] Open
Abstract
Absolute quantification of mitochondrial DNA copy number (mCN) provides important insights in many fields of research including cancer, cardiovascular and reproductive health. Droplet digital PCR (ddPCR) natively reports absolute copy number, and we have developed a single-dye, multiplex assay to measure rat mCN that is accurate, precise and affordable. We demonstrate simple methods to optimize this assay and to determine nuclear reference pseudogene copy number to extend the range of mCN that can be measured with this assay. We evaluated two commonly used mitochondrial DNA reference loci to determine mCN, the ND1 gene and the D-Loop. Harnessing the absolute measures of ddPCR, we found that the D-Loop amplifies with a copy number of ~1.0–1.5 relative to other sites on the mitochondrial genome. This anomalous copy number varied significantly between rats and tissues (aorta, brain, heart, liver, soleus muscle). We advocate for avoiding the D-Loop as a mitochondrial reference in future studies of mCN. Further, we report a novel approach to quantifying immunolabelled mitochondrial DNA that provides single-cell estimates of mCN that closely agree with the population analyses by ddPCR. The combination of these assays represents a cost-effective and powerful suite of tools to study mCN.
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139
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Mitochondrial DNA variants modulate genetic susceptibility to Parkinson's disease in Han Chinese. Neurobiol Dis 2018; 114:17-23. [DOI: 10.1016/j.nbd.2018.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/18/2018] [Accepted: 02/21/2018] [Indexed: 12/26/2022] Open
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140
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Wiehe RS, Gole B, Chatre L, Walther P, Calzia E, Ricchetti M, Wiesmüller L. Endonuclease G promotes mitochondrial genome cleavage and replication. Oncotarget 2018; 9:18309-18326. [PMID: 29719607 PMCID: PMC5915074 DOI: 10.18632/oncotarget.24822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/12/2018] [Indexed: 12/26/2022] Open
Abstract
Endonuclease G (EndoG) is a nuclear-encoded endonuclease, mostly localised in mitochondria. In the nucleus EndoG participates in site-specific cleavage during replication stress and genome-wide DNA degradation during apoptosis. However, the impact of EndoG on mitochondrial DNA (mtDNA) metabolism is poorly understood. Here, we investigated whether EndoG is involved in the regulation of mtDNA replication and removal of aberrant copies. We applied the single-cell mitochondrial Transcription and Replication Imaging Protocol (mTRIP) and PCR-based strategies on human cells after knockdown/knockout and re-expression of EndoG. Our analysis revealed that EndoG stimulates both mtDNA replication initiation and mtDNA depletion, the two events being interlinked and dependent on EndoG's nuclease activity. Stimulation of mtDNA replication by EndoG was independent of 7S DNA processing at the replication origin. Importantly, both mtDNA-directed activities of EndoG were promoted by oxidative stress. Inhibition of base excision repair (BER) that repairs oxidative stress-induced DNA damage unveiled a pronounced effect of EndoG on mtDNA removal, reminiscent of recently discovered links between EndoG and BER in the nucleus. Altogether with the downstream effects on mitochondrial transcription, protein expression, redox status and morphology, this study demonstrates that removal of damaged mtDNA by EndoG and compensatory replication play a critical role in mitochondria homeostasis.
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Affiliation(s)
| | - Boris Gole
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
- Present address: Centre for Human Molecular Genetics and Pharmacogenomics, Medical Faculty, University of Maribor, Maribor, SI-2000, Slovenia
| | - Laurent Chatre
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, 89081, Germany
| | - Enrico Calzia
- Institute of Anesthesiological Pathophysiology and Process Engineering, Ulm University Hospital, Ulm, 89081, Germany
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
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141
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Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria. Nat Commun 2018; 9:1202. [PMID: 29572490 PMCID: PMC5865154 DOI: 10.1038/s41467-018-03552-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/21/2018] [Indexed: 12/17/2022] Open
Abstract
Replication of mammalian mitochondrial DNA (mtDNA) is an essential process that requires high fidelity and control at multiple levels to ensure proper mitochondrial function. Mutations in the mitochondrial genome maintenance exonuclease 1 (MGME1) gene were recently reported in mitochondrial disease patients. Here, to study disease pathophysiology, we generated Mgme1 knockout mice and report that homozygous knockouts develop depletion and multiple deletions of mtDNA. The mtDNA replication stalling phenotypes vary dramatically in different tissues of Mgme1 knockout mice. Mice with MGME1 deficiency accumulate a long linear subgenomic mtDNA species, similar to the one found in mtDNA mutator mice, but do not develop progeria. This finding resolves a long-standing debate by showing that point mutations of mtDNA are the main cause of progeria in mtDNA mutator mice. We also propose a role for MGME1 in the regulation of replication and transcription termination at the end of the control region of mtDNA. It has been debated whether premature ageing in mitochondrial DNA mutator mice is driven by point mutations or deletions of mtDNA. Matic et al generate Mgme1 knockout mice and show here that these mice have tissue-specific replication stalling and accumulate deleted mtDNA, without developing progeria.
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142
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Kang I, Chu CT, Kaufman BA. The mitochondrial transcription factor TFAM in neurodegeneration: emerging evidence and mechanisms. FEBS Lett 2018; 592:793-811. [PMID: 29364506 PMCID: PMC5851836 DOI: 10.1002/1873-3468.12989] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 12/30/2022]
Abstract
The mitochondrial transcription factor A, or TFAM, is a mitochondrial DNA (mtDNA)-binding protein essential for genome maintenance. TFAM functions in determining the abundance of the mitochondrial genome by regulating packaging, stability, and replication. More recently, TFAM has been shown to play a central role in the mtDNA stress-mediated inflammatory response. Emerging evidence indicates that decreased mtDNA copy number is associated with several aging-related pathologies; however, little is known about the association of TFAM abundance and disease. In this Review, we evaluate the potential associations of altered TFAM levels or mtDNA copy number with neurodegeneration. We also describe potential mechanisms by which mtDNA replication, transcription initiation, and TFAM-mediated endogenous danger signals may impact mitochondrial homeostasis in Alzheimer, Huntington, Parkinson, and other neurodegenerative diseases.
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Affiliation(s)
- Inhae Kang
- Department of Food Science and Nutrition, Jeju National University, Jeju, Korea
- Division of Cardiology, Vascular Medicine Institute, Department of Medicine Center for Metabolic and Mitochondrial Medicine (C3M), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Charleen T. Chu
- Department of Pathology, Center for Neuroscience, Pittsburgh Institute for Neurodegenerative Diseases, Conformational Protein Diseases Center, and the McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Brett A. Kaufman
- Division of Cardiology, Vascular Medicine Institute, Department of Medicine Center for Metabolic and Mitochondrial Medicine (C3M), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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143
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Abstract
Mitochondrial DNA (mtDNA), which is essential for mitochondrial and cell function, is replicated and transcribed in the organelle by proteins that are entirely coded in the nucleus. Replication of mtDNA is challenged not only by threats related to the replication machinery and orchestration of DNA synthesis, but also by factors linked to the peculiarity of this genome. Indeed the architecture, organization, copy number, and location of mtDNA, which are markedly distinct from the nuclear genome, require ad hoc and complex regulation to ensure coordinated replication. As a consequence sub-optimal mtDNA replication, which results from compromised regulation of these factors, is generally associated with mitochondrial dysfunction and disease. Mitochondrial DNA replication should be considered in the context of the organelle and the whole cell, and not just a single genome or a single replication event. Major threats to mtDNA replication are linked to its dependence on both mitochondrial and nuclear factors, which require exquisite coordination of these crucial subcellular compartments. Moreover, regulation of replication events deals with a dynamic population of multiple mtDNA molecules rather than with a fixed number of genome copies, as it is the case for nuclear DNA. Importantly, the mechanistic aspects of mtDNA replication are still debated. We describe here major challenges for human mtDNA replication, the mechanistic aspects of the process that are to a large extent original, and their consequences on disease.
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Affiliation(s)
- Miria Ricchetti
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Stem Cells and Development, 75724 Cedex15, Paris, France; Team Stability of Nuclear and Mitochondrial DNA, CNRS UMR 3738, 75724, Cedex15, Paris, France.
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144
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Craven L, Tang MX, Gorman GS, De Sutter P, Heindryckx B. Novel reproductive technologies to prevent mitochondrial disease. Hum Reprod Update 2018. [PMID: 28651360 DOI: 10.1093/humupd/dmx018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The use of nuclear transfer (NT) has been proposed as a novel reproductive treatment to overcome the transmission of maternally-inherited mitochondrial DNA (mtDNA) mutations. Pathogenic mutations in mtDNA can cause a wide-spectrum of life-limiting disorders, collectively known as mtDNA disease, for which there are currently few effective treatments and no known cures. The many unique features of mtDNA make genetic counselling challenging for women harbouring pathogenic mtDNA mutations but reproductive options that involve medical intervention are available that will minimize the risk of mtDNA disease in their offspring. This includes PGD, which is currently offered as a clinical treatment but will not be suitable for all. The potential for NT to reduce transmission of mtDNA mutations has been demonstrated in both animal and human models, and has recently been clinically applied not only to prevent mtDNA disease but also for some infertility cases. In this review, we will interrogate the different NT techniques, including a discussion on the available safety and efficacy data of these technologies for mtDNA disease prevention. In addition, we appraise the evidence for the translational use of NT technologies in infertility. OBJECTIVE AND RATIONALE We propose to review the current scientific evidence regarding the clinical use of NT to prevent mitochondrial disease. SEARCH METHODS The scientific literature was investigated by searching PubMed database until Jan 2017. Relevant documents from Human Fertilisation and Embryology Authority as well as reports from both the scientific and popular media were also implemented. The above searches were based on the following key words: 'mitochondria', 'mitochondrial DNA'; 'mitochondrial DNA disease', 'fertility'; 'preimplantation genetic diagnosis', 'nuclear transfer', 'mitochondrial replacement' and 'mitochondrial donation'. OUTCOMES While NT techniques have been shown to effectively reduce the transmission of heteroplasmic mtDNA variants in animal models, and increasing evidence supports their use to prevent the transmission of human mtDNA disease, the need for robust, long-term evaluation is still warranted. Moreover, prenatal screening would still be strongly advocated in combination with the use of these IVF-based technologies. Scientific evidence to support the use of NT and other novel reproductive techniques for infertility is currently lacking. WIDER IMPLICATIONS It is mandatory that any new ART treatments are first adequately assessed in both animal and human models before the cautious implementation of these new therapeutic approaches is clinically undertaken. There is growing evidence to suggest that the translation of these innovative technologies into clinical practice should be cautiously adopted only in highly selected patients. Indeed, given the limited safety and efficacy data, close monitoring of any offspring remains paramount.
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Affiliation(s)
- Lyndsey Craven
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Mao-Xing Tang
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Petra De Sutter
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
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145
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Kullar PJ, Gomez-Duran A, Gammage PA, Garone C, Minczuk M, Golder Z, Wilson J, Montoya J, Häkli S, Kärppä M, Horvath R, Majamaa K, Chinnery PF. Heterozygous SSBP1 start loss mutation co-segregates with hearing loss and the m.1555A>G mtDNA variant in a large multigenerational family. Brain 2018; 141:55-62. [PMID: 29182774 PMCID: PMC5837410 DOI: 10.1093/brain/awx295] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/10/2017] [Accepted: 09/25/2017] [Indexed: 11/30/2022] Open
Abstract
The m.1555A>G mtDNA variant causes maternally inherited deafness, but the reasons for the highly variable clinical penetrance are not known. Exome sequencing identified a heterozygous start loss mutation in SSBP1, encoding the single stranded binding protein 1 (SSBP1), segregating with hearing loss in a multi-generational family transmitting m.1555A>G, associated with mtDNA depletion and multiple deletions in skeletal muscle. The SSBP1 mutation reduced steady state SSBP1 levels leading to a perturbation of mtDNA metabolism, likely compounding the intra-mitochondrial translation defect due to m.1555A>G in a tissue-specific manner. This family demonstrates the importance of rare trans-acting genetic nuclear modifiers in the clinical expression of mtDNA disease.
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Affiliation(s)
- Peter J Kullar
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Aurora Gomez-Duran
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Payam A Gammage
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Caterina Garone
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Michal Minczuk
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Zoe Golder
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Janet Wilson
- Institute of Health and Society, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Julio Montoya
- Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón, Spain
| | - Sanna Häkli
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Mikko Kärppä
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, UK
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Patrick F Chinnery
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
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146
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Lee EJ, Hwang I, Lee JY, Park JN, Kim KC, Kim GH, Kang CM, Kim I, Lee SY, Kim HS. Hepatocyte Growth Factor Improves the Therapeutic Efficacy of Human Bone Marrow Mesenchymal Stem Cells via RAD51. Mol Ther 2017; 26:845-859. [PMID: 29398486 DOI: 10.1016/j.ymthe.2017.12.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023] Open
Abstract
Human embryonic stem cell-derived mesenchymal stem cells (hE-MSCs) have greater proliferative capacity than other human mesenchymal stem cells (hMSCs), suggesting that they may have wider applications in regenerative cellular therapy. In this study, to uncover the anti-senescence mechanism in hE-MSCs, we compared hE-MSCs with adult bone marrow (hBM-MSCs) and found that hepatocyte growth factor (HGF) was more abundantly expressed in hE-MSCs than in hBM-MSCs and that it induced the transcription of RAD51 and facilitated its SUMOylation at K70. RAD51 induction/modification by HGF not only increased telomere length but also increased mtDNA replication, leading to increased ATP generation. Moreover, HGF-treated hBM-MSCs showed significantly better therapeutic efficacy than naive hBM-MSCs. Together, the data suggest that the RAD51-mediated effects of HGF prevent hMSC senescence by promoting telomere lengthening and inducing mtDNA replication and function, which opens the prospect of developing novel therapies for liver disease.
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Affiliation(s)
- Eun Ju Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Injoo Hwang
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ji Yeon Lee
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong Nam Park
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Keun Cheon Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Gi-Hwan Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Chang-Mo Kang
- Korea Institute of Radiological & Medical Sciences, Seoul, Republic of Korea
| | - Irene Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seo-Yeon Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyo-Soo Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
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147
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Hertweck KL, Dasgupta S. The Landscape of mtDNA Modifications in Cancer: A Tale of Two Cities. Front Oncol 2017; 7:262. [PMID: 29164061 PMCID: PMC5673620 DOI: 10.3389/fonc.2017.00262] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 10/18/2017] [Indexed: 12/25/2022] Open
Abstract
Mitochondria from normal and cancerous cells represent a tale of two cities, wherein both execute similar processes but with different cellular and molecular effects. Given the number of reviews currently available which describe the functional implications of mitochondrial mutations in cancer, this article focuses on documenting current knowledge in the abundance and distribution of somatic mitochondrial mutations, followed by elucidation of processes which affect the fate of mutations in cancer cells. The conclusion includes an overview of translational implications for mtDNA mutations, as well as recommendations for future research uniting mitochondrial variants and tumorigenesis.
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Affiliation(s)
- Kate L Hertweck
- Department of Biology, The University of Texas at Tyler, Tyler, TX, United States
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
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148
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Hopkins JF, Sabelnykova VY, Weischenfeldt J, Simon R, Aguiar JA, Alkallas R, Heisler LE, Zhang J, Watson JD, Chua MLK, Fraser M, Favero F, Lawerenz C, Plass C, Sauter G, McPherson JD, van der Kwast T, Korbel J, Schlomm T, Bristow RG, Boutros PC. Mitochondrial mutations drive prostate cancer aggression. Nat Commun 2017; 8:656. [PMID: 28939825 PMCID: PMC5610241 DOI: 10.1038/s41467-017-00377-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/26/2017] [Indexed: 12/26/2022] Open
Abstract
Nuclear mutations are well known to drive tumor incidence, aggression and response to therapy. By contrast, the frequency and roles of mutations in the maternally inherited mitochondrial genome are poorly understood. Here we sequence the mitochondrial genomes of 384 localized prostate cancer patients, and identify a median of one mitochondrial single-nucleotide variant (mtSNV) per patient. Some of these mtSNVs occur in recurrent mutational hotspots and associate with aggressive disease. Younger patients have fewer mtSNVs than those who diagnosed at an older age. We demonstrate strong links between mitochondrial and nuclear mutational profiles, with co-occurrence between specific mutations. For example, certain control region mtSNVs co-occur with gain of the MYC oncogene, and these mutations are jointly associated with patient survival. These data demonstrate frequent mitochondrial mutation in prostate cancer, and suggest interplay between nuclear and mitochondrial mutational profiles in prostate cancer. In prostate cancer, the role of mutations in the maternally-inherited mitochondrial genome are not well known. Here, the authors demonstrate frequent, age-dependent mitochondrial mutation in prostate cancer. Strong links between mitochondrial and nuclear mutational profiles are associated with clinical aggressivity.
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Affiliation(s)
- Julia F Hopkins
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3.
| | - Veronica Y Sabelnykova
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3
| | - Joachim Weischenfeldt
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69120, Germany.,Biotech Research & Innovation Centre (BRIC) and Finsen Laboratory, Copenhagen, 2200, Denmark
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Jennifer A Aguiar
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3
| | - Rached Alkallas
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3
| | - Lawrence E Heisler
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3
| | - Junyan Zhang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, M5G 1L7
| | - John D Watson
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3
| | - Melvin L K Chua
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, M5G 1L7
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, M5G 1L7
| | - Francesco Favero
- Biotech Research & Innovation Centre (BRIC) and Finsen Laboratory, Copenhagen, 2200, Denmark
| | - Chris Lawerenz
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - John D McPherson
- Genome Technologies Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital/University Health Network, Toronto, ON, Canada, M5G 2C4
| | - Jan Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69120, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, M5G 1L7. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada, M5G 1L7. .,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada, M5T 1P5.
| | - Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada, M5G 1L7. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada, M5S 1A8.
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149
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Wolf DP, Hayama T, Mitalipov S. Mitochondrial genome inheritance and replacement in the human germline. EMBO J 2017; 36:2177-2181. [PMID: 28679504 DOI: 10.15252/embj.201797606] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mitochondria, the ubiquitous power packs in nearly every eukaryotic cell, contain their own DNA, known as mtDNA, which is inherited exclusively from the mother. The number of mitochondrial genomes varies depending on the cell's energy needs. The mature oocyte contains the highest number of mitochondria of any cell type, although there is little if any mtDNA replication after fertilization until the embryo implants. This has potential repercussions for mitochondrial replacement therapy (MRT; see description of currently employed methods below) used to prevent the transmission of mtDNA-based disorders. If only a few mitochondria with defective mtDNA are left in the embryo and undergo extensive replication, it might therefore thwart the purpose of MRT In order to improve the safety and efficacy of this experimental therapy, we need a better understanding of how and which mtDNA is tagged for replication versus transcription after fertilization of the oocyte.
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Affiliation(s)
- Don P Wolf
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR, USA.,Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Tomonari Hayama
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR, USA.,Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Shoukhrat Mitalipov
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR, USA.,Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
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Li H, Shen L, Hu P, Huang R, Cao Y, Deng J, Yuan W, Liu D, Yang J, Gu H, Bai Y. Aging-associated mitochondrial DNA mutations alter oxidative phosphorylation machinery and cause mitochondrial dysfunctions. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2266-2273. [PMID: 28559044 DOI: 10.1016/j.bbadis.2017.05.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/14/2022]
Abstract
Our previous study generated a series of cybrids containing mitochondria of synaptosomes from mice at different ages. The following functional analysis on these cybrids revealed an age-dependent decline of mitochondrial function. To understand the underlying mechanisms that contribute to the age-related mitochondrial dysfunction, we focused on three cybrids carrying mitochondria derived from synaptosomes of the old mice that exhibited severe respiratory deficiencies. In particular, we started with a comprehensive analysis of mitochondrial genome by high resolution, high sensitive deep sequencing method. Compared with young control, we detected a significant accumulation of heteroplasmic mtDNA mutations. These mutations included six alterations in main control region that has been shown to regulate overall gene-expression, and four alterations in protein coding region, two of which led to significant changes in complex I subunit ND5 and complex III subunit CytB. Interestingly, a reduced mtDNA-encoded protein synthesis was associated with the changes in the main control region. Likewise, mutations in ND5 and CytB were associated with defects in assembly of respiratory complexes. Altogether, the identified age-dependent accumulation of mtDNA mutations in mouse brain likely contributes to the decline in mitochondrial function.
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Affiliation(s)
- Hongzhi Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Luxi Shen
- Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Peiqing Hu
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rong Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Ying Cao
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Janice Deng
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Weihua Yuan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Danhui Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jifeng Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Haihua Gu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Yidong Bai
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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